output/shovill/Serratia/shovill.log Version 1
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
SEEK ID: https://fairdomhub.org/documents/2578?version=1
Filename:
output/shovill/Serratia/shovill.log
Format: Plain text document
Size: 922 KB
[shovill] Hello administrator [shovill] You ran: /home/administrator/conda2/envs/shovill/bin/shovill --force --outdir ./shovill/Serratia/ --R1 ./fq/incl615_R1.fastq --R2 ./fq/incl615_R2.fastq --gsize 5M --cpus 30 --ram 240 --minlen 200 --kmers 31,41,51,61,71,81,91,101,111,121 --assembler spades [shovill] This is shovill 1.1.0 [shovill] Written by Torsten Seemann [shovill] Homepage is https://github.com/tseemann/shovill [shovill] Operating system is linux [shovill] Perl version is v5.26.2 [shovill] Machine has 32 CPU cores and 251.58 GB RAM [shovill] Using bwa - /home/administrator/conda2/envs/shovill/bin/bwa | Version: 0.7.17-r1188 [shovill] Using flash - /home/administrator/conda2/envs/shovill/bin/flash | FLASH v1.2.11 [shovill] Using java - /home/administrator/conda2/envs/shovill/bin/java | openjdk version "11.0.8-internal" 2020-07-14 [shovill] Using kmc - /home/administrator/conda2/envs/shovill/bin/kmc | K-Mer Counter (KMC) ver. 3.1.1 (2019-05-19) [shovill] Using lighter - /home/administrator/conda2/envs/shovill/bin/lighter | Lighter v1.1.2 [shovill] Using megahit - /home/administrator/conda2/envs/shovill/bin/megahit | MEGAHIT v1.2.9 [shovill] Using megahit_toolkit - /home/administrator/conda2/envs/shovill/bin/megahit_toolkit | v1.2.9 [shovill] Using pigz - /home/administrator/conda2/envs/shovill/bin/pigz | pigz 2.3.4 [shovill] Using pilon - /home/administrator/conda2/envs/shovill/bin/pilon | Pilon version 1.23 Mon Nov 26 16:04:05 2018 -0500 [shovill] Using samclip - /home/administrator/conda2/envs/shovill/bin/samclip | samclip 0.4.0 [shovill] Using samtools - /home/administrator/conda2/envs/shovill/bin/samtools | Version: 1.10 (using htslib 1.10.2) [shovill] Using seqtk - /home/administrator/conda2/envs/shovill/bin/seqtk | Version: 1.3-r106 [shovill] Using skesa - /home/administrator/conda2/envs/shovill/bin/skesa | SKESA 2.4.0 [shovill] Using spades.py - /home/administrator/conda2/envs/shovill/bin/spades.py | SPAdes genome assembler v3.14.1 [shovill] Using trimmomatic - /home/administrator/conda2/envs/shovill/bin/trimmomatic | 0.39 [shovill] Using velvetg - /home/administrator/conda2/envs/shovill/bin/velvetg | Version 1.2.10 [shovill] Using velveth - /home/administrator/conda2/envs/shovill/bin/velveth | Version 1.2.10 [shovill] Found spades version: 003014000 [shovill] Will use spades 003014000 options: --isolate and --merged [shovill] Forced overwrite of existing --outdir ./shovill/Serratia/ [shovill] Using tempdir: /tmp/7pScLI1Yr4 [shovill] Changing into folder: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia [shovill] Collecting raw read statistics with 'seqtk' [shovill] Running: seqtk fqchk -q3 \/DATB\/markop\/CPB\/CPB_rcf_DNAseq\/fq\/incl615_R1\.fastq >/tmp/2WWgc7M_kX 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log [shovill] Read stats: max_len = 150 [shovill] Read stats: min_len = 150 [shovill] Read stats: total_bp = 17811269400 [shovill] Read stats: avg_len = 150 [shovill] Using genome size 5000000 bp [shovill] Estimated sequencing depth: 3562 x [shovill] Subsampling reads by factor 0.042 to get from 3562x to 150x [shovill] Running: seqtk sample \/DATB\/markop\/CPB\/CPB_rcf_DNAseq\/fq\/incl615_R1\.fastq 0.042 | pigz --fast -c -p 30 > R1.sub.fq.gz 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log [shovill] Running: seqtk sample \/DATB\/markop\/CPB\/CPB_rcf_DNAseq\/fq\/incl615_R2\.fastq 0.042 | pigz --fast -c -p 30 > R2.sub.fq.gz 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log [shovill] Appending -Xmx240g to _JAVA_OPTIONS [shovill] Running: ln -sf R1\.sub\.fq\.gz R1.fq.gz 2>&1 | sed 's/^/[ln] /' | tee -a shovill.log [shovill] Running: ln -sf R2\.sub\.fq\.gz R2.fq.gz 2>&1 | sed 's/^/[ln] /' | tee -a shovill.log [shovill] Average read length looks like 150 bp [shovill] Examing provided --kmers 31,41,51,61,71,81,91,101,111,121 [shovill] Using kmers: 31,41,51,61,71,81,91,101,111,121 [shovill] Correcting reads with 'Lighter' [shovill] Running: lighter -od . -r R1.fq.gz -r R2.fq.gz -K 32 5000000 -t 30 -maxcor 1 2>&1 | sed 's/^/[lighter] /' | tee -a shovill.log [lighter] [2021-01-20 23:52:25] =============Start==================== [lighter] [2021-01-20 23:52:25] Scanning the input files to infer alpha(sampling rate) [lighter] [2021-01-20 23:52:33] Average coverage is 149.634 and alpha is 0.047 [lighter] [2021-01-20 23:52:35] Bad quality threshold is "7" [lighter] [2021-01-20 23:53:11] Finish sampling kmers [lighter] [2021-01-20 23:53:11] Bloom filter A's false positive rate: 0.007479 [lighter] [2021-01-20 23:53:31] Finish storing trusted kmers [lighter] [2021-01-20 23:54:10] Finish error correction [lighter] Processed 4987788 reads: [lighter] 4144946 are error-free [lighter] Corrected 1326188 bases(1.573472 corrections for reads with errors) [lighter] Trimmed 0 reads with average trimmed bases 0.000000 [lighter] Discard 0 reads [shovill] Overlapping/stitching PE reads with 'FLASH' [shovill] Running: flash -m 20 -M 150 -d . -o flash -z -t 30 R1.cor.fq.gz R2.cor.fq.gz 2>&1 | sed 's/^//' | tee -a shovill.log [FLASH] Starting FLASH v1.2.11 [FLASH] Fast Length Adjustment of SHort reads [FLASH] [FLASH] Input files: [FLASH] R1.cor.fq.gz [FLASH] R2.cor.fq.gz [FLASH] [FLASH] Output files: [FLASH] ./flash.extendedFrags.fastq.gz [FLASH] ./flash.notCombined_1.fastq.gz [FLASH] ./flash.notCombined_2.fastq.gz [FLASH] ./flash.hist [FLASH] ./flash.histogram [FLASH] [FLASH] Parameters: [FLASH] Min overlap: 20 [FLASH] Max overlap: 150 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: false [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 30 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH] [FLASH] Starting reader and writer threads [FLASH] Starting 30 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 175000 read pairs [FLASH] Processed 200000 read pairs [FLASH] Processed 225000 read pairs [FLASH] Processed 250000 read pairs [FLASH] Processed 275000 read pairs [FLASH] Processed 300000 read pairs [FLASH] Processed 325000 read pairs [FLASH] Processed 350000 read pairs [FLASH] Processed 375000 read pairs [FLASH] Processed 400000 read pairs [FLASH] Processed 425000 read pairs [FLASH] Processed 450000 read pairs [FLASH] Processed 475000 read pairs [FLASH] Processed 500000 read pairs [FLASH] Processed 525000 read pairs [FLASH] Processed 550000 read pairs [FLASH] Processed 575000 read pairs [FLASH] Processed 600000 read pairs [FLASH] Processed 625000 read pairs [FLASH] Processed 650000 read pairs [FLASH] Processed 675000 read pairs [FLASH] Processed 700000 read pairs [FLASH] Processed 725000 read pairs [FLASH] Processed 750000 read pairs [FLASH] Processed 775000 read pairs [FLASH] Processed 800000 read pairs [FLASH] Processed 825000 read pairs [FLASH] Processed 850000 read pairs [FLASH] Processed 875000 read pairs [FLASH] Processed 900000 read pairs [FLASH] Processed 925000 read pairs [FLASH] Processed 950000 read pairs [FLASH] Processed 975000 read pairs [FLASH] Processed 1000000 read pairs [FLASH] Processed 1025000 read pairs [FLASH] Processed 1050000 read pairs [FLASH] Processed 1075000 read pairs [FLASH] Processed 1100000 read pairs [FLASH] Processed 1125000 read pairs [FLASH] Processed 1150000 read pairs [FLASH] Processed 1175000 read pairs [FLASH] Processed 1200000 read pairs [FLASH] Processed 1225000 read pairs [FLASH] Processed 1250000 read pairs [FLASH] Processed 1275000 read pairs [FLASH] Processed 1300000 read pairs [FLASH] Processed 1325000 read pairs [FLASH] Processed 1350000 read pairs [FLASH] Processed 1375000 read pairs [FLASH] Processed 1400000 read pairs [FLASH] Processed 1425000 read pairs [FLASH] Processed 1450000 read pairs [FLASH] Processed 1475000 read pairs [FLASH] Processed 1500000 read pairs [FLASH] Processed 1525000 read pairs [FLASH] Processed 1550000 read pairs [FLASH] Processed 1575000 read pairs [FLASH] Processed 1600000 read pairs [FLASH] Processed 1625000 read pairs [FLASH] Processed 1650000 read pairs [FLASH] Processed 1675000 read pairs [FLASH] Processed 1700000 read pairs [FLASH] Processed 1725000 read pairs [FLASH] Processed 1750000 read pairs [FLASH] Processed 1775000 read pairs [FLASH] Processed 1800000 read pairs [FLASH] Processed 1825000 read pairs [FLASH] Processed 1850000 read pairs [FLASH] Processed 1875000 read pairs [FLASH] Processed 1900000 read pairs [FLASH] Processed 1925000 read pairs [FLASH] Processed 1950000 read pairs [FLASH] Processed 1975000 read pairs [FLASH] Processed 2000000 read pairs [FLASH] Processed 2025000 read pairs [FLASH] Processed 2050000 read pairs [FLASH] Processed 2075000 read pairs [FLASH] Processed 2100000 read pairs [FLASH] Processed 2125000 read pairs [FLASH] Processed 2150000 read pairs [FLASH] Processed 2175000 read pairs [FLASH] Processed 2200000 read pairs [FLASH] Processed 2225000 read pairs [FLASH] Processed 2250000 read pairs [FLASH] Processed 2275000 read pairs [FLASH] Processed 2300000 read pairs [FLASH] Processed 2325000 read pairs [FLASH] Processed 2350000 read pairs [FLASH] Processed 2375000 read pairs [FLASH] Processed 2400000 read pairs [FLASH] Processed 2425000 read pairs [FLASH] Processed 2450000 read pairs [FLASH] Processed 2475000 read pairs [FLASH] Processed 2493894 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 2493894 [FLASH] Combined pairs: 1003406 [FLASH] Uncombined pairs: 1490488 [FLASH] Percent combined: 40.23% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v1.2.11 complete! [FLASH] 79.173 seconds elapsed [shovill] Assembling reads with 'spades' [shovill] Running: spades.py -1 flash.notCombined_1.fastq.gz -2 flash.notCombined_2.fastq.gz --isolate --threads 30 --memory 240 -o spades --tmp-dir /tmp/7pScLI1Yr4 -k 31,41,51,61,71,81,91,101,111,121 --merged flash.extendedFrags.fastq.gz 2>&1 | sed 's/^/[spades] /' | tee -a shovill.log [spades] Command line: /home/administrator/conda2/envs/shovill/bin/spades.py -1 /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/flash.notCombined_1.fastq.gz -2 /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/flash.notCombined_2.fastq.gz --isolate --threads 30 --memory 240 -o /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades --tmp-dir /tmp/7pScLI1Yr4 -k 31,41,51,61,71,81,91,101,111,121 --merged /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/flash.extendedFrags.fastq.gz [spades] [spades] System information: [spades] SPAdes version: 3.14.1 [spades] Python version: 3.8.5 [spades] OS: Linux-4.13.0-41-generic-x86_64-with-glibc2.10 [spades] [spades] Output dir: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades [spades] Mode: ONLY assembling (without read error correction) [spades] Debug mode is turned OFF [spades] [spades] Dataset parameters: [spades] Isolate mode [spades] Reads: [spades] Library number: 1, library type: paired-end [spades] orientation: fr [spades] left reads: ['/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/flash.notCombined_1.fastq.gz'] [spades] right reads: ['/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/flash.notCombined_2.fastq.gz'] [spades] interlaced reads: not specified [spades] single reads: not specified [spades] merged reads: ['/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/flash.extendedFrags.fastq.gz'] [spades] Assembly parameters: [spades] k: [31, 41, 51, 61, 71, 81, 91, 101, 111, 121] [spades] Repeat resolution is enabled [spades] Mismatch careful mode is turned OFF [spades] MismatchCorrector will be SKIPPED [spades] Coverage cutoff is turned OFF [spades] Other parameters: [spades] Dir for temp files: /tmp/7pScLI1Yr4 [spades] Threads: 30 [spades] Memory limit (in Gb): 240 [spades] [spades] [spades] ======= SPAdes pipeline started. Log can be found here: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/spades.log [spades] [spades] /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/flash.notCombined_1.fastq.gz: max reads length: 150 [spades] /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/flash.notCombined_2.fastq.gz: max reads length: 150 [spades] Files with merged reads were ignored. [spades] [spades] Reads length: 150 [spades] [spades] [spades] ===== Before start started. [spades] [spades] [spades] ===== Assembling started. [spades] [spades] [spades] ===== K31 started. [spades] [spades] [spades] == Running: /home/administrator/conda2/envs/shovill/bin/spades-core /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K31/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K31/configs/isolate_mode.info [spades] [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is tmp_contigs.fasta [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K31/configs/config.info [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K31/configs/isolate_mode.info [spades] 0:00:00.001 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/dataset.info) with K=31 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 30 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 194) SPAdes started [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0 [spades] 0:00:00.002 7M / 9M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion [spades] 0:00:00.005 7M / 9M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) [spades] 0:00:00.005 7M / 9M INFO General (read_converter.cpp : 73) Converting paired reads [spades] 0:00:00.935 204M / 204M INFO General (binary_converter.cpp : 96) 16384 reads processed [spades] 0:00:01.007 223M / 223M INFO General (binary_converter.cpp : 96) 32768 reads processed [spades] 0:00:01.174 262M / 262M INFO General (binary_converter.cpp : 96) 65536 reads processed [spades] 0:00:01.485 306M / 306M INFO General (binary_converter.cpp : 96) 131072 reads processed [spades] 0:00:02.196 421M / 421M INFO General (binary_converter.cpp : 96) 262144 reads processed [spades] 0:00:04.019 616M / 616M INFO General (binary_converter.cpp : 96) 524288 reads processed [spades] 0:00:06.822 851M / 851M INFO General (binary_converter.cpp : 96) 1048576 reads processed [spades] 0:00:08.991 971M / 971M INFO General (binary_converter.cpp : 111) 1490488 reads written [spades] 0:00:08.995 947M / 966M INFO General (read_converter.cpp : 81) Converting single reads [spades] 0:00:08.997 957M / 966M INFO General (binary_converter.cpp : 111) 0 reads written [spades] 0:00:08.998 947M / 966M INFO General (read_converter.cpp : 87) Converting merged reads [spades] 0:00:09.662 1023M / 1023M INFO General (binary_converter.cpp : 96) 16384 reads processed [spades] 0:00:09.703 1023M / 1023M INFO General (binary_converter.cpp : 96) 32768 reads processed [spades] 0:00:09.789 1023M / 1023M INFO General (binary_converter.cpp : 96) 65536 reads processed [spades] 0:00:10.329 997M / 2G INFO General (binary_converter.cpp : 96) 131072 reads processed [spades] 0:00:11.089 2G / 2G INFO General (binary_converter.cpp : 96) 262144 reads processed [spades] 0:00:12.821 2G / 2G INFO General (binary_converter.cpp : 96) 524288 reads processed [spades] 0:00:16.012 2G / 2G INFO General (binary_converter.cpp : 111) 1003406 reads written [spades] 0:00:16.054 90M / 2G INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:16.063 90M / 2G INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:16.064 90M / 2G INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:16.064 90M / 2G INFO General (construction.cpp : 156) Average read length 173.568 [spades] 0:00:16.065 90M / 2G INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:16.065 90M / 2G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:16.068 90M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:16.069 90M / 2G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66664 Gb [spades] 0:00:16.070 90M / 2G INFO General (kmer_splitters.hpp : 97) Using cell size of 74565 [spades] 0:00:22.487 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 7968764 reads [spades] 0:00:22.869 326M / 5G INFO General (kmer_splitters.hpp : 293) Used 7968764 reads [spades] 0:00:22.870 326M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:23.240 243M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 12501337 kmers in total. [spades] 0:00:23.242 243M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:23.369 237M / 5G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:23.370 237M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:23.370 237M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:23.371 237M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:23.372 237M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:23.372 237M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 [spades] 0:00:23.972 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 12501337 kmers [spades] 0:00:23.973 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 12501337 kmers. [spades] 0:00:24.041 215M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:24.259 215M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 12502300 kmers in total. [spades] 0:00:24.260 215M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:24.368 215M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:24.674 224M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:24.836 224M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5805464 bytes occupied (3.71481 bits per kmer). [spades] 0:00:24.855 236M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:25.253 236M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:25.257 236M / 5G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping [spades] 0:00:25.258 236M / 5G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) [spades] 0:00:25.260 236M / 5G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping [spades] 0:00:25.677 242M / 5G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 71381 [spades] 0:00:25.681 242M / 5G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 71739 [spades] 0:00:25.693 242M / 5G INFO Early tip clipping (early_simplification.hpp : 30) 3256421 32-mers were removed by early tip clipper [spades] 0:00:25.694 242M / 5G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:25.696 242M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:26.106 203M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 87385 sequences extracted [spades] 0:00:26.333 203M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:26.458 203M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 5 loops collected [spades] 0:00:26.834 204M / 5G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:26.835 204M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:26.836 204M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:27.033 221M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5812608 bytes occupied (3.71967 bits per kmer). [spades] 0:00:27.066 269M / 5G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:35.382 268M / 5G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:35.666 268M / 5G INFO General (construction.cpp : 505) Processed 174730 edges [spades] 0:00:35.717 207M / 5G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:35.719 207M / 5G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 15 [spades] 0:00:35.720 207M / 5G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 110 [spades] 0:00:35.721 207M / 5G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 110. Coverage mad: 22.239 [spades] 0:00:35.721 207M / 5G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:35.823 207M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:36.103 207M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:37.085 207M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:38.128 207M / 5G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 110.953. Fitted coverage std. dev: 20.1203 [spades] 0:00:38.133 207M / 5G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.999767 [spades] 0:00:38.133 207M / 5G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 70 [spades] 0:00:38.134 207M / 5G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 62 [spades] 0:00:38.135 207M / 5G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 4908515 [spades] 0:00:38.135 207M / 5G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 110.953 [spades] 0:00:38.136 207M / 5G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 62 [spades] 0:00:38.137 207M / 5G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:38.137 207M / 5G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:38.144 207M / 5G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:38.147 207M / 5G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:38.149 207M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:38.162 207M / 5G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:38.163 207M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:38.165 207M / 5G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:38.166 207M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:38.167 207M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:38.168 207M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:38.199 139M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 835 times [spades] 0:00:38.200 139M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:38.725 127M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 15329 times [spades] 0:00:38.726 127M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:38.897 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5435 times [spades] 0:00:38.898 128M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:38.899 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:38.922 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 403 times [spades] 0:00:38.923 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:38.925 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 16 times [spades] 0:00:38.925 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:38.931 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 130 times [spades] 0:00:38.931 128M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:38.932 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:38.934 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 11 times [spades] 0:00:38.934 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:38.935 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times [spades] 0:00:38.935 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:38.938 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 69 times [spades] 0:00:38.938 128M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:38.939 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:38.940 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8 times [spades] 0:00:38.941 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:38.941 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:38.942 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:38.943 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 37 times [spades] 0:00:38.944 128M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:38.944 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:38.945 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times [spades] 0:00:38.946 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:38.946 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:38.947 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:38.949 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 27 times [spades] 0:00:38.949 128M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:38.950 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:38.951 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:38.951 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:38.952 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:38.952 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:38.953 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times [spades] 0:00:38.954 128M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:38.954 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:38.955 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:38.956 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:38.956 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:38.957 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:38.958 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times [spades] 0:00:38.958 128M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:38.959 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:38.959 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:38.960 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:38.961 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:38.961 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:38.962 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8 times [spades] 0:00:38.963 128M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:38.964 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:38.964 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:38.965 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:38.965 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:38.966 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:38.967 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:38.967 128M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:38.968 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:38.968 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:38.969 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:38.969 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:38.970 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:38.971 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6 times [spades] 0:00:38.971 128M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:38.972 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:38.977 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times [spades] 0:00:38.978 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:38.984 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:38.985 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:38.989 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:38.990 128M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 [spades] 0:00:38.991 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:38.992 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:38.993 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:38.994 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:38.995 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:38.996 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:39.000 128M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:39.001 128M / 5G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:39.001 128M / 5G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:39.002 128M / 5G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:39.003 128M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:39.004 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:39.009 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:39.010 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:39.015 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:39.016 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:39.020 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:39.021 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:39.027 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:39.027 128M / 5G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:39.046 128M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:39.104 128M / 5G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 21414 times [spades] 0:00:39.105 128M / 5G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:39.108 128M / 5G INFO General (simplification.cpp : 502) Average coverage = 101.799 [spades] 0:00:39.108 128M / 5G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:39.115 128M / 5G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K31/simplified_contigs [spades] 0:00:39.124 132M / 5G INFO General (binary_converter.cpp : 111) 1912 reads written [spades] 0:00:39.128 132M / 5G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:39.139 132M / 5G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 39 seconds [spades] [spades] ===== K31 finished. [spades] [spades] [spades] ===== K41 started. [spades] [spades] [spades] == Running: /home/administrator/conda2/envs/shovill/bin/spades-core /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K41/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K41/configs/isolate_mode.info [spades] [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K31/simplified_contigs [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K41/configs/config.info [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K41/configs/isolate_mode.info [spades] 0:00:00.001 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/dataset.info) with K=41 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 30 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 194) SPAdes started [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0 [spades] 0:00:00.001 7M / 9M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion [spades] 0:00:00.003 7M / 9M INFO General (read_converter.cpp : 53) Binary reads detected [spades] 0:00:00.004 8M / 9M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:00.005 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K31/simplified_contigs [spades] 0:00:00.010 8M / 9M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.010 8M / 9M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.010 8M / 9M INFO General (construction.cpp : 156) Average read length 173.568 [spades] 0:00:00.010 8M / 9M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.010 8M / 9M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.012 8M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.012 8M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.012 8M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 37282 [spades] 0:00:07.528 20G / 20G INFO General (kmer_splitters.hpp : 287) Processed 7972588 reads [spades] 0:00:08.248 212M / 9G INFO General (kmer_splitters.hpp : 293) Used 7972588 reads [spades] 0:00:08.249 212M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:08.661 212M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 12430189 kmers in total. [spades] 0:00:08.662 212M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:08.872 212M / 9G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:08.872 212M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:08.873 212M / 9G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:08.873 212M / 9G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:08.874 212M / 9G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:08.874 212M / 9G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:09.500 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 12430189 kmers [spades] 0:00:09.505 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 12430189 kmers. [spades] 0:00:09.599 240M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:09.880 236M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 12441600 kmers in total. [spades] 0:00:09.881 236M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:10.082 236M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:10.372 239M / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:10.719 239M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5777224 bytes occupied (3.71478 bits per kmer). [spades] 0:00:10.737 251M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:11.265 251M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:11.271 231M / 9G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping [spades] 0:00:11.273 231M / 9G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) [spades] 0:00:11.275 231M / 9G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping [spades] 0:00:11.723 233M / 9G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 69828 [spades] 0:00:11.728 233M / 9G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 70172 [spades] 0:00:11.743 233M / 9G INFO Early tip clipping (early_simplification.hpp : 30) 3059253 42-mers were removed by early tip clipper [spades] 0:00:11.744 233M / 9G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:11.747 233M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:12.171 205M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 73665 sequences extracted [spades] 0:00:12.421 205M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:12.542 205M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 5 loops collected [spades] 0:00:12.898 199M / 9G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:12.899 199M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:12.900 199M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:13.090 202M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5779488 bytes occupied (3.71965 bits per kmer). [spades] 0:00:13.124 250M / 9G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:20.988 250M / 9G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:21.284 250M / 9G INFO General (construction.cpp : 505) Processed 147315 edges [spades] 0:00:21.350 122M / 9G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:21.352 122M / 9G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 15 [spades] 0:00:21.353 122M / 9G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 102 [spades] 0:00:21.353 122M / 9G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 102. Coverage mad: 20.7564 [spades] 0:00:21.354 122M / 9G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:21.451 122M / 9G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:21.713 122M / 9G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:22.631 122M / 9G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:23.771 122M / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 103.093. Fitted coverage std. dev: 18.9614 [spades] 0:00:23.776 122M / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.999532 [spades] 0:00:23.776 122M / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 64 [spades] 0:00:23.777 122M / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 59 [spades] 0:00:23.778 122M / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 4899035 [spades] 0:00:23.778 122M / 9G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 103.093 [spades] 0:00:23.779 122M / 9G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 59 [spades] 0:00:23.779 122M / 9G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:23.780 122M / 9G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:23.781 122M / 9G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:23.781 122M / 9G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:23.782 122M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:23.791 122M / 9G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:23.791 122M / 9G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:23.792 122M / 9G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:23.793 122M / 9G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:23.794 122M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:23.795 122M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:23.815 122M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 768 times [spades] 0:00:23.816 122M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.234 105M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11818 times [spades] 0:00:24.235 105M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.377 106M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3076 times [spades] 0:00:24.378 106M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:24.379 106M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.400 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 190 times [spades] 0:00:24.400 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.402 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 14 times [spades] 0:00:24.403 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.406 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 82 times [spades] 0:00:24.407 107M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:24.408 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.410 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 10 times [spades] 0:00:24.411 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.412 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.412 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.414 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 58 times [spades] 0:00:24.414 107M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:24.415 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.417 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8 times [spades] 0:00:24.417 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.418 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.418 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.420 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 34 times [spades] 0:00:24.421 107M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:24.421 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.422 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 5 times [spades] 0:00:24.423 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.424 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:24.424 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.425 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 18 times [spades] 0:00:24.426 107M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:24.426 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.428 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times [spades] 0:00:24.428 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.429 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.429 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.430 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times [spades] 0:00:24.431 107M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:24.431 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.432 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times [spades] 0:00:24.433 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.433 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.434 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.435 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8 times [spades] 0:00:24.436 107M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:24.436 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.437 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.437 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.438 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.439 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.440 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:24.441 107M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:24.441 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.442 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.442 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.443 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.444 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.444 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:24.445 107M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:24.446 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.446 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.447 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.447 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.448 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.450 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6 times [spades] 0:00:24.450 107M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:24.451 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.457 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times [spades] 0:00:24.458 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.463 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.464 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.468 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:24.469 107M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 [spades] 0:00:24.470 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.471 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.472 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.472 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.473 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.474 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:24.478 107M / 9G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:24.479 107M / 9G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:24.479 107M / 9G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:24.480 107M / 9G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:24.481 107M / 9G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:24.482 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.486 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.487 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.492 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.493 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.497 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.498 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.503 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.504 107M / 9G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:24.524 107M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:24.585 107M / 9G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 25657 times [spades] 0:00:24.586 107M / 9G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:24.588 107M / 9G INFO General (simplification.cpp : 502) Average coverage = 94.2657 [spades] 0:00:24.589 107M / 9G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:24.590 107M / 9G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K41/simplified_contigs [spades] 0:00:24.594 111M / 9G INFO General (binary_converter.cpp : 111) 1469 reads written [spades] 0:00:24.596 112M / 9G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:24.602 112M / 9G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 24 seconds [spades] [spades] ===== K41 finished. [spades] [spades] [spades] ===== K51 started. [spades] [spades] [spades] == Running: /home/administrator/conda2/envs/shovill/bin/spades-core /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K51/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K51/configs/isolate_mode.info [spades] [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K41/simplified_contigs [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K51/configs/config.info [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K51/configs/isolate_mode.info [spades] 0:00:00.000 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/dataset.info) with K=51 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 30 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 194) SPAdes started [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0 [spades] 0:00:00.001 7M / 9M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion [spades] 0:00:00.003 7M / 9M INFO General (read_converter.cpp : 53) Binary reads detected [spades] 0:00:00.004 8M / 9M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:00.004 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K41/simplified_contigs [spades] 0:00:00.009 8M / 10M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.009 8M / 10M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.009 8M / 10M INFO General (construction.cpp : 156) Average read length 173.568 [spades] 0:00:00.009 8M / 10M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.009 8M / 10M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.010 8M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.010 8M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.010 8M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 37282 [spades] 0:00:07.053 20G / 20G INFO General (kmer_splitters.hpp : 287) Processed 7971702 reads [spades] 0:00:07.714 212M / 8G INFO General (kmer_splitters.hpp : 293) Used 7971702 reads [spades] 0:00:07.715 212M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:08.127 212M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 12274122 kmers in total. [spades] 0:00:08.128 212M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:08.326 212M / 8G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:08.327 212M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:08.328 212M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:08.328 212M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:08.329 212M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:08.329 212M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:08.940 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 12274122 kmers [spades] 0:00:08.941 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 12274122 kmers. [spades] 0:00:09.025 238M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:09.307 238M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 12292661 kmers in total. [spades] 0:00:09.308 238M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:09.504 238M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:09.794 238M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:10.102 238M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5708392 bytes occupied (3.71499 bits per kmer). [spades] 0:00:10.123 250M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:10.541 250M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:10.545 236M / 8G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping [spades] 0:00:10.547 236M / 8G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) [spades] 0:00:10.549 236M / 8G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping [spades] 0:00:10.961 238M / 8G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 68650 [spades] 0:00:10.964 238M / 8G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 68989 [spades] 0:00:10.978 238M / 8G INFO Early tip clipping (early_simplification.hpp : 30) 2903061 52-mers were removed by early tip clipper [spades] 0:00:10.979 238M / 8G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:10.981 238M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:11.397 222M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 66652 sequences extracted [spades] 0:00:11.645 222M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:11.765 206M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 2 loops collected [spades] 0:00:12.101 204M / 8G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:12.102 204M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:12.103 204M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:12.302 210M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5707280 bytes occupied (3.71988 bits per kmer). [spades] 0:00:12.334 258M / 8G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:19.659 258M / 8G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:19.948 258M / 8G INFO General (construction.cpp : 505) Processed 133298 edges [spades] 0:00:20.012 121M / 8G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:20.014 121M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 30 [spades] 0:00:20.015 121M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 93 [spades] 0:00:20.015 121M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 95. Coverage mad: 19.2738 [spades] 0:00:20.016 121M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:20.107 121M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:20.347 121M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:21.212 121M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:22.137 121M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 95.2532. Fitted coverage std. dev: 17.7965 [spades] 0:00:22.141 121M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.921719 [spades] 0:00:22.141 121M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 59 [spades] 0:00:22.142 121M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 59 [spades] 0:00:22.143 121M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 4855989 [spades] 0:00:22.143 121M / 8G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 95.2532 [spades] 0:00:22.144 121M / 8G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 59 [spades] 0:00:22.145 121M / 8G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:22.145 121M / 8G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:22.146 121M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:22.146 121M / 8G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:22.147 121M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:22.156 121M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:22.156 121M / 8G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:22.157 121M / 8G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:22.158 121M / 8G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:22.159 121M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:22.160 121M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.197 121M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 727 times [spades] 0:00:22.198 121M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.558 107M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 9497 times [spades] 0:00:22.559 107M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:22.691 109M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1924 times [spades] 0:00:22.692 109M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:22.693 109M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.708 110M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 84 times [spades] 0:00:22.708 110M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.712 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 10 times [spades] 0:00:22.712 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:22.717 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 74 times [spades] 0:00:22.718 111M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:22.719 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.721 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times [spades] 0:00:22.721 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.722 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:22.722 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:22.724 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 56 times [spades] 0:00:22.725 111M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:22.725 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.727 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times [spades] 0:00:22.728 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.728 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:22.729 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:22.730 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 24 times [spades] 0:00:22.731 111M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:22.731 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.733 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times [spades] 0:00:22.733 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.734 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:22.734 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:22.735 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 12 times [spades] 0:00:22.736 111M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:22.736 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.737 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:22.738 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.739 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:22.739 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:22.740 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:22.741 111M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:22.741 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.742 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times [spades] 0:00:22.743 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.743 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:22.744 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:22.745 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:22.745 111M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:22.746 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.747 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:22.747 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.748 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:22.749 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:22.750 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:22.750 111M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:22.751 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.752 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:22.752 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.753 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:22.753 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:22.755 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:22.755 111M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:22.756 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.757 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:22.757 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.758 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:22.759 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:22.760 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6 times [spades] 0:00:22.761 111M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:22.762 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.766 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:22.767 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.773 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:22.774 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:22.779 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:22.783 111M / 8G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:22.784 111M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:22.784 111M / 8G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:22.785 111M / 8G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:22.786 111M / 8G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:22.787 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.792 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:22.793 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.798 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:22.798 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.803 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:22.804 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.809 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:22.810 111M / 8G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:22.831 111M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:22.899 111M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 29180 times [spades] 0:00:22.900 111M / 8G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:22.902 111M / 8G INFO General (simplification.cpp : 502) Average coverage = 86.9077 [spades] 0:00:22.903 111M / 8G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:22.904 111M / 8G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K51/simplified_contigs [spades] 0:00:22.909 115M / 8G INFO General (binary_converter.cpp : 111) 1378 reads written [spades] 0:00:22.911 115M / 8G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:22.918 115M / 8G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 22 seconds [spades] [spades] ===== K51 finished. [spades] [spades] [spades] ===== K61 started. [spades] [spades] [spades] == Running: /home/administrator/conda2/envs/shovill/bin/spades-core /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K61/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K61/configs/isolate_mode.info [spades] [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K51/simplified_contigs [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K61/configs/config.info [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K61/configs/isolate_mode.info [spades] 0:00:00.001 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/dataset.info) with K=61 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 30 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 194) SPAdes started [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 218) Will need read mapping, kmer mapper will be attached [spades] 0:00:00.001 7M / 9M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion [spades] 0:00:00.003 7M / 9M INFO General (read_converter.cpp : 53) Binary reads detected [spades] 0:00:00.004 8M / 9M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:00.004 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K51/simplified_contigs [spades] 0:00:00.008 8M / 9M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.008 8M / 9M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.008 8M / 9M INFO General (construction.cpp : 156) Average read length 173.568 [spades] 0:00:00.008 8M / 9M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.008 8M / 9M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.009 8M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.009 8M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.009 8M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 37282 [spades] 0:00:06.423 20G / 20G INFO General (kmer_splitters.hpp : 287) Processed 7971520 reads [spades] 0:00:07.043 215M / 8G INFO General (kmer_splitters.hpp : 293) Used 7971520 reads [spades] 0:00:07.044 215M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:07.447 210M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 12056183 kmers in total. [spades] 0:00:07.449 210M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:07.655 210M / 8G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:07.656 210M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:07.656 210M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:07.657 210M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:07.658 210M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:07.658 210M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:08.299 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 12056183 kmers [spades] 0:00:08.304 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 12056183 kmers. [spades] 0:00:08.395 239M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:08.670 236M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 12080372 kmers in total. [spades] 0:00:08.672 236M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:08.862 236M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:09.143 230M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:09.442 230M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5609848 bytes occupied (3.71502 bits per kmer). [spades] 0:00:09.463 242M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:09.957 242M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:09.964 224M / 8G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:09.971 224M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:10.456 217M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 196756 sequences extracted [spades] 0:00:10.761 213M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:10.879 213M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected [spades] 0:00:11.790 231M / 8G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:11.791 231M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:11.792 231M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:11.975 239M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5605952 bytes occupied (3.71989 bits per kmer). [spades] 0:00:12.008 287M / 8G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:18.783 286M / 8G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:19.156 286M / 8G INFO General (construction.cpp : 505) Processed 393506 edges [spades] 0:00:19.221 155M / 8G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:19.223 155M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 26 [spades] 0:00:19.224 155M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 84 [spades] 0:00:19.224 155M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 87. Coverage mad: 17.7912 [spades] 0:00:19.225 155M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:19.307 155M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:19.524 155M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:20.220 155M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:20.971 155M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 87.4166. Fitted coverage std. dev: 16.624 [spades] 0:00:20.976 155M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.933563 [spades] 0:00:20.976 155M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 54 [spades] 0:00:20.977 155M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 54 [spades] 0:00:20.978 155M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 4853341 [spades] 0:00:20.978 155M / 8G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 87.4166 [spades] 0:00:20.979 155M / 8G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 54 [spades] 0:00:20.979 155M / 8G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:20.980 155M / 8G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:20.981 155M / 8G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:20.981 155M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:20.982 155M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:20.983 155M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:20.984 155M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66591 Gb [spades] 0:00:20.985 155M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:21.338 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 393506 edges [spades] 0:00:21.341 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 393506 sequences. [spades] 0:00:21.407 212M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:21.711 209M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 12056183 kmers in total. [spades] 0:00:21.712 209M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:21.899 209M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:22.206 206M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:22.495 206M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5598648 bytes occupied (3.71504 bits per kmer). [spades] 0:00:22.610 398M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:22.843 398M / 8G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:22.845 398M / 8G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:23.127 408M / 8G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:24.108 395M / 8G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:24.110 395M / 8G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:24.174 396M / 8G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:24.363 389M / 8G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 89 gaps after checking 1075 candidates [spades] 0:00:24.419 389M / 8G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:24.429 197M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:24.430 197M / 8G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:24.431 197M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:24.443 197M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:24.444 197M / 8G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:24.445 197M / 8G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:24.446 197M / 8G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:24.447 197M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:24.448 197M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.175 185M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 68034 times [spades] 0:00:25.176 185M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.596 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7845 times [spades] 0:00:26.597 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.727 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1300 times [spades] 0:00:26.728 213M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:26.728 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.736 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 43 times [spades] 0:00:26.737 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.742 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 10 times [spades] 0:00:26.743 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.745 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 66 times [spades] 0:00:26.746 213M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:26.746 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.748 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times [spades] 0:00:26.748 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.750 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:26.750 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.752 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 51 times [spades] 0:00:26.752 213M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:26.753 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.754 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.754 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.755 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.755 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.757 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 25 times [spades] 0:00:26.757 213M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:26.758 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.759 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:26.760 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.760 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.761 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.762 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 12 times [spades] 0:00:26.762 213M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:26.763 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.764 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times [spades] 0:00:26.765 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.766 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.766 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.767 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:26.767 213M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:26.768 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.769 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.769 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.770 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.770 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.772 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:26.772 213M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:26.773 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.774 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.774 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.775 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.775 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.776 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:26.777 213M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:26.777 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.778 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.778 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.779 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.780 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.782 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:26.782 213M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:26.783 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.783 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.784 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.785 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.785 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.787 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:26.787 213M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:26.788 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.797 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:26.798 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.806 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.807 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.814 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:26.815 213M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 [spades] 0:00:26.816 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.817 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.817 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.818 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.819 213M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.820 213M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:26.827 213M / 8G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:26.828 213M / 8G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:26.829 213M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:26.829 213M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:26.831 213M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:26.832 213M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66523 Gb [spades] 0:00:26.833 213M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:27.082 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 67542 edges [spades] 0:00:27.083 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 67542 sequences. [spades] 0:00:27.140 237M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:27.359 236M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8538815 kmers in total. [spades] 0:00:27.362 236M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:27.517 236M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:27.718 230M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:27.936 230M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3967680 bytes occupied (3.71731 bits per kmer). [spades] 0:00:28.050 390M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:28.282 390M / 8G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:28.285 390M / 8G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:28.387 394M / 8G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:29.379 380M / 8G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:29.380 380M / 8G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:29.428 379M / 8G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:29.475 379M / 8G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 19 gaps after checking 549 candidates [spades] 0:00:29.501 372M / 8G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:29.502 372M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:29.503 372M / 8G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:29.504 372M / 8G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:29.505 372M / 8G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:29.505 372M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:29.513 372M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:29.514 372M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:29.521 372M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:29.522 372M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:29.529 372M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:29.530 372M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:29.537 372M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:29.538 372M / 8G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:29.570 372M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:31.303 364M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 32390 times [spades] 0:00:31.304 364M / 8G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:31.307 364M / 8G INFO General (simplification.cpp : 502) Average coverage = 79.5989 [spades] 0:00:31.308 364M / 8G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:31.309 364M / 8G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K61/simplified_contigs [spades] 0:00:31.321 368M / 8G INFO General (binary_converter.cpp : 111) 1362 reads written [spades] 0:00:31.326 367M / 8G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:31.479 199M / 8G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 31 seconds [spades] [spades] ===== K61 finished. [spades] [spades] [spades] ===== K71 started. [spades] [spades] [spades] == Running: /home/administrator/conda2/envs/shovill/bin/spades-core /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K71/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K71/configs/isolate_mode.info [spades] [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K61/simplified_contigs [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K71/configs/config.info [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K71/configs/isolate_mode.info [spades] 0:00:00.001 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/dataset.info) with K=71 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 30 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 194) SPAdes started [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 218) Will need read mapping, kmer mapper will be attached [spades] 0:00:00.001 7M / 9M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion [spades] 0:00:00.002 7M / 9M INFO General (read_converter.cpp : 53) Binary reads detected [spades] 0:00:00.004 8M / 9M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:00.005 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K61/simplified_contigs [spades] 0:00:00.010 8M / 9M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.010 8M / 9M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.010 8M / 9M INFO General (construction.cpp : 156) Average read length 173.568 [spades] 0:00:00.010 8M / 9M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.011 8M / 9M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.012 8M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.012 8M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.013 8M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 24855 [spades] 0:00:06.641 20G / 20G INFO General (kmer_splitters.hpp : 287) Processed 7971488 reads [spades] 0:00:07.462 203M / 10G INFO General (kmer_splitters.hpp : 293) Used 7971488 reads [spades] 0:00:07.463 203M / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:07.916 203M / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 11787061 kmers in total. [spades] 0:00:07.918 203M / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:08.219 203M / 10G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:08.219 203M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:08.220 203M / 10G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:08.220 203M / 10G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:08.221 203M / 10G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:08.221 203M / 10G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:08.946 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 11787061 kmers [spades] 0:00:08.951 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 11787061 kmers. [spades] 0:00:09.051 242M / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:09.365 242M / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 11816640 kmers in total. [spades] 0:00:09.367 242M / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:09.632 242M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:09.946 245M / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:10.395 245M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5487544 bytes occupied (3.71513 bits per kmer). [spades] 0:00:10.414 257M / 10G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:10.924 257M / 10G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:10.929 238M / 10G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:10.941 238M / 10G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:11.429 220M / 10G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 190723 sequences extracted [spades] 0:00:11.752 220M / 10G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:11.872 220M / 10G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:12.772 225M / 10G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:12.773 225M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:12.774 225M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:12.975 230M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5481168 bytes occupied (3.72013 bits per kmer). [spades] 0:00:13.006 278M / 10G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:19.337 278M / 10G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:19.722 213M / 10G INFO General (construction.cpp : 505) Processed 381445 edges [spades] 0:00:19.796 153M / 10G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:19.798 153M / 10G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 26 [spades] 0:00:19.799 153M / 10G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 78 [spades] 0:00:19.800 153M / 10G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 79. Coverage mad: 17.7912 [spades] 0:00:19.800 153M / 10G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:19.875 153M / 10G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:20.077 153M / 10G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:20.800 153M / 10G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:21.823 153M / 10G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 79.591. Fitted coverage std. dev: 15.4422 [spades] 0:00:21.826 153M / 10G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.845257 [spades] 0:00:21.827 153M / 10G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 49 [spades] 0:00:21.827 153M / 10G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 49 [spades] 0:00:21.828 153M / 10G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 4849855 [spades] 0:00:21.829 153M / 10G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 79.591 [spades] 0:00:21.829 153M / 10G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 49 [spades] 0:00:21.830 153M / 10G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:21.831 153M / 10G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:21.831 153M / 10G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:21.832 153M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:21.833 153M / 10G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:21.834 153M / 10G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:21.835 153M / 10G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66594 Gb [spades] 0:00:21.835 153M / 10G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:22.232 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 381445 edges [spades] 0:00:22.233 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 381445 sequences. [spades] 0:00:22.300 212M / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:22.606 205M / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 11787061 kmers in total. [spades] 0:00:22.608 205M / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:22.874 205M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:23.176 206M / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:23.592 206M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5474016 bytes occupied (3.71527 bits per kmer). [spades] 0:00:23.709 398M / 10G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:23.955 398M / 10G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:23.958 398M / 10G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:24.238 408M / 10G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:25.144 389M / 10G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:25.146 389M / 10G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:25.205 390M / 10G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:25.390 382M / 10G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 25 gaps after checking 1021 candidates [spades] 0:00:25.426 382M / 10G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:25.436 190M / 10G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:25.437 190M / 10G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:25.438 190M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:25.461 190M / 10G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:25.463 190M / 10G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:25.463 190M / 10G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:25.464 190M / 10G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:25.465 190M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:25.466 190M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.191 187M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 65900 times [spades] 0:00:26.192 187M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.588 237M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6443 times [spades] 0:00:27.590 237M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:27.708 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 911 times [spades] 0:00:27.709 239M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:27.709 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.713 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 24 times [spades] 0:00:27.714 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.720 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11 times [spades] 0:00:27.721 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:27.723 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 55 times [spades] 0:00:27.724 239M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:27.725 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.725 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.726 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.727 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:27.727 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:27.729 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 49 times [spades] 0:00:27.729 239M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:27.730 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.731 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.731 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.732 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:27.733 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:27.734 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 20 times [spades] 0:00:27.735 239M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:27.735 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.736 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.737 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.737 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:27.738 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:27.739 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 14 times [spades] 0:00:27.739 239M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:27.740 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.741 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.741 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.742 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:27.742 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:27.743 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times [spades] 0:00:27.744 239M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:27.745 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.745 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.746 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.747 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:27.747 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:27.748 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:27.749 239M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:27.750 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.750 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.751 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.751 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:27.752 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:27.753 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:27.754 239M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:27.754 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.755 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.755 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.756 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:27.757 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:27.758 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:27.759 239M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:27.760 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.760 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.761 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.762 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:27.762 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:27.763 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:27.763 239M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:27.764 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.772 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.773 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.782 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:27.783 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:27.791 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:27.792 239M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 [spades] 0:00:27.793 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.794 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.795 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.796 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:27.797 239M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:27.798 239M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:27.806 239M / 10G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:27.807 239M / 10G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:27.808 239M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:27.808 239M / 10G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:27.810 239M / 10G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:27.812 239M / 10G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.665 Gb [spades] 0:00:27.812 239M / 10G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:28.118 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 74754 edges [spades] 0:00:28.121 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 74754 sequences. [spades] 0:00:28.189 251M / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:28.443 251M / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8502028 kmers in total. [spades] 0:00:28.445 251M / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:28.641 251M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:28.868 253M / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:29.180 253M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3950544 bytes occupied (3.71727 bits per kmer). [spades] 0:00:29.304 413M / 10G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:29.503 413M / 10G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:29.506 413M / 10G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:29.611 417M / 10G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:30.555 400M / 10G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:30.556 400M / 10G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:30.607 400M / 10G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:30.658 400M / 10G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 5 gaps after checking 511 candidates [spades] 0:00:30.674 396M / 10G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:30.675 396M / 10G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:30.676 396M / 10G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:30.677 396M / 10G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:30.678 396M / 10G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:30.679 396M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:30.687 396M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:30.688 396M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:30.695 396M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:30.696 396M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:30.704 396M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:30.705 396M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:30.713 396M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:30.714 396M / 10G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:30.747 396M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:32.580 382M / 10G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 36064 times [spades] 0:00:32.582 382M / 10G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:32.585 382M / 10G INFO General (simplification.cpp : 502) Average coverage = 72.6466 [spades] 0:00:32.585 382M / 10G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:32.587 382M / 10G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K71/simplified_contigs [spades] 0:00:32.598 386M / 10G INFO General (binary_converter.cpp : 111) 1308 reads written [spades] 0:00:32.602 386M / 10G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:32.780 222M / 10G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 32 seconds [spades] [spades] ===== K71 finished. [spades] [spades] [spades] ===== K81 started. [spades] [spades] [spades] == Running: /home/administrator/conda2/envs/shovill/bin/spades-core /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K81/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K81/configs/isolate_mode.info [spades] [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K71/simplified_contigs [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K81/configs/config.info [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K81/configs/isolate_mode.info [spades] 0:00:00.001 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/dataset.info) with K=81 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 30 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 194) SPAdes started [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 218) Will need read mapping, kmer mapper will be attached [spades] 0:00:00.001 7M / 9M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion [spades] 0:00:00.003 7M / 9M INFO General (read_converter.cpp : 53) Binary reads detected [spades] 0:00:00.005 8M / 9M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:00.006 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K71/simplified_contigs [spades] 0:00:00.011 8M / 10M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.011 8M / 10M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.011 8M / 10M INFO General (construction.cpp : 156) Average read length 173.568 [spades] 0:00:00.012 8M / 10M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.013 8M / 10M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.015 8M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.015 8M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.015 8M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 24855 [spades] 0:00:06.209 20G / 20G INFO General (kmer_splitters.hpp : 287) Processed 7971380 reads [spades] 0:00:06.939 217M / 9G INFO General (kmer_splitters.hpp : 293) Used 7971380 reads [spades] 0:00:06.939 217M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:07.381 217M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 11460785 kmers in total. [spades] 0:00:07.384 217M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:07.656 210M / 9G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:07.657 210M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:07.657 210M / 9G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:07.658 210M / 9G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:07.659 210M / 9G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:07.659 210M / 9G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:08.390 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 11460785 kmers [spades] 0:00:08.393 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 11460785 kmers. [spades] 0:00:08.494 243M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:08.801 243M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 11495689 kmers in total. [spades] 0:00:08.803 243M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:09.070 243M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:09.369 246M / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:09.817 246M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5338664 bytes occupied (3.71525 bits per kmer). [spades] 0:00:09.839 258M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:10.283 258M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:10.290 234M / 9G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:10.296 234M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:10.785 215M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 185112 sequences extracted [spades] 0:00:11.104 215M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:11.217 215M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:12.121 226M / 9G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:12.123 226M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:12.123 226M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:12.317 229M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5329920 bytes occupied (3.72046 bits per kmer). [spades] 0:00:12.349 277M / 9G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:18.103 267M / 9G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:18.479 267M / 9G INFO General (construction.cpp : 505) Processed 370225 edges [spades] 0:00:18.551 207M / 9G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:18.553 207M / 9G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 24 [spades] 0:00:18.554 207M / 9G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 70 [spades] 0:00:18.554 207M / 9G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 71. Coverage mad: 16.3086 [spades] 0:00:18.555 207M / 9G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:18.624 207M / 9G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:18.807 207M / 9G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:19.488 207M / 9G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:20.648 207M / 9G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:20.925 207M / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 71.7733. Fitted coverage std. dev: 14.2459 [spades] 0:00:20.928 207M / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.780511 [spades] 0:00:20.929 207M / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 43 [spades] 0:00:20.929 207M / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 43 [spades] 0:00:20.930 207M / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 4861732 [spades] 0:00:20.930 207M / 9G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 71.7733 [spades] 0:00:20.931 207M / 9G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 43 [spades] 0:00:20.932 207M / 9G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:20.932 207M / 9G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:20.933 207M / 9G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:20.933 207M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:20.934 207M / 9G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:20.936 148M / 9G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:20.937 148M / 9G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66597 Gb [spades] 0:00:20.938 148M / 9G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:21.331 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 370225 edges [spades] 0:00:21.333 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 370225 sequences. [spades] 0:00:21.398 182M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:21.701 181M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 11460785 kmers in total. [spades] 0:00:21.703 181M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:21.964 181M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:22.258 178M / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:22.687 178M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5322544 bytes occupied (3.71531 bits per kmer). [spades] 0:00:22.799 370M / 9G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:23.050 366M / 9G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:23.052 366M / 9G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:23.334 377M / 9G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:24.186 354M / 9G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:24.188 354M / 9G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:24.248 355M / 9G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:24.433 359M / 9G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 31 gaps after checking 998 candidates [spades] 0:00:24.478 359M / 9G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:24.488 167M / 9G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:24.489 167M / 9G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:24.490 167M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:24.502 167M / 9G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:24.503 167M / 9G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:24.504 167M / 9G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:24.505 167M / 9G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:24.506 167M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:24.507 167M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.200 161M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 63010 times [spades] 0:00:25.201 161M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.457 216M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5332 times [spades] 0:00:26.459 216M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.571 218M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 692 times [spades] 0:00:26.572 218M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:26.573 218M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.577 218M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 14 times [spades] 0:00:26.577 218M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.584 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 8 times [spades] 0:00:26.584 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.587 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 47 times [spades] 0:00:26.588 219M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:26.588 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.589 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.590 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.590 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.591 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.599 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 48 times [spades] 0:00:26.600 219M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:26.600 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.601 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.601 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.602 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.603 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.604 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 24 times [spades] 0:00:26.604 219M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:26.605 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.606 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.606 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.607 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.607 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.608 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 12 times [spades] 0:00:26.609 219M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:26.609 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.610 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.611 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.611 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.612 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.613 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6 times [spades] 0:00:26.613 219M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:26.614 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.615 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.615 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.616 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.616 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.618 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:26.618 219M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:26.619 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.620 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.620 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.621 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.621 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.623 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:26.623 219M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:26.624 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.624 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.625 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.626 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.626 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.627 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:26.628 219M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:26.629 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.629 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.630 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.630 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.631 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.633 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:26.633 219M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:26.634 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.642 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.643 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.652 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.653 219M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.661 219M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:26.669 219M / 9G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:26.669 219M / 9G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:26.670 219M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:26.671 219M / 9G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:26.672 219M / 9G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:26.674 219M / 9G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.6651 Gb [spades] 0:00:26.675 219M / 9G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:27.002 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 82532 edges [spades] 0:00:27.004 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 82532 sequences. [spades] 0:00:27.066 261M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:27.319 260M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8413366 kmers in total. [spades] 0:00:27.321 260M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:27.509 260M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:27.728 256M / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:28.049 256M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3909528 bytes occupied (3.71744 bits per kmer). [spades] 0:00:28.169 416M / 9G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:28.420 410M / 9G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:28.423 410M / 9G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:28.536 415M / 9G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:29.764 404M / 9G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:29.766 404M / 9G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:29.841 404M / 9G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:29.903 396M / 9G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 6 gaps after checking 551 candidates [spades] 0:00:29.924 396M / 9G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:29.925 396M / 9G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:29.926 396M / 9G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:29.927 396M / 9G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:29.928 396M / 9G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:29.929 396M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:29.939 396M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:29.940 396M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:29.971 396M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:29.972 396M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:30.003 396M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:30.004 396M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:30.035 396M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:30.036 396M / 9G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:30.072 396M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:32.102 378M / 9G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 40069 times [spades] 0:00:32.103 378M / 9G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:32.106 378M / 9G INFO General (simplification.cpp : 502) Average coverage = 65.7835 [spades] 0:00:32.106 378M / 9G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:32.108 378M / 9G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K81/simplified_contigs [spades] 0:00:32.116 382M / 9G INFO General (binary_converter.cpp : 111) 1191 reads written [spades] 0:00:32.121 382M / 9G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:32.304 211M / 9G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 32 seconds [spades] [spades] ===== K81 finished. [spades] [spades] [spades] ===== K91 started. [spades] [spades] [spades] == Running: /home/administrator/conda2/envs/shovill/bin/spades-core /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K91/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K91/configs/isolate_mode.info [spades] [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K81/simplified_contigs [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K91/configs/config.info [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K91/configs/isolate_mode.info [spades] 0:00:00.000 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/dataset.info) with K=91 [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 30 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 194) SPAdes started [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 218) Will need read mapping, kmer mapper will be attached [spades] 0:00:00.001 7M / 9M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion [spades] 0:00:00.002 7M / 9M INFO General (read_converter.cpp : 53) Binary reads detected [spades] 0:00:00.004 8M / 9M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:00.004 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K81/simplified_contigs [spades] 0:00:00.008 9M / 9M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.008 9M / 9M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.009 9M / 9M INFO General (construction.cpp : 156) Average read length 173.568 [spades] 0:00:00.009 9M / 9M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.009 9M / 9M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.010 9M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.010 9M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.010 9M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 24855 [spades] 0:00:05.553 20G / 20G INFO General (kmer_splitters.hpp : 287) Processed 7971146 reads [spades] 0:00:06.185 227M / 8G INFO General (kmer_splitters.hpp : 293) Used 7971146 reads [spades] 0:00:06.185 227M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:06.651 222M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 11076379 kmers in total. [spades] 0:00:06.652 222M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:06.920 222M / 8G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:06.921 222M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:06.921 222M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:06.922 222M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:06.922 222M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:06.923 222M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:07.580 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 11076379 kmers [spades] 0:00:07.581 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 11076379 kmers. [spades] 0:00:07.674 281M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:07.986 281M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 11117593 kmers in total. [spades] 0:00:07.987 281M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:08.233 281M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:08.502 284M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:08.919 284M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5163320 bytes occupied (3.71542 bits per kmer). [spades] 0:00:08.940 296M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:09.338 296M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:09.344 279M / 8G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:09.348 279M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:09.877 269M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 178703 sequences extracted [spades] 0:00:10.189 262M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:10.296 262M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:11.130 260M / 8G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:11.131 260M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:11.132 260M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:11.328 259M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5151304 bytes occupied (3.72057 bits per kmer). [spades] 0:00:11.357 307M / 8G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:16.529 307M / 8G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:16.885 307M / 8G INFO General (construction.cpp : 505) Processed 357408 edges [spades] 0:00:16.957 247M / 8G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:16.960 152M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 21 [spades] 0:00:16.961 152M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 63 [spades] 0:00:16.961 152M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 64. Coverage mad: 14.826 [spades] 0:00:16.962 152M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:17.026 152M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:17.188 152M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:17.781 152M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:18.794 152M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:19.029 152M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 63.9652. Fitted coverage std. dev: 13.0279 [spades] 0:00:19.032 152M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.754367 [spades] 0:00:19.032 152M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 38 [spades] 0:00:19.033 152M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 38 [spades] 0:00:19.033 152M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 4859484 [spades] 0:00:19.034 152M / 8G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 63.9652 [spades] 0:00:19.035 152M / 8G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 38 [spades] 0:00:19.035 152M / 8G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:19.036 152M / 8G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:19.037 152M / 8G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:19.037 152M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:19.038 152M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:19.039 152M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:19.040 152M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66596 Gb [spades] 0:00:19.041 152M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:19.422 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 357408 edges [spades] 0:00:19.423 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 357408 sequences. [spades] 0:00:19.487 199M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:19.801 198M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 11076379 kmers in total. [spades] 0:00:19.803 198M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:20.056 198M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:20.353 196M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:20.766 196M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 5144184 bytes occupied (3.71543 bits per kmer). [spades] 0:00:20.881 388M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:21.104 388M / 8G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:21.106 388M / 8G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:21.429 400M / 8G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:22.287 378M / 8G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:22.289 378M / 8G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:22.363 374M / 8G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:22.553 372M / 8G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 35 gaps after checking 943 candidates [spades] 0:00:22.584 372M / 8G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:22.594 180M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:22.595 180M / 8G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:22.595 180M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:22.606 180M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:22.607 180M / 8G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:22.608 180M / 8G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:22.609 180M / 8G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:22.610 180M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:22.611 180M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:23.274 172M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 59151 times [spades] 0:00:23.275 172M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.408 209M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4179 times [spades] 0:00:24.409 209M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.528 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 578 times [spades] 0:00:24.529 211M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:24.530 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.532 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 10 times [spades] 0:00:24.533 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.537 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5 times [spades] 0:00:24.538 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.546 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 56 times [spades] 0:00:24.547 211M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:24.547 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.548 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.549 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.549 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.550 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.555 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 42 times [spades] 0:00:24.556 211M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:24.556 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.557 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.557 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.558 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.559 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.561 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 23 times [spades] 0:00:24.561 211M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:24.562 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.563 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.563 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.564 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.564 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.565 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 9 times [spades] 0:00:24.566 211M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:24.566 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.567 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.567 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.568 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.568 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.570 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8 times [spades] 0:00:24.571 211M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:24.571 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.572 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.573 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.573 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.574 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.575 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:24.576 211M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:24.576 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.577 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.577 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.578 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.578 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.580 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:24.580 211M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:24.581 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.581 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.582 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.582 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.583 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.584 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:24.585 211M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:24.585 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.586 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.587 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.587 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.588 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.589 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:24.590 211M / 8G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:24.590 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.614 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.615 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.642 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.643 211M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.678 211M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:24.706 211M / 8G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:24.706 211M / 8G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:24.707 211M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:24.708 211M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:24.709 211M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:24.711 211M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66522 Gb [spades] 0:00:24.712 211M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:25.017 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 92526 edges [spades] 0:00:25.019 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 92526 sequences. [spades] 0:00:25.080 242M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:25.344 242M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8311600 kmers in total. [spades] 0:00:25.346 242M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:25.523 242M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:25.733 237M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:26.028 237M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3862416 bytes occupied (3.71761 bits per kmer). [spades] 0:00:26.157 365M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:26.387 357M / 8G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:26.390 357M / 8G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:26.502 363M / 8G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:27.311 352M / 8G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:27.313 352M / 8G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:27.383 353M / 8G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:27.451 346M / 8G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 6 gaps after checking 585 candidates [spades] 0:00:27.473 346M / 8G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:27.474 346M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:27.475 346M / 8G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:27.476 346M / 8G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:27.477 346M / 8G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:27.477 346M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.487 346M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.488 346M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.496 346M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:27.497 346M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.506 346M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.507 346M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.515 346M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:27.516 346M / 8G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:27.554 346M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:29.473 335M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 45126 times [spades] 0:00:29.474 335M / 8G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:29.477 335M / 8G INFO General (simplification.cpp : 502) Average coverage = 58.8028 [spades] 0:00:29.478 335M / 8G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:29.479 335M / 8G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K91/simplified_contigs [spades] 0:00:29.486 335M / 8G INFO General (binary_converter.cpp : 111) 1131 reads written [spades] 0:00:29.489 335M / 8G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:29.617 200M / 8G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 29 seconds [spades] [spades] ===== K91 finished. [spades] [spades] [spades] ===== K101 started. [spades] [spades] [spades] == Running: /home/administrator/conda2/envs/shovill/bin/spades-core /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K101/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K101/configs/isolate_mode.info [spades] [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K91/simplified_contigs [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K101/configs/config.info [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K101/configs/isolate_mode.info [spades] 0:00:00.001 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/dataset.info) with K=101 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 30 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 194) SPAdes started [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 218) Will need read mapping, kmer mapper will be attached [spades] 0:00:00.001 7M / 9M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion [spades] 0:00:00.003 7M / 9M INFO General (read_converter.cpp : 53) Binary reads detected [spades] 0:00:00.004 8M / 9M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:00.004 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K91/simplified_contigs [spades] 0:00:00.007 8M / 10M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.007 8M / 10M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.008 8M / 10M INFO General (construction.cpp : 156) Average read length 173.568 [spades] 0:00:00.008 8M / 10M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.008 8M / 10M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.009 8M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.009 8M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.009 8M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 18641 [spades] 0:00:05.540 20G / 20G INFO General (kmer_splitters.hpp : 287) Processed 7971026 reads [spades] 0:00:06.303 217M / 10G INFO General (kmer_splitters.hpp : 293) Used 7971026 reads [spades] 0:00:06.304 217M / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:06.757 217M / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 10623466 kmers in total. [spades] 0:00:06.759 217M / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:07.094 210M / 10G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:07.095 210M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:07.095 210M / 10G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:07.096 210M / 10G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:07.097 210M / 10G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:07.097 210M / 10G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:07.885 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 10623466 kmers [spades] 0:00:07.893 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 10623466 kmers. [spades] 0:00:08.011 280M / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:08.355 280M / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 10671867 kmers in total. [spades] 0:00:08.356 280M / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:08.677 280M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:08.972 273M / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:09.488 273M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4956472 bytes occupied (3.71554 bits per kmer). [spades] 0:00:09.505 285M / 10G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:09.987 285M / 10G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:09.994 251M / 10G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:10.001 251M / 10G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:10.450 223M / 10G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 171551 sequences extracted [spades] 0:00:10.758 223M / 10G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:10.864 223M / 10G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:11.708 228M / 10G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:11.709 228M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:11.710 228M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:11.891 238M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4942008 bytes occupied (3.72158 bits per kmer). [spades] 0:00:11.919 286M / 10G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:16.555 286M / 10G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:16.909 286M / 10G INFO General (construction.cpp : 505) Processed 343104 edges [spades] 0:00:16.991 155M / 10G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:16.992 155M / 10G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 19 [spades] 0:00:16.993 155M / 10G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 53 [spades] 0:00:16.994 155M / 10G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 56. Coverage mad: 13.3434 [spades] 0:00:16.994 155M / 10G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:17.049 155M / 10G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:17.193 155M / 10G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:17.691 155M / 10G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:18.612 155M / 10G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:18.612 155M / 10G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 56.1704. Fitted coverage std. dev: 11.7904 [spades] 0:00:18.615 155M / 10G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.652281 [spades] 0:00:18.616 155M / 10G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 33 [spades] 0:00:18.618 155M / 10G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 33 [spades] 0:00:18.618 155M / 10G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 4857365 [spades] 0:00:18.619 155M / 10G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 56.1704 [spades] 0:00:18.619 155M / 10G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 33 [spades] 0:00:18.620 155M / 10G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:18.621 155M / 10G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:18.621 155M / 10G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:18.622 155M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:18.623 155M / 10G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:18.623 155M / 10G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:18.625 155M / 10G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66596 Gb [spades] 0:00:18.625 155M / 10G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:19.058 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 343104 edges [spades] 0:00:19.059 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 343104 sequences. [spades] 0:00:19.129 234M / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:19.446 228M / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 10623466 kmers in total. [spades] 0:00:19.449 228M / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:19.771 228M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:20.078 227M / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:20.604 227M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4934160 bytes occupied (3.71567 bits per kmer). [spades] 0:00:20.708 419M / 10G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:20.941 415M / 10G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:20.944 415M / 10G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:21.224 427M / 10G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:21.988 400M / 10G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:22.000 400M / 10G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:22.064 401M / 10G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:22.242 393M / 10G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 40 gaps after checking 913 candidates [spades] 0:00:22.285 393M / 10G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:22.298 201M / 10G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:22.299 201M / 10G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:22.300 201M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:22.311 201M / 10G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:22.312 201M / 10G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:22.313 201M / 10G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:22.314 201M / 10G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:22.315 201M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:22.316 201M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.937 200M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 54541 times [spades] 0:00:22.938 200M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:23.898 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2997 times [spades] 0:00:23.899 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.016 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 471 times [spades] 0:00:24.017 232M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:24.018 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.020 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 7 times [spades] 0:00:24.021 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.024 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times [spades] 0:00:24.024 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.032 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 54 times [spades] 0:00:24.033 232M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:24.034 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.034 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.035 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.036 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:24.037 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.040 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 34 times [spades] 0:00:24.040 232M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:24.041 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.041 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.042 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.043 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.043 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.048 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 21 times [spades] 0:00:24.049 232M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:24.049 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.050 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.050 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.051 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.052 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.053 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 12 times [spades] 0:00:24.054 232M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:24.054 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.055 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.055 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.056 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.057 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.059 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6 times [spades] 0:00:24.059 232M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:24.060 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.061 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.061 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.062 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.063 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.065 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:24.065 232M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:24.066 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.067 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.067 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.068 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.068 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.069 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:24.070 232M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:24.070 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.071 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.072 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.072 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.073 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.074 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:24.075 232M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:24.076 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.076 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.077 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.078 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.078 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.080 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:24.081 232M / 10G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:24.081 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.100 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.101 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.132 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.133 232M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:24.164 232M / 10G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:24.198 232M / 10G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:24.199 232M / 10G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:24.200 232M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:24.200 232M / 10G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:24.202 232M / 10G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:24.203 232M / 10G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.6653 Gb [spades] 0:00:24.204 232M / 10G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:24.571 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 104246 edges [spades] 0:00:24.572 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 104246 sequences. [spades] 0:00:24.637 241M / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:24.913 241M / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8160186 kmers in total. [spades] 0:00:24.915 241M / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:25.162 241M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:25.386 242M / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:25.784 242M / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3792288 bytes occupied (3.71784 bits per kmer). [spades] 0:00:25.919 370M / 10G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:26.127 362M / 10G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:26.130 362M / 10G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:26.253 370M / 10G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:27.028 345M / 10G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:27.029 345M / 10G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:27.106 347M / 10G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:27.189 340M / 10G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 4 gaps after checking 650 candidates [spades] 0:00:27.227 340M / 10G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:27.228 340M / 10G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:27.229 340M / 10G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:27.230 340M / 10G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:27.230 340M / 10G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:27.231 340M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.239 340M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.240 340M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.250 340M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:27.251 340M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:27.261 340M / 10G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:27.262 340M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:27.271 340M / 10G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:27.272 340M / 10G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:27.313 340M / 10G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:29.262 317M / 10G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 51036 times [spades] 0:00:29.263 317M / 10G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:29.266 317M / 10G INFO General (simplification.cpp : 502) Average coverage = 51.7995 [spades] 0:00:29.267 317M / 10G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:29.268 317M / 10G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K101/simplified_contigs [spades] 0:00:29.279 321M / 10G INFO General (binary_converter.cpp : 111) 1083 reads written [spades] 0:00:29.283 322M / 10G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:29.410 191M / 10G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 29 seconds [spades] [spades] ===== K101 finished. [spades] [spades] [spades] ===== K111 started. [spades] [spades] [spades] == Running: /home/administrator/conda2/envs/shovill/bin/spades-core /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K111/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K111/configs/isolate_mode.info [spades] [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K101/simplified_contigs [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K111/configs/config.info [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K111/configs/isolate_mode.info [spades] 0:00:00.001 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/dataset.info) with K=111 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 30 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 194) SPAdes started [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 218) Will need read mapping, kmer mapper will be attached [spades] 0:00:00.001 7M / 9M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion [spades] 0:00:00.003 7M / 9M INFO General (read_converter.cpp : 53) Binary reads detected [spades] 0:00:00.005 8M / 9M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:00.005 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K101/simplified_contigs [spades] 0:00:00.008 8M / 9M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.008 8M / 9M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.008 8M / 9M INFO General (construction.cpp : 156) Average read length 173.568 [spades] 0:00:00.009 8M / 9M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.009 8M / 9M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.010 8M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.010 8M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.010 8M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 18641 [spades] 0:00:05.006 20G / 20G INFO General (kmer_splitters.hpp : 287) Processed 7970930 reads [spades] 0:00:05.652 211M / 9G INFO General (kmer_splitters.hpp : 293) Used 7970930 reads [spades] 0:00:05.653 211M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:06.110 211M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 10093007 kmers in total. [spades] 0:00:06.112 211M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:06.436 204M / 9G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:06.437 204M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:06.437 204M / 9G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:06.438 204M / 9G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:06.439 204M / 9G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:06.439 204M / 9G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:07.159 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 10093007 kmers [spades] 0:00:07.160 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 10093007 kmers. [spades] 0:00:07.273 271M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:07.617 271M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 10149644 kmers in total. [spades] 0:00:07.618 271M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:07.920 271M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:08.188 266M / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:08.703 266M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4714552 bytes occupied (3.71603 bits per kmer). [spades] 0:00:08.723 276M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:09.097 276M / 9G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:09.104 251M / 9G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:09.109 251M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:09.542 229M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 163590 sequences extracted [spades] 0:00:09.839 226M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:09.939 226M / 9G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:10.767 224M / 9G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:10.768 224M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:10.769 224M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:10.950 231M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4695904 bytes occupied (3.72211 bits per kmer). [spades] 0:00:10.978 271M / 9G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:15.014 271M / 9G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:15.350 271M / 9G INFO General (construction.cpp : 505) Processed 327182 edges [spades] 0:00:15.432 221M / 9G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:15.433 221M / 9G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 17 [spades] 0:00:15.434 221M / 9G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 47 [spades] 0:00:15.435 221M / 9G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 48. Coverage mad: 11.8608 [spades] 0:00:15.435 221M / 9G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:15.482 221M / 9G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:15.603 221M / 9G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:16.047 221M / 9G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:16.795 221M / 9G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:16.795 221M / 9G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 48.3834. Fitted coverage std. dev: 10.5393 [spades] 0:00:16.798 221M / 9G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.508916 [spades] 0:00:16.798 221M / 9G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 28 [spades] 0:00:16.799 221M / 9G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 28 [spades] 0:00:16.799 221M / 9G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 4855896 [spades] 0:00:16.800 221M / 9G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 48.3834 [spades] 0:00:16.801 221M / 9G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 28 [spades] 0:00:16.801 221M / 9G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:16.802 221M / 9G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:16.803 221M / 9G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:16.803 221M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:16.804 221M / 9G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:16.805 221M / 9G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:16.806 221M / 9G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66601 Gb [spades] 0:00:16.807 221M / 9G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:17.235 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 327182 edges [spades] 0:00:17.238 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 327182 sequences. [spades] 0:00:17.313 265M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:17.618 257M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 10093007 kmers in total. [spades] 0:00:17.621 257M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:17.909 257M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:18.164 257M / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:18.677 257M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4688336 bytes occupied (3.71611 bits per kmer). [spades] 0:00:18.782 417M / 9G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:18.984 417M / 9G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:18.986 417M / 9G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:19.273 429M / 9G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:19.944 405M / 9G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:19.946 405M / 9G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:20.008 406M / 9G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:20.183 402M / 9G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 44 gaps after checking 877 candidates [spades] 0:00:20.221 394M / 9G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:20.229 234M / 9G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:20.230 234M / 9G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:20.231 234M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:20.247 234M / 9G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:20.248 234M / 9G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:20.248 234M / 9G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:20.249 234M / 9G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:20.250 234M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:20.251 234M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:20.841 229M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 48961 times [spades] 0:00:20.843 229M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:21.444 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1792 times [spades] 0:00:21.445 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:21.548 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 393 times [spades] 0:00:21.549 233M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:21.550 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:21.551 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 4 times [spades] 0:00:21.552 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:21.554 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times [spades] 0:00:21.555 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:21.567 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 54 times [spades] 0:00:21.567 233M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:21.568 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:21.569 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:21.569 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:21.570 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:21.570 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:21.572 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 25 times [spades] 0:00:21.572 233M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:21.573 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:21.574 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:21.574 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:21.575 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:21.575 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:21.581 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 21 times [spades] 0:00:21.582 233M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:21.582 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:21.583 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:21.584 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:21.584 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:21.585 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:21.586 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times [spades] 0:00:21.587 233M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:21.587 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:21.588 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:21.589 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:21.589 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:21.590 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:21.592 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times [spades] 0:00:21.593 233M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:21.593 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:21.594 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:21.595 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:21.595 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:21.596 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:21.597 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:21.598 233M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:21.599 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:21.599 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:21.600 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:21.600 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:21.601 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:21.602 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:21.602 233M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:21.603 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:21.603 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:21.604 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:21.605 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:21.605 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:21.607 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:21.607 233M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:21.608 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:21.609 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:21.609 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:21.610 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:21.611 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:21.612 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:21.613 233M / 9G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:21.613 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:21.633 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:21.637 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:21.669 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:21.670 233M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:21.701 233M / 9G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:21.713 233M / 9G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:21.714 233M / 9G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:21.715 233M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:21.716 233M / 9G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:21.717 233M / 9G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:21.719 233M / 9G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66559 Gb [spades] 0:00:21.719 233M / 9G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:22.095 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 118098 edges [spades] 0:00:22.096 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 118098 sequences. [spades] 0:00:22.161 249M / 9G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:22.461 249M / 9G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7948075 kmers in total. [spades] 0:00:22.463 249M / 9G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:22.678 249M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:22.886 240M / 9G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:23.278 240M / 9G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3693696 bytes occupied (3.71783 bits per kmer). [spades] 0:00:23.405 368M / 9G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:23.655 352M / 9G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:23.660 352M / 9G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:23.832 360M / 9G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:24.580 334M / 9G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:24.582 334M / 9G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:24.673 331M / 9G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:24.783 326M / 9G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 3 gaps after checking 671 candidates [spades] 0:00:24.806 326M / 9G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:24.807 326M / 9G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:24.808 326M / 9G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:24.809 326M / 9G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:24.810 326M / 9G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:24.811 326M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.821 326M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.823 326M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.833 326M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.834 326M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:24.844 326M / 9G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:24.846 326M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:24.856 326M / 9G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:24.857 326M / 9G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:24.901 321M / 9G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:26.892 299M / 9G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 58008 times [spades] 0:00:26.894 299M / 9G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:26.896 299M / 9G INFO General (simplification.cpp : 502) Average coverage = 44.7665 [spades] 0:00:26.897 299M / 9G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:26.898 299M / 9G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K111/simplified_contigs [spades] 0:00:26.905 299M / 9G INFO General (binary_converter.cpp : 111) 1038 reads written [spades] 0:00:26.907 300M / 9G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:27.008 170M / 9G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 27 seconds [spades] [spades] ===== K111 finished. [spades] [spades] [spades] ===== K121 started. [spades] [spades] [spades] == Running: /home/administrator/conda2/envs/shovill/bin/spades-core /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/configs/isolate_mode.info [spades] [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K111/simplified_contigs [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/configs/config.info [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/configs/isolate_mode.info [spades] 0:00:00.001 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/dataset.info) with K=121 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 30 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 194) SPAdes started [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 218) Will need read mapping, kmer mapper will be attached [spades] 0:00:00.001 7M / 9M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion [spades] 0:00:00.003 7M / 9M INFO General (read_converter.cpp : 53) Binary reads detected [spades] 0:00:00.005 8M / 9M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:00.005 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K111/simplified_contigs [spades] 0:00:00.008 8M / 9M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.008 8M / 9M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.008 8M / 9M INFO General (construction.cpp : 156) Average read length 173.568 [spades] 0:00:00.008 8M / 9M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.009 8M / 9M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.009 8M / 9M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.010 8M / 9M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.010 8M / 9M INFO General (kmer_splitters.hpp : 97) Using cell size of 18641 [spades] 0:00:04.299 20G / 20G INFO General (kmer_splitters.hpp : 287) Processed 7970840 reads [spades] 0:00:04.841 216M / 7G INFO General (kmer_splitters.hpp : 293) Used 7970840 reads [spades] 0:00:04.842 216M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:05.269 218M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 9475843 kmers in total. [spades] 0:00:05.271 218M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:05.577 211M / 7G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:05.578 211M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:05.580 211M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:05.580 211M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:05.581 211M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:05.581 211M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:06.240 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 9475843 kmers [spades] 0:00:06.241 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 9475843 kmers. [spades] 0:00:06.341 270M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:06.653 270M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 9541614 kmers in total. [spades] 0:00:06.654 270M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:06.957 270M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:07.262 260M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:07.750 260M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4432688 bytes occupied (3.71651 bits per kmer). [spades] 0:00:07.767 270M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:08.208 270M / 7G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:08.221 247M / 7G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:08.225 247M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:08.636 231M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 154166 sequences extracted [spades] 0:00:08.927 231M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:09.020 231M / 7G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:09.833 228M / 7G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:09.835 228M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:09.836 228M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:10.000 233M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4409232 bytes occupied (3.7225 bits per kmer). [spades] 0:00:10.026 273M / 7G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:13.499 263M / 7G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:13.819 263M / 7G INFO General (construction.cpp : 505) Processed 308334 edges [spades] 0:00:13.889 213M / 7G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:13.890 213M / 7G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 13 [spades] 0:00:13.891 213M / 7G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 39 [spades] 0:00:13.892 213M / 7G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 40. Coverage mad: 10.3782 [spades] 0:00:13.892 213M / 7G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:13.932 213M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:14.034 213M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:14.366 213M / 7G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:14.845 213M / 7G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 40.6106. Fitted coverage std. dev: 9.26849 [spades] 0:00:14.847 213M / 7G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.545805 [spades] 0:00:14.848 213M / 7G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 23 [spades] 0:00:14.848 213M / 7G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 23 [spades] 0:00:14.849 213M / 7G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 4855221 [spades] 0:00:14.850 213M / 7G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 40.6106 [spades] 0:00:14.850 213M / 7G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 23 [spades] 0:00:14.851 213M / 7G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:14.851 213M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:14.852 213M / 7G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:14.853 213M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:14.853 213M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:14.855 144M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:14.857 144M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66601 Gb [spades] 0:00:14.857 144M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:15.259 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 308334 edges [spades] 0:00:15.261 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 308334 sequences. [spades] 0:00:15.332 167M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:15.621 161M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 9475843 kmers in total. [spades] 0:00:15.623 161M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:15.907 161M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:16.159 157M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:16.652 157M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 4402136 bytes occupied (3.71651 bits per kmer). [spades] 0:00:16.754 317M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:16.943 317M / 7G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:16.946 317M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:17.240 337M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:17.851 316M / 7G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:17.853 316M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:17.920 317M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:18.092 320M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 47 gaps after checking 824 candidates [spades] 0:00:18.130 320M / 7G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:18.139 160M / 7G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:18.140 160M / 7G INFO General (simplification.cpp : 63) Most init cleaning disabled on main iteration [spades] 0:00:18.141 160M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:18.152 160M / 7G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:18.153 160M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:18.154 160M / 7G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:18.154 160M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:18.155 160M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:18.156 160M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:18.684 157M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 41730 times [spades] 0:00:18.685 157M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:19.012 162M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 843 times [spades] 0:00:19.013 162M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:19.124 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 315 times [spades] 0:00:19.125 163M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:19.125 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:19.129 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 6 times [spades] 0:00:19.129 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:19.131 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times [spades] 0:00:19.132 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:19.142 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 40 times [spades] 0:00:19.143 163M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:19.143 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:19.144 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:19.144 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:19.145 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:19.146 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:19.148 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 26 times [spades] 0:00:19.148 163M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:19.149 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:19.149 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:19.150 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:19.151 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:19.151 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:19.155 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 15 times [spades] 0:00:19.156 163M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:19.156 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:19.157 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:19.158 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:19.158 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:19.159 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:19.161 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times [spades] 0:00:19.162 163M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:19.162 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:19.163 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:19.163 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:19.164 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:19.165 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:19.168 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10 times [spades] 0:00:19.168 163M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:19.169 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:19.170 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:19.170 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:19.171 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:19.171 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:19.172 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:19.173 163M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:19.173 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:19.174 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:19.174 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:19.175 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:19.176 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:19.176 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:19.177 163M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:19.178 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:19.178 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:19.179 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:19.179 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:19.180 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:19.182 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:19.182 163M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:19.183 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:19.184 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:19.184 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:19.185 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:19.185 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:19.186 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:19.187 163M / 7G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:19.187 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:19.211 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:19.212 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:19.242 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:19.243 163M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:19.274 163M / 7G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:19.301 163M / 7G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:19.302 163M / 7G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:19.304 163M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:19.305 163M / 7G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:19.307 163M / 7G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:19.308 163M / 7G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66579 Gb [spades] 0:00:19.309 163M / 7G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:19.678 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 134264 edges [spades] 0:00:19.679 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 134264 sequences. [spades] 0:00:19.742 218M / 7G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:20.011 218M / 7G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7661859 kmers in total. [spades] 0:00:20.014 218M / 7G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:20.250 218M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:20.474 215M / 7G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:20.877 215M / 7G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3561064 bytes occupied (3.71822 bits per kmer). [spades] 0:00:21.003 343M / 7G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:21.275 337M / 7G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:21.280 337M / 7G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:21.481 347M / 7G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:22.125 335M / 7G INFO General (gap_closer.cpp : 126) Used 1490488 paired reads [spades] 0:00:22.127 335M / 7G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:22.235 338M / 7G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:22.349 330M / 7G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 5 gaps after checking 714 candidates [spades] 0:00:22.380 330M / 7G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:22.381 330M / 7G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:22.382 330M / 7G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:22.383 330M / 7G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:22.384 330M / 7G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:22.385 330M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.396 330M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:22.397 330M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.407 330M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:22.408 330M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:22.419 330M / 7G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:22.420 330M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:22.431 330M / 7G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:22.432 330M / 7G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:22.479 330M / 7G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:24.393 302M / 7G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 66127 times [spades] 0:00:24.395 302M / 7G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:24.398 302M / 7G INFO General (simplification.cpp : 502) Average coverage = 37.701 [spades] 0:00:24.398 302M / 7G INFO StageManager (stage.cpp : 166) STAGE == Mismatch Correction [spades] 0:00:24.399 302M / 7G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 209854 kmers to process [spades] 0:00:24.448 309M / 7G INFO General (graph_pack.hpp : 115) Normalizing done [spades] 0:00:28.906 306M / 7G INFO General (mismatch_shall_not_pass.hp: 195) Finished collecting potential mismatches positions [spades] 0:00:28.978 293M / 7G INFO General (mismatch_shall_not_pass.hp: 310) All edges processed [spades] 0:00:28.980 293M / 7G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides [spades] 0:00:28.982 281M / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:28.983 281M / 7G INFO General (contig_output.hpp : 21) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/before_rr.fasta [spades] 0:00:29.070 281M / 7G INFO General (contig_output_stage.cpp : 146) Writing GFA graph to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/assembly_graph_after_simplification.gfa [spades] 0:00:29.120 280M / 7G INFO StageManager (stage.cpp : 166) STAGE == Paired Information Counting [spades] 0:00:29.125 280M / 7G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 209854 kmers to process [spades] 0:00:29.126 280M / 7G INFO General (graph_pack.hpp : 115) Normalizing done [spades] 0:00:29.127 280M / 7G INFO General (pair_info_count.cpp : 322) Min edge length for estimation: 170136 [spades] 0:00:29.128 280M / 7G INFO General (pair_info_count.cpp : 333) Estimating insert size for library #0 [spades] 0:00:29.128 280M / 7G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) [spades] 0:00:29.401 776M / 7G INFO General (pair_info_count.cpp : 39) Selecting usual mapper [spades] 0:00:31.132 754M / 7G INFO General (sequence_mapper_notifier.h: 94) Total 2493894 reads processed [spades] 0:00:31.218 754M / 7G INFO General (pair_info_count.cpp : 208) Edge pairs: 4230 [spades] 0:00:31.219 754M / 7G INFO General (pair_info_count.cpp : 212) 1292942 paired reads (51.8443% of all) aligned to long edges [spades] 0:00:31.241 258M / 7G INFO General (pair_info_count.cpp : 356) Insert size = 294.85, deviation = 56.3599, left quantile = 225, right quantile = 366, read length = 150 [spades] 0:00:31.242 258M / 7G INFO General (pair_info_count.cpp : 373) Filtering data for library #0 [spades] 0:00:31.243 258M / 7G INFO General (pair_info_count.cpp : 39) Selecting usual mapper [spades] 0:00:32.373 257M / 7G INFO General (sequence_mapper_notifier.h: 94) Total 2493894 reads processed [spades] 0:00:32.375 257M / 7G INFO General (pair_info_count.cpp : 385) Mapping library #0 [spades] 0:00:32.377 257M / 7G INFO General (pair_info_count.cpp : 387) Mapping paired reads (takes a while) [spades] 0:00:32.380 257M / 7G INFO General (pair_info_count.cpp : 288) Left insert size quantile 225, right insert size quantile 366, filtering threshold 2, rounding threshold 0 [spades] 0:00:32.397 265M / 7G INFO General (pair_info_count.cpp : 39) Selecting usual mapper [spades] 0:00:33.679 266M / 7G INFO General (sequence_mapper_notifier.h: 94) Total 2493894 reads processed [spades] 0:00:33.693 257M / 7G INFO StageManager (stage.cpp : 166) STAGE == Distance Estimation [spades] 0:00:33.694 257M / 7G INFO General (distance_estimation.cpp : 174) Processing library #0 [spades] 0:00:33.696 257M / 7G INFO General (distance_estimation.cpp : 150) Weight Filter Done [spades] 0:00:33.697 257M / 7G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator [spades] 0:00:33.704 257M / 7G INFO General (distance_estimation.cpp : 35) Filtering info [spades] 0:00:33.704 257M / 7G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2746 [spades] 0:00:33.707 257M / 7G INFO General (pair_info_filters.hpp : 263) Done filtering [spades] 0:00:33.707 257M / 7G INFO General (distance_estimation.cpp : 157) Refining clustered pair information [spades] 0:00:33.709 257M / 7G INFO General (distance_estimation.cpp : 159) The refining of clustered pair information has been finished [spades] 0:00:33.710 257M / 7G INFO General (distance_estimation.cpp : 161) Improving paired information [spades] 0:00:33.717 257M / 7G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 29; contradictional = 14 [spades] 0:00:33.722 257M / 7G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 [spades] 0:00:33.723 257M / 7G INFO General (distance_estimation.cpp : 104) Filling scaffolding index [spades] 0:00:33.724 257M / 7G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator [spades] 0:00:33.728 259M / 7G INFO General (distance_estimation.cpp : 35) Filtering info [spades] 0:00:33.728 259M / 7G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2050 [spades] 0:00:33.730 259M / 7G INFO General (pair_info_filters.hpp : 263) Done filtering [spades] 0:00:33.731 259M / 7G INFO General (distance_estimation.cpp : 183) Clearing raw paired index [spades] 0:00:33.733 259M / 7G INFO StageManager (stage.cpp : 166) STAGE == Repeat Resolving [spades] 0:00:33.733 259M / 7G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving [spades] 0:00:33.734 259M / 7G INFO General (launcher.cpp : 538) ExSPAnder repeat resolving tool started [spades] 0:00:33.743 261M / 7G INFO General (launcher.cpp : 404) Creating main extenders, unique edge length = 2000 [spades] 0:00:33.747 261M / 7G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #0 is 37.701 [spades] 0:00:33.749 261M / 7G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #0 is 37.701 [spades] 0:00:33.754 261M / 7G INFO General (extenders_logic.cpp : 519) Using 1 paired-end library [spades] 0:00:33.754 261M / 7G INFO General (extenders_logic.cpp : 520) Using 1 paired-end scaffolding library [spades] 0:00:33.755 261M / 7G INFO General (extenders_logic.cpp : 521) Using 0 single read libraries [spades] 0:00:33.756 261M / 7G INFO General (launcher.cpp : 432) Total number of extenders is 3 [spades] 0:00:33.757 261M / 7G INFO General (path_extender.hpp : 894) Processed 0 paths from 994 (0%) [spades] 0:00:33.783 261M / 7G INFO General (path_extender.hpp : 894) Processed 100 paths from 994 (10%) [spades] 0:00:33.786 261M / 7G INFO General (path_extender.hpp : 892) Processed 128 paths from 994 (12%) [spades] 0:00:33.792 262M / 7G INFO General (path_extender.hpp : 894) Processed 200 paths from 994 (20%) [spades] 0:00:33.797 262M / 7G INFO General (path_extender.hpp : 892) Processed 256 paths from 994 (25%) [spades] 0:00:33.800 262M / 7G INFO General (path_extender.hpp : 894) Processed 300 paths from 994 (30%) [spades] 0:00:33.807 263M / 7G INFO General (path_extender.hpp : 894) Processed 400 paths from 994 (40%) [spades] 0:00:33.815 264M / 7G INFO General (path_extender.hpp : 894) Processed 500 paths from 994 (50%) [spades] 0:00:33.816 264M / 7G INFO General (path_extender.hpp : 892) Processed 512 paths from 994 (51%) [spades] 0:00:33.823 265M / 7G INFO General (path_extender.hpp : 894) Processed 600 paths from 994 (60%) [spades] 0:00:33.830 266M / 7G INFO General (path_extender.hpp : 894) Processed 700 paths from 994 (70%) [spades] 0:00:33.837 266M / 7G INFO General (path_extender.hpp : 894) Processed 800 paths from 994 (80%) [spades] 0:00:33.844 267M / 7G INFO General (path_extender.hpp : 894) Processed 900 paths from 994 (90%) [spades] 0:00:33.851 268M / 7G INFO General (launcher.cpp : 244) Finalizing paths [spades] 0:00:33.852 268M / 7G INFO General (launcher.cpp : 246) Deduplicating paths [spades] 0:00:33.855 268M / 7G INFO General (launcher.cpp : 250) Paths deduplicated [spades] 0:00:33.856 268M / 7G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps [spades] 0:00:33.856 268M / 7G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths [spades] 0:00:33.858 268M / 7G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps [spades] 0:00:33.858 268M / 7G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps [spades] 0:00:33.860 268M / 7G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps [spades] 0:00:33.863 268M / 7G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths [spades] 0:00:33.864 268M / 7G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths [spades] 0:00:33.865 268M / 7G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed [spades] 0:00:33.868 268M / 7G INFO General (launcher.cpp : 267) Paths finalized [spades] 0:00:33.869 268M / 7G INFO General (launcher.cpp : 439) Closing gaps in paths [spades] 0:00:33.874 268M / 7G INFO General (launcher.cpp : 467) Gap closing completed [spades] 0:00:33.877 268M / 7G INFO General (launcher.cpp : 296) Traversing tandem repeats [spades] 0:00:33.885 268M / 7G INFO General (launcher.cpp : 306) Traversed 2 loops [spades] 0:00:33.886 268M / 7G INFO General (launcher.cpp : 244) Finalizing paths [spades] 0:00:33.887 268M / 7G INFO General (launcher.cpp : 246) Deduplicating paths [spades] 0:00:33.888 268M / 7G INFO General (launcher.cpp : 250) Paths deduplicated [spades] 0:00:33.889 268M / 7G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps [spades] 0:00:33.889 268M / 7G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths [spades] 0:00:33.890 268M / 7G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps [spades] 0:00:33.891 268M / 7G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps [spades] 0:00:33.893 268M / 7G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps [spades] 0:00:33.895 268M / 7G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths [spades] 0:00:33.896 268M / 7G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths [spades] 0:00:33.897 268M / 7G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed [spades] 0:00:33.899 268M / 7G INFO General (launcher.cpp : 267) Paths finalized [spades] 0:00:33.900 268M / 7G INFO General (launcher.cpp : 596) ExSPAnder repeat resolving tool finished [spades] 0:00:33.904 268M / 7G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:33.905 268M / 7G INFO General (contig_output.hpp : 21) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/before_rr.fasta [spades] 0:00:33.992 269M / 7G INFO General (contig_output_stage.cpp : 146) Writing GFA graph to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/assembly_graph_with_scaffolds.gfa [spades] 0:00:34.062 269M / 7G INFO General (contig_output_stage.cpp : 160) Outputting FastG graph to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/assembly_graph.fastg [spades] 0:00:34.349 269M / 7G INFO General (contig_output_stage.cpp : 190) Breaking scaffolds [spades] 0:00:34.421 271M / 7G INFO General (contig_output_stage.cpp : 95) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/final_contigs.fasta [spades] 0:00:34.498 272M / 7G INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/final_contigs.paths [spades] 0:00:34.558 272M / 7G INFO General (contig_output_stage.cpp : 95) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/scaffolds.fasta [spades] 0:00:34.634 272M / 7G INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/scaffolds.paths [spades] 0:00:34.637 272M / 7G INFO General (contig_output_stage.cpp : 108) Populating GFA with scaffold paths [spades] 0:00:34.639 270M / 7G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:34.725 140M / 7G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 34 seconds [spades] [spades] ===== K121 finished. [spades] [spades] [spades] ===== Copy files started. [spades] [spades] [spades] == Running: /home/administrator/conda2/envs/shovill/bin/python /home/administrator/conda2/envs/shovill/share/spades/spades_pipeline/scripts/copy_files.py /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/before_rr.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/before_rr.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/assembly_graph_after_simplification.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/assembly_graph_after_simplification.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/final_contigs.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/contigs.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/first_pe_contigs.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/first_pe_contigs.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/strain_graph.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/strain_graph.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/scaffolds.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/scaffolds.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/scaffolds.paths /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/scaffolds.paths /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/assembly_graph_with_scaffolds.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/assembly_graph_with_scaffolds.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/assembly_graph.fastg /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/assembly_graph.fastg /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/K121/final_contigs.paths /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/contigs.paths [spades] [spades] [spades] ===== Copy files finished. [spades] [spades] [spades] ===== Assembling finished. [spades] [spades] [spades] ===== Breaking scaffolds started. [spades] [spades] [spades] == Running: /home/administrator/conda2/envs/shovill/bin/python /home/administrator/conda2/envs/shovill/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/scaffolds.fasta --misc_dir /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/misc --threshold_for_breaking_scaffolds 3 [spades] [spades] [spades] ===== Breaking scaffolds finished. [spades] [spades] [spades] ===== Terminate started. [spades] [spades] [spades] ===== Terminate finished. [spades] [spades] * Assembled contigs are in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/contigs.fasta [spades] * Assembled scaffolds are in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/scaffolds.fasta [spades] * Paths in the assembly graph corresponding to the contigs are in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/contigs.paths [spades] * Paths in the assembly graph corresponding to the scaffolds are in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/scaffolds.paths [spades] * Assembly graph is in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/assembly_graph.fastg [spades] * Assembly graph in GFA format is in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/assembly_graph_with_scaffolds.gfa [spades] [spades] ======= SPAdes pipeline finished. [spades] [spades] SPAdes log can be found here: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/spades/spades.log [spades] [spades] Thank you for using SPAdes! [shovill] Checking for assembly errors in spades.fasta [shovill] Running: bwa index spades.fasta 2>&1 | sed 's/^/[bwa-index] /' | tee -a shovill.log [bwa-index] [bwa_index] Pack FASTA... 0.06 sec [bwa-index] [bwa_index] Construct BWT for the packed sequence... [bwa-index] [bwa_index] 1.68 seconds elapse. [bwa-index] [bwa_index] Update BWT... 0.05 sec [bwa-index] [bwa_index] Pack forward-only FASTA... 0.05 sec [bwa-index] [bwa_index] Construct SA from BWT and Occ... 0.62 sec [bwa-index] [main] Version: 0.7.17-r1188 [bwa-index] [main] CMD: bwa index spades.fasta [bwa-index] [main] Real time: 2.827 sec; CPU: 2.458 sec [shovill] Running: samtools faidx spades.fasta 2>&1 | sed 's/^/[faidx] /' | tee -a shovill.log [shovill] Running: (bwa mem -v 3 -x intractg -t 30 spades.fasta R1.fq.gz R2.fq.gz | samclip --ref spades.fasta.fai | samtools sort --threads 7 -m 17554m --reference spades.fasta -T /tmp/7pScLI1Yr4 -o shovill.bam) 2>&1 | sed 's/^/[bwa+samtools-sort] /' | tee -a shovill.log [bwa+samtools-sort] [M::bwa_idx_load_from_disk] read 0 ALT contigs [bwa+samtools-sort] [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [bwa+samtools-sort] [samclip] Loading: spades.fasta.fai [bwa+samtools-sort] [samclip] Found 937 sequences in spades.fasta.fai [bwa+samtools-sort] [M::process] read 2000000 sequences (300000000 bp)... [bwa+samtools-sort] [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 986092, 4, 5) [bwa+samtools-sort] [M::mem_pestat] skip orientation FF as there are not enough pairs [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation FR... [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (257, 290, 327) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (117, 467) [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (292.57, 53.03) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (47, 537) [bwa+samtools-sort] [M::mem_pestat] skip orientation RF as there are not enough pairs [bwa+samtools-sort] [M::mem_pestat] skip orientation RR as there are not enough pairs [bwa+samtools-sort] [M::mem_process_seqs] Processed 2000000 reads in 234.226 CPU sec, 13.813 real sec [bwa+samtools-sort] [samclip] Processed 100000 records... [bwa+samtools-sort] [samclip] Processed 200000 records... [bwa+samtools-sort] [samclip] Processed 300000 records... [bwa+samtools-sort] [samclip] Processed 400000 records... [bwa+samtools-sort] [samclip] Processed 500000 records... [bwa+samtools-sort] [samclip] Processed 600000 records... [bwa+samtools-sort] [samclip] Processed 700000 records... [bwa+samtools-sort] [samclip] Processed 800000 records... [bwa+samtools-sort] [M::process] read 2000000 sequences (300000000 bp)... [bwa+samtools-sort] [samclip] Processed 900000 records... [bwa+samtools-sort] [samclip] Processed 1000000 records... [bwa+samtools-sort] [samclip] Processed 1100000 records... [bwa+samtools-sort] [samclip] Processed 1200000 records... [bwa+samtools-sort] [samclip] Processed 1300000 records... [bwa+samtools-sort] [samclip] Processed 1400000 records... [bwa+samtools-sort] [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 987850, 0, 4) [bwa+samtools-sort] [M::mem_pestat] skip orientation FF as there are not enough pairs [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation FR... [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (256, 292, 330) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (108, 478) [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (293.42, 56.30) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (34, 552) [bwa+samtools-sort] [M::mem_pestat] skip orientation RF as there are not enough pairs [bwa+samtools-sort] [M::mem_pestat] skip orientation RR as there are not enough pairs [bwa+samtools-sort] [samclip] Processed 1500000 records... [bwa+samtools-sort] [M::mem_process_seqs] Processed 2000000 reads in 208.981 CPU sec, 9.410 real sec [bwa+samtools-sort] [samclip] Processed 1600000 records... [bwa+samtools-sort] [samclip] Processed 1700000 records... [bwa+samtools-sort] [samclip] Processed 1800000 records... [bwa+samtools-sort] [samclip] Processed 1900000 records... [bwa+samtools-sort] [samclip] Processed 2000000 records... [bwa+samtools-sort] [samclip] Processed 2100000 records... [bwa+samtools-sort] [samclip] Processed 2200000 records... [bwa+samtools-sort] [samclip] Processed 2300000 records... [bwa+samtools-sort] [samclip] Processed 2400000 records... [bwa+samtools-sort] [samclip] Processed 2500000 records... [bwa+samtools-sort] [samclip] Processed 2600000 records... [bwa+samtools-sort] [samclip] Processed 2700000 records... [bwa+samtools-sort] [samclip] Processed 2800000 records... [bwa+samtools-sort] [samclip] Processed 2900000 records... [bwa+samtools-sort] [samclip] Processed 3000000 records... [bwa+samtools-sort] [M::process] read 987788 sequences (148168200 bp)... [bwa+samtools-sort] [samclip] Processed 3100000 records... [bwa+samtools-sort] [samclip] Processed 3200000 records... [bwa+samtools-sort] [samclip] Processed 3300000 records... [bwa+samtools-sort] [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 487193, 2, 2) [bwa+samtools-sort] [M::mem_pestat] skip orientation FF as there are not enough pairs [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation FR... [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (256, 293, 331) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (106, 481) [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (293.70, 56.94) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (31, 556) [bwa+samtools-sort] [M::mem_pestat] skip orientation RF as there are not enough pairs [bwa+samtools-sort] [M::mem_pestat] skip orientation RR as there are not enough pairs [bwa+samtools-sort] [samclip] Processed 3400000 records... [bwa+samtools-sort] [M::mem_process_seqs] Processed 987788 reads in 97.487 CPU sec, 3.757 real sec [bwa+samtools-sort] [samclip] Processed 3500000 records... [bwa+samtools-sort] [samclip] Processed 3600000 records... [bwa+samtools-sort] [samclip] Processed 3700000 records... [bwa+samtools-sort] [samclip] Processed 3800000 records... [bwa+samtools-sort] [samclip] Processed 3900000 records... [bwa+samtools-sort] [samclip] Processed 4000000 records... [bwa+samtools-sort] [samclip] Processed 4100000 records... [bwa+samtools-sort] [samclip] Processed 4200000 records... [bwa+samtools-sort] [samclip] Processed 4300000 records... [bwa+samtools-sort] [samclip] Processed 4400000 records... [bwa+samtools-sort] [samclip] Processed 4500000 records... [bwa+samtools-sort] [samclip] Processed 4600000 records... [bwa+samtools-sort] [samclip] Processed 4700000 records... [bwa+samtools-sort] [samclip] Processed 4800000 records... [bwa+samtools-sort] [samclip] Processed 4900000 records... [bwa+samtools-sort] [main] Version: 0.7.17-r1188 [bwa+samtools-sort] [main] CMD: bwa mem -v 3 -x intractg -t 30 spades.fasta R1.fq.gz R2.fq.gz [bwa+samtools-sort] [main] Real time: 44.805 sec; CPU: 559.312 sec [bwa+samtools-sort] [samclip] Total SAM records 4992067, removed 112998, allowed 108135, passed 4879069 [bwa+samtools-sort] [samclip] Header contained 938 lines [bwa+samtools-sort] [samclip] Done. [bwa+samtools-sort] [bam_sort_core] merging from 0 files and 7 in-memory blocks... [shovill] Running: samtools index shovill.bam 2>&1 | sed 's/^/[samtools-index] /' | tee -a shovill.log [shovill] Correcting errors in spades.fasta [shovill] Running: pilon --genome spades.fasta --frags shovill.bam --minmq 60 --minqual 3 --fix bases --output pilon --threads 30 --changes --mindepth 0.25 2>&1 | sed 's/^/[pilon] /' | tee -a shovill.log [pilon] Picked up _JAVA_OPTIONS: -Xmx240g [pilon] Pilon version 1.23 Mon Nov 26 16:04:05 2018 -0500 [pilon] Genome: spades.fasta [pilon] Fixing snps, indels [pilon] Input genome size: 5558245 [pilon] Processing NODE_143_length_849_cov_11.251374:1-849 [pilon] Processing NODE_812_length_431_cov_1.306452:1-431 [pilon] Processing NODE_194_length_767_cov_3.058824:1-767 [pilon] Processing NODE_897_length_404_cov_2.787986:1-404 [pilon] Processing NODE_230_length_724_cov_4.943615:1-724 [pilon] Processing NODE_330_length_644_cov_7.353728:1-644 [pilon] Processing NODE_243_length_710_cov_9.393888:1-710 [pilon] Processing NODE_125_length_940_cov_17.301587:1-940 [pilon] Processing NODE_451_length_573_cov_0.865044:1-573 [pilon] Processing NODE_304_length_661_cov_3.374074:1-661 [pilon] Processing NODE_615_length_502_cov_3.490814:1-502 [pilon] Processing NODE_142_length_852_cov_1.573187:1-852 [pilon] Processing NODE_395_length_601_cov_1.741667:1-601 [pilon] Processing NODE_151_length_836_cov_7.868531:1-836 [pilon] Processing NODE_191_length_769_cov_3.649691:1-769 [pilon] Processing NODE_586_length_513_cov_2.084184:1-513 [pilon] Processing NODE_167_length_809_cov_20.085756:1-809 [pilon] Processing NODE_201_length_756_cov_8.740157:1-756 [pilon] Processing NODE_751_length_451_cov_0.939394:1-451 [pilon] Processing NODE_697_length_471_cov_1.057143:1-471 [pilon] Processing NODE_729_length_458_cov_7.721068:1-458 [pilon] Processing NODE_12_length_161867_cov_46.822283:1-161867 [pilon] Processing NODE_907_length_402_cov_2.704626:1-402 [pilon] Processing NODE_578_length_515_cov_1.868020:1-515 [pilon] Processing NODE_46_length_3713_cov_27.868875:1-3713 [pilon] Processing NODE_198_length_760_cov_9.341158:1-760 [pilon] Processing NODE_647_length_490_cov_1.132791:1-490 [pilon] Processing NODE_71_length_1564_cov_90.154539:1-1564 [pilon] Processing NODE_361_length_622_cov_1.826347:1-622 [pilon] Processing NODE_716_length_465_cov_2.866279:1-465 [pilon] NODE_451_length_573_cov_0.865044:1-573 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 573 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_451_length_573_cov_0.865044:1-573 [pilon] NODE_897_length_404_cov_2.787986:1-404 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 26, Coverage: 6, minDepth: 5 [pilon] Confirmed 166 of 404 bases (41.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_897_length_404_cov_2.787986:1-404 [pilon] Processing NODE_700_length_470_cov_3.160458:1-470 [pilon] NODE_697_length_471_cov_1.057143:1-471 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 122 of 471 bases (25.90%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_697_length_471_cov_1.057143:1-471 [pilon] Processing NODE_898_length_404_cov_1.795053:1-404 [pilon] NODE_751_length_451_cov_0.939394:1-451 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 149 of 451 bases (33.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_751_length_451_cov_0.939394:1-451 [pilon] Processing NODE_701_length_470_cov_2.902579:1-470 [pilon] NODE_647_length_490_cov_1.132791:1-490 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 13, Coverage: 3, minDepth: 5 [pilon] Confirmed 171 of 490 bases (34.90%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_647_length_490_cov_1.132791:1-490 [pilon] Processing NODE_32_length_23617_cov_34.984721:1-23617 [pilon] NODE_395_length_601_cov_1.741667:1-601 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 25, Coverage: 5, minDepth: 5 [pilon] Confirmed 279 of 601 bases (46.42%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_395_length_601_cov_1.741667:1-601 [pilon] Processing NODE_873_length_411_cov_1.644828:1-411 [pilon] NODE_361_length_622_cov_1.826347:1-622 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 25, Coverage: 5, minDepth: 5 [pilon] Confirmed 269 of 622 bases (43.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_361_length_622_cov_1.826347:1-622 [pilon] Processing NODE_343_length_637_cov_10.397287:1-637 [pilon] NODE_812_length_431_cov_1.306452:1-431 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 224 of 431 bases (51.97%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_812_length_431_cov_1.306452:1-431 [pilon] NODE_578_length_515_cov_1.868020:1-515 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 29, Coverage: 7, minDepth: 5 [pilon] Confirmed 331 of 515 bases (64.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_578_length_515_cov_1.868020:1-515 [pilon] Processing NODE_271_length_687_cov_9.517668:1-687 [pilon] NODE_586_length_513_cov_2.084184:1-513 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 19, Coverage: 5, minDepth: 5 [pilon] Confirmed 227 of 513 bases (44.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_586_length_513_cov_2.084184:1-513 [pilon] Processing NODE_145_length_846_cov_11.144828:1-846 [pilon] Processing NODE_126_length_933_cov_4.070197:1-933 [pilon] Processing NODE_852_length_418_cov_3.343434:1-418 [pilon] NODE_194_length_767_cov_3.058824:1-767 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 47, Coverage: 8, minDepth: 5 [pilon] Confirmed 409 of 767 bases (53.32%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_194_length_767_cov_3.058824:1-767 [pilon] Processing NODE_625_length_498_cov_0.941645:1-498 [pilon] NODE_615_length_502_cov_3.490814:1-502 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 42, Coverage: 11, minDepth: 5 [pilon] Confirmed 382 of 502 bases (76.10%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_615_length_502_cov_3.490814:1-502 [pilon] Processing NODE_933_length_240_cov_55.739496:1-240 [pilon] NODE_230_length_724_cov_4.943615:1-724 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 70, Coverage: 13, minDepth: 5 [pilon] Confirmed 471 of 724 bases (65.06%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_230_length_724_cov_4.943615:1-724 [pilon] Processing NODE_6_length_324215_cov_45.379603:1-324215 [pilon] NODE_151_length_836_cov_7.868531:1-836 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 114, Coverage: 17, minDepth: 5 [pilon] Confirmed 524 of 836 bases (62.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_151_length_836_cov_7.868531:1-836 [pilon] Processing NODE_347_length_631_cov_7.131373:1-631 [pilon] NODE_142_length_852_cov_1.573187:1-852 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 40, Coverage: 5, minDepth: 5 [pilon] Confirmed 433 of 852 bases (50.82%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_191_length_769_cov_3.649691:1-769 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 50, Coverage: 8, minDepth: 5 [pilon] Confirmed 453 of 769 bases (58.91%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_191_length_769_cov_3.649691:1-769 [pilon] NODE_143_length_849_cov_11.251374:1-849 log: [pilon] frags shovill.bam: coverage 27 [pilon] Total Reads: 182, Coverage: 27, minDepth: 7 [pilon] Confirmed 710 of 849 bases (83.63%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_143_length_849_cov_11.251374:1-849 [pilon] Processing NODE_883_length_408_cov_0.404181:1-408 [pilon] NODE_716_length_465_cov_2.866279:1-465 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 25, Coverage: 6, minDepth: 5 [pilon] Confirmed 234 of 465 bases (50.32%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_243_length_710_cov_9.393888:1-710 log: [pilon] Finished processing NODE_716_length_465_cov_2.866279:1-465 [pilon] NODE_167_length_809_cov_20.085756:1-809 log: [pilon] frags shovill.bam: coverage 63 [pilon] Total Reads: 398, Coverage: 63, minDepth: 16 [pilon] Confirmed 611 of 809 bases (75.53%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_330_length_644_cov_7.353728:1-644 log: [pilon] frags shovill.bam: coverage 19 [pilon] Total Reads: 95, Coverage: 19, minDepth: 5 [pilon] Confirmed 468 of 644 bases (72.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_330_length_644_cov_7.353728:1-644 [pilon] Processing NODE_372_length_616_cov_2.371717:1-616 [pilon] NODE_198_length_760_cov_9.341158:1-760 log: [pilon] frags shovill.bam: coverage 24 [pilon] Total Reads: 143, Coverage: 24, minDepth: 6 [pilon] Confirmed 484 of 760 bases (63.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_198_length_760_cov_9.341158:1-760 [pilon] Processing NODE_399_length_599_cov_11.370293:1-599 [pilon] NODE_729_length_458_cov_7.721068:1-458 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 56, Coverage: 15, minDepth: 5 [pilon] Confirmed 361 of 458 bases (78.82%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_807_length_434_cov_0.463259:1-434 [pilon] Finished processing NODE_142_length_852_cov_1.573187:1-852 [pilon] Finished processing NODE_729_length_458_cov_7.721068:1-458 [pilon] Processing NODE_184_length_780_cov_8.930197:1-780 [pilon] NODE_125_length_940_cov_17.301587:1-940 log: [pilon] NODE_304_length_661_cov_3.374074:1-661 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 49, Coverage: 9, minDepth: 5 [pilon] Confirmed 424 of 661 bases (64.15%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_167_length_809_cov_20.085756:1-809 [pilon] NODE_907_length_402_cov_2.704626:1-402 log: [pilon] frags shovill.bam: coverage 22 [pilon] Total Reads: 120, Coverage: 22, minDepth: 6 [pilon] Confirmed 516 of 710 bases (72.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 19, Coverage: 6, minDepth: 5 [pilon] Confirmed 216 of 402 bases (53.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] frags shovill.bam: coverage 45 [pilon] Total Reads: 327, Coverage: 45, minDepth: 11 [pilon] Confirmed 623 of 940 bases (66.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_660_length_484_cov_14.564738:1-484 [pilon] Finished processing NODE_125_length_940_cov_17.301587:1-940 [pilon] Finished processing NODE_907_length_402_cov_2.704626:1-402 [pilon] Finished processing NODE_243_length_710_cov_9.393888:1-710 [pilon] Processing NODE_475_length_562_cov_2.623583:1-562 [pilon] Processing NODE_795_length_436_cov_2.041270:1-436 [pilon] Processing NODE_376_length_614_cov_1.245436:1-614 [pilon] Processing NODE_424_length_587_cov_2.729614:1-587 [pilon] NODE_201_length_756_cov_8.740157:1-756 log: [pilon] frags shovill.bam: coverage 26 [pilon] Total Reads: 153, Coverage: 26, minDepth: 7 [pilon] Confirmed 560 of 756 bases (74.07%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_201_length_756_cov_8.740157:1-756 [pilon] Processing NODE_261_length_694_cov_5.057592:1-694 [pilon] Finished processing NODE_304_length_661_cov_3.374074:1-661 [pilon] Processing NODE_543_length_533_cov_4.640777:1-533 [pilon] Processing NODE_859_length_416_cov_0.294915:1-416 [pilon] NODE_852_length_418_cov_3.343434:1-418 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 22, Coverage: 5, minDepth: 5 [pilon] Confirmed 197 of 418 bases (47.13%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_852_length_418_cov_3.343434:1-418 [pilon] Processing NODE_438_length_578_cov_1.271335:1-578 [pilon] NODE_700_length_470_cov_3.160458:1-470 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 24, Coverage: 7, minDepth: 5 [pilon] Confirmed 246 of 470 bases (52.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_700_length_470_cov_3.160458:1-470 [pilon] Processing NODE_298_length_666_cov_2.227523:1-666 [pilon] NODE_873_length_411_cov_1.644828:1-411 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 129 of 411 bases (31.39%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_873_length_411_cov_1.644828:1-411 [pilon] Processing NODE_388_length_604_cov_4.625259:1-604 [pilon] NODE_898_length_404_cov_1.795053:1-404 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 130 of 404 bases (32.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_898_length_404_cov_1.795053:1-404 [pilon] Processing NODE_735_length_456_cov_4.352239:1-456 [pilon] NODE_701_length_470_cov_2.902579:1-470 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 30, Coverage: 8, minDepth: 5 [pilon] Confirmed 319 of 470 bases (67.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_701_length_470_cov_2.902579:1-470 [pilon] Processing NODE_616_length_502_cov_3.451444:1-502 [pilon] NODE_625_length_498_cov_0.941645:1-498 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 19, Coverage: 5, minDepth: 5 [pilon] Confirmed 219 of 498 bases (43.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_625_length_498_cov_0.941645:1-498 [pilon] Processing NODE_386_length_607_cov_0.742798:1-607 [pilon] NODE_475_length_562_cov_2.623583:1-562 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 40, Coverage: 9, minDepth: 5 [pilon] Confirmed 408 of 562 bases (72.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_475_length_562_cov_2.623583:1-562 [pilon] Processing NODE_64_length_2049_cov_28.913900:1-2049 [pilon] NODE_807_length_434_cov_0.463259:1-434 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 6, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 434 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_807_length_434_cov_0.463259:1-434 [pilon] Processing NODE_259_length_697_cov_2.095486:1-697 [pilon] NODE_795_length_436_cov_2.041270:1-436 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 22, Coverage: 7, minDepth: 5 [pilon] Confirmed 284 of 436 bases (65.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_795_length_436_cov_2.041270:1-436 [pilon] Processing NODE_657_length_485_cov_11.313187:1-485 [pilon] NODE_933_length_240_cov_55.739496:1-240 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 140, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 240 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_933_length_240_cov_55.739496:1-240 [pilon] Processing NODE_924_length_244_cov_85.203252:1-244 [pilon] NODE_660_length_484_cov_14.564738:1-484 log: [pilon] frags shovill.bam: coverage 28 [pilon] Total Reads: 106, Coverage: 28, minDepth: 7 [pilon] Confirmed 411 of 484 bases (84.92%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_660_length_484_cov_14.564738:1-484 [pilon] Processing NODE_811_length_432_cov_1.360129:1-432 [pilon] NODE_883_length_408_cov_0.404181:1-408 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 4, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 408 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_883_length_408_cov_0.404181:1-408 [pilon] Processing NODE_441_length_577_cov_1.447368:1-577 [pilon] NODE_343_length_637_cov_10.397287:1-637 log: [pilon] frags shovill.bam: coverage 29 [pilon] Total Reads: 146, Coverage: 29, minDepth: 7 [pilon] Confirmed 475 of 637 bases (74.57%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_343_length_637_cov_10.397287:1-637 [pilon] Processing NODE_403_length_597_cov_5.792017:1-597 [pilon] NODE_424_length_587_cov_2.729614:1-587 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 34, Coverage: 7, minDepth: 5 [pilon] Confirmed 446 of 587 bases (75.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_376_length_614_cov_1.245436:1-614 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 16, Coverage: 3, minDepth: 5 [pilon] Confirmed 100 of 614 bases (16.29%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_376_length_614_cov_1.245436:1-614 [pilon] Processing NODE_836_length_423_cov_5.794702:1-423 [pilon] NODE_543_length_533_cov_4.640777:1-533 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 44, Coverage: 11, minDepth: 5 [pilon] Confirmed 367 of 533 bases (68.86%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_543_length_533_cov_4.640777:1-533 [pilon] Processing NODE_630_length_495_cov_3.577540:1-495 [pilon] Finished processing NODE_424_length_587_cov_2.729614:1-587 [pilon] Processing NODE_73_length_1546_cov_14.455439:1-1546 [pilon] NODE_859_length_416_cov_0.294915:1-416 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 6, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 416 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_859_length_416_cov_0.294915:1-416 [pilon] Processing NODE_445_length_576_cov_1.593407:1-576 [pilon] NODE_145_length_846_cov_11.144828:1-846 log: [pilon] frags shovill.bam: coverage 26 [pilon] Total Reads: 180, Coverage: 26, minDepth: 7 [pilon] Confirmed 612 of 846 bases (72.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_145_length_846_cov_11.144828:1-846 [pilon] Processing NODE_56_length_2632_cov_23.807248:1-2632 [pilon] NODE_347_length_631_cov_7.131373:1-631 log: [pilon] frags shovill.bam: coverage 27 [pilon] Total Reads: 132, Coverage: 27, minDepth: 7 [pilon] Confirmed 496 of 631 bases (78.61%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_347_length_631_cov_7.131373:1-631 [pilon] Processing NODE_322_length_648_cov_5.081594:1-648 [pilon] NODE_399_length_599_cov_11.370293:1-599 log: [pilon] frags shovill.bam: coverage 24 [pilon] Total Reads: 112, Coverage: 24, minDepth: 6 [pilon] Confirmed 461 of 599 bases (76.96%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_399_length_599_cov_11.370293:1-599 [pilon] Processing NODE_339_length_641_cov_0.930769:1-641 [pilon] NODE_735_length_456_cov_4.352239:1-456 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 43, Coverage: 11, minDepth: 5 [pilon] Confirmed 317 of 456 bases (69.52%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_735_length_456_cov_4.352239:1-456 [pilon] Processing NODE_530_length_537_cov_13.817308:1-537 [pilon] NODE_126_length_933_cov_4.070197:1-933 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 91, Coverage: 12, minDepth: 5 [pilon] Confirmed 712 of 933 bases (76.31%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_126_length_933_cov_4.070197:1-933 [pilon] Processing NODE_598_length_508_cov_1.550388:1-508 [pilon] NODE_438_length_578_cov_1.271335:1-578 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 17, Coverage: 3, minDepth: 5 [pilon] Confirmed 200 of 578 bases (34.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_386_length_607_cov_0.742798:1-607 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 14, Coverage: 3, minDepth: 5 [pilon] Confirmed 102 of 607 bases (16.80%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_386_length_607_cov_0.742798:1-607 [pilon] Processing NODE_280_length_680_cov_6.016100:1-680 [pilon] NODE_616_length_502_cov_3.451444:1-502 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 29, Coverage: 8, minDepth: 5 [pilon] Confirmed 280 of 502 bases (55.78%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_616_length_502_cov_3.451444:1-502 [pilon] Processing NODE_870_length_412_cov_1.364261:1-412 [pilon] NODE_657_length_485_cov_11.313187:1-485 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 78, Coverage: 21, minDepth: 5 [pilon] Confirmed 399 of 485 bases (82.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_657_length_485_cov_11.313187:1-485 [pilon] Processing NODE_433_length_582_cov_2.464208:1-582 [pilon] NODE_261_length_694_cov_5.057592:1-694 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 74, Coverage: 14, minDepth: 5 [pilon] Confirmed 499 of 694 bases (71.90%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_261_length_694_cov_5.057592:1-694 [pilon] Processing NODE_121_length_956_cov_2.796407:1-956 [pilon] NODE_372_length_616_cov_2.371717:1-616 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 26, Coverage: 5, minDepth: 5 [pilon] Confirmed 282 of 616 bases (45.78%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_372_length_616_cov_2.371717:1-616 [pilon] Processing NODE_601_length_507_cov_0.917098:1-507 [pilon] Finished processing NODE_438_length_578_cov_1.271335:1-578 [pilon] Processing NODE_474_length_563_cov_1.601810:1-563 [pilon] NODE_298_length_666_cov_2.227523:1-666 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 34, Coverage: 7, minDepth: 5 [pilon] Confirmed 396 of 666 bases (59.46%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_298_length_666_cov_2.227523:1-666 [pilon] Processing NODE_275_length_685_cov_5.287234:1-685 [pilon] NODE_271_length_687_cov_9.517668:1-687 log: [pilon] frags shovill.bam: coverage 22 [pilon] Total Reads: 116, Coverage: 22, minDepth: 6 [pilon] Confirmed 506 of 687 bases (73.65%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_271_length_687_cov_9.517668:1-687 [pilon] Processing NODE_512_length_548_cov_1.957845:1-548 [pilon] NODE_184_length_780_cov_8.930197:1-780 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 124, Coverage: 21, minDepth: 5 [pilon] Confirmed 468 of 780 bases (60.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_184_length_780_cov_8.930197:1-780 [pilon] Processing NODE_27_length_38554_cov_39.888481:1-38554 [pilon] NODE_924_length_244_cov_85.203252:1-244 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 233, Coverage: 9, minDepth: 5 [pilon] Confirmed 188 of 244 bases (77.05%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_924_length_244_cov_85.203252:1-244 [pilon] Processing NODE_778_length_442_cov_1.221184:1-442 [pilon] NODE_811_length_432_cov_1.360129:1-432 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 432 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_811_length_432_cov_1.360129:1-432 [pilon] Processing NODE_711_length_467_cov_1.242775:1-467 [pilon] NODE_259_length_697_cov_2.095486:1-697 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 40, Coverage: 7, minDepth: 5 [pilon] Confirmed 461 of 697 bases (66.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_259_length_697_cov_2.095486:1-697 [pilon] Processing NODE_457_length_569_cov_3.955357:1-569 [pilon] NODE_870_length_412_cov_1.364261:1-412 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 53 of 412 bases (12.86%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_870_length_412_cov_1.364261:1-412 [pilon] Processing NODE_864_length_414_cov_1.255973:1-414 [pilon] NODE_630_length_495_cov_3.577540:1-495 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 38, Coverage: 10, minDepth: 5 [pilon] Confirmed 262 of 495 bases (52.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_630_length_495_cov_3.577540:1-495 [pilon] Processing NODE_596_length_508_cov_1.614987:1-508 [pilon] NODE_441_length_577_cov_1.447368:1-577 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 24, Coverage: 5, minDepth: 5 [pilon] Confirmed 282 of 577 bases (48.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_441_length_577_cov_1.447368:1-577 [pilon] Processing NODE_574_length_517_cov_2.780303:1-517 [pilon] NODE_836_length_423_cov_5.794702:1-423 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 36, Coverage: 11, minDepth: 5 [pilon] Confirmed 276 of 423 bases (65.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_836_length_423_cov_5.794702:1-423 [pilon] Processing NODE_908_length_402_cov_2.448399:1-402 [pilon] NODE_339_length_641_cov_0.930769:1-641 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 17, Coverage: 3, minDepth: 5 [pilon] Confirmed 129 of 641 bases (20.12%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_339_length_641_cov_0.930769:1-641 [pilon] Processing NODE_237_length_715_cov_10.309764:1-715 [pilon] NODE_601_length_507_cov_0.917098:1-507 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 15, Coverage: 4, minDepth: 5 [pilon] Confirmed 166 of 507 bases (32.74%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_601_length_507_cov_0.917098:1-507 [pilon] Processing NODE_798_length_436_cov_0.701587:1-436 [pilon] NODE_445_length_576_cov_1.593407:1-576 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 27, Coverage: 6, minDepth: 5 [pilon] Confirmed 278 of 576 bases (48.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_445_length_576_cov_1.593407:1-576 [pilon] Processing NODE_710_length_467_cov_2.164740:1-467 [pilon] NODE_433_length_582_cov_2.464208:1-582 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 36, Coverage: 8, minDepth: 5 [pilon] Confirmed 438 of 582 bases (75.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_433_length_582_cov_2.464208:1-582 [pilon] Processing NODE_562_length_521_cov_3.597500:1-521 [pilon] NODE_778_length_442_cov_1.221184:1-442 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 19, Coverage: 6, minDepth: 5 [pilon] Confirmed 261 of 442 bases (59.05%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_598_length_508_cov_1.550388:1-508 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 19, Coverage: 4, minDepth: 5 [pilon] Confirmed 181 of 508 bases (35.63%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_388_length_604_cov_4.625259:1-604 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 56, Coverage: 12, minDepth: 5 [pilon] Confirmed 457 of 604 bases (75.66%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_598_length_508_cov_1.550388:1-508 [pilon] Finished processing NODE_778_length_442_cov_1.221184:1-442 [pilon] Processing NODE_329_length_646_cov_0.761905:1-646 [pilon] Processing NODE_558_length_525_cov_1.509901:1-525 [pilon] Finished processing NODE_388_length_604_cov_4.625259:1-604 [pilon] Processing NODE_430_length_584_cov_0.552916:1-584 [pilon] NODE_403_length_597_cov_5.792017:1-597 log: [pilon] frags shovill.bam: coverage 23 [pilon] Total Reads: 105, Coverage: 23, minDepth: 6 [pilon] Confirmed 375 of 597 bases (62.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_403_length_597_cov_5.792017:1-597 [pilon] Processing NODE_113_length_1014_cov_3.965286:1-1014 [pilon] NODE_512_length_548_cov_1.957845:1-548 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 18, Coverage: 4, minDepth: 5 [pilon] Confirmed 198 of 548 bases (36.13%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_512_length_548_cov_1.957845:1-548 [pilon] Processing NODE_819_length_428_cov_5.026059:1-428 [pilon] NODE_864_length_414_cov_1.255973:1-414 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 11, Coverage: 3, minDepth: 5 [pilon] Confirmed 129 of 414 bases (31.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_864_length_414_cov_1.255973:1-414 [pilon] Processing NODE_877_length_408_cov_4.003484:1-408 [pilon] NODE_711_length_467_cov_1.242775:1-467 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 24 of 467 bases (5.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_711_length_467_cov_1.242775:1-467 [pilon] Processing NODE_60_length_2263_cov_6.024743:1-2263 [pilon] NODE_275_length_685_cov_5.287234:1-685 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 80, Coverage: 15, minDepth: 5 [pilon] Confirmed 461 of 685 bases (67.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_275_length_685_cov_5.287234:1-685 [pilon] Processing NODE_66_length_1897_cov_28.582770:1-1897 [pilon] NODE_596_length_508_cov_1.614987:1-508 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 19, Coverage: 5, minDepth: 5 [pilon] Confirmed 194 of 508 bases (38.19%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_596_length_508_cov_1.614987:1-508 [pilon] Processing NODE_434_length_581_cov_1.110870:1-581 [pilon] NODE_474_length_563_cov_1.601810:1-563 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 29, Coverage: 6, minDepth: 5 [pilon] Confirmed 363 of 563 bases (64.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_474_length_563_cov_1.601810:1-563 [pilon] Processing NODE_492_length_555_cov_1.419355:1-555 [pilon] NODE_121_length_956_cov_2.796407:1-956 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 67, Coverage: 9, minDepth: 5 [pilon] Confirmed 660 of 956 bases (69.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_121_length_956_cov_2.796407:1-956 [pilon] NODE_457_length_569_cov_3.955357:1-569 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 46, Coverage: 10, minDepth: 5 [pilon] Confirmed 327 of 569 bases (57.47%) [pilon] Corrected 1 snps; 1 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_245_length_708_cov_2.270869:1-708 [pilon] Finished processing NODE_457_length_569_cov_3.955357:1-569 [pilon] Processing NODE_331_length_643_cov_3.398467:1-643 [pilon] NODE_530_length_537_cov_13.817308:1-537 log: [pilon] frags shovill.bam: coverage 27 [pilon] Total Reads: 110, Coverage: 27, minDepth: 7 [pilon] Confirmed 394 of 537 bases (73.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_530_length_537_cov_13.817308:1-537 [pilon] Processing NODE_248_length_706_cov_4.246154:1-706 [pilon] NODE_322_length_648_cov_5.081594:1-648 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 59, Coverage: 11, minDepth: 5 [pilon] Confirmed 376 of 648 bases (58.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_322_length_648_cov_5.081594:1-648 [pilon] Processing NODE_264_length_693_cov_5.673077:1-693 [pilon] NODE_71_length_1564_cov_90.154539:1-1564 log: [pilon] frags shovill.bam: coverage 231 [pilon] Total Reads: 3093, Coverage: 231, minDepth: 58 [pilon] Confirmed 1456 of 1564 bases (93.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_71_length_1564_cov_90.154539:1-1564 [pilon] Processing NODE_486_length_557_cov_3.717890:1-557 [pilon] NODE_280_length_680_cov_6.016100:1-680 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 91, Coverage: 16, minDepth: 5 [pilon] Confirmed 530 of 680 bases (77.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_280_length_680_cov_6.016100:1-680 [pilon] Processing NODE_695_length_471_cov_10.322857:1-471 [pilon] NODE_558_length_525_cov_1.509901:1-525 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 19, Coverage: 4, minDepth: 5 [pilon] Confirmed 167 of 525 bases (31.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_558_length_525_cov_1.509901:1-525 [pilon] Processing NODE_340_length_640_cov_2.533719:1-640 [pilon] NODE_798_length_436_cov_0.701587:1-436 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 99 of 436 bases (22.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_798_length_436_cov_0.701587:1-436 [pilon] Processing NODE_132_length_899_cov_8.776350:1-899 [pilon] NODE_908_length_402_cov_2.448399:1-402 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 25, Coverage: 7, minDepth: 5 [pilon] Confirmed 280 of 402 bases (69.65%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_908_length_402_cov_2.448399:1-402 [pilon] Processing NODE_624_length_498_cov_3.225464:1-498 [pilon] NODE_710_length_467_cov_2.164740:1-467 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 25, Coverage: 5, minDepth: 5 [pilon] Confirmed 230 of 467 bases (49.25%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_710_length_467_cov_2.164740:1-467 [pilon] Processing NODE_518_length_546_cov_2.468235:1-546 [pilon] NODE_877_length_408_cov_4.003484:1-408 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 23, Coverage: 7, minDepth: 5 [pilon] Confirmed 258 of 408 bases (63.24%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_877_length_408_cov_4.003484:1-408 [pilon] Processing NODE_772_length_443_cov_1.645963:1-443 [pilon] NODE_434_length_581_cov_1.110870:1-581 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 18, Coverage: 4, minDepth: 5 [pilon] Confirmed 248 of 581 bases (42.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_434_length_581_cov_1.110870:1-581 [pilon] Processing NODE_57_length_2590_cov_24.109356:1-2590 [pilon] NODE_430_length_584_cov_0.552916:1-584 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 584 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_430_length_584_cov_0.552916:1-584 [pilon] NODE_237_length_715_cov_10.309764:1-715 log: [pilon] frags shovill.bam: coverage 28 [pilon] Total Reads: 154, Coverage: 28, minDepth: 7 [pilon] Confirmed 488 of 715 bases (68.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_237_length_715_cov_10.309764:1-715 [pilon] Processing NODE_256_length_700_cov_10.943005:1-700 [pilon] Processing NODE_39_length_5426_cov_45.750236:1-5426 [pilon] NODE_574_length_517_cov_2.780303:1-517 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 33, Coverage: 7, minDepth: 5 [pilon] Confirmed 313 of 517 bases (60.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_574_length_517_cov_2.780303:1-517 [pilon] Processing NODE_896_length_404_cov_90.671378:1-404 [pilon] NODE_562_length_521_cov_3.597500:1-521 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 37, Coverage: 9, minDepth: 5 [pilon] Confirmed 358 of 521 bases (68.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_562_length_521_cov_3.597500:1-521 [pilon] Processing NODE_22_length_72603_cov_36.721489:1-72603 [pilon] NODE_695_length_471_cov_10.322857:1-471 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 64, Coverage: 18, minDepth: 5 [pilon] Confirmed 380 of 471 bases (80.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_695_length_471_cov_10.322857:1-471 [pilon] Processing NODE_828_length_426_cov_0.645902:1-426 [pilon] NODE_819_length_428_cov_5.026059:1-428 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 35, Coverage: 11, minDepth: 5 [pilon] Confirmed 347 of 428 bases (81.07%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_819_length_428_cov_5.026059:1-428 [pilon] Processing NODE_327_length_646_cov_3.708571:1-646 [pilon] NODE_329_length_646_cov_0.761905:1-646 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 12, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 646 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_329_length_646_cov_0.761905:1-646 [pilon] Processing NODE_891_length_406_cov_0.757895:1-406 [pilon] NODE_492_length_555_cov_1.419355:1-555 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 14, Coverage: 3, minDepth: 5 [pilon] Confirmed 148 of 555 bases (26.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_492_length_555_cov_1.419355:1-555 [pilon] Processing NODE_845_length_421_cov_0.993333:1-421 [pilon] NODE_46_length_3713_cov_27.868875:1-3713 log: [pilon] frags shovill.bam: coverage 83 [pilon] Total Reads: 2372, Coverage: 83, minDepth: 21 [pilon] Confirmed 3187 of 3713 bases (85.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_46_length_3713_cov_27.868875:1-3713 [pilon] Processing NODE_810_length_432_cov_3.016077:1-432 [pilon] NODE_331_length_643_cov_3.398467:1-643 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 62, Coverage: 13, minDepth: 5 [pilon] Confirmed 453 of 643 bases (70.45%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_331_length_643_cov_3.398467:1-643 [pilon] Processing NODE_640_length_493_cov_1.413978:1-493 [pilon] NODE_248_length_706_cov_4.246154:1-706 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 66, Coverage: 12, minDepth: 5 [pilon] Confirmed 497 of 706 bases (70.40%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_248_length_706_cov_4.246154:1-706 [pilon] Processing NODE_792_length_437_cov_1.060127:1-437 [pilon] NODE_264_length_693_cov_5.673077:1-693 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 78, Coverage: 15, minDepth: 5 [pilon] Confirmed 381 of 693 bases (54.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_264_length_693_cov_5.673077:1-693 [pilon] Processing NODE_207_length_750_cov_6.608903:1-750 [pilon] NODE_486_length_557_cov_3.717890:1-557 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 46, Coverage: 11, minDepth: 5 [pilon] Confirmed 447 of 557 bases (80.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_486_length_557_cov_3.717890:1-557 [pilon] Processing NODE_580_length_515_cov_0.791878:1-515 [pilon] NODE_624_length_498_cov_3.225464:1-498 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 31, Coverage: 8, minDepth: 5 [pilon] Confirmed 301 of 498 bases (60.44%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_624_length_498_cov_3.225464:1-498 [pilon] Processing NODE_637_length_494_cov_1.126005:1-494 [pilon] NODE_245_length_708_cov_2.270869:1-708 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 45, Coverage: 8, minDepth: 5 [pilon] Confirmed 361 of 708 bases (50.99%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_245_length_708_cov_2.270869:1-708 [pilon] Processing NODE_55_length_2727_cov_44.844973:1-2727 [pilon] NODE_340_length_640_cov_2.533719:1-640 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 60, Coverage: 12, minDepth: 5 [pilon] Confirmed 543 of 640 bases (84.84%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_340_length_640_cov_2.533719:1-640 [pilon] Processing NODE_639_length_493_cov_2.107527:1-493 [pilon] NODE_64_length_2049_cov_28.913900:1-2049 log: [pilon] frags shovill.bam: coverage 72 [pilon] Total Reads: 1327, Coverage: 72, minDepth: 18 [pilon] Confirmed 1723 of 2049 bases (84.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_64_length_2049_cov_28.913900:1-2049 [pilon] Processing NODE_156_length_826_cov_13.026950:1-826 [pilon] NODE_772_length_443_cov_1.645963:1-443 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 146 of 443 bases (32.96%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_772_length_443_cov_1.645963:1-443 [pilon] Processing NODE_345_length_634_cov_2.976608:1-634 [pilon] NODE_73_length_1546_cov_14.455439:1-1546 log: [pilon] frags shovill.bam: coverage 40 [pilon] Total Reads: 480, Coverage: 40, minDepth: 10 [pilon] Confirmed 1122 of 1546 bases (72.57%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_73_length_1546_cov_14.455439:1-1546 [pilon] Processing NODE_302_length_661_cov_12.557407:1-661 [pilon] NODE_891_length_406_cov_0.757895:1-406 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 406 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_891_length_406_cov_0.757895:1-406 [pilon] Processing NODE_644_length_491_cov_3.045946:1-491 [pilon] NODE_113_length_1014_cov_3.965286:1-1014 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 89, Coverage: 11, minDepth: 5 [pilon] Confirmed 677 of 1014 bases (66.77%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_113_length_1014_cov_3.965286:1-1014 [pilon] Processing NODE_550_length_527_cov_7.167488:1-527 [pilon] NODE_845_length_421_cov_0.993333:1-421 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 12, Coverage: 4, minDepth: 5 [pilon] Confirmed 138 of 421 bases (32.78%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_845_length_421_cov_0.993333:1-421 [pilon] Processing NODE_269_length_689_cov_2.417254:1-689 [pilon] NODE_792_length_437_cov_1.060127:1-437 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 437 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_792_length_437_cov_1.060127:1-437 [pilon] Processing NODE_371_length_616_cov_2.884848:1-616 [pilon] NODE_810_length_432_cov_3.016077:1-432 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 29, Coverage: 8, minDepth: 5 [pilon] Confirmed 299 of 432 bases (69.21%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_810_length_432_cov_3.016077:1-432 [pilon] Processing NODE_440_length_577_cov_1.548246:1-577 [pilon] NODE_828_length_426_cov_0.645902:1-426 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 426 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_828_length_426_cov_0.645902:1-426 [pilon] Processing NODE_725_length_461_cov_2.061765:1-461 [pilon] NODE_640_length_493_cov_1.413978:1-493 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 60 of 493 bases (12.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_640_length_493_cov_1.413978:1-493 [pilon] Processing NODE_15_length_107429_cov_46.392263:1-107429 [pilon] NODE_896_length_404_cov_90.671378:1-404 log: [pilon] frags shovill.bam: coverage 96 [pilon] Total Reads: 636, Coverage: 96, minDepth: 24 [pilon] Confirmed 357 of 404 bases (88.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_896_length_404_cov_90.671378:1-404 [pilon] Processing NODE_238_length_714_cov_11.553120:1-714 [pilon] NODE_580_length_515_cov_0.791878:1-515 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 7, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 515 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_580_length_515_cov_0.791878:1-515 [pilon] Processing NODE_224_length_735_cov_2.224756:1-735 [pilon] NODE_327_length_646_cov_3.708571:1-646 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 50, Coverage: 10, minDepth: 5 [pilon] Confirmed 552 of 646 bases (85.45%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_327_length_646_cov_3.708571:1-646 [pilon] Processing NODE_353_length_628_cov_1.211045:1-628 [pilon] NODE_637_length_494_cov_1.126005:1-494 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 132 of 494 bases (26.72%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_637_length_494_cov_1.126005:1-494 [pilon] Processing NODE_108_length_1050_cov_11.834230:1-1050 [pilon] NODE_639_length_493_cov_2.107527:1-493 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 204 of 493 bases (41.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_639_length_493_cov_2.107527:1-493 [pilon] Processing NODE_820_length_428_cov_3.618893:1-428 [pilon] NODE_518_length_546_cov_2.468235:1-546 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 31, Coverage: 7, minDepth: 5 [pilon] Confirmed 321 of 546 bases (58.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_518_length_546_cov_2.468235:1-546 [pilon] Processing NODE_94_length_1172_cov_6.336822:1-1172 [pilon] NODE_256_length_700_cov_10.943005:1-700 log: [pilon] frags shovill.bam: coverage 32 [pilon] Total Reads: 171, Coverage: 32, minDepth: 8 [pilon] Confirmed 473 of 700 bases (67.57%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_256_length_700_cov_10.943005:1-700 [pilon] Processing NODE_363_length_621_cov_1.536000:1-621 [pilon] NODE_132_length_899_cov_8.776350:1-899 log: [pilon] frags shovill.bam: coverage 28 [pilon] Total Reads: 194, Coverage: 28, minDepth: 7 [pilon] Confirmed 598 of 899 bases (66.52%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_132_length_899_cov_8.776350:1-899 [pilon] Processing NODE_784_length_440_cov_2.858934:1-440 [pilon] NODE_207_length_750_cov_6.608903:1-750 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 94, Coverage: 16, minDepth: 5 [pilon] Confirmed 549 of 750 bases (73.20%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_207_length_750_cov_6.608903:1-750 [pilon] Processing NODE_929_length_243_cov_44.868852:1-243 [pilon] NODE_644_length_491_cov_3.045946:1-491 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 22, Coverage: 6, minDepth: 5 [pilon] Confirmed 277 of 491 bases (56.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_644_length_491_cov_3.045946:1-491 [pilon] Processing NODE_587_length_513_cov_1.696429:1-513 [pilon] NODE_345_length_634_cov_2.976608:1-634 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 38, Coverage: 8, minDepth: 5 [pilon] Confirmed 374 of 634 bases (58.99%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_345_length_634_cov_2.976608:1-634 [pilon] Processing NODE_493_length_554_cov_1.586605:1-554 [pilon] NODE_725_length_461_cov_2.061765:1-461 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 22, Coverage: 5, minDepth: 5 [pilon] Confirmed 270 of 461 bases (58.57%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_725_length_461_cov_2.061765:1-461 [pilon] Processing NODE_679_length_478_cov_1.364146:1-478 [pilon] NODE_371_length_616_cov_2.884848:1-616 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 34, Coverage: 7, minDepth: 5 [pilon] Confirmed 348 of 616 bases (56.49%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_371_length_616_cov_2.884848:1-616 [pilon] Processing NODE_67_length_1824_cov_7.270112:1-1824 [pilon] NODE_269_length_689_cov_2.417254:1-689 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 44, Coverage: 8, minDepth: 5 [pilon] Confirmed 499 of 689 bases (72.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_269_length_689_cov_2.417254:1-689 [pilon] Processing NODE_721_length_463_cov_1.137427:1-463 [pilon] NODE_353_length_628_cov_1.211045:1-628 log: [pilon] NODE_550_length_527_cov_7.167488:1-527 log: [pilon] frags shovill.bam: coverage 23 [pilon] Total Reads: 94, Coverage: 23, minDepth: 6 [pilon] Confirmed 356 of 527 bases (67.55%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_550_length_527_cov_7.167488:1-527 [pilon] Processing NODE_95_length_1170_cov_6.428980:1-1170 [pilon] NODE_440_length_577_cov_1.548246:1-577 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 18, Coverage: 4, minDepth: 5 [pilon] Confirmed 148 of 577 bases (25.65%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_156_length_826_cov_13.026950:1-826 log: [pilon] frags shovill.bam: coverage 40 [pilon] Total Reads: 258, Coverage: 40, minDepth: 10 [pilon] Confirmed 513 of 826 bases (62.11%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_156_length_826_cov_13.026950:1-826 [pilon] Processing NODE_436_length_579_cov_9.914847:1-579 [pilon] NODE_224_length_735_cov_2.224756:1-735 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 32, Coverage: 6, minDepth: 5 [pilon] Confirmed 366 of 735 bases (49.80%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_224_length_735_cov_2.224756:1-735 [pilon] Processing NODE_838_length_423_cov_2.384106:1-423 [pilon] NODE_820_length_428_cov_3.618893:1-428 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 24, Coverage: 7, minDepth: 5 [pilon] Confirmed 283 of 428 bases (66.12%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_302_length_661_cov_12.557407:1-661 log: [pilon] frags shovill.bam: coverage 27 [pilon] Total Reads: 140, Coverage: 27, minDepth: 7 [pilon] Confirmed 435 of 661 bases (65.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_66_length_1897_cov_28.582770:1-1897 log: [pilon] Finished processing NODE_302_length_661_cov_12.557407:1-661 [pilon] Processing NODE_520_length_544_cov_9.387707:1-544 [pilon] Finished processing NODE_820_length_428_cov_3.618893:1-428 [pilon] Finished processing NODE_440_length_577_cov_1.548246:1-577 [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 20, Coverage: 4, minDepth: 5 [pilon] Confirmed 218 of 628 bases (34.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] frags shovill.bam: coverage 80 [pilon] Total Reads: 1172, Coverage: 80, minDepth: 20 [pilon] Confirmed 1581 of 1897 bases (83.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_937_length_122_cov_58.000000:1-122 [pilon] Processing NODE_502_length_550_cov_7.286713:1-550 [pilon] Finished processing NODE_353_length_628_cov_1.211045:1-628 [pilon] Finished processing NODE_66_length_1897_cov_28.582770:1-1897 [pilon] Processing NODE_472_length_563_cov_7.088235:1-563 [pilon] Processing NODE_921_length_270_cov_27.093960:1-270 [pilon] NODE_784_length_440_cov_2.858934:1-440 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 28, Coverage: 8, minDepth: 5 [pilon] Confirmed 271 of 440 bases (61.59%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_784_length_440_cov_2.858934:1-440 [pilon] Processing NODE_746_length_452_cov_2.232628:1-452 [pilon] NODE_60_length_2263_cov_6.024743:1-2263 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 305, Coverage: 18, minDepth: 5 [pilon] Confirmed 1605 of 2263 bases (70.92%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_60_length_2263_cov_6.024743:1-2263 [pilon] Processing NODE_548_length_529_cov_1.431373:1-529 [pilon] NODE_108_length_1050_cov_11.834230:1-1050 log: [pilon] frags shovill.bam: coverage 30 [pilon] Total Reads: 249, Coverage: 30, minDepth: 8 [pilon] Confirmed 807 of 1050 bases (76.86%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_108_length_1050_cov_11.834230:1-1050 [pilon] NODE_929_length_243_cov_44.868852:1-243 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 84, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 243 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_929_length_243_cov_44.868852:1-243 [pilon] Processing NODE_905_length_403_cov_0.500000:1-403 [pilon] NODE_56_length_2632_cov_23.807248:1-2632 log: [pilon] frags shovill.bam: coverage 68 [pilon] Total Reads: 1386, Coverage: 68, minDepth: 17 [pilon] Confirmed 2376 of 2632 bases (90.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_56_length_2632_cov_23.807248:1-2632 [pilon] Processing NODE_18_length_88019_cov_41.386914:1-88019 [pilon] NODE_238_length_714_cov_11.553120:1-714 log: [pilon] frags shovill.bam: coverage 29 [pilon] Total Reads: 161, Coverage: 29, minDepth: 7 [pilon] Confirmed 533 of 714 bases (74.65%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_238_length_714_cov_11.553120:1-714 [pilon] Processing NODE_175_length_799_cov_4.877581:1-799 [pilon] NODE_587_length_513_cov_1.696429:1-513 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 24, Coverage: 6, minDepth: 5 [pilon] Confirmed 300 of 513 bases (58.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_587_length_513_cov_1.696429:1-513 [pilon] Processing NODE_267_length_690_cov_8.441125:1-690 [pilon] NODE_363_length_621_cov_1.536000:1-621 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 18, Coverage: 4, minDepth: 5 [pilon] Confirmed 177 of 621 bases (28.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_363_length_621_cov_1.536000:1-621 [pilon] Processing NODE_522_length_544_cov_1.345154:1-544 [pilon] NODE_493_length_554_cov_1.586605:1-554 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 19, Coverage: 4, minDepth: 5 [pilon] Confirmed 212 of 554 bases (38.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_493_length_554_cov_1.586605:1-554 [pilon] Processing NODE_890_length_406_cov_1.101754:1-406 [pilon] NODE_921_length_270_cov_27.093960:1-270 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 133, Coverage: 9, minDepth: 5 [pilon] Confirmed 206 of 270 bases (76.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_921_length_270_cov_27.093960:1-270 [pilon] Processing NODE_260_length_696_cov_4.808696:1-696 [pilon] NODE_679_length_478_cov_1.364146:1-478 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 13, Coverage: 4, minDepth: 5 [pilon] Confirmed 167 of 478 bases (34.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_679_length_478_cov_1.364146:1-478 [pilon] Processing NODE_540_length_535_cov_2.193237:1-535 [pilon] NODE_838_length_423_cov_2.384106:1-423 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 16, Coverage: 5, minDepth: 5 [pilon] Confirmed 211 of 423 bases (49.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_838_length_423_cov_2.384106:1-423 [pilon] Processing NODE_544_length_533_cov_1.235437:1-533 [pilon] NODE_721_length_463_cov_1.137427:1-463 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 109 of 463 bases (23.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_721_length_463_cov_1.137427:1-463 [pilon] Processing NODE_740_length_454_cov_5.174174:1-454 [pilon] NODE_57_length_2590_cov_24.109356:1-2590 log: [pilon] frags shovill.bam: coverage 70 [pilon] Total Reads: 1403, Coverage: 70, minDepth: 18 [pilon] Confirmed 2264 of 2590 bases (87.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_57_length_2590_cov_24.109356:1-2590 [pilon] Processing NODE_817_length_429_cov_4.000000:1-429 [pilon] NODE_937_length_122_cov_58.000000:1-122 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 5, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 122 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_937_length_122_cov_58.000000:1-122 [pilon] Processing NODE_833_length_424_cov_1.283828:1-424 [pilon] NODE_94_length_1172_cov_6.336822:1-1172 log: [pilon] frags shovill.bam: coverage 20 [pilon] Total Reads: 177, Coverage: 20, minDepth: 5 [pilon] Confirmed 982 of 1172 bases (83.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_94_length_1172_cov_6.336822:1-1172 [pilon] Processing NODE_227_length_727_cov_3.968647:1-727 [pilon] NODE_905_length_403_cov_0.500000:1-403 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 5, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 403 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_905_length_403_cov_0.500000:1-403 [pilon] Processing NODE_157_length_825_cov_4.169034:1-825 [pilon] NODE_520_length_544_cov_9.387707:1-544 log: [pilon] frags shovill.bam: coverage 24 [pilon] Total Reads: 101, Coverage: 24, minDepth: 6 [pilon] Confirmed 367 of 544 bases (67.46%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_520_length_544_cov_9.387707:1-544 [pilon] Processing NODE_428_length_584_cov_2.097192:1-584 [pilon] NODE_436_length_579_cov_9.914847:1-579 log: [pilon] frags shovill.bam: coverage 24 [pilon] Total Reads: 109, Coverage: 24, minDepth: 6 [pilon] Confirmed 461 of 579 bases (79.62%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_436_length_579_cov_9.914847:1-579 [pilon] Processing NODE_688_length_473_cov_2.355114:1-473 [pilon] NODE_548_length_529_cov_1.431373:1-529 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 16, Coverage: 3, minDepth: 5 [pilon] Confirmed 136 of 529 bases (25.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_548_length_529_cov_1.431373:1-529 [pilon] Processing NODE_44_length_4154_cov_17.558889:1-4154 [pilon] NODE_472_length_563_cov_7.088235:1-563 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 66, Coverage: 15, minDepth: 5 [pilon] Confirmed 431 of 563 bases (76.55%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_472_length_563_cov_7.088235:1-563 [pilon] Processing NODE_514_length_547_cov_5.532864:1-547 [pilon] NODE_746_length_452_cov_2.232628:1-452 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 25, Coverage: 7, minDepth: 5 [pilon] Confirmed 312 of 452 bases (69.03%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_746_length_452_cov_2.232628:1-452 [pilon] Processing NODE_889_length_406_cov_1.396491:1-406 [pilon] NODE_502_length_550_cov_7.286713:1-550 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 90, Coverage: 21, minDepth: 5 [pilon] Confirmed 448 of 550 bases (81.45%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_502_length_550_cov_7.286713:1-550 [pilon] NODE_175_length_799_cov_4.877581:1-799 log: [pilon] Processing NODE_82_length_1299_cov_12.027165:1-1299 [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 89, Coverage: 14, minDepth: 5 [pilon] Confirmed 516 of 799 bases (64.58%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_175_length_799_cov_4.877581:1-799 [pilon] NODE_522_length_544_cov_1.345154:1-544 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 164 of 544 bases (30.15%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_522_length_544_cov_1.345154:1-544 [pilon] Processing NODE_465_length_566_cov_3.964045:1-566 [pilon] NODE_267_length_690_cov_8.441125:1-690 log: [pilon] frags shovill.bam: coverage 24 [pilon] Total Reads: 130, Coverage: 24, minDepth: 6 [pilon] Confirmed 551 of 690 bases (79.86%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_267_length_690_cov_8.441125:1-690 [pilon] Processing NODE_815_length_430_cov_1.165049:1-430 [pilon] NODE_890_length_406_cov_1.101754:1-406 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 8, Coverage: 3, minDepth: 5 [pilon] Confirmed 104 of 406 bases (25.62%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_890_length_406_cov_1.101754:1-406 [pilon] Processing NODE_262_length_693_cov_18.087413:1-693 [pilon] NODE_95_length_1170_cov_6.428980:1-1170 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 150, Coverage: 17, minDepth: 5 [pilon] Confirmed 830 of 1170 bases (70.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_95_length_1170_cov_6.428980:1-1170 [pilon] Processing NODE_555_length_526_cov_2.797531:1-526 [pilon] NODE_544_length_533_cov_1.235437:1-533 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 21, Coverage: 5, minDepth: 5 [pilon] Confirmed 224 of 533 bases (42.03%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_544_length_533_cov_1.235437:1-533 [pilon] Processing NODE_656_length_486_cov_3.769863:1-486 [pilon] NODE_740_length_454_cov_5.174174:1-454 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 36, Coverage: 10, minDepth: 5 [pilon] Confirmed 295 of 454 bases (64.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_740_length_454_cov_5.174174:1-454 [pilon] Processing NODE_140_length_858_cov_24.404342:1-858 [pilon] NODE_817_length_429_cov_4.000000:1-429 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 31, Coverage: 9, minDepth: 5 [pilon] Confirmed 313 of 429 bases (72.96%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_817_length_429_cov_4.000000:1-429 [pilon] NODE_540_length_535_cov_2.193237:1-535 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 24, Coverage: 6, minDepth: 5 [pilon] Confirmed 343 of 535 bases (64.11%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_540_length_535_cov_2.193237:1-535 [pilon] Processing NODE_634_length_495_cov_1.278075:1-495 [pilon] Processing NODE_595_length_509_cov_1.961340:1-509 [pilon] NODE_833_length_424_cov_1.283828:1-424 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 13, Coverage: 3, minDepth: 5 [pilon] Confirmed 128 of 424 bases (30.19%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_833_length_424_cov_1.283828:1-424 [pilon] Processing NODE_354_length_627_cov_0.901186:1-627 [pilon] NODE_514_length_547_cov_5.532864:1-547 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 85, Coverage: 15, minDepth: 5 [pilon] Confirmed 340 of 547 bases (62.16%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_514_length_547_cov_5.532864:1-547 [pilon] Processing NODE_404_length_597_cov_3.235294:1-597 [pilon] NODE_227_length_727_cov_3.968647:1-727 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 68, Coverage: 12, minDepth: 5 [pilon] Confirmed 489 of 727 bases (67.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_55_length_2727_cov_44.844973:1-2727 log: [pilon] frags shovill.bam: coverage 133 [pilon] Total Reads: 2804, Coverage: 133, minDepth: 33 [pilon] Confirmed 2232 of 2727 bases (81.85%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_55_length_2727_cov_44.844973:1-2727 [pilon] Processing NODE_552_length_527_cov_3.625616:1-527 [pilon] Finished processing NODE_227_length_727_cov_3.968647:1-727 [pilon] Processing NODE_199_length_758_cov_12.158556:1-758 [pilon] NODE_688_length_473_cov_2.355114:1-473 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 22, Coverage: 6, minDepth: 5 [pilon] Confirmed 221 of 473 bases (46.72%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_688_length_473_cov_2.355114:1-473 [pilon] Processing NODE_253_length_702_cov_10.481928:1-702 [pilon] NODE_260_length_696_cov_4.808696:1-696 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 79, Coverage: 15, minDepth: 5 [pilon] Confirmed 445 of 696 bases (63.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_260_length_696_cov_4.808696:1-696 [pilon] NODE_428_length_584_cov_2.097192:1-584 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 20, Coverage: 4, minDepth: 5 [pilon] Confirmed 278 of 584 bases (47.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_428_length_584_cov_2.097192:1-584 [pilon] Processing NODE_494_length_554_cov_1.124711:1-554 [pilon] Processing NODE_306_length_660_cov_4.077922:1-660 [pilon] NODE_157_length_825_cov_4.169034:1-825 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 71, Coverage: 11, minDepth: 5 [pilon] Confirmed 709 of 825 bases (85.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_157_length_825_cov_4.169034:1-825 [pilon] Processing NODE_426_length_585_cov_3.517241:1-585 [pilon] NODE_889_length_406_cov_1.396491:1-406 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 9, Coverage: 2, minDepth: 5 [pilon] Confirmed 7 of 406 bases (1.72%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_889_length_406_cov_1.396491:1-406 [pilon] Processing NODE_460_length_568_cov_10.100671:1-568 [pilon] NODE_815_length_430_cov_1.165049:1-430 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 98 of 430 bases (22.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_815_length_430_cov_1.165049:1-430 [pilon] Processing NODE_912_length_402_cov_0.523132:1-402 [pilon] NODE_67_length_1824_cov_7.270112:1-1824 log: [pilon] frags shovill.bam: coverage 23 [pilon] Total Reads: 322, Coverage: 23, minDepth: 6 [pilon] Confirmed 1290 of 1824 bases (70.72%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_67_length_1824_cov_7.270112:1-1824 [pilon] Processing NODE_228_length_726_cov_13.768595:1-726 [pilon] NODE_656_length_486_cov_3.769863:1-486 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 37, Coverage: 9, minDepth: 5 [pilon] Confirmed 291 of 486 bases (59.88%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_656_length_486_cov_3.769863:1-486 [pilon] Processing NODE_702_length_470_cov_1.716332:1-470 [pilon] NODE_555_length_526_cov_2.797531:1-526 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 45, Coverage: 9, minDepth: 5 [pilon] Confirmed 423 of 526 bases (80.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_555_length_526_cov_2.797531:1-526 [pilon] Processing NODE_102_length_1098_cov_3.344933:1-1098 [pilon] NODE_634_length_495_cov_1.278075:1-495 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 18, Coverage: 5, minDepth: 5 [pilon] Confirmed 261 of 495 bases (52.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_634_length_495_cov_1.278075:1-495 [pilon] Processing NODE_421_length_587_cov_11.553648:1-587 [pilon] NODE_595_length_509_cov_1.961340:1-509 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 22, Coverage: 6, minDepth: 5 [pilon] Confirmed 283 of 509 bases (55.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_595_length_509_cov_1.961340:1-509 [pilon] Processing NODE_901_length_403_cov_3.290780:1-403 [pilon] NODE_465_length_566_cov_3.964045:1-566 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 51, Coverage: 12, minDepth: 5 [pilon] Confirmed 485 of 566 bases (85.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_465_length_566_cov_3.964045:1-566 [pilon] Processing NODE_177_length_794_cov_4.732541:1-794 [pilon] NODE_354_length_627_cov_0.901186:1-627 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 15, Coverage: 3, minDepth: 5 [pilon] Confirmed 116 of 627 bases (18.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_354_length_627_cov_0.901186:1-627 [pilon] Processing NODE_381_length_609_cov_3.153689:1-609 [pilon] NODE_494_length_554_cov_1.124711:1-554 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 17, Coverage: 4, minDepth: 5 [pilon] Confirmed 254 of 554 bases (45.85%) [pilon] Corrected 5 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_494_length_554_cov_1.124711:1-554 [pilon] Processing NODE_346_length_632_cov_1.418787:1-632 [pilon] NODE_404_length_597_cov_3.235294:1-597 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 36, Coverage: 8, minDepth: 5 [pilon] Confirmed 414 of 597 bases (69.35%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_404_length_597_cov_3.235294:1-597 [pilon] Processing NODE_333_length_642_cov_4.161228:1-642 [pilon] NODE_912_length_402_cov_0.523132:1-402 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 402 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_912_length_402_cov_0.523132:1-402 [pilon] NODE_262_length_693_cov_18.087413:1-693 log: [pilon] frags shovill.bam: coverage 47 [pilon] Total Reads: 251, Coverage: 47, minDepth: 12 [pilon] Confirmed 543 of 693 bases (78.35%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_262_length_693_cov_18.087413:1-693 [pilon] Processing NODE_279_length_680_cov_8.694097:1-680 [pilon] NODE_552_length_527_cov_3.625616:1-527 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 38, Coverage: 9, minDepth: 5 [pilon] Confirmed 403 of 527 bases (76.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_552_length_527_cov_3.625616:1-527 [pilon] Processing NODE_661_length_483_cov_1.726519:1-483 [pilon] NODE_306_length_660_cov_4.077922:1-660 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 50, Coverage: 10, minDepth: 5 [pilon] Confirmed 448 of 660 bases (67.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_306_length_660_cov_4.077922:1-660 [pilon] Processing NODE_87_length_1232_cov_4.632763:1-1232 [pilon] NODE_460_length_568_cov_10.100671:1-568 log: [pilon] frags shovill.bam: coverage 23 [pilon] Total Reads: 102, Coverage: 23, minDepth: 6 [pilon] Confirmed 443 of 568 bases (77.99%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_460_length_568_cov_10.100671:1-568 [pilon] Processing NODE_5_length_326645_cov_43.335586:1-326645 [pilon] NODE_426_length_585_cov_3.517241:1-585 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 56, Coverage: 12, minDepth: 5 [pilon] Confirmed 447 of 585 bases (76.41%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_426_length_585_cov_3.517241:1-585 [pilon] Processing NODE_664_length_483_cov_1.215470:1-483 [pilon] NODE_253_length_702_cov_10.481928:1-702 log: [pilon] frags shovill.bam: coverage 27 [pilon] Total Reads: 147, Coverage: 27, minDepth: 7 [pilon] Confirmed 504 of 702 bases (71.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_253_length_702_cov_10.481928:1-702 [pilon] Processing NODE_765_length_445_cov_1.546296:1-445 [pilon] NODE_199_length_758_cov_12.158556:1-758 log: [pilon] frags shovill.bam: coverage 29 [pilon] Total Reads: 172, Coverage: 29, minDepth: 7 [pilon] Confirmed 574 of 758 bases (75.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_199_length_758_cov_12.158556:1-758 [pilon] Processing NODE_70_length_1613_cov_190.256032:1-1613 [pilon] NODE_702_length_470_cov_1.716332:1-470 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 21, Coverage: 4, minDepth: 5 [pilon] Confirmed 135 of 470 bases (28.72%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_702_length_470_cov_1.716332:1-470 [pilon] Processing NODE_355_length_627_cov_0.723320:1-627 [pilon] Processing NODE_384_length_607_cov_3.839506:1-607 [pilon] Processing NODE_638_length_494_cov_1.048257:1-494 [pilon] NODE_140_length_858_cov_24.404342:1-858 log: [pilon] frags shovill.bam: coverage 64 [pilon] Total Reads: 429, Coverage: 64, minDepth: 16 [pilon] Confirmed 587 of 858 bases (68.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_140_length_858_cov_24.404342:1-858 [pilon] Processing NODE_769_length_444_cov_1.272446:1-444 [pilon] NODE_228_length_726_cov_13.768595:1-726 log: [pilon] frags shovill.bam: coverage 35 [pilon] Total Reads: 205, Coverage: 35, minDepth: 9 [pilon] Confirmed 449 of 726 bases (61.85%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_228_length_726_cov_13.768595:1-726 [pilon] Processing NODE_362_length_622_cov_0.612774:1-622 [pilon] NODE_901_length_403_cov_3.290780:1-403 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 26, Coverage: 8, minDepth: 5 [pilon] Confirmed 301 of 403 bases (74.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_901_length_403_cov_3.290780:1-403 [pilon] Processing NODE_170_length_803_cov_5.054252:1-803 [pilon] NODE_82_length_1299_cov_12.027165:1-1299 log: [pilon] frags shovill.bam: coverage 46 [pilon] Total Reads: 466, Coverage: 46, minDepth: 12 [pilon] Confirmed 1047 of 1299 bases (80.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_82_length_1299_cov_12.027165:1-1299 [pilon] Processing NODE_554_length_526_cov_2.827160:1-526 [pilon] NODE_421_length_587_cov_11.553648:1-587 log: [pilon] frags shovill.bam: coverage 26 [pilon] Total Reads: 119, Coverage: 26, minDepth: 7 [pilon] Confirmed 445 of 587 bases (75.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_421_length_587_cov_11.553648:1-587 [pilon] Processing NODE_48_length_3613_cov_14.987113:1-3613 [pilon] NODE_177_length_794_cov_4.732541:1-794 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 83, Coverage: 14, minDepth: 5 [pilon] Confirmed 654 of 794 bases (82.37%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_177_length_794_cov_4.732541:1-794 [pilon] Processing NODE_553_length_527_cov_1.901478:1-527 [pilon] NODE_102_length_1098_cov_3.344933:1-1098 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 78, Coverage: 9, minDepth: 5 [pilon] Confirmed 746 of 1098 bases (67.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_102_length_1098_cov_3.344933:1-1098 [pilon] Processing NODE_594_length_510_cov_1.971722:1-510 [pilon] NODE_381_length_609_cov_3.153689:1-609 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 38, Coverage: 8, minDepth: 5 [pilon] Confirmed 380 of 609 bases (62.40%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_381_length_609_cov_3.153689:1-609 [pilon] Processing NODE_281_length_678_cov_15.633752:1-678 [pilon] NODE_661_length_483_cov_1.726519:1-483 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 22, Coverage: 6, minDepth: 5 [pilon] Confirmed 289 of 483 bases (59.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_661_length_483_cov_1.726519:1-483 [pilon] Processing NODE_197_length_761_cov_7.173438:1-761 [pilon] NODE_333_length_642_cov_4.161228:1-642 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 56, Coverage: 11, minDepth: 5 [pilon] Confirmed 456 of 642 bases (71.03%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_333_length_642_cov_4.161228:1-642 [pilon] Processing NODE_604_length_506_cov_3.267532:1-506 [pilon] NODE_664_length_483_cov_1.215470:1-483 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 168 of 483 bases (34.78%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_664_length_483_cov_1.215470:1-483 [pilon] Processing NODE_736_length_456_cov_3.922388:1-456 [pilon] NODE_765_length_445_cov_1.546296:1-445 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 123 of 445 bases (27.64%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_765_length_445_cov_1.546296:1-445 [pilon] Processing NODE_239_length_714_cov_4.460371:1-714 [pilon] NODE_279_length_680_cov_8.694097:1-680 log: [pilon] frags shovill.bam: coverage 27 [pilon] Total Reads: 142, Coverage: 27, minDepth: 7 [pilon] Confirmed 486 of 680 bases (71.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_279_length_680_cov_8.694097:1-680 [pilon] Processing NODE_926_length_243_cov_50.122951:1-243 [pilon] NODE_346_length_632_cov_1.418787:1-632 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 22, Coverage: 5, minDepth: 5 [pilon] Confirmed 291 of 632 bases (46.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_346_length_632_cov_1.418787:1-632 [pilon] Processing NODE_150_length_836_cov_9.173427:1-836 [pilon] NODE_638_length_494_cov_1.048257:1-494 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 124 of 494 bases (25.10%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_638_length_494_cov_1.048257:1-494 [pilon] Processing NODE_755_length_448_cov_2.556575:1-448 [pilon] NODE_769_length_444_cov_1.272446:1-444 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 109 of 444 bases (24.55%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_769_length_444_cov_1.272446:1-444 [pilon] Processing NODE_914_length_345_cov_42.709821:1-345 [pilon] NODE_362_length_622_cov_0.612774:1-622 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 10, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 622 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_362_length_622_cov_0.612774:1-622 [pilon] NODE_355_length_627_cov_0.723320:1-627 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 10, Coverage: 2, minDepth: 5 [pilon] Confirmed 29 of 627 bases (4.63%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_355_length_627_cov_0.723320:1-627 [pilon] Processing NODE_563_length_521_cov_3.055000:1-521 [pilon] Processing NODE_216_length_740_cov_13.583199:1-740 [pilon] NODE_384_length_607_cov_3.839506:1-607 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 42, Coverage: 9, minDepth: 5 [pilon] Confirmed 299 of 607 bases (49.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_384_length_607_cov_3.839506:1-607 [pilon] Processing NODE_642_length_492_cov_1.908356:1-492 [pilon] NODE_554_length_526_cov_2.827160:1-526 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 28, Coverage: 7, minDepth: 5 [pilon] Confirmed 348 of 526 bases (66.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_554_length_526_cov_2.827160:1-526 [pilon] Processing NODE_692_length_473_cov_0.417614:1-473 [pilon] NODE_170_length_803_cov_5.054252:1-803 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 87, Coverage: 14, minDepth: 5 [pilon] Confirmed 526 of 803 bases (65.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_170_length_803_cov_5.054252:1-803 [pilon] Processing NODE_680_length_478_cov_0.591036:1-478 [pilon] NODE_553_length_527_cov_1.901478:1-527 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 17, Coverage: 4, minDepth: 5 [pilon] Confirmed 209 of 527 bases (39.66%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_736_length_456_cov_3.922388:1-456 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 34, Coverage: 9, minDepth: 5 [pilon] Confirmed 294 of 456 bases (64.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_755_length_448_cov_2.556575:1-448 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 25, Coverage: 6, minDepth: 5 [pilon] Confirmed 292 of 448 bases (65.18%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_604_length_506_cov_3.267532:1-506 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 30, Coverage: 8, minDepth: 5 [pilon] Confirmed 323 of 506 bases (63.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_594_length_510_cov_1.971722:1-510 log: [pilon] NODE_87_length_1232_cov_4.632763:1-1232 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 113, Coverage: 12, minDepth: 5 [pilon] Confirmed 819 of 1232 bases (66.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_87_length_1232_cov_4.632763:1-1232 [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 20, Coverage: 5, minDepth: 5 [pilon] Confirmed 301 of 510 bases (59.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_604_length_506_cov_3.267532:1-506 [pilon] Finished processing NODE_755_length_448_cov_2.556575:1-448 [pilon] Finished processing NODE_736_length_456_cov_3.922388:1-456 [pilon] Finished processing NODE_553_length_527_cov_1.901478:1-527 [pilon] Processing NODE_348_length_630_cov_6.960707:1-630 [pilon] Processing NODE_783_length_441_cov_1.387500:1-441 [pilon] NODE_281_length_678_cov_15.633752:1-678 log: [pilon] frags shovill.bam: coverage 36 [pilon] Total Reads: 189, Coverage: 36, minDepth: 9 [pilon] Confirmed 490 of 678 bases (72.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_281_length_678_cov_15.633752:1-678 [pilon] Processing NODE_857_length_416_cov_1.081356:1-416 [pilon] Finished processing NODE_594_length_510_cov_1.971722:1-510 [pilon] Processing NODE_14_length_120159_cov_46.979490:1-120159 [pilon] Processing NODE_536_length_536_cov_1.077108:1-536 [pilon] Processing NODE_285_length_673_cov_6.056159:1-673 [pilon] Processing NODE_794_length_436_cov_4.212698:1-436 [pilon] NODE_239_length_714_cov_4.460371:1-714 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 82, Coverage: 15, minDepth: 5 [pilon] Confirmed 483 of 714 bases (67.65%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_239_length_714_cov_4.460371:1-714 [pilon] Processing NODE_841_length_422_cov_0.710963:1-422 [pilon] NODE_197_length_761_cov_7.173438:1-761 log: [pilon] frags shovill.bam: coverage 19 [pilon] Total Reads: 113, Coverage: 19, minDepth: 5 [pilon] Confirmed 560 of 761 bases (73.59%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_197_length_761_cov_7.173438:1-761 [pilon] Processing NODE_406_length_597_cov_2.689076:1-597 [pilon] NODE_150_length_836_cov_9.173427:1-836 log: [pilon] frags shovill.bam: coverage 22 [pilon] Total Reads: 148, Coverage: 22, minDepth: 6 [pilon] Confirmed 765 of 836 bases (91.51%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_150_length_836_cov_9.173427:1-836 [pilon] Processing NODE_483_length_558_cov_2.189931:1-558 [pilon] NODE_926_length_243_cov_50.122951:1-243 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 146, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 243 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_926_length_243_cov_50.122951:1-243 [pilon] Processing NODE_775_length_442_cov_1.545171:1-442 [pilon] NODE_563_length_521_cov_3.055000:1-521 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 34, Coverage: 8, minDepth: 5 [pilon] Confirmed 325 of 521 bases (62.38%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_563_length_521_cov_3.055000:1-521 [pilon] Processing NODE_81_length_1306_cov_7.258228:1-1306 [pilon] NODE_914_length_345_cov_42.709821:1-345 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 226, Coverage: 5, minDepth: 5 [pilon] Confirmed 148 of 345 bases (42.90%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_914_length_345_cov_42.709821:1-345 [pilon] Processing NODE_673_length_479_cov_9.251397:1-479 [pilon] NODE_44_length_4154_cov_17.558889:1-4154 log: [pilon] frags shovill.bam: coverage 50 [pilon] Total Reads: 2362, Coverage: 50, minDepth: 13 [pilon] Confirmed 3007 of 4154 bases (72.39%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_44_length_4154_cov_17.558889:1-4154 [pilon] Processing NODE_232_length_721_cov_1.846667:1-721 [pilon] NODE_642_length_492_cov_1.908356:1-492 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 18, Coverage: 5, minDepth: 5 [pilon] Confirmed 255 of 492 bases (51.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_642_length_492_cov_1.908356:1-492 [pilon] Processing NODE_782_length_441_cov_1.571875:1-441 [pilon] NODE_216_length_740_cov_13.583199:1-740 log: [pilon] frags shovill.bam: coverage 61 [pilon] Total Reads: 349, Coverage: 61, minDepth: 15 [pilon] Confirmed 554 of 740 bases (74.86%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_216_length_740_cov_13.583199:1-740 [pilon] Processing NODE_541_length_534_cov_3.578692:1-534 [pilon] NODE_48_length_3613_cov_14.987113:1-3613 log: [pilon] frags shovill.bam: coverage 46 [pilon] Total Reads: 1273, Coverage: 46, minDepth: 12 [pilon] Confirmed 2454 of 3613 bases (67.92%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_48_length_3613_cov_14.987113:1-3613 [pilon] Processing NODE_653_length_487_cov_2.789617:1-487 [pilon] NODE_39_length_5426_cov_45.750236:1-5426 log: [pilon] frags shovill.bam: coverage 131 [pilon] Total Reads: 5649, Coverage: 131, minDepth: 33 [pilon] Confirmed 5289 of 5426 bases (97.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_39_length_5426_cov_45.750236:1-5426 [pilon] Processing NODE_829_length_426_cov_0.570492:1-426 [pilon] NODE_692_length_473_cov_0.417614:1-473 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 473 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_692_length_473_cov_0.417614:1-473 [pilon] Processing NODE_158_length_824_cov_2.116643:1-824 [pilon] NODE_680_length_478_cov_0.591036:1-478 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 7, Coverage: 2, minDepth: 5 [pilon] Confirmed 10 of 478 bases (2.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_680_length_478_cov_0.591036:1-478 [pilon] Processing NODE_538_length_535_cov_2.850242:1-535 [pilon] NODE_857_length_416_cov_1.081356:1-416 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 8, Coverage: 3, minDepth: 5 [pilon] Confirmed 80 of 416 bases (19.23%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_857_length_416_cov_1.081356:1-416 [pilon] Processing NODE_442_length_577_cov_1.396930:1-577 [pilon] NODE_783_length_441_cov_1.387500:1-441 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 15, Coverage: 4, minDepth: 5 [pilon] Confirmed 234 of 441 bases (53.06%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_783_length_441_cov_1.387500:1-441 [pilon] Processing NODE_900_length_404_cov_0.621908:1-404 [pilon] NODE_841_length_422_cov_0.710963:1-422 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 422 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_841_length_422_cov_0.710963:1-422 [pilon] Processing NODE_487_length_557_cov_0.983945:1-557 [pilon] NODE_483_length_558_cov_2.189931:1-558 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 18, Coverage: 4, minDepth: 5 [pilon] Confirmed 275 of 558 bases (49.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_483_length_558_cov_2.189931:1-558 [pilon] Processing NODE_884_length_408_cov_0.202091:1-408 [pilon] NODE_536_length_536_cov_1.077108:1-536 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 15, Coverage: 3, minDepth: 5 [pilon] Confirmed 162 of 536 bases (30.22%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_536_length_536_cov_1.077108:1-536 [pilon] Processing NODE_249_length_705_cov_10.506849:1-705 [pilon] NODE_794_length_436_cov_4.212698:1-436 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 43, Coverage: 13, minDepth: 5 [pilon] Confirmed 334 of 436 bases (76.61%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_794_length_436_cov_4.212698:1-436 [pilon] Processing NODE_290_length_671_cov_5.743636:1-671 [pilon] NODE_775_length_442_cov_1.545171:1-442 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 28, Coverage: 4, minDepth: 5 [pilon] Confirmed 221 of 442 bases (50.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_775_length_442_cov_1.545171:1-442 [pilon] Processing NODE_816_length_430_cov_0.708738:1-430 [pilon] NODE_406_length_597_cov_2.689076:1-597 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 34, Coverage: 7, minDepth: 5 [pilon] Confirmed 380 of 597 bases (63.65%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_406_length_597_cov_2.689076:1-597 [pilon] Processing NODE_90_length_1212_cov_6.421632:1-1212 [pilon] NODE_348_length_630_cov_6.960707:1-630 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 81, Coverage: 17, minDepth: 5 [pilon] Confirmed 524 of 630 bases (83.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_348_length_630_cov_6.960707:1-630 [pilon] Processing NODE_383_length_608_cov_2.195072:1-608 [pilon] NODE_232_length_721_cov_1.846667:1-721 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 38, Coverage: 6, minDepth: 5 [pilon] Confirmed 448 of 721 bases (62.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_232_length_721_cov_1.846667:1-721 [pilon] Processing NODE_904_length_403_cov_0.882979:1-403 [pilon] NODE_673_length_479_cov_9.251397:1-479 log: [pilon] frags shovill.bam: coverage 24 [pilon] Total Reads: 91, Coverage: 24, minDepth: 6 [pilon] Confirmed 366 of 479 bases (76.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_673_length_479_cov_9.251397:1-479 [pilon] NODE_81_length_1306_cov_7.258228:1-1306 log: [pilon] frags shovill.bam: coverage 24 [pilon] Total Reads: 248, Coverage: 24, minDepth: 6 [pilon] Confirmed 807 of 1306 bases (61.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_81_length_1306_cov_7.258228:1-1306 [pilon] Processing NODE_4_length_326788_cov_39.039413:1-326788 [pilon] Processing NODE_116_length_1006_cov_1.476836:1-1006 [pilon] NODE_285_length_673_cov_6.056159:1-673 log: [pilon] frags shovill.bam: coverage 24 [pilon] Total Reads: 127, Coverage: 24, minDepth: 6 [pilon] Confirmed 434 of 673 bases (64.49%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_285_length_673_cov_6.056159:1-673 [pilon] Processing NODE_196_length_761_cov_8.310937:1-761 [pilon] NODE_541_length_534_cov_3.578692:1-534 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 32, Coverage: 8, minDepth: 5 [pilon] Confirmed 366 of 534 bases (68.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_541_length_534_cov_3.578692:1-534 [pilon] Processing NODE_730_length_458_cov_7.433234:1-458 [pilon] NODE_829_length_426_cov_0.570492:1-426 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 426 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_829_length_426_cov_0.570492:1-426 [pilon] Processing NODE_8_length_244740_cov_43.085002:1-244740 [pilon] NODE_782_length_441_cov_1.571875:1-441 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 18, Coverage: 5, minDepth: 5 [pilon] Confirmed 282 of 441 bases (63.95%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_782_length_441_cov_1.571875:1-441 [pilon] Processing NODE_139_length_869_cov_15.966578:1-869 [pilon] NODE_538_length_535_cov_2.850242:1-535 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 30, Coverage: 7, minDepth: 5 [pilon] Confirmed 339 of 535 bases (63.36%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_538_length_535_cov_2.850242:1-535 [pilon] Processing NODE_69_length_1792_cov_6.403351:1-1792 [pilon] NODE_900_length_404_cov_0.621908:1-404 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 10, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 404 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_158_length_824_cov_2.116643:1-824 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 41, Coverage: 6, minDepth: 5 [pilon] Confirmed 444 of 824 bases (53.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_158_length_824_cov_2.116643:1-824 [pilon] NODE_442_length_577_cov_1.396930:1-577 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 22, Coverage: 5, minDepth: 5 [pilon] Confirmed 296 of 577 bases (51.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_442_length_577_cov_1.396930:1-577 [pilon] Processing NODE_823_length_428_cov_0.716612:1-428 [pilon] NODE_249_length_705_cov_10.506849:1-705 log: [pilon] frags shovill.bam: coverage 24 [pilon] Total Reads: 136, Coverage: 24, minDepth: 6 [pilon] Confirmed 503 of 705 bases (71.35%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_249_length_705_cov_10.506849:1-705 [pilon] NODE_816_length_430_cov_0.708738:1-430 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 5, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 430 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_884_length_408_cov_0.202091:1-408 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 4, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 408 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_884_length_408_cov_0.202091:1-408 [pilon] NODE_487_length_557_cov_0.983945:1-557 log: [pilon] Processing NODE_392_length_603_cov_1.765560:1-603 [pilon] Finished processing NODE_816_length_430_cov_0.708738:1-430 [pilon] Processing NODE_851_length_419_cov_0.617450:1-419 [pilon] Processing NODE_880_length_408_cov_1.236934:1-408 [pilon] Processing NODE_645_length_491_cov_0.581081:1-491 [pilon] Finished processing NODE_900_length_404_cov_0.621908:1-404 [pilon] NODE_383_length_608_cov_2.195072:1-608 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 26, Coverage: 6, minDepth: 5 [pilon] Confirmed 311 of 608 bases (51.15%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 11, Coverage: 2, minDepth: 5 [pilon] Confirmed 125 of 557 bases (22.44%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_383_length_608_cov_2.195072:1-608 [pilon] Processing NODE_114_length_1009_cov_11.805180:1-1009 [pilon] Processing NODE_111_length_1038_cov_10.586696:1-1038 [pilon] Finished processing NODE_487_length_557_cov_0.983945:1-557 [pilon] Processing NODE_320_length_649_cov_4.556818:1-649 [pilon] NODE_653_length_487_cov_2.789617:1-487 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 24, Coverage: 6, minDepth: 5 [pilon] Confirmed 269 of 487 bases (55.24%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_653_length_487_cov_2.789617:1-487 [pilon] Processing NODE_913_length_399_cov_99.758993:1-399 [pilon] NODE_290_length_671_cov_5.743636:1-671 log: [pilon] frags shovill.bam: coverage 19 [pilon] Total Reads: 101, Coverage: 19, minDepth: 5 [pilon] Confirmed 535 of 671 bases (79.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_290_length_671_cov_5.743636:1-671 [pilon] Processing NODE_605_length_506_cov_1.724675:1-506 [pilon] NODE_90_length_1212_cov_6.421632:1-1212 log: [pilon] frags shovill.bam: coverage 23 [pilon] Total Reads: 217, Coverage: 23, minDepth: 6 [pilon] Confirmed 779 of 1212 bases (64.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_90_length_1212_cov_6.421632:1-1212 [pilon] Processing NODE_504_length_550_cov_3.918415:1-550 [pilon] NODE_70_length_1613_cov_190.256032:1-1613 log: [pilon] frags shovill.bam: coverage 463 [pilon] Total Reads: 6733, Coverage: 463, minDepth: 116 [pilon] Confirmed 1360 of 1613 bases (84.31%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_70_length_1613_cov_190.256032:1-1613 [pilon] Processing NODE_591_length_511_cov_0.435897:1-511 [pilon] NODE_116_length_1006_cov_1.476836:1-1006 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 40, Coverage: 5, minDepth: 5 [pilon] Confirmed 410 of 1006 bases (40.76%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_116_length_1006_cov_1.476836:1-1006 [pilon] Processing NODE_43_length_4199_cov_27.804316:1-4199 [pilon] NODE_139_length_869_cov_15.966578:1-869 log: [pilon] frags shovill.bam: coverage 39 [pilon] Total Reads: 265, Coverage: 39, minDepth: 10 [pilon] Confirmed 537 of 869 bases (61.80%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_139_length_869_cov_15.966578:1-869 [pilon] Processing NODE_148_length_838_cov_5.747559:1-838 [pilon] NODE_851_length_419_cov_0.617450:1-419 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 419 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_851_length_419_cov_0.617450:1-419 [pilon] Processing NODE_2_length_407886_cov_34.907846:1-407886 [pilon] NODE_392_length_603_cov_1.765560:1-603 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 18, Coverage: 4, minDepth: 5 [pilon] Confirmed 214 of 603 bases (35.49%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_823_length_428_cov_0.716612:1-428 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 428 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_392_length_603_cov_1.765560:1-603 [pilon] Finished processing NODE_823_length_428_cov_0.716612:1-428 [pilon] Processing NODE_412_length_594_cov_16.319239:1-594 [pilon] Processing NODE_270_length_688_cov_2.793651:1-688 [pilon] NODE_880_length_408_cov_1.236934:1-408 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 99 of 408 bases (24.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_880_length_408_cov_1.236934:1-408 [pilon] Processing NODE_773_length_443_cov_1.043478:1-443 [pilon] NODE_196_length_761_cov_8.310937:1-761 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 125, Coverage: 21, minDepth: 5 [pilon] Confirmed 552 of 761 bases (72.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_196_length_761_cov_8.310937:1-761 [pilon] Processing NODE_52_length_2905_cov_24.298132:1-2905 [pilon] NODE_904_length_403_cov_0.882979:1-403 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 18, Coverage: 3, minDepth: 5 [pilon] Confirmed 70 of 403 bases (17.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_904_length_403_cov_0.882979:1-403 [pilon] Processing NODE_127_length_929_cov_1.813119:1-929 [pilon] NODE_320_length_649_cov_4.556818:1-649 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 61, Coverage: 12, minDepth: 5 [pilon] Confirmed 525 of 649 bases (80.89%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_320_length_649_cov_4.556818:1-649 [pilon] Processing NODE_368_length_618_cov_3.501006:1-618 [pilon] NODE_645_length_491_cov_0.581081:1-491 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 9, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 491 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_645_length_491_cov_0.581081:1-491 [pilon] Processing NODE_686_length_474_cov_1.118980:1-474 [pilon] NODE_69_length_1792_cov_6.403351:1-1792 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 256, Coverage: 18, minDepth: 5 [pilon] Confirmed 1590 of 1792 bases (88.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_69_length_1792_cov_6.403351:1-1792 [pilon] Processing NODE_277_length_682_cov_6.190731:1-682 [pilon] NODE_114_length_1009_cov_11.805180:1-1009 log: [pilon] frags shovill.bam: coverage 31 [pilon] Total Reads: 238, Coverage: 31, minDepth: 8 [pilon] Confirmed 724 of 1009 bases (71.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_114_length_1009_cov_11.805180:1-1009 [pilon] Processing NODE_739_length_454_cov_9.126126:1-454 [pilon] NODE_111_length_1038_cov_10.586696:1-1038 log: [pilon] NODE_504_length_550_cov_3.918415:1-550 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 55, Coverage: 10, minDepth: 5 [pilon] Confirmed 421 of 550 bases (76.55%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_913_length_399_cov_99.758993:1-399 log: [pilon] frags shovill.bam: coverage 110 [pilon] Total Reads: 652, Coverage: 110, minDepth: 28 [pilon] Confirmed 356 of 399 bases (89.22%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] frags shovill.bam: coverage 34 [pilon] Total Reads: 271, Coverage: 34, minDepth: 9 [pilon] Confirmed 764 of 1038 bases (73.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_504_length_550_cov_3.918415:1-550 [pilon] Processing NODE_61_length_2178_cov_37.741857:1-2178 [pilon] Finished processing NODE_913_length_399_cov_99.758993:1-399 [pilon] Processing NODE_129_length_909_cov_2.441624:1-909 [pilon] Finished processing NODE_111_length_1038_cov_10.586696:1-1038 [pilon] Processing NODE_394_length_602_cov_1.147609:1-602 [pilon] NODE_730_length_458_cov_7.433234:1-458 log: [pilon] frags shovill.bam: coverage 26 [pilon] Total Reads: 116, Coverage: 26, minDepth: 7 [pilon] Confirmed 348 of 458 bases (75.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_730_length_458_cov_7.433234:1-458 [pilon] Processing NODE_527_length_538_cov_1.733813:1-538 [pilon] NODE_591_length_511_cov_0.435897:1-511 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 511 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_591_length_511_cov_0.435897:1-511 [pilon] Processing NODE_328_length_646_cov_0.775238:1-646 [pilon] NODE_32_length_23617_cov_34.984721:1-23617 log: [pilon] frags shovill.bam: coverage 106 [pilon] Total Reads: 19370, Coverage: 106, minDepth: 27 [pilon] Confirmed 22468 of 23617 bases (95.13%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_32_length_23617_cov_34.984721:1-23617 [pilon] Processing NODE_337_length_641_cov_20.051923:1-641 [pilon] NODE_605_length_506_cov_1.724675:1-506 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 15, Coverage: 4, minDepth: 5 [pilon] Confirmed 130 of 506 bases (25.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_605_length_506_cov_1.724675:1-506 [pilon] Processing NODE_791_length_437_cov_1.363924:1-437 [pilon] NODE_148_length_838_cov_5.747559:1-838 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 96, Coverage: 15, minDepth: 5 [pilon] Confirmed 670 of 838 bases (79.95%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_148_length_838_cov_5.747559:1-838 [pilon] Processing NODE_469_length_565_cov_6.002252:1-565 [pilon] NODE_368_length_618_cov_3.501006:1-618 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 40, Coverage: 8, minDepth: 5 [pilon] Confirmed 428 of 618 bases (69.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_368_length_618_cov_3.501006:1-618 [pilon] Processing NODE_427_length_584_cov_4.844492:1-584 [pilon] NODE_412_length_594_cov_16.319239:1-594 log: [pilon] frags shovill.bam: coverage 40 [pilon] Total Reads: 183, Coverage: 40, minDepth: 10 [pilon] Confirmed 477 of 594 bases (80.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_412_length_594_cov_16.319239:1-594 [pilon] Processing NODE_58_length_2458_cov_28.578947:1-2458 [pilon] NODE_270_length_688_cov_2.793651:1-688 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 49, Coverage: 9, minDepth: 5 [pilon] Confirmed 489 of 688 bases (71.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_270_length_688_cov_2.793651:1-688 [pilon] Processing NODE_878_length_408_cov_3.770035:1-408 [pilon] NODE_773_length_443_cov_1.043478:1-443 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 443 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_773_length_443_cov_1.043478:1-443 [pilon] Processing NODE_467_length_566_cov_0.833708:1-566 [pilon] NODE_127_length_929_cov_1.813119:1-929 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 43, Coverage: 6, minDepth: 5 [pilon] Confirmed 526 of 929 bases (56.62%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_127_length_929_cov_1.813119:1-929 [pilon] Processing NODE_917_length_297_cov_40.056818:1-297 [pilon] NODE_686_length_474_cov_1.118980:1-474 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 129 of 474 bases (27.22%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_686_length_474_cov_1.118980:1-474 [pilon] Processing NODE_3_length_343968_cov_36.406323:1-343968 [pilon] NODE_739_length_454_cov_9.126126:1-454 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 66, Coverage: 18, minDepth: 5 [pilon] Confirmed 360 of 454 bases (79.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_739_length_454_cov_9.126126:1-454 [pilon] Processing NODE_109_length_1044_cov_3.619718:1-1044 [pilon] NODE_277_length_682_cov_6.190731:1-682 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 89, Coverage: 17, minDepth: 5 [pilon] Confirmed 487 of 682 bases (71.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_277_length_682_cov_6.190731:1-682 [pilon] Processing NODE_684_length_474_cov_2.334278:1-474 [pilon] NODE_394_length_602_cov_1.147609:1-602 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 19, Coverage: 4, minDepth: 5 [pilon] Confirmed 146 of 602 bases (24.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_394_length_602_cov_1.147609:1-602 [pilon] Processing NODE_321_length_649_cov_2.943182:1-649 [pilon] NODE_129_length_909_cov_2.441624:1-909 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 53, Coverage: 8, minDepth: 5 [pilon] Confirmed 457 of 909 bases (50.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_129_length_909_cov_2.441624:1-909 [pilon] Processing NODE_717_length_465_cov_1.183140:1-465 [pilon] NODE_791_length_437_cov_1.363924:1-437 log: [pilon] NODE_328_length_646_cov_0.775238:1-646 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 12, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 646 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_328_length_646_cov_0.775238:1-646 [pilon] Processing NODE_631_length_495_cov_2.147059:1-495 [pilon] NODE_527_length_538_cov_1.733813:1-538 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 7, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 437 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 17, Coverage: 4, minDepth: 5 [pilon] Confirmed 256 of 538 bases (47.58%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_791_length_437_cov_1.363924:1-437 [pilon] Finished processing NODE_527_length_538_cov_1.733813:1-538 [pilon] Processing NODE_101_length_1100_cov_7.600613:1-1100 [pilon] Processing NODE_617_length_502_cov_1.545932:1-502 [pilon] NODE_337_length_641_cov_20.051923:1-641 log: [pilon] frags shovill.bam: coverage 51 [pilon] Total Reads: 253, Coverage: 51, minDepth: 13 [pilon] Confirmed 501 of 641 bases (78.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_337_length_641_cov_20.051923:1-641 [pilon] Processing NODE_909_length_402_cov_2.437722:1-402 [pilon] NODE_878_length_408_cov_3.770035:1-408 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 23, Coverage: 7, minDepth: 5 [pilon] Confirmed 267 of 408 bases (65.44%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_878_length_408_cov_3.770035:1-408 [pilon] Processing NODE_435_length_581_cov_0.717391:1-581 [pilon] NODE_469_length_565_cov_6.002252:1-565 log: [pilon] frags shovill.bam: coverage 19 [pilon] Total Reads: 88, Coverage: 19, minDepth: 5 [pilon] Confirmed 443 of 565 bases (78.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_469_length_565_cov_6.002252:1-565 [pilon] Processing NODE_276_length_684_cov_5.488455:1-684 [pilon] NODE_427_length_584_cov_4.844492:1-584 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 63, Coverage: 13, minDepth: 5 [pilon] Confirmed 423 of 584 bases (72.43%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_427_length_584_cov_4.844492:1-584 [pilon] Processing NODE_80_length_1327_cov_10.440299:1-1327 [pilon] NODE_467_length_566_cov_0.833708:1-566 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 19, Coverage: 4, minDepth: 5 [pilon] Confirmed 194 of 566 bases (34.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_467_length_566_cov_0.833708:1-566 [pilon] Processing NODE_313_length_654_cov_2.236398:1-654 [pilon] NODE_917_length_297_cov_40.056818:1-297 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 159, Coverage: 17, minDepth: 5 [pilon] Confirmed 265 of 297 bases (89.23%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_917_length_297_cov_40.056818:1-297 [pilon] Processing NODE_485_length_557_cov_5.697248:1-557 [pilon] NODE_684_length_474_cov_2.334278:1-474 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 20, Coverage: 5, minDepth: 5 [pilon] Confirmed 284 of 474 bases (59.92%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_684_length_474_cov_2.334278:1-474 [pilon] Processing NODE_508_length_549_cov_7.191589:1-549 [pilon] NODE_43_length_4199_cov_27.804316:1-4199 log: [pilon] frags shovill.bam: coverage 82 [pilon] Total Reads: 2656, Coverage: 82, minDepth: 21 [pilon] Confirmed 3472 of 4199 bases (82.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_43_length_4199_cov_27.804316:1-4199 [pilon] Processing NODE_336_length_642_cov_0.660269:1-642 [pilon] NODE_109_length_1044_cov_3.619718:1-1044 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 102, Coverage: 12, minDepth: 5 [pilon] Confirmed 965 of 1044 bases (92.43%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_109_length_1044_cov_3.619718:1-1044 [pilon] Processing NODE_308_length_657_cov_3.386194:1-657 [pilon] NODE_61_length_2178_cov_37.741857:1-2178 log: [pilon] frags shovill.bam: coverage 107 [pilon] Total Reads: 1803, Coverage: 107, minDepth: 27 [pilon] Confirmed 1569 of 2178 bases (72.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_61_length_2178_cov_37.741857:1-2178 [pilon] Processing NODE_374_length_615_cov_1.866397:1-615 [pilon] NODE_321_length_649_cov_2.943182:1-649 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 37, Coverage: 7, minDepth: 5 [pilon] Confirmed 429 of 649 bases (66.10%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_321_length_649_cov_2.943182:1-649 [pilon] Processing NODE_319_length_650_cov_4.007561:1-650 [pilon] NODE_52_length_2905_cov_24.298132:1-2905 log: [pilon] frags shovill.bam: coverage 72 [pilon] Total Reads: 1621, Coverage: 72, minDepth: 18 [pilon] Confirmed 2290 of 2905 bases (78.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_52_length_2905_cov_24.298132:1-2905 [pilon] Processing NODE_317_length_651_cov_2.745283:1-651 [pilon] NODE_717_length_465_cov_1.183140:1-465 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 9, Coverage: 3, minDepth: 5 [pilon] Confirmed 28 of 465 bases (6.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_717_length_465_cov_1.183140:1-465 [pilon] Processing NODE_425_length_585_cov_7.530172:1-585 [pilon] NODE_617_length_502_cov_1.545932:1-502 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 26, Coverage: 7, minDepth: 5 [pilon] Confirmed 303 of 502 bases (60.36%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_617_length_502_cov_1.545932:1-502 [pilon] Processing NODE_335_length_642_cov_1.644914:1-642 [pilon] NODE_631_length_495_cov_2.147059:1-495 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 22, Coverage: 6, minDepth: 5 [pilon] Confirmed 290 of 495 bases (58.59%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_631_length_495_cov_2.147059:1-495 [pilon] Processing NODE_117_length_997_cov_4.005708:1-997 [pilon] NODE_909_length_402_cov_2.437722:1-402 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 16, Coverage: 5, minDepth: 5 [pilon] Confirmed 172 of 402 bases (42.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_276_length_684_cov_5.488455:1-684 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 75, Coverage: 14, minDepth: 5 [pilon] Confirmed 496 of 684 bases (72.51%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_276_length_684_cov_5.488455:1-684 [pilon] Processing NODE_221_length_739_cov_2.076052:1-739 [pilon] NODE_435_length_581_cov_0.717391:1-581 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 10, Coverage: 2, minDepth: 5 [pilon] Confirmed 23 of 581 bases (3.96%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_435_length_581_cov_0.717391:1-581 [pilon] Processing NODE_911_length_402_cov_1.007117:1-402 [pilon] Finished processing NODE_909_length_402_cov_2.437722:1-402 [pilon] NODE_101_length_1100_cov_7.600613:1-1100 log: [pilon] frags shovill.bam: coverage 22 [pilon] Total Reads: 186, Coverage: 22, minDepth: 6 [pilon] Confirmed 776 of 1100 bases (70.55%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_101_length_1100_cov_7.600613:1-1100 [pilon] Processing NODE_666_length_482_cov_4.121884:1-482 [pilon] NODE_58_length_2458_cov_28.578947:1-2458 log: [pilon] frags shovill.bam: coverage 86 [pilon] Total Reads: 1629, Coverage: 86, minDepth: 22 [pilon] Confirmed 2206 of 2458 bases (89.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_58_length_2458_cov_28.578947:1-2458 [pilon] Processing NODE_30_length_25829_cov_44.046017:1-25829 [pilon] NODE_313_length_654_cov_2.236398:1-654 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 34, Coverage: 6, minDepth: 5 [pilon] Confirmed 406 of 654 bases (62.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_313_length_654_cov_2.236398:1-654 [pilon] Processing NODE_534_length_536_cov_2.457831:1-536 [pilon] NODE_485_length_557_cov_5.697248:1-557 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 79, Coverage: 17, minDepth: 5 [pilon] Confirmed 406 of 557 bases (72.89%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_485_length_557_cov_5.697248:1-557 [pilon] Processing NODE_669_length_482_cov_0.850416:1-482 [pilon] NODE_80_length_1327_cov_10.440299:1-1327 log: [pilon] frags shovill.bam: coverage 31 [pilon] Total Reads: 322, Coverage: 31, minDepth: 8 [pilon] Confirmed 1077 of 1327 bases (81.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_80_length_1327_cov_10.440299:1-1327 [pilon] Processing NODE_47_length_3711_cov_34.911699:1-3711 [pilon] NODE_336_length_642_cov_0.660269:1-642 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 19, Coverage: 4, minDepth: 5 [pilon] Confirmed 209 of 642 bases (32.55%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_336_length_642_cov_0.660269:1-642 [pilon] Processing NODE_910_length_402_cov_2.049822:1-402 [pilon] NODE_508_length_549_cov_7.191589:1-549 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 65, Coverage: 15, minDepth: 5 [pilon] Confirmed 454 of 549 bases (82.70%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_508_length_549_cov_7.191589:1-549 [pilon] Processing NODE_34_length_9773_cov_31.265334:1-9773 [pilon] NODE_374_length_615_cov_1.866397:1-615 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 29, Coverage: 6, minDepth: 5 [pilon] Confirmed 343 of 615 bases (55.77%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_374_length_615_cov_1.866397:1-615 [pilon] Processing NODE_551_length_527_cov_4.490148:1-527 [pilon] NODE_308_length_657_cov_3.386194:1-657 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 52, Coverage: 10, minDepth: 5 [pilon] Confirmed 471 of 657 bases (71.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_308_length_657_cov_3.386194:1-657 [pilon] Processing NODE_477_length_561_cov_2.334091:1-561 [pilon] NODE_317_length_651_cov_2.745283:1-651 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 46, Coverage: 9, minDepth: 5 [pilon] Confirmed 413 of 651 bases (63.44%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_317_length_651_cov_2.745283:1-651 [pilon] Processing NODE_200_length_758_cov_3.084772:1-758 [pilon] NODE_319_length_650_cov_4.007561:1-650 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 66, Coverage: 13, minDepth: 5 [pilon] Confirmed 452 of 650 bases (69.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_319_length_650_cov_4.007561:1-650 [pilon] Processing NODE_704_length_470_cov_1.512894:1-470 [pilon] NODE_117_length_997_cov_4.005708:1-997 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 90, Coverage: 12, minDepth: 5 [pilon] Confirmed 818 of 997 bases (82.05%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_117_length_997_cov_4.005708:1-997 [pilon] Processing NODE_902_length_403_cov_1.453901:1-403 [pilon] NODE_425_length_585_cov_7.530172:1-585 log: [pilon] frags shovill.bam: coverage 19 [pilon] Total Reads: 95, Coverage: 19, minDepth: 5 [pilon] Confirmed 496 of 585 bases (84.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_425_length_585_cov_7.530172:1-585 [pilon] Processing NODE_871_length_411_cov_2.048276:1-411 [pilon] NODE_335_length_642_cov_1.644914:1-642 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 27, Coverage: 5, minDepth: 5 [pilon] Confirmed 264 of 642 bases (41.12%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_335_length_642_cov_1.644914:1-642 [pilon] Processing NODE_844_length_421_cov_1.536667:1-421 [pilon] NODE_911_length_402_cov_1.007117:1-402 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 402 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_911_length_402_cov_1.007117:1-402 [pilon] Processing NODE_364_length_620_cov_3.044088:1-620 [pilon] NODE_221_length_739_cov_2.076052:1-739 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 37, Coverage: 7, minDepth: 5 [pilon] Confirmed 323 of 739 bases (43.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_221_length_739_cov_2.076052:1-739 [pilon] Processing NODE_266_length_690_cov_13.720562:1-690 [pilon] NODE_666_length_482_cov_4.121884:1-482 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 42, Coverage: 11, minDepth: 5 [pilon] Confirmed 388 of 482 bases (80.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_666_length_482_cov_4.121884:1-482 [pilon] Processing NODE_188_length_773_cov_15.803681:1-773 [pilon] NODE_534_length_536_cov_2.457831:1-536 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 24, Coverage: 6, minDepth: 5 [pilon] Confirmed 280 of 536 bases (52.24%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_534_length_536_cov_2.457831:1-536 [pilon] NODE_669_length_482_cov_0.850416:1-482 log: [pilon] NODE_910_length_402_cov_2.049822:1-402 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 18, Coverage: 5, minDepth: 5 [pilon] Confirmed 242 of 402 bases (60.20%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_910_length_402_cov_2.049822:1-402 [pilon] Processing NODE_539_length_535_cov_2.376812:1-535 [pilon] Processing NODE_785_length_440_cov_1.241379:1-440 [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 7, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 482 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_669_length_482_cov_0.850416:1-482 [pilon] Processing NODE_564_length_520_cov_3.781955:1-520 [pilon] NODE_551_length_527_cov_4.490148:1-527 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 44, Coverage: 10, minDepth: 5 [pilon] Confirmed 324 of 527 bases (61.48%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_551_length_527_cov_4.490148:1-527 [pilon] Processing NODE_161_length_819_cov_2.855301:1-819 [pilon] NODE_477_length_561_cov_2.334091:1-561 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 28, Coverage: 6, minDepth: 5 [pilon] Confirmed 270 of 561 bases (48.13%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_477_length_561_cov_2.334091:1-561 [pilon] Processing NODE_318_length_650_cov_4.098299:1-650 [pilon] NODE_704_length_470_cov_1.512894:1-470 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 15, Coverage: 4, minDepth: 5 [pilon] Confirmed 211 of 470 bases (44.89%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_704_length_470_cov_1.512894:1-470 [pilon] Processing NODE_745_length_452_cov_87.323263:1-452 [pilon] NODE_200_length_758_cov_3.084772:1-758 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 50, Coverage: 9, minDepth: 5 [pilon] Confirmed 464 of 758 bases (61.21%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_200_length_758_cov_3.084772:1-758 [pilon] Processing NODE_53_length_2821_cov_26.718519:1-2821 [pilon] NODE_871_length_411_cov_2.048276:1-411 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 19, Coverage: 6, minDepth: 5 [pilon] Confirmed 237 of 411 bases (57.66%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_871_length_411_cov_2.048276:1-411 [pilon] Processing NODE_495_length_553_cov_1.171296:1-553 [pilon] NODE_844_length_421_cov_1.536667:1-421 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 20, Coverage: 6, minDepth: 5 [pilon] Confirmed 285 of 421 bases (67.70%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_844_length_421_cov_1.536667:1-421 [pilon] Processing NODE_342_length_637_cov_19.019380:1-637 [pilon] NODE_902_length_403_cov_1.453901:1-403 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 9, Coverage: 3, minDepth: 5 [pilon] Confirmed 12 of 403 bases (2.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_902_length_403_cov_1.453901:1-403 [pilon] Processing NODE_761_length_445_cov_5.623457:1-445 [pilon] NODE_564_length_520_cov_3.781955:1-520 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 58, Coverage: 14, minDepth: 5 [pilon] Confirmed 406 of 520 bases (78.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_564_length_520_cov_3.781955:1-520 [pilon] Processing NODE_513_length_548_cov_1.515222:1-548 [pilon] NODE_364_length_620_cov_3.044088:1-620 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 40, Coverage: 8, minDepth: 5 [pilon] Confirmed 440 of 620 bases (70.97%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_364_length_620_cov_3.044088:1-620 [pilon] Processing NODE_68_length_1819_cov_5.074205:1-1819 [pilon] NODE_539_length_535_cov_2.376812:1-535 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 27, Coverage: 6, minDepth: 5 [pilon] Confirmed 328 of 535 bases (61.31%) [pilon] Corrected 4 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_539_length_535_cov_2.376812:1-535 [pilon] Processing NODE_733_length_457_cov_3.083333:1-457 [pilon] NODE_266_length_690_cov_13.720562:1-690 log: [pilon] frags shovill.bam: coverage 47 [pilon] Total Reads: 248, Coverage: 47, minDepth: 12 [pilon] Confirmed 489 of 690 bases (70.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_266_length_690_cov_13.720562:1-690 [pilon] Processing NODE_324_length_647_cov_13.633080:1-647 [pilon] NODE_161_length_819_cov_2.855301:1-819 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 53, Coverage: 8, minDepth: 5 [pilon] Confirmed 410 of 819 bases (50.06%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_161_length_819_cov_2.855301:1-819 [pilon] Processing NODE_830_length_426_cov_0.413115:1-426 [pilon] NODE_785_length_440_cov_1.241379:1-440 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 111 of 440 bases (25.23%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_785_length_440_cov_1.241379:1-440 [pilon] Processing NODE_826_length_426_cov_5.003279:1-426 [pilon] NODE_188_length_773_cov_15.803681:1-773 log: [pilon] frags shovill.bam: coverage 41 [pilon] Total Reads: 245, Coverage: 41, minDepth: 10 [pilon] Confirmed 571 of 773 bases (73.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_188_length_773_cov_15.803681:1-773 [pilon] Processing NODE_734_length_457_cov_1.136905:1-457 [pilon] NODE_318_length_650_cov_4.098299:1-650 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 67, Coverage: 13, minDepth: 5 [pilon] Confirmed 348 of 650 bases (53.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_318_length_650_cov_4.098299:1-650 [pilon] Processing NODE_764_length_445_cov_2.015432:1-445 [pilon] NODE_761_length_445_cov_5.623457:1-445 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 47, Coverage: 13, minDepth: 5 [pilon] Confirmed 318 of 445 bases (71.46%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_761_length_445_cov_5.623457:1-445 [pilon] Processing NODE_714_length_466_cov_0.820290:1-466 [pilon] NODE_342_length_637_cov_19.019380:1-637 log: [pilon] frags shovill.bam: coverage 47 [pilon] Total Reads: 234, Coverage: 47, minDepth: 12 [pilon] Confirmed 441 of 637 bases (69.23%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_342_length_637_cov_19.019380:1-637 [pilon] Processing NODE_206_length_750_cov_12.383148:1-750 [pilon] NODE_495_length_553_cov_1.171296:1-553 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 11, Coverage: 3, minDepth: 5 [pilon] Confirmed 109 of 553 bases (19.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_495_length_553_cov_1.171296:1-553 [pilon] NODE_745_length_452_cov_87.323263:1-452 log: [pilon] frags shovill.bam: coverage 112 [pilon] Total Reads: 709, Coverage: 112, minDepth: 28 [pilon] Confirmed 387 of 452 bases (85.62%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_745_length_452_cov_87.323263:1-452 [pilon] Processing NODE_602_length_507_cov_0.505181:1-507 [pilon] NODE_733_length_457_cov_3.083333:1-457 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 31, Coverage: 7, minDepth: 5 [pilon] Confirmed 245 of 457 bases (53.61%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_733_length_457_cov_3.083333:1-457 [pilon] Processing NODE_579_length_515_cov_1.614213:1-515 [pilon] NODE_830_length_426_cov_0.413115:1-426 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 426 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_830_length_426_cov_0.413115:1-426 [pilon] Processing NODE_437_length_578_cov_1.682713:1-578 [pilon] NODE_826_length_426_cov_5.003279:1-426 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 35, Coverage: 8, minDepth: 5 [pilon] Confirmed 259 of 426 bases (60.80%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_826_length_426_cov_5.003279:1-426 [pilon] Processing NODE_571_length_518_cov_4.347607:1-518 [pilon] NODE_513_length_548_cov_1.515222:1-548 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 19, Coverage: 4, minDepth: 5 [pilon] Confirmed 275 of 548 bases (50.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_513_length_548_cov_1.515222:1-548 [pilon] Processing NODE_233_length_720_cov_2.071786:1-720 [pilon] NODE_324_length_647_cov_13.633080:1-647 log: [pilon] frags shovill.bam: coverage 42 [pilon] Total Reads: 207, Coverage: 42, minDepth: 11 [pilon] Confirmed 482 of 647 bases (74.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_324_length_647_cov_13.633080:1-647 [pilon] Processing NODE_23_length_65675_cov_40.839644:1-65675 [pilon] NODE_764_length_445_cov_2.015432:1-445 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 19, Coverage: 5, minDepth: 5 [pilon] Confirmed 209 of 445 bases (46.97%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_734_length_457_cov_1.136905:1-457 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 11, Coverage: 3, minDepth: 5 [pilon] Confirmed 115 of 457 bases (25.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_734_length_457_cov_1.136905:1-457 [pilon] Processing NODE_213_length_742_cov_0.743961:1-742 [pilon] NODE_68_length_1819_cov_5.074205:1-1819 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 219, Coverage: 16, minDepth: 5 [pilon] Confirmed 1229 of 1819 bases (67.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_68_length_1819_cov_5.074205:1-1819 [pilon] Processing NODE_16_length_93240_cov_43.502379:1-93240 [pilon] Finished processing NODE_764_length_445_cov_2.015432:1-445 [pilon] Processing NODE_159_length_822_cov_2.813124:1-822 [pilon] NODE_714_length_466_cov_0.820290:1-466 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 466 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_714_length_466_cov_0.820290:1-466 [pilon] Processing NODE_479_length_561_cov_1.650000:1-561 [pilon] NODE_602_length_507_cov_0.505181:1-507 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 507 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_579_length_515_cov_1.614213:1-515 log: [pilon] Finished processing NODE_602_length_507_cov_0.505181:1-507 [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 26, Coverage: 7, minDepth: 5 [pilon] Confirmed 260 of 515 bases (50.49%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_822_length_428_cov_1.267101:1-428 [pilon] Finished processing NODE_579_length_515_cov_1.614213:1-515 [pilon] Processing NODE_893_length_405_cov_2.873239:1-405 [pilon] NODE_53_length_2821_cov_26.718519:1-2821 log: [pilon] frags shovill.bam: coverage 82 [pilon] Total Reads: 1790, Coverage: 82, minDepth: 21 [pilon] Confirmed 2146 of 2821 bases (76.07%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_53_length_2821_cov_26.718519:1-2821 [pilon] Processing NODE_875_length_409_cov_2.204861:1-409 [pilon] NODE_437_length_578_cov_1.682713:1-578 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 24, Coverage: 5, minDepth: 5 [pilon] Confirmed 327 of 578 bases (56.57%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_437_length_578_cov_1.682713:1-578 [pilon] Processing NODE_25_length_46794_cov_38.082832:1-46794 [pilon] NODE_571_length_518_cov_4.347607:1-518 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 44, Coverage: 11, minDepth: 5 [pilon] Confirmed 423 of 518 bases (81.66%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_571_length_518_cov_4.347607:1-518 [pilon] Processing NODE_79_length_1387_cov_156.505529:1-1387 [pilon] NODE_233_length_720_cov_2.071786:1-720 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 43, Coverage: 7, minDepth: 5 [pilon] Confirmed 528 of 720 bases (73.33%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_233_length_720_cov_2.071786:1-720 [pilon] Processing NODE_690_length_473_cov_1.758523:1-473 [pilon] NODE_47_length_3711_cov_34.911699:1-3711 log: [pilon] frags shovill.bam: coverage 104 [pilon] Total Reads: 2980, Coverage: 104, minDepth: 26 [pilon] Confirmed 3398 of 3711 bases (91.57%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_47_length_3711_cov_34.911699:1-3711 [pilon] Processing NODE_542_length_534_cov_1.515738:1-534 [pilon] Processing NODE_715_length_466_cov_0.753623:1-466 [pilon] NODE_213_length_742_cov_0.743961:1-742 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 10, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 742 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_213_length_742_cov_0.743961:1-742 [pilon] Processing NODE_273_length_686_cov_4.472566:1-686 [pilon] NODE_479_length_561_cov_1.650000:1-561 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 15, Coverage: 3, minDepth: 5 [pilon] Confirmed 136 of 561 bases (24.24%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_479_length_561_cov_1.650000:1-561 [pilon] NODE_159_length_822_cov_2.813124:1-822 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 68, Coverage: 11, minDepth: 5 [pilon] Confirmed 599 of 822 bases (72.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_159_length_822_cov_2.813124:1-822 [pilon] Processing NODE_694_length_471_cov_18.674286:1-471 [pilon] Processing NODE_410_length_595_cov_2.067511:1-595 [pilon] NODE_822_length_428_cov_1.267101:1-428 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 82 of 428 bases (19.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_822_length_428_cov_1.267101:1-428 [pilon] Processing NODE_54_length_2785_cov_55.135135:1-2785 [pilon] NODE_690_length_473_cov_1.758523:1-473 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 185 of 473 bases (39.11%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_690_length_473_cov_1.758523:1-473 [pilon] Processing NODE_78_length_1390_cov_5.759653:1-1390 [pilon] NODE_893_length_405_cov_2.873239:1-405 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 23, Coverage: 7, minDepth: 5 [pilon] Confirmed 217 of 405 bases (53.58%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_893_length_405_cov_2.873239:1-405 [pilon] Processing NODE_648_length_489_cov_4.967391:1-489 [pilon] NODE_542_length_534_cov_1.515738:1-534 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 14, Coverage: 3, minDepth: 5 [pilon] Confirmed 185 of 534 bases (34.64%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_273_length_686_cov_4.472566:1-686 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 57, Coverage: 10, minDepth: 5 [pilon] Confirmed 406 of 686 bases (59.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_410_length_595_cov_2.067511:1-595 log: [pilon] NODE_875_length_409_cov_2.204861:1-409 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 25, Coverage: 7, minDepth: 5 [pilon] Confirmed 249 of 409 bases (60.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_715_length_466_cov_0.753623:1-466 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 189 of 466 bases (40.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_715_length_466_cov_0.753623:1-466 [pilon] Finished processing NODE_875_length_409_cov_2.204861:1-409 [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 30, Coverage: 6, minDepth: 5 [pilon] Confirmed 320 of 595 bases (53.78%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_410_length_595_cov_2.067511:1-595 [pilon] Processing NODE_903_length_403_cov_0.929078:1-403 [pilon] Processing NODE_658_length_485_cov_2.060440:1-485 [pilon] Finished processing NODE_273_length_686_cov_4.472566:1-686 [pilon] Finished processing NODE_542_length_534_cov_1.515738:1-534 [pilon] Processing NODE_164_length_816_cov_5.598561:1-816 [pilon] Processing NODE_450_length_573_cov_4.059735:1-573 [pilon] Processing NODE_803_length_434_cov_2.204473:1-434 [pilon] NODE_694_length_471_cov_18.674286:1-471 log: [pilon] frags shovill.bam: coverage 39 [pilon] Total Reads: 144, Coverage: 39, minDepth: 10 [pilon] Confirmed 366 of 471 bases (77.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_694_length_471_cov_18.674286:1-471 [pilon] NODE_206_length_750_cov_12.383148:1-750 log: [pilon] frags shovill.bam: coverage 48 [pilon] Total Reads: 278, Coverage: 48, minDepth: 12 [pilon] Confirmed 470 of 750 bases (62.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_206_length_750_cov_12.383148:1-750 [pilon] Processing NODE_526_length_539_cov_0.894737:1-539 [pilon] Processing NODE_842_length_421_cov_2.793333:1-421 [pilon] NODE_450_length_573_cov_4.059735:1-573 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 48, Coverage: 11, minDepth: 5 [pilon] Confirmed 452 of 573 bases (78.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_450_length_573_cov_4.059735:1-573 [pilon] Processing NODE_378_length_613_cov_1.747967:1-613 [pilon] NODE_903_length_403_cov_0.929078:1-403 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 8, Coverage: 3, minDepth: 5 [pilon] Confirmed 37 of 403 bases (9.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_903_length_403_cov_0.929078:1-403 [pilon] Processing NODE_236_length_716_cov_3.312605:1-716 [pilon] NODE_658_length_485_cov_2.060440:1-485 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 22, Coverage: 5, minDepth: 5 [pilon] Confirmed 258 of 485 bases (53.20%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_658_length_485_cov_2.060440:1-485 [pilon] Processing NODE_45_length_4048_cov_21.660300:1-4048 [pilon] NODE_842_length_421_cov_2.793333:1-421 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 16, Coverage: 5, minDepth: 5 [pilon] Confirmed 168 of 421 bases (39.90%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_842_length_421_cov_2.793333:1-421 [pilon] Processing NODE_646_length_490_cov_1.785908:1-490 [pilon] NODE_526_length_539_cov_0.894737:1-539 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 11, Coverage: 3, minDepth: 5 [pilon] Confirmed 26 of 539 bases (4.82%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_526_length_539_cov_0.894737:1-539 [pilon] Processing NODE_411_length_595_cov_2.040084:1-595 [pilon] NODE_803_length_434_cov_2.204473:1-434 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 154 of 434 bases (35.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_803_length_434_cov_2.204473:1-434 [pilon] Processing NODE_663_length_483_cov_1.342541:1-483 [pilon] NODE_78_length_1390_cov_5.759653:1-1390 log: [pilon] frags shovill.bam: coverage 19 [pilon] Total Reads: 205, Coverage: 19, minDepth: 5 [pilon] Confirmed 1076 of 1390 bases (77.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_78_length_1390_cov_5.759653:1-1390 [pilon] Processing NODE_521_length_544_cov_3.744681:1-544 [pilon] NODE_648_length_489_cov_4.967391:1-489 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 42, Coverage: 10, minDepth: 5 [pilon] Confirmed 394 of 489 bases (80.57%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_648_length_489_cov_4.967391:1-489 [pilon] Processing NODE_423_length_587_cov_3.555794:1-587 [pilon] NODE_164_length_816_cov_5.598561:1-816 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 107, Coverage: 17, minDepth: 5 [pilon] Confirmed 559 of 816 bases (68.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_164_length_816_cov_5.598561:1-816 [pilon] Processing NODE_296_length_667_cov_2.014652:1-667 [pilon] NODE_646_length_490_cov_1.785908:1-490 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 20, Coverage: 5, minDepth: 5 [pilon] Confirmed 280 of 490 bases (57.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_646_length_490_cov_1.785908:1-490 [pilon] Processing NODE_856_length_416_cov_1.623729:1-416 [pilon] NODE_378_length_613_cov_1.747967:1-613 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 42, Coverage: 9, minDepth: 5 [pilon] Confirmed 386 of 613 bases (62.97%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_378_length_613_cov_1.747967:1-613 [pilon] Processing NODE_299_length_666_cov_0.715596:1-666 [pilon] NODE_236_length_716_cov_3.312605:1-716 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 57, Coverage: 10, minDepth: 5 [pilon] Confirmed 456 of 716 bases (63.69%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_236_length_716_cov_3.312605:1-716 [pilon] Processing NODE_505_length_550_cov_3.151515:1-550 [pilon] NODE_663_length_483_cov_1.342541:1-483 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 97 of 483 bases (20.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_663_length_483_cov_1.342541:1-483 [pilon] Processing NODE_307_length_658_cov_2.163873:1-658 [pilon] NODE_521_length_544_cov_3.744681:1-544 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 44, Coverage: 10, minDepth: 5 [pilon] Confirmed 360 of 544 bases (66.18%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_521_length_544_cov_3.744681:1-544 [pilon] Processing NODE_282_length_675_cov_3.539711:1-675 [pilon] NODE_411_length_595_cov_2.040084:1-595 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 23, Coverage: 5, minDepth: 5 [pilon] Confirmed 202 of 595 bases (33.95%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_411_length_595_cov_2.040084:1-595 [pilon] Processing NODE_756_length_448_cov_2.027523:1-448 [pilon] NODE_423_length_587_cov_3.555794:1-587 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 34, Coverage: 7, minDepth: 5 [pilon] Confirmed 453 of 587 bases (77.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_423_length_587_cov_3.555794:1-587 [pilon] Processing NODE_446_length_576_cov_1.351648:1-576 [pilon] NODE_296_length_667_cov_2.014652:1-667 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 37, Coverage: 7, minDepth: 5 [pilon] Confirmed 298 of 667 bases (44.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_296_length_667_cov_2.014652:1-667 [pilon] Processing NODE_813_length_431_cov_1.167742:1-431 [pilon] NODE_856_length_416_cov_1.623729:1-416 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 25, Coverage: 4, minDepth: 5 [pilon] Confirmed 137 of 416 bases (32.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_856_length_416_cov_1.623729:1-416 [pilon] Processing NODE_226_length_731_cov_4.532787:1-731 [pilon] NODE_299_length_666_cov_0.715596:1-666 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 10, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 666 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_299_length_666_cov_0.715596:1-666 [pilon] Processing NODE_489_length_555_cov_5.700461:1-555 [pilon] NODE_505_length_550_cov_3.151515:1-550 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 39, Coverage: 9, minDepth: 5 [pilon] Confirmed 325 of 550 bases (59.09%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_505_length_550_cov_3.151515:1-550 [pilon] Processing NODE_498_length_552_cov_1.018561:1-552 [pilon] NODE_446_length_576_cov_1.351648:1-576 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 21, Coverage: 3, minDepth: 5 [pilon] Confirmed 111 of 576 bases (19.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_446_length_576_cov_1.351648:1-576 [pilon] Processing NODE_128_length_922_cov_10.159800:1-922 [pilon] NODE_756_length_448_cov_2.027523:1-448 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 227 of 448 bases (50.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_756_length_448_cov_2.027523:1-448 [pilon] Processing NODE_137_length_877_cov_3.000000:1-877 [pilon] NODE_307_length_658_cov_2.163873:1-658 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 31, Coverage: 6, minDepth: 5 [pilon] Confirmed 347 of 658 bases (52.74%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_307_length_658_cov_2.163873:1-658 [pilon] Processing NODE_305_length_661_cov_1.529630:1-661 [pilon] NODE_282_length_675_cov_3.539711:1-675 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 73, Coverage: 14, minDepth: 5 [pilon] Confirmed 390 of 675 bases (57.78%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_282_length_675_cov_3.539711:1-675 [pilon] Processing NODE_887_length_407_cov_0.916084:1-407 [pilon] NODE_813_length_431_cov_1.167742:1-431 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 51 of 431 bases (11.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_813_length_431_cov_1.167742:1-431 [pilon] Processing NODE_606_length_505_cov_7.375000:1-505 [pilon] NODE_226_length_731_cov_4.532787:1-731 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 72, Coverage: 13, minDepth: 5 [pilon] Confirmed 477 of 731 bases (65.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_226_length_731_cov_4.532787:1-731 [pilon] Processing NODE_35_length_9076_cov_59.737353:1-9076 [pilon] NODE_34_length_9773_cov_31.265334:1-9773 log: [pilon] frags shovill.bam: coverage 95 [pilon] Total Reads: 7211, Coverage: 95, minDepth: 24 [pilon] Confirmed 8855 of 9773 bases (90.61%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_34_length_9773_cov_31.265334:1-9773 [pilon] Processing NODE_93_length_1188_cov_3.535145:1-1188 [pilon] NODE_54_length_2785_cov_55.135135:1-2785 log: [pilon] frags shovill.bam: coverage 165 [pilon] Total Reads: 3554, Coverage: 165, minDepth: 41 [pilon] Confirmed 2178 of 2785 bases (78.20%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_54_length_2785_cov_55.135135:1-2785 [pilon] Processing NODE_650_length_488_cov_0.945504:1-488 [pilon] NODE_498_length_552_cov_1.018561:1-552 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 65 of 552 bases (11.78%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_498_length_552_cov_1.018561:1-552 [pilon] Processing NODE_607_length_505_cov_5.414062:1-505 [pilon] NODE_489_length_555_cov_5.700461:1-555 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 60, Coverage: 14, minDepth: 5 [pilon] Confirmed 453 of 555 bases (81.62%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_489_length_555_cov_5.700461:1-555 [pilon] NODE_79_length_1387_cov_156.505529:1-1387 log: [pilon] frags shovill.bam: coverage 360 [pilon] Total Reads: 4863, Coverage: 360, minDepth: 90 [pilon] Confirmed 1338 of 1387 bases (96.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_79_length_1387_cov_156.505529:1-1387 [pilon] Processing NODE_251_length_703_cov_2.912371:1-703 [pilon] Processing NODE_654_length_487_cov_1.333333:1-487 [pilon] NODE_137_length_877_cov_3.000000:1-877 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 58, Coverage: 9, minDepth: 5 [pilon] Confirmed 415 of 877 bases (47.32%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_137_length_877_cov_3.000000:1-877 [pilon] Processing NODE_776_length_442_cov_1.417445:1-442 [pilon] NODE_128_length_922_cov_10.159800:1-922 log: [pilon] frags shovill.bam: coverage 42 [pilon] Total Reads: 312, Coverage: 42, minDepth: 11 [pilon] Confirmed 802 of 922 bases (86.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_128_length_922_cov_10.159800:1-922 [pilon] Processing NODE_713_length_467_cov_0.624277:1-467 [pilon] NODE_305_length_661_cov_1.529630:1-661 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 26, Coverage: 5, minDepth: 5 [pilon] Confirmed 311 of 661 bases (47.05%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_305_length_661_cov_1.529630:1-661 [pilon] Processing NODE_407_length_597_cov_2.407563:1-597 [pilon] NODE_887_length_407_cov_0.916084:1-407 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 407 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_887_length_407_cov_0.916084:1-407 [pilon] Processing NODE_506_length_550_cov_2.547786:1-550 [pilon] NODE_93_length_1188_cov_3.535145:1-1188 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 107, Coverage: 12, minDepth: 5 [pilon] Confirmed 728 of 1188 bases (61.28%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_93_length_1188_cov_3.535145:1-1188 [pilon] Processing NODE_38_length_5880_cov_24.816461:1-5880 [pilon] NODE_45_length_4048_cov_21.660300:1-4048 log: [pilon] frags shovill.bam: coverage 64 [pilon] Total Reads: 2001, Coverage: 64, minDepth: 16 [pilon] Confirmed 3471 of 4048 bases (85.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_45_length_4048_cov_21.660300:1-4048 [pilon] Processing NODE_779_length_442_cov_1.180685:1-442 [pilon] NODE_606_length_505_cov_7.375000:1-505 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 63, Coverage: 16, minDepth: 5 [pilon] Confirmed 394 of 505 bases (78.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_606_length_505_cov_7.375000:1-505 [pilon] Processing NODE_416_length_592_cov_4.552017:1-592 [pilon] NODE_650_length_488_cov_0.945504:1-488 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 15, Coverage: 4, minDepth: 5 [pilon] Confirmed 143 of 488 bases (29.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_650_length_488_cov_0.945504:1-488 [pilon] Processing NODE_51_length_3042_cov_23.091065:1-3042 [pilon] NODE_776_length_442_cov_1.417445:1-442 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 203 of 442 bases (45.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_776_length_442_cov_1.417445:1-442 [pilon] NODE_654_length_487_cov_1.333333:1-487 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 99 of 487 bases (20.33%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_654_length_487_cov_1.333333:1-487 [pilon] NODE_607_length_505_cov_5.414062:1-505 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 52, Coverage: 13, minDepth: 5 [pilon] Confirmed 411 of 505 bases (81.39%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_629_length_495_cov_4.328877:1-495 [pilon] NODE_407_length_597_cov_2.407563:1-597 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 34, Coverage: 7, minDepth: 5 [pilon] Confirmed 289 of 597 bases (48.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_607_length_505_cov_5.414062:1-505 [pilon] NODE_713_length_467_cov_0.624277:1-467 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 467 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_407_length_597_cov_2.407563:1-597 [pilon] Finished processing NODE_713_length_467_cov_0.624277:1-467 [pilon] Processing NODE_100_length_1118_cov_11.091274:1-1118 [pilon] Processing NODE_240_length_714_cov_0.691400:1-714 [pilon] Processing NODE_800_length_435_cov_2.630573:1-435 [pilon] NODE_251_length_703_cov_2.912371:1-703 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 55, Coverage: 10, minDepth: 5 [pilon] Confirmed 490 of 703 bases (69.70%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_251_length_703_cov_2.912371:1-703 [pilon] Processing NODE_916_length_308_cov_40.363636:1-308 [pilon] NODE_506_length_550_cov_2.547786:1-550 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 34, Coverage: 8, minDepth: 5 [pilon] Confirmed 455 of 550 bases (82.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_506_length_550_cov_2.547786:1-550 [pilon] Processing NODE_72_length_1553_cov_5.699022:1-1553 [pilon] NODE_779_length_442_cov_1.180685:1-442 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 12, Coverage: 2, minDepth: 5 [pilon] Confirmed 92 of 442 bases (20.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_779_length_442_cov_1.180685:1-442 [pilon] Processing NODE_462_length_568_cov_1.662192:1-568 [pilon] NODE_416_length_592_cov_4.552017:1-592 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 57, Coverage: 13, minDepth: 5 [pilon] Confirmed 486 of 592 bases (82.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_416_length_592_cov_4.552017:1-592 [pilon] Processing NODE_576_length_516_cov_4.445570:1-516 [pilon] NODE_462_length_568_cov_1.662192:1-568 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 18, Coverage: 4, minDepth: 5 [pilon] Confirmed 212 of 568 bases (37.32%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_462_length_568_cov_1.662192:1-568 [pilon] Processing NODE_770_length_443_cov_1.981366:1-443 [pilon] NODE_100_length_1118_cov_11.091274:1-1118 log: [pilon] frags shovill.bam: coverage 34 [pilon] Total Reads: 299, Coverage: 34, minDepth: 9 [pilon] Confirmed 536 of 1118 bases (47.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_100_length_1118_cov_11.091274:1-1118 [pilon] Processing NODE_17_length_89057_cov_42.425002:1-89057 [pilon] NODE_800_length_435_cov_2.630573:1-435 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 23, Coverage: 6, minDepth: 5 [pilon] Confirmed 318 of 435 bases (73.10%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_800_length_435_cov_2.630573:1-435 [pilon] Processing NODE_380_length_610_cov_3.396728:1-610 [pilon] NODE_629_length_495_cov_4.328877:1-495 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 37, Coverage: 9, minDepth: 5 [pilon] Confirmed 378 of 495 bases (76.36%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_629_length_495_cov_4.328877:1-495 [pilon] Processing NODE_868_length_412_cov_1.797251:1-412 [pilon] NODE_240_length_714_cov_0.691400:1-714 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 14, Coverage: 3, minDepth: 5 [pilon] Confirmed 124 of 714 bases (17.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_240_length_714_cov_0.691400:1-714 [pilon] Processing NODE_641_length_492_cov_7.970350:1-492 [pilon] NODE_916_length_308_cov_40.363636:1-308 log: [pilon] frags shovill.bam: coverage 30 [pilon] Total Reads: 203, Coverage: 30, minDepth: 8 [pilon] Confirmed 239 of 308 bases (77.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_916_length_308_cov_40.363636:1-308 [pilon] Processing NODE_681_length_477_cov_2.002809:1-477 [pilon] NODE_27_length_38554_cov_39.888481:1-38554 log: [pilon] frags shovill.bam: coverage 122 [pilon] Total Reads: 36351, Coverage: 122, minDepth: 31 [pilon] Confirmed 38104 of 38554 bases (98.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_27_length_38554_cov_39.888481:1-38554 [pilon] Processing NODE_255_length_702_cov_1.733219:1-702 [pilon] NODE_576_length_516_cov_4.445570:1-516 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 45, Coverage: 11, minDepth: 5 [pilon] Confirmed 346 of 516 bases (67.05%) [pilon] Corrected 3 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_576_length_516_cov_4.445570:1-516 [pilon] Processing NODE_698_length_471_cov_0.974286:1-471 [pilon] NODE_770_length_443_cov_1.981366:1-443 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 20, Coverage: 6, minDepth: 5 [pilon] Confirmed 234 of 443 bases (52.82%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_770_length_443_cov_1.981366:1-443 [pilon] Processing NODE_351_length_629_cov_0.990157:1-629 [pilon] NODE_72_length_1553_cov_5.699022:1-1553 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 196, Coverage: 16, minDepth: 5 [pilon] Confirmed 1161 of 1553 bases (74.76%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_72_length_1553_cov_5.699022:1-1553 [pilon] Processing NODE_189_length_770_cov_1.961479:1-770 [pilon] NODE_868_length_412_cov_1.797251:1-412 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 181 of 412 bases (43.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_868_length_412_cov_1.797251:1-412 [pilon] NODE_380_length_610_cov_3.396728:1-610 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 52, Coverage: 10, minDepth: 5 [pilon] Confirmed 446 of 610 bases (73.11%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_380_length_610_cov_3.396728:1-610 [pilon] Processing NODE_499_length_551_cov_2.186047:1-551 [pilon] Processing NODE_862_length_414_cov_1.331058:1-414 [pilon] NODE_641_length_492_cov_7.970350:1-492 log: [pilon] frags shovill.bam: coverage 30 [pilon] Total Reads: 116, Coverage: 30, minDepth: 8 [pilon] Confirmed 352 of 492 bases (71.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_641_length_492_cov_7.970350:1-492 [pilon] Processing NODE_748_length_451_cov_2.118182:1-451 [pilon] NODE_681_length_477_cov_2.002809:1-477 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 20, Coverage: 5, minDepth: 5 [pilon] Confirmed 152 of 477 bases (31.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_681_length_477_cov_2.002809:1-477 [pilon] Processing NODE_932_length_241_cov_38.241667:1-241 [pilon] NODE_351_length_629_cov_0.990157:1-629 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 25, Coverage: 5, minDepth: 5 [pilon] Confirmed 273 of 629 bases (43.40%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_351_length_629_cov_0.990157:1-629 [pilon] Processing NODE_894_length_405_cov_1.165493:1-405 [pilon] NODE_255_length_702_cov_1.733219:1-702 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 30, Coverage: 5, minDepth: 5 [pilon] Confirmed 416 of 702 bases (59.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_255_length_702_cov_1.733219:1-702 [pilon] Processing NODE_834_length_424_cov_1.237624:1-424 [pilon] NODE_698_length_471_cov_0.974286:1-471 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 119 of 471 bases (25.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_698_length_471_cov_0.974286:1-471 [pilon] Processing NODE_523_length_543_cov_0.696682:1-543 [pilon] NODE_51_length_3042_cov_23.091065:1-3042 log: [pilon] frags shovill.bam: coverage 66 [pilon] Total Reads: 1567, Coverage: 66, minDepth: 17 [pilon] Confirmed 2514 of 3042 bases (82.64%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_51_length_3042_cov_23.091065:1-3042 [pilon] Processing NODE_203_length_753_cov_3.724684:1-753 [pilon] NODE_189_length_770_cov_1.961479:1-770 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 34, Coverage: 6, minDepth: 5 [pilon] Confirmed 480 of 770 bases (62.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_189_length_770_cov_1.961479:1-770 [pilon] Processing NODE_464_length_566_cov_4.561798:1-566 [pilon] NODE_38_length_5880_cov_24.816461:1-5880 log: [pilon] frags shovill.bam: coverage 74 [pilon] Total Reads: 3349, Coverage: 74, minDepth: 19 [pilon] Confirmed 4701 of 5880 bases (79.95%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_38_length_5880_cov_24.816461:1-5880 [pilon] Processing NODE_613_length_503_cov_0.960733:1-503 [pilon] Processing NODE_466_length_566_cov_3.494382:1-566 [pilon] NODE_499_length_551_cov_2.186047:1-551 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 23, Coverage: 5, minDepth: 5 [pilon] Confirmed 238 of 551 bases (43.19%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_499_length_551_cov_2.186047:1-551 [pilon] NODE_862_length_414_cov_1.331058:1-414 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 16, Coverage: 5, minDepth: 5 [pilon] Confirmed 187 of 414 bases (45.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_268_length_689_cov_5.595070:1-689 [pilon] Finished processing NODE_862_length_414_cov_1.331058:1-414 [pilon] Processing NODE_927_length_243_cov_45.827869:1-243 [pilon] NODE_894_length_405_cov_1.165493:1-405 log: [pilon] NODE_748_length_451_cov_2.118182:1-451 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 21, Coverage: 6, minDepth: 5 [pilon] Confirmed 176 of 451 bases (39.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_748_length_451_cov_2.118182:1-451 [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 8, Coverage: 3, minDepth: 5 [pilon] Confirmed 9 of 405 bases (2.22%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_894_length_405_cov_1.165493:1-405 [pilon] NODE_932_length_241_cov_38.241667:1-241 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 92, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 241 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_932_length_241_cov_38.241667:1-241 [pilon] Processing NODE_459_length_569_cov_0.763393:1-569 [pilon] Processing NODE_98_length_1148_cov_0.789679:1-1148 [pilon] Processing NODE_209_length_748_cov_4.261563:1-748 [pilon] NODE_834_length_424_cov_1.237624:1-424 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 129 of 424 bases (30.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_834_length_424_cov_1.237624:1-424 [pilon] Processing NODE_510_length_549_cov_1.546729:1-549 [pilon] NODE_523_length_543_cov_0.696682:1-543 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 8, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 543 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_523_length_543_cov_0.696682:1-543 [pilon] Processing NODE_272_length_687_cov_9.204947:1-687 [pilon] NODE_613_length_503_cov_0.960733:1-503 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 9, Coverage: 2, minDepth: 5 [pilon] Confirmed 32 of 503 bases (6.36%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_613_length_503_cov_0.960733:1-503 [pilon] Processing NODE_370_length_617_cov_0.774194:1-617 [pilon] NODE_464_length_566_cov_4.561798:1-566 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 65, Coverage: 14, minDepth: 5 [pilon] Confirmed 425 of 566 bases (75.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_464_length_566_cov_4.561798:1-566 [pilon] Processing NODE_187_length_777_cov_18.288110:1-777 [pilon] NODE_203_length_753_cov_3.724684:1-753 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 56, Coverage: 10, minDepth: 5 [pilon] Confirmed 472 of 753 bases (62.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_203_length_753_cov_3.724684:1-753 [pilon] Processing NODE_292_length_671_cov_1.358182:1-671 [pilon] NODE_459_length_569_cov_0.763393:1-569 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 8, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 569 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_459_length_569_cov_0.763393:1-569 [pilon] Processing NODE_350_length_629_cov_3.021654:1-629 [pilon] NODE_466_length_566_cov_3.494382:1-566 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 28, Coverage: 6, minDepth: 5 [pilon] Confirmed 286 of 566 bases (50.53%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_466_length_566_cov_3.494382:1-566 [pilon] Processing NODE_766_length_445_cov_1.274691:1-445 [pilon] NODE_927_length_243_cov_45.827869:1-243 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 52, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 243 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_927_length_243_cov_45.827869:1-243 [pilon] Processing NODE_796_length_436_cov_1.904762:1-436 [pilon] NODE_268_length_689_cov_5.595070:1-689 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 67, Coverage: 13, minDepth: 5 [pilon] Confirmed 471 of 689 bases (68.36%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_268_length_689_cov_5.595070:1-689 [pilon] Processing NODE_471_length_564_cov_4.591422:1-564 [pilon] NODE_209_length_748_cov_4.261563:1-748 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 76, Coverage: 13, minDepth: 5 [pilon] Confirmed 614 of 748 bases (82.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_209_length_748_cov_4.261563:1-748 [pilon] Processing NODE_589_length_512_cov_0.864450:1-512 [pilon] NODE_98_length_1148_cov_0.789679:1-1148 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 24, Coverage: 2, minDepth: 5 [pilon] Confirmed 48 of 1148 bases (4.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_98_length_1148_cov_0.789679:1-1148 [pilon] Processing NODE_369_length_618_cov_2.336016:1-618 [pilon] NODE_510_length_549_cov_1.546729:1-549 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 20, Coverage: 5, minDepth: 5 [pilon] Confirmed 243 of 549 bases (44.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_510_length_549_cov_1.546729:1-549 [pilon] Processing NODE_418_length_592_cov_2.409766:1-592 [pilon] NODE_370_length_617_cov_0.774194:1-617 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 10, Coverage: 2, minDepth: 5 [pilon] Confirmed 9 of 617 bases (1.46%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_370_length_617_cov_0.774194:1-617 [pilon] Processing NODE_9_length_223393_cov_42.039651:1-223393 [pilon] NODE_187_length_777_cov_18.288110:1-777 log: [pilon] frags shovill.bam: coverage 50 [pilon] Total Reads: 300, Coverage: 50, minDepth: 13 [pilon] Confirmed 539 of 777 bases (69.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_187_length_777_cov_18.288110:1-777 [pilon] Processing NODE_387_length_606_cov_1.863918:1-606 [pilon] NODE_272_length_687_cov_9.204947:1-687 log: [pilon] frags shovill.bam: coverage 26 [pilon] Total Reads: 142, Coverage: 26, minDepth: 7 [pilon] Confirmed 446 of 687 bases (64.92%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_272_length_687_cov_9.204947:1-687 [pilon] Processing NODE_532_length_536_cov_4.913253:1-536 [pilon] NODE_350_length_629_cov_3.021654:1-629 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 38, Coverage: 8, minDepth: 5 [pilon] Confirmed 389 of 629 bases (61.84%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_292_length_671_cov_1.358182:1-671 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 28, Coverage: 5, minDepth: 5 [pilon] Confirmed 371 of 671 bases (55.29%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_350_length_629_cov_3.021654:1-629 [pilon] Finished processing NODE_292_length_671_cov_1.358182:1-671 [pilon] Processing NODE_182_length_784_cov_6.437406:1-784 [pilon] Processing NODE_805_length_434_cov_1.562300:1-434 [pilon] NODE_796_length_436_cov_1.904762:1-436 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 23, Coverage: 7, minDepth: 5 [pilon] Confirmed 281 of 436 bases (64.45%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_796_length_436_cov_1.904762:1-436 [pilon] Processing NODE_208_length_748_cov_9.604466:1-748 [pilon] NODE_766_length_445_cov_1.274691:1-445 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 2 of 445 bases (0.45%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_766_length_445_cov_1.274691:1-445 [pilon] Processing NODE_835_length_424_cov_0.689769:1-424 [pilon] NODE_387_length_606_cov_1.863918:1-606 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 22, Coverage: 5, minDepth: 5 [pilon] Confirmed 277 of 606 bases (45.71%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_387_length_606_cov_1.863918:1-606 [pilon] Processing NODE_727_length_460_cov_3.401180:1-460 [pilon] NODE_589_length_512_cov_0.864450:1-512 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 147 of 512 bases (28.71%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_589_length_512_cov_0.864450:1-512 [pilon] Processing NODE_936_length_122_cov_4573.000000:1-122 [pilon] NODE_471_length_564_cov_4.591422:1-564 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 38, Coverage: 9, minDepth: 5 [pilon] Confirmed 326 of 564 bases (57.80%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_471_length_564_cov_4.591422:1-564 [pilon] Processing NODE_138_length_876_cov_1.023841:1-876 [pilon] NODE_418_length_592_cov_2.409766:1-592 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 32, Coverage: 7, minDepth: 5 [pilon] Confirmed 330 of 592 bases (55.74%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_418_length_592_cov_2.409766:1-592 [pilon] Processing NODE_231_length_721_cov_3.973333:1-721 [pilon] NODE_369_length_618_cov_2.336016:1-618 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 36, Coverage: 7, minDepth: 5 [pilon] Confirmed 377 of 618 bases (61.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_369_length_618_cov_2.336016:1-618 [pilon] Processing NODE_752_length_450_cov_1.425532:1-450 [pilon] NODE_532_length_536_cov_4.913253:1-536 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 65, Coverage: 13, minDepth: 5 [pilon] Confirmed 327 of 536 bases (61.01%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_532_length_536_cov_4.913253:1-536 [pilon] Processing NODE_500_length_551_cov_1.555814:1-551 [pilon] NODE_805_length_434_cov_1.562300:1-434 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 18, Coverage: 5, minDepth: 5 [pilon] Confirmed 282 of 434 bases (64.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_805_length_434_cov_1.562300:1-434 [pilon] Processing NODE_480_length_561_cov_1.459091:1-561 [pilon] NODE_182_length_784_cov_6.437406:1-784 log: [pilon] frags shovill.bam: coverage 23 [pilon] Total Reads: 140, Coverage: 23, minDepth: 6 [pilon] Confirmed 625 of 784 bases (79.72%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_182_length_784_cov_6.437406:1-784 [pilon] Processing NODE_1_length_490052_cov_33.720238:1-490052 [pilon] NODE_208_length_748_cov_9.604466:1-748 log: [pilon] frags shovill.bam: coverage 25 [pilon] Total Reads: 145, Coverage: 25, minDepth: 6 [pilon] Confirmed 544 of 748 bases (72.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_208_length_748_cov_9.604466:1-748 [pilon] Processing NODE_696_length_471_cov_1.554286:1-471 [pilon] NODE_835_length_424_cov_0.689769:1-424 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 9, Coverage: 3, minDepth: 5 [pilon] Confirmed 31 of 424 bases (7.31%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_835_length_424_cov_0.689769:1-424 [pilon] Processing NODE_497_length_552_cov_2.109049:1-552 [pilon] NODE_752_length_450_cov_1.425532:1-450 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 21, Coverage: 5, minDepth: 5 [pilon] Confirmed 169 of 450 bases (37.56%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_752_length_450_cov_1.425532:1-450 [pilon] Processing NODE_934_length_134_cov_36.384615:1-134 [pilon] NODE_727_length_460_cov_3.401180:1-460 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 36, Coverage: 9, minDepth: 5 [pilon] Confirmed 342 of 460 bases (74.35%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_727_length_460_cov_3.401180:1-460 [pilon] Processing NODE_827_length_426_cov_1.180328:1-426 [pilon] NODE_138_length_876_cov_1.023841:1-876 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 21, Coverage: 3, minDepth: 5 [pilon] Confirmed 213 of 876 bases (24.32%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_138_length_876_cov_1.023841:1-876 [pilon] Processing NODE_325_length_647_cov_6.089354:1-647 [pilon] NODE_936_length_122_cov_4573.000000:1-122 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 306, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 122 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_936_length_122_cov_4573.000000:1-122 [pilon] Processing NODE_278_length_682_cov_5.737968:1-682 [pilon] NODE_500_length_551_cov_1.555814:1-551 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 20, Coverage: 5, minDepth: 5 [pilon] Confirmed 252 of 551 bases (45.74%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_500_length_551_cov_1.555814:1-551 [pilon] Processing NODE_84_length_1289_cov_7.542808:1-1289 [pilon] NODE_231_length_721_cov_3.973333:1-721 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 55, Coverage: 10, minDepth: 5 [pilon] Confirmed 470 of 721 bases (65.19%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_231_length_721_cov_3.973333:1-721 [pilon] Processing NODE_628_length_496_cov_15.306667:1-496 [pilon] NODE_480_length_561_cov_1.459091:1-561 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 17, Coverage: 4, minDepth: 5 [pilon] Confirmed 171 of 561 bases (30.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_480_length_561_cov_1.459091:1-561 [pilon] Processing NODE_105_length_1066_cov_12.984127:1-1066 [pilon] NODE_696_length_471_cov_1.554286:1-471 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 189 of 471 bases (40.13%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_696_length_471_cov_1.554286:1-471 [pilon] Processing NODE_252_length_703_cov_2.020619:1-703 [pilon] NODE_497_length_552_cov_2.109049:1-552 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 25, Coverage: 4, minDepth: 5 [pilon] Confirmed 272 of 552 bases (49.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_497_length_552_cov_2.109049:1-552 [pilon] Processing NODE_393_length_602_cov_7.295218:1-602 [pilon] NODE_934_length_134_cov_36.384615:1-134 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 0, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 134 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_934_length_134_cov_36.384615:1-134 [pilon] Processing NODE_635_length_494_cov_9.292225:1-494 [pilon] NODE_827_length_426_cov_1.180328:1-426 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 7 of 426 bases (1.64%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_827_length_426_cov_1.180328:1-426 [pilon] Processing NODE_708_length_468_cov_3.763689:1-468 [pilon] NODE_278_length_682_cov_5.737968:1-682 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 96, Coverage: 16, minDepth: 5 [pilon] Confirmed 464 of 682 bases (68.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_278_length_682_cov_5.737968:1-682 [pilon] Processing NODE_846_length_421_cov_0.366667:1-421 [pilon] NODE_325_length_647_cov_6.089354:1-647 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 68, Coverage: 13, minDepth: 5 [pilon] Confirmed 492 of 647 bases (76.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_325_length_647_cov_6.089354:1-647 [pilon] Processing NODE_429_length_584_cov_1.611231:1-584 [pilon] NODE_628_length_496_cov_15.306667:1-496 log: [pilon] frags shovill.bam: coverage 32 [pilon] Total Reads: 125, Coverage: 32, minDepth: 8 [pilon] Confirmed 417 of 496 bases (84.07%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_628_length_496_cov_15.306667:1-496 [pilon] Processing NODE_787_length_439_cov_0.468553:1-439 [pilon] NODE_252_length_703_cov_2.020619:1-703 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 35, Coverage: 5, minDepth: 5 [pilon] Confirmed 357 of 703 bases (50.78%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_105_length_1066_cov_12.984127:1-1066 log: [pilon] frags shovill.bam: coverage 35 [pilon] Total Reads: 287, Coverage: 35, minDepth: 9 [pilon] Confirmed 672 of 1066 bases (63.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_105_length_1066_cov_12.984127:1-1066 [pilon] Finished processing NODE_252_length_703_cov_2.020619:1-703 [pilon] Processing NODE_301_length_662_cov_1.837338:1-662 [pilon] Processing NODE_863_length_414_cov_1.262799:1-414 [pilon] NODE_84_length_1289_cov_7.542808:1-1289 log: [pilon] frags shovill.bam: coverage 20 [pilon] Total Reads: 207, Coverage: 20, minDepth: 5 [pilon] Confirmed 1100 of 1289 bases (85.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_84_length_1289_cov_7.542808:1-1289 [pilon] Processing NODE_246_length_706_cov_12.011966:1-706 [pilon] NODE_708_length_468_cov_3.763689:1-468 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 29, Coverage: 8, minDepth: 5 [pilon] Confirmed 309 of 468 bases (66.03%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_708_length_468_cov_3.763689:1-468 [pilon] Processing NODE_283_length_674_cov_4.443038:1-674 [pilon] NODE_393_length_602_cov_7.295218:1-602 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 98, Coverage: 18, minDepth: 5 [pilon] Confirmed 427 of 602 bases (70.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_393_length_602_cov_7.295218:1-602 [pilon] Processing NODE_847_length_420_cov_0.959866:1-420 [pilon] NODE_846_length_421_cov_0.366667:1-421 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 7, Coverage: 2, minDepth: 5 [pilon] Confirmed 9 of 421 bases (2.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_846_length_421_cov_0.366667:1-421 [pilon] Processing NODE_593_length_510_cov_3.740360:1-510 [pilon] NODE_635_length_494_cov_9.292225:1-494 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 70, Coverage: 18, minDepth: 5 [pilon] Confirmed 375 of 494 bases (75.91%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_635_length_494_cov_9.292225:1-494 [pilon] Processing NODE_557_length_526_cov_0.708642:1-526 [pilon] NODE_429_length_584_cov_1.611231:1-584 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 26, Coverage: 6, minDepth: 5 [pilon] Confirmed 283 of 584 bases (48.46%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_429_length_584_cov_1.611231:1-584 [pilon] Processing NODE_134_length_895_cov_1.293282:1-895 [pilon] NODE_787_length_439_cov_0.468553:1-439 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 439 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_787_length_439_cov_0.468553:1-439 [pilon] Processing NODE_866_length_413_cov_2.428082:1-413 [pilon] NODE_863_length_414_cov_1.262799:1-414 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 76 of 414 bases (18.36%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_863_length_414_cov_1.262799:1-414 [pilon] Processing NODE_848_length_419_cov_2.550336:1-419 [pilon] NODE_301_length_662_cov_1.837338:1-662 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 26, Coverage: 5, minDepth: 5 [pilon] Confirmed 277 of 662 bases (41.84%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_301_length_662_cov_1.837338:1-662 [pilon] Processing NODE_178_length_792_cov_11.068554:1-792 [pilon] NODE_847_length_420_cov_0.959866:1-420 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 44 of 420 bases (10.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_847_length_420_cov_0.959866:1-420 [pilon] NODE_283_length_674_cov_4.443038:1-674 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 54, Coverage: 10, minDepth: 5 [pilon] Confirmed 411 of 674 bases (60.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_283_length_674_cov_4.443038:1-674 [pilon] Processing NODE_804_length_434_cov_1.642173:1-434 [pilon] NODE_246_length_706_cov_12.011966:1-706 log: [pilon] frags shovill.bam: coverage 36 [pilon] Total Reads: 193, Coverage: 36, minDepth: 9 [pilon] Confirmed 493 of 706 bases (69.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_246_length_706_cov_12.011966:1-706 [pilon] Processing NODE_186_length_778_cov_2.202435:1-778 [pilon] Processing NODE_706_length_469_cov_5.272989:1-469 [pilon] NODE_593_length_510_cov_3.740360:1-510 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 42, Coverage: 11, minDepth: 5 [pilon] Confirmed 378 of 510 bases (74.12%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_593_length_510_cov_3.740360:1-510 [pilon] Processing NODE_223_length_735_cov_17.998371:1-735 [pilon] NODE_134_length_895_cov_1.293282:1-895 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 35, Coverage: 5, minDepth: 5 [pilon] Confirmed 310 of 895 bases (34.64%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_134_length_895_cov_1.293282:1-895 [pilon] Processing NODE_869_length_412_cov_1.501718:1-412 [pilon] NODE_557_length_526_cov_0.708642:1-526 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 15, Coverage: 4, minDepth: 5 [pilon] Confirmed 180 of 526 bases (34.22%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_557_length_526_cov_0.708642:1-526 [pilon] Processing NODE_582_length_514_cov_2.391858:1-514 [pilon] NODE_848_length_419_cov_2.550336:1-419 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 21, Coverage: 5, minDepth: 5 [pilon] Confirmed 221 of 419 bases (52.74%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_848_length_419_cov_2.550336:1-419 [pilon] Processing NODE_36_length_8792_cov_31.574559:1-8792 [pilon] NODE_866_length_413_cov_2.428082:1-413 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 26, Coverage: 8, minDepth: 5 [pilon] Confirmed 338 of 413 bases (81.84%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_866_length_413_cov_2.428082:1-413 [pilon] Processing NODE_153_length_834_cov_11.768583:1-834 [pilon] NODE_178_length_792_cov_11.068554:1-792 log: [pilon] frags shovill.bam: coverage 27 [pilon] Total Reads: 164, Coverage: 27, minDepth: 7 [pilon] Confirmed 529 of 792 bases (66.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_178_length_792_cov_11.068554:1-792 [pilon] Processing NODE_349_length_629_cov_12.068898:1-629 [pilon] NODE_804_length_434_cov_1.642173:1-434 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 48 of 434 bases (11.06%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_804_length_434_cov_1.642173:1-434 [pilon] NODE_706_length_469_cov_5.272989:1-469 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 48, Coverage: 13, minDepth: 5 [pilon] Confirmed 327 of 469 bases (69.72%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_415_length_592_cov_8.649682:1-592 [pilon] NODE_186_length_778_cov_2.202435:1-778 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 45, Coverage: 7, minDepth: 5 [pilon] Confirmed 341 of 778 bases (43.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_186_length_778_cov_2.202435:1-778 [pilon] Processing NODE_546_length_529_cov_5.019608:1-529 [pilon] Finished processing NODE_706_length_469_cov_5.272989:1-469 [pilon] Processing NODE_41_length_4807_cov_50.648314:1-4807 [pilon] NODE_869_length_412_cov_1.501718:1-412 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 13, Coverage: 3, minDepth: 5 [pilon] Confirmed 122 of 412 bases (29.61%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_869_length_412_cov_1.501718:1-412 [pilon] Processing NODE_569_length_518_cov_6.191436:1-518 [pilon] NODE_223_length_735_cov_17.998371:1-735 log: [pilon] frags shovill.bam: coverage 48 [pilon] Total Reads: 271, Coverage: 48, minDepth: 12 [pilon] Confirmed 534 of 735 bases (72.65%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_223_length_735_cov_17.998371:1-735 [pilon] Processing NODE_356_length_626_cov_2.227723:1-626 [pilon] NODE_582_length_514_cov_2.391858:1-514 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 25, Coverage: 6, minDepth: 5 [pilon] Confirmed 244 of 514 bases (47.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_582_length_514_cov_2.391858:1-514 [pilon] Processing NODE_85_length_1260_cov_4.128183:1-1260 [pilon] NODE_35_length_9076_cov_59.737353:1-9076 log: [pilon] frags shovill.bam: coverage 181 [pilon] Total Reads: 12749, Coverage: 181, minDepth: 45 [pilon] Confirmed 8243 of 9076 bases (90.82%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_35_length_9076_cov_59.737353:1-9076 [pilon] Processing NODE_627_length_497_cov_2.901596:1-497 [pilon] NODE_153_length_834_cov_11.768583:1-834 log: [pilon] frags shovill.bam: coverage 36 [pilon] Total Reads: 235, Coverage: 36, minDepth: 9 [pilon] Confirmed 662 of 834 bases (79.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_153_length_834_cov_11.768583:1-834 [pilon] Processing NODE_10_length_218666_cov_45.518241:1-218666 [pilon] NODE_349_length_629_cov_12.068898:1-629 log: [pilon] frags shovill.bam: coverage 37 [pilon] Total Reads: 180, Coverage: 37, minDepth: 9 [pilon] Confirmed 506 of 629 bases (80.45%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_349_length_629_cov_12.068898:1-629 [pilon] Processing NODE_567_length_519_cov_0.748744:1-519 [pilon] NODE_569_length_518_cov_6.191436:1-518 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 63, Coverage: 15, minDepth: 5 [pilon] Confirmed 359 of 518 bases (69.31%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_569_length_518_cov_6.191436:1-518 [pilon] Processing NODE_808_length_433_cov_6.464744:1-433 [pilon] NODE_415_length_592_cov_8.649682:1-592 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 96, Coverage: 21, minDepth: 5 [pilon] Confirmed 465 of 592 bases (78.55%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_415_length_592_cov_8.649682:1-592 [pilon] Processing NODE_155_length_831_cov_32.573239:1-831 [pilon] NODE_546_length_529_cov_5.019608:1-529 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 51, Coverage: 12, minDepth: 5 [pilon] Confirmed 369 of 529 bases (69.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_546_length_529_cov_5.019608:1-529 [pilon] Processing NODE_507_length_550_cov_1.172494:1-550 [pilon] NODE_356_length_626_cov_2.227723:1-626 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 35, Coverage: 6, minDepth: 5 [pilon] Confirmed 312 of 626 bases (49.84%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_356_length_626_cov_2.227723:1-626 [pilon] Processing NODE_396_length_600_cov_13.361169:1-600 [pilon] NODE_627_length_497_cov_2.901596:1-497 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 32, Coverage: 8, minDepth: 5 [pilon] Confirmed 396 of 497 bases (79.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_627_length_497_cov_2.901596:1-497 [pilon] Processing NODE_449_length_574_cov_1.578366:1-574 [pilon] NODE_85_length_1260_cov_4.128183:1-1260 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 120, Coverage: 12, minDepth: 5 [pilon] Confirmed 758 of 1260 bases (60.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_85_length_1260_cov_4.128183:1-1260 [pilon] Processing NODE_219_length_739_cov_13.367314:1-739 [pilon] NODE_567_length_519_cov_0.748744:1-519 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 17 of 519 bases (3.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_567_length_519_cov_0.748744:1-519 [pilon] Processing NODE_545_length_530_cov_109.266504:1-530 [pilon] NODE_808_length_433_cov_6.464744:1-433 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 46, Coverage: 13, minDepth: 5 [pilon] Confirmed 302 of 433 bases (69.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_808_length_433_cov_6.464744:1-433 [pilon] Processing NODE_303_length_661_cov_10.912963:1-661 [pilon] NODE_507_length_550_cov_1.172494:1-550 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 9, Coverage: 2, minDepth: 5 [pilon] Confirmed 26 of 550 bases (4.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_507_length_550_cov_1.172494:1-550 [pilon] Processing NODE_458_length_569_cov_1.357143:1-569 [pilon] NODE_396_length_600_cov_13.361169:1-600 log: [pilon] frags shovill.bam: coverage 32 [pilon] Total Reads: 147, Coverage: 32, minDepth: 8 [pilon] Confirmed 404 of 600 bases (67.33%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_396_length_600_cov_13.361169:1-600 [pilon] Processing NODE_247_length_706_cov_7.126496:1-706 [pilon] NODE_449_length_574_cov_1.578366:1-574 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 17, Coverage: 4, minDepth: 5 [pilon] Confirmed 164 of 574 bases (28.57%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_449_length_574_cov_1.578366:1-574 [pilon] Processing NODE_821_length_428_cov_2.817590:1-428 [pilon] NODE_155_length_831_cov_32.573239:1-831 log: [pilon] frags shovill.bam: coverage 91 [pilon] Total Reads: 583, Coverage: 91, minDepth: 23 [pilon] Confirmed 592 of 831 bases (71.24%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_155_length_831_cov_32.573239:1-831 [pilon] Processing NODE_365_length_620_cov_1.148297:1-620 [pilon] NODE_219_length_739_cov_13.367314:1-739 log: [pilon] frags shovill.bam: coverage 33 [pilon] Total Reads: 192, Coverage: 33, minDepth: 8 [pilon] Confirmed 527 of 739 bases (71.31%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_219_length_739_cov_13.367314:1-739 [pilon] Processing NODE_831_length_425_cov_1.289474:1-425 [pilon] NODE_303_length_661_cov_10.912963:1-661 log: [pilon] frags shovill.bam: coverage 43 [pilon] Total Reads: 219, Coverage: 43, minDepth: 11 [pilon] Confirmed 470 of 661 bases (71.10%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_303_length_661_cov_10.912963:1-661 [pilon] Processing NODE_147_length_842_cov_10.613037:1-842 [pilon] NODE_545_length_530_cov_109.266504:1-530 log: [pilon] frags shovill.bam: coverage 130 [pilon] Total Reads: 955, Coverage: 130, minDepth: 33 [pilon] Confirmed 444 of 530 bases (83.77%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_545_length_530_cov_109.266504:1-530 [pilon] Processing NODE_719_length_464_cov_1.702624:1-464 [pilon] NODE_458_length_569_cov_1.357143:1-569 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 15, Coverage: 3, minDepth: 5 [pilon] Confirmed 177 of 569 bases (31.11%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_458_length_569_cov_1.357143:1-569 [pilon] Processing NODE_63_length_2135_cov_25.848560:1-2135 [pilon] NODE_247_length_706_cov_7.126496:1-706 log: [pilon] frags shovill.bam: coverage 19 [pilon] Total Reads: 105, Coverage: 19, minDepth: 5 [pilon] Confirmed 557 of 706 bases (78.90%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_247_length_706_cov_7.126496:1-706 [pilon] Processing NODE_825_length_427_cov_0.901961:1-427 [pilon] NODE_821_length_428_cov_2.817590:1-428 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 43, Coverage: 9, minDepth: 5 [pilon] Confirmed 313 of 428 bases (73.13%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_821_length_428_cov_2.817590:1-428 [pilon] Processing NODE_149_length_838_cov_0.669456:1-838 [pilon] NODE_365_length_620_cov_1.148297:1-620 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 20, Coverage: 4, minDepth: 5 [pilon] Confirmed 252 of 620 bases (40.65%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_365_length_620_cov_1.148297:1-620 [pilon] Processing NODE_572_length_518_cov_2.743073:1-518 [pilon] NODE_30_length_25829_cov_44.046017:1-25829 log: [pilon] frags shovill.bam: coverage 132 [pilon] Total Reads: 26654, Coverage: 132, minDepth: 33 [pilon] Confirmed 25532 of 25829 bases (98.85%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_30_length_25829_cov_44.046017:1-25829 [pilon] Processing NODE_212_length_743_cov_0.860129:1-743 [pilon] NODE_831_length_425_cov_1.289474:1-425 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 191 of 425 bases (44.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_831_length_425_cov_1.289474:1-425 [pilon] Processing NODE_790_length_437_cov_2.594937:1-437 [pilon] NODE_825_length_427_cov_0.901961:1-427 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 9, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 427 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_825_length_427_cov_0.901961:1-427 [pilon] Processing NODE_171_length_802_cov_1.945668:1-802 [pilon] NODE_719_length_464_cov_1.702624:1-464 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 239 of 464 bases (51.51%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_719_length_464_cov_1.702624:1-464 [pilon] Processing NODE_358_length_624_cov_6.866799:1-624 [pilon] NODE_147_length_842_cov_10.613037:1-842 log: [pilon] frags shovill.bam: coverage 38 [pilon] Total Reads: 255, Coverage: 38, minDepth: 10 [pilon] Confirmed 541 of 842 bases (64.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_147_length_842_cov_10.613037:1-842 [pilon] Processing NODE_205_length_750_cov_16.674086:1-750 [pilon] NODE_149_length_838_cov_0.669456:1-838 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 16, Coverage: 2, minDepth: 5 [pilon] Confirmed 57 of 838 bases (6.80%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_149_length_838_cov_0.669456:1-838 [pilon] Processing NODE_622_length_499_cov_2.269841:1-499 [pilon] NODE_572_length_518_cov_2.743073:1-518 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 24, Coverage: 6, minDepth: 5 [pilon] Confirmed 335 of 518 bases (64.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_572_length_518_cov_2.743073:1-518 [pilon] Processing NODE_511_length_548_cov_2.377049:1-548 [pilon] NODE_212_length_743_cov_0.860129:1-743 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 16, Coverage: 3, minDepth: 5 [pilon] Confirmed 139 of 743 bases (18.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_212_length_743_cov_0.860129:1-743 [pilon] Processing NODE_107_length_1063_cov_2.485138:1-1063 [pilon] NODE_790_length_437_cov_2.594937:1-437 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 17, Coverage: 5, minDepth: 5 [pilon] Confirmed 238 of 437 bases (54.46%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_790_length_437_cov_2.594937:1-437 [pilon] Processing NODE_899_length_404_cov_1.544170:1-404 [pilon] NODE_41_length_4807_cov_50.648314:1-4807 log: [pilon] frags shovill.bam: coverage 147 [pilon] Total Reads: 5461, Coverage: 147, minDepth: 37 [pilon] Confirmed 3944 of 4807 bases (82.05%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_41_length_4807_cov_50.648314:1-4807 [pilon] Processing NODE_169_length_805_cov_0.739766:1-805 [pilon] NODE_63_length_2135_cov_25.848560:1-2135 log: [pilon] frags shovill.bam: coverage 72 [pilon] Total Reads: 1191, Coverage: 72, minDepth: 18 [pilon] Confirmed 1849 of 2135 bases (86.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_63_length_2135_cov_25.848560:1-2135 [pilon] Processing NODE_549_length_528_cov_1.393120:1-528 [pilon] NODE_622_length_499_cov_2.269841:1-499 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 17, Coverage: 4, minDepth: 5 [pilon] Confirmed 215 of 499 bases (43.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_622_length_499_cov_2.269841:1-499 [pilon] Processing NODE_767_length_445_cov_0.580247:1-445 [pilon] NODE_205_length_750_cov_16.674086:1-750 log: [pilon] frags shovill.bam: coverage 55 [pilon] Total Reads: 319, Coverage: 55, minDepth: 14 [pilon] Confirmed 472 of 750 bases (62.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_205_length_750_cov_16.674086:1-750 [pilon] NODE_511_length_548_cov_2.377049:1-548 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 23, Coverage: 5, minDepth: 5 [pilon] Confirmed 362 of 548 bases (66.06%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_511_length_548_cov_2.377049:1-548 [pilon] Processing NODE_344_length_636_cov_4.460194:1-636 [pilon] Processing NODE_806_length_434_cov_1.172524:1-434 [pilon] NODE_358_length_624_cov_6.866799:1-624 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 82, Coverage: 17, minDepth: 5 [pilon] Confirmed 491 of 624 bases (78.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_358_length_624_cov_6.866799:1-624 [pilon] Processing NODE_92_length_1208_cov_7.812328:1-1208 [pilon] NODE_899_length_404_cov_1.544170:1-404 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 16, Coverage: 5, minDepth: 5 [pilon] Confirmed 237 of 404 bases (58.66%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_899_length_404_cov_1.544170:1-404 [pilon] Processing NODE_455_length_569_cov_4.328125:1-569 [pilon] NODE_171_length_802_cov_1.945668:1-802 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 41, Coverage: 6, minDepth: 5 [pilon] Confirmed 371 of 802 bases (46.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_171_length_802_cov_1.945668:1-802 [pilon] NODE_169_length_805_cov_0.739766:1-805 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 18, Coverage: 3, minDepth: 5 [pilon] Confirmed 124 of 805 bases (15.40%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_169_length_805_cov_0.739766:1-805 [pilon] Processing NODE_906_length_402_cov_91.327402:1-402 [pilon] NODE_107_length_1063_cov_2.485138:1-1063 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 67, Coverage: 7, minDepth: 5 [pilon] Confirmed 692 of 1063 bases (65.10%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_107_length_1063_cov_2.485138:1-1063 [pilon] Processing NODE_33_length_10685_cov_34.309447:1-10685 [pilon] NODE_36_length_8792_cov_31.574559:1-8792 log: [pilon] frags shovill.bam: coverage 95 [pilon] Total Reads: 6546, Coverage: 95, minDepth: 24 [pilon] Confirmed 8101 of 8792 bases (92.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_36_length_8792_cov_31.574559:1-8792 [pilon] Processing NODE_468_length_565_cov_6.135135:1-565 [pilon] NODE_767_length_445_cov_0.580247:1-445 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 10, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 445 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_767_length_445_cov_0.580247:1-445 [pilon] Processing NODE_482_length_559_cov_0.958904:1-559 [pilon] NODE_549_length_528_cov_1.393120:1-528 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 10, Coverage: 2, minDepth: 5 [pilon] Confirmed 97 of 528 bases (18.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_549_length_528_cov_1.393120:1-528 [pilon] Processing NODE_86_length_1257_cov_11.625880:1-1257 [pilon] NODE_806_length_434_cov_1.172524:1-434 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 9 of 434 bases (2.07%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_806_length_434_cov_1.172524:1-434 [pilon] Processing NODE_154_length_832_cov_1.753868:1-832 [pilon] NODE_344_length_636_cov_4.460194:1-636 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 50, Coverage: 10, minDepth: 5 [pilon] Confirmed 435 of 636 bases (68.40%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_344_length_636_cov_4.460194:1-636 [pilon] Processing NODE_789_length_438_cov_1.056782:1-438 [pilon] NODE_455_length_569_cov_4.328125:1-569 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 48, Coverage: 11, minDepth: 5 [pilon] Confirmed 407 of 569 bases (71.53%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_455_length_569_cov_4.328125:1-569 [pilon] Processing NODE_920_length_273_cov_36.506579:1-273 [pilon] NODE_468_length_565_cov_6.135135:1-565 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 58, Coverage: 13, minDepth: 5 [pilon] Confirmed 330 of 565 bases (58.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_468_length_565_cov_6.135135:1-565 [pilon] Processing NODE_366_length_619_cov_9.184739:1-619 [pilon] NODE_92_length_1208_cov_7.812328:1-1208 log: [pilon] frags shovill.bam: coverage 22 [pilon] Total Reads: 210, Coverage: 22, minDepth: 6 [pilon] Confirmed 826 of 1208 bases (68.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_92_length_1208_cov_7.812328:1-1208 [pilon] Processing NODE_573_length_517_cov_6.219697:1-517 [pilon] NODE_906_length_402_cov_91.327402:1-402 log: [pilon] frags shovill.bam: coverage 99 [pilon] Total Reads: 603, Coverage: 99, minDepth: 25 [pilon] Confirmed 353 of 402 bases (87.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_906_length_402_cov_91.327402:1-402 [pilon] Processing NODE_448_length_575_cov_4.389868:1-575 [pilon] NODE_920_length_273_cov_36.506579:1-273 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 118, Coverage: 8, minDepth: 5 [pilon] Confirmed 203 of 273 bases (74.36%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_920_length_273_cov_36.506579:1-273 [pilon] Processing NODE_621_length_500_cov_2.366755:1-500 [pilon] NODE_789_length_438_cov_1.056782:1-438 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 438 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_789_length_438_cov_1.056782:1-438 [pilon] Processing NODE_419_length_591_cov_3.208511:1-591 [pilon] NODE_154_length_832_cov_1.753868:1-832 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 34, Coverage: 5, minDepth: 5 [pilon] Confirmed 515 of 832 bases (61.90%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_154_length_832_cov_1.753868:1-832 [pilon] Processing NODE_771_length_443_cov_1.807453:1-443 [pilon] NODE_482_length_559_cov_0.958904:1-559 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 110 of 559 bases (19.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_482_length_559_cov_0.958904:1-559 [pilon] Processing NODE_447_length_575_cov_4.718062:1-575 [pilon] NODE_86_length_1257_cov_11.625880:1-1257 log: [pilon] frags shovill.bam: coverage 36 [pilon] Total Reads: 347, Coverage: 36, minDepth: 9 [pilon] Confirmed 787 of 1257 bases (62.61%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_573_length_517_cov_6.219697:1-517 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 58, Coverage: 14, minDepth: 5 [pilon] Confirmed 393 of 517 bases (76.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_86_length_1257_cov_11.625880:1-1257 [pilon] Finished processing NODE_573_length_517_cov_6.219697:1-517 [pilon] Processing NODE_915_length_328_cov_30.048309:1-328 [pilon] Processing NODE_699_length_471_cov_0.662857:1-471 [pilon] NODE_366_length_619_cov_9.184739:1-619 log: [pilon] frags shovill.bam: coverage 24 [pilon] Total Reads: 116, Coverage: 24, minDepth: 6 [pilon] Confirmed 513 of 619 bases (82.88%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_366_length_619_cov_9.184739:1-619 [pilon] Processing NODE_146_length_846_cov_4.600000:1-846 [pilon] NODE_448_length_575_cov_4.389868:1-575 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 68, Coverage: 15, minDepth: 5 [pilon] Confirmed 487 of 575 bases (84.70%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_448_length_575_cov_4.389868:1-575 [pilon] Processing NODE_509_length_549_cov_1.934579:1-549 [pilon] NODE_447_length_575_cov_4.718062:1-575 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 50, Coverage: 11, minDepth: 5 [pilon] Confirmed 364 of 575 bases (63.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_447_length_575_cov_4.718062:1-575 [pilon] Processing NODE_677_length_478_cov_4.187675:1-478 [pilon] NODE_621_length_500_cov_2.366755:1-500 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 21, Coverage: 5, minDepth: 5 [pilon] Confirmed 261 of 500 bases (52.20%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_621_length_500_cov_2.366755:1-500 [pilon] Processing NODE_293_length_671_cov_1.327273:1-671 [pilon] NODE_771_length_443_cov_1.807453:1-443 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 174 of 443 bases (39.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_771_length_443_cov_1.807453:1-443 [pilon] Processing NODE_390_length_604_cov_1.343685:1-604 [pilon] NODE_419_length_591_cov_3.208511:1-591 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 38, Coverage: 8, minDepth: 5 [pilon] Confirmed 402 of 591 bases (68.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_419_length_591_cov_3.208511:1-591 [pilon] Processing NODE_133_length_896_cov_12.440000:1-896 [pilon] NODE_699_length_471_cov_0.662857:1-471 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 471 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_699_length_471_cov_0.662857:1-471 [pilon] Processing NODE_633_length_495_cov_1.304813:1-495 [pilon] NODE_915_length_328_cov_30.048309:1-328 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 102, Coverage: 3, minDepth: 5 [pilon] Confirmed 98 of 328 bases (29.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_915_length_328_cov_30.048309:1-328 [pilon] Processing NODE_454_length_570_cov_0.556793:1-570 [pilon] Processing NODE_760_length_446_cov_0.907692:1-446 [pilon] NODE_509_length_549_cov_1.934579:1-549 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 26, Coverage: 6, minDepth: 5 [pilon] Confirmed 259 of 549 bases (47.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_509_length_549_cov_1.934579:1-549 [pilon] Processing NODE_456_length_569_cov_4.133929:1-569 [pilon] NODE_146_length_846_cov_4.600000:1-846 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 107, Coverage: 16, minDepth: 5 [pilon] Confirmed 633 of 846 bases (74.82%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_146_length_846_cov_4.600000:1-846 [pilon] Processing NODE_174_length_799_cov_7.619469:1-799 [pilon] NODE_677_length_478_cov_4.187675:1-478 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 37, Coverage: 10, minDepth: 5 [pilon] Confirmed 331 of 478 bases (69.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_677_length_478_cov_4.187675:1-478 [pilon] Processing NODE_590_length_511_cov_2.210256:1-511 [pilon] NODE_293_length_671_cov_1.327273:1-671 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 22, Coverage: 4, minDepth: 5 [pilon] Confirmed 270 of 671 bases (40.24%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_293_length_671_cov_1.327273:1-671 [pilon] Processing NODE_886_length_407_cov_0.944056:1-407 [pilon] NODE_390_length_604_cov_1.343685:1-604 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 23, Coverage: 5, minDepth: 5 [pilon] Confirmed 221 of 604 bases (36.59%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_390_length_604_cov_1.343685:1-604 [pilon] Processing NODE_723_length_462_cov_1.307918:1-462 [pilon] NODE_133_length_896_cov_12.440000:1-896 log: [pilon] frags shovill.bam: coverage 32 [pilon] Total Reads: 224, Coverage: 32, minDepth: 8 [pilon] Confirmed 550 of 896 bases (61.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_133_length_896_cov_12.440000:1-896 [pilon] Processing NODE_738_length_455_cov_8.790419:1-455 [pilon] NODE_760_length_446_cov_0.907692:1-446 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 446 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_633_length_495_cov_1.304813:1-495 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 130 of 495 bases (26.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_633_length_495_cov_1.304813:1-495 [pilon] Finished processing NODE_760_length_446_cov_0.907692:1-446 [pilon] Processing NODE_309_length_656_cov_4.977570:1-656 [pilon] Processing NODE_793_length_437_cov_0.787975:1-437 [pilon] NODE_454_length_570_cov_0.556793:1-570 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 7, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 570 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_454_length_570_cov_0.556793:1-570 [pilon] Processing NODE_763_length_445_cov_2.472222:1-445 [pilon] NODE_456_length_569_cov_4.133929:1-569 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 46, Coverage: 10, minDepth: 5 [pilon] Confirmed 447 of 569 bases (78.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_456_length_569_cov_4.133929:1-569 [pilon] Processing NODE_385_length_607_cov_2.683128:1-607 [pilon] NODE_590_length_511_cov_2.210256:1-511 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 23, Coverage: 5, minDepth: 5 [pilon] Confirmed 233 of 511 bases (45.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_590_length_511_cov_2.210256:1-511 [pilon] Processing NODE_287_length_672_cov_135.872958:1-672 [pilon] NODE_174_length_799_cov_7.619469:1-799 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 130, Coverage: 21, minDepth: 5 [pilon] Confirmed 607 of 799 bases (75.97%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_174_length_799_cov_7.619469:1-799 [pilon] Processing NODE_707_length_469_cov_1.566092:1-469 [pilon] NODE_738_length_455_cov_8.790419:1-455 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 73, Coverage: 18, minDepth: 5 [pilon] Confirmed 365 of 455 bases (80.22%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_738_length_455_cov_8.790419:1-455 [pilon] Processing NODE_250_length_703_cov_13.702749:1-703 [pilon] NODE_886_length_407_cov_0.944056:1-407 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 126 of 407 bases (30.96%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_886_length_407_cov_0.944056:1-407 [pilon] Processing NODE_581_length_514_cov_4.358779:1-514 [pilon] NODE_723_length_462_cov_1.307918:1-462 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 17, Coverage: 5, minDepth: 5 [pilon] Confirmed 133 of 462 bases (28.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_723_length_462_cov_1.307918:1-462 [pilon] Processing NODE_409_length_595_cov_2.453586:1-595 [pilon] NODE_309_length_656_cov_4.977570:1-656 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 66, Coverage: 13, minDepth: 5 [pilon] Confirmed 589 of 656 bases (89.79%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_309_length_656_cov_4.977570:1-656 [pilon] Processing NODE_731_length_458_cov_1.655786:1-458 [pilon] NODE_793_length_437_cov_0.787975:1-437 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 13, Coverage: 3, minDepth: 5 [pilon] Confirmed 130 of 437 bases (29.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_793_length_437_cov_0.787975:1-437 [pilon] Processing NODE_211_length_743_cov_8.315113:1-743 [pilon] NODE_763_length_445_cov_2.472222:1-445 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 18, Coverage: 5, minDepth: 5 [pilon] Confirmed 230 of 445 bases (51.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_763_length_445_cov_2.472222:1-445 [pilon] Processing NODE_444_length_576_cov_2.457143:1-576 [pilon] NODE_385_length_607_cov_2.683128:1-607 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 34, Coverage: 7, minDepth: 5 [pilon] Confirmed 447 of 607 bases (73.64%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_385_length_607_cov_2.683128:1-607 [pilon] Processing NODE_858_length_416_cov_0.461017:1-416 [pilon] NODE_250_length_703_cov_13.702749:1-703 log: [pilon] frags shovill.bam: coverage 31 [pilon] Total Reads: 171, Coverage: 31, minDepth: 8 [pilon] Confirmed 470 of 703 bases (66.86%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_250_length_703_cov_13.702749:1-703 [pilon] Processing NODE_229_length_726_cov_1.993388:1-726 [pilon] NODE_707_length_469_cov_1.566092:1-469 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 23, Coverage: 6, minDepth: 5 [pilon] Confirmed 283 of 469 bases (60.34%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_707_length_469_cov_1.566092:1-469 [pilon] NODE_581_length_514_cov_4.358779:1-514 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 52, Coverage: 13, minDepth: 5 [pilon] Confirmed 457 of 514 bases (88.91%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_581_length_514_cov_4.358779:1-514 [pilon] Processing NODE_310_length_656_cov_1.218692:1-656 [pilon] NODE_409_length_595_cov_2.453586:1-595 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 37, Coverage: 8, minDepth: 5 [pilon] Confirmed 377 of 595 bases (63.36%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_409_length_595_cov_2.453586:1-595 [pilon] Processing NODE_96_length_1166_cov_18.626794:1-1166 [pilon] NODE_444_length_576_cov_2.457143:1-576 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 26, Coverage: 6, minDepth: 5 [pilon] Confirmed 352 of 576 bases (61.11%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_444_length_576_cov_2.457143:1-576 [pilon] Processing NODE_537_length_535_cov_3.253623:1-535 [pilon] NODE_731_length_458_cov_1.655786:1-458 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 212 of 458 bases (46.29%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_229_length_726_cov_1.993388:1-726 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 37, Coverage: 7, minDepth: 5 [pilon] Confirmed 453 of 726 bases (62.40%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_229_length_726_cov_1.993388:1-726 [pilon] Finished processing NODE_731_length_458_cov_1.655786:1-458 [pilon] Processing NODE_750_length_451_cov_1.569697:1-451 [pilon] Processing NODE_726_length_460_cov_3.766962:1-460 [pilon] NODE_858_length_416_cov_0.461017:1-416 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 9, Coverage: 3, minDepth: 5 [pilon] Confirmed 0 of 416 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_858_length_416_cov_0.461017:1-416 [pilon] Processing NODE_732_length_458_cov_1.370920:1-458 [pilon] NODE_211_length_743_cov_8.315113:1-743 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 123, Coverage: 21, minDepth: 5 [pilon] Confirmed 523 of 743 bases (70.39%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_211_length_743_cov_8.315113:1-743 [pilon] Processing NODE_152_length_836_cov_4.925874:1-836 [pilon] NODE_310_length_656_cov_1.218692:1-656 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 26, Coverage: 5, minDepth: 5 [pilon] Confirmed 337 of 656 bases (51.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_310_length_656_cov_1.218692:1-656 [pilon] Processing NODE_632_length_495_cov_1.462567:1-495 [pilon] NODE_287_length_672_cov_135.872958:1-672 log: [pilon] frags shovill.bam: coverage 214 [pilon] Total Reads: 1689, Coverage: 214, minDepth: 54 [pilon] Confirmed 588 of 672 bases (87.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_287_length_672_cov_135.872958:1-672 [pilon] Processing NODE_288_length_672_cov_5.842105:1-672 [pilon] NODE_750_length_451_cov_1.569697:1-451 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 13, Coverage: 3, minDepth: 5 [pilon] Confirmed 127 of 451 bases (28.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_750_length_451_cov_1.569697:1-451 [pilon] Processing NODE_689_length_473_cov_1.911932:1-473 [pilon] NODE_537_length_535_cov_3.253623:1-535 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 36, Coverage: 9, minDepth: 5 [pilon] Confirmed 317 of 535 bases (59.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_537_length_535_cov_3.253623:1-535 [pilon] Processing NODE_923_length_244_cov_169.414634:1-244 [pilon] NODE_732_length_458_cov_1.370920:1-458 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 60 of 458 bases (13.10%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_732_length_458_cov_1.370920:1-458 [pilon] NODE_726_length_460_cov_3.766962:1-460 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 24, Coverage: 7, minDepth: 5 [pilon] Confirmed 302 of 460 bases (65.65%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_338_length_641_cov_2.815385:1-641 [pilon] Finished processing NODE_726_length_460_cov_3.766962:1-460 [pilon] Processing NODE_234_length_718_cov_4.132328:1-718 [pilon] NODE_96_length_1166_cov_18.626794:1-1166 log: [pilon] frags shovill.bam: coverage 50 [pilon] Total Reads: 450, Coverage: 50, minDepth: 13 [pilon] Confirmed 858 of 1166 bases (73.58%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_96_length_1166_cov_18.626794:1-1166 [pilon] Processing NODE_603_length_506_cov_5.558442:1-506 [pilon] Processing NODE_401_length_599_cov_3.085774:1-599 [pilon] NODE_689_length_473_cov_1.911932:1-473 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 151 of 473 bases (31.92%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_689_length_473_cov_1.911932:1-473 [pilon] Processing NODE_670_length_482_cov_0.202216:1-482 [pilon] NODE_152_length_836_cov_4.925874:1-836 log: [pilon] frags shovill.bam: coverage 26 [pilon] Total Reads: 166, Coverage: 26, minDepth: 7 [pilon] Confirmed 554 of 836 bases (66.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_152_length_836_cov_4.925874:1-836 [pilon] Processing NODE_168_length_805_cov_6.302632:1-805 [pilon] NODE_632_length_495_cov_1.462567:1-495 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 11, Coverage: 3, minDepth: 5 [pilon] Confirmed 130 of 495 bases (26.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_632_length_495_cov_1.462567:1-495 [pilon] Processing NODE_839_length_422_cov_2.694352:1-422 [pilon] NODE_33_length_10685_cov_34.309447:1-10685 log: [pilon] frags shovill.bam: coverage 104 [pilon] Total Reads: 8571, Coverage: 104, minDepth: 26 [pilon] Confirmed 9874 of 10685 bases (92.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_33_length_10685_cov_34.309447:1-10685 [pilon] Processing NODE_131_length_900_cov_0.893453:1-900 [pilon] NODE_288_length_672_cov_5.842105:1-672 log: [pilon] frags shovill.bam: coverage 19 [pilon] Total Reads: 96, Coverage: 19, minDepth: 5 [pilon] Confirmed 531 of 672 bases (79.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_288_length_672_cov_5.842105:1-672 [pilon] Processing NODE_531_length_537_cov_1.574519:1-537 [pilon] NODE_234_length_718_cov_4.132328:1-718 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 56, Coverage: 10, minDepth: 5 [pilon] Confirmed 460 of 718 bases (64.07%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_234_length_718_cov_4.132328:1-718 [pilon] Processing NODE_720_length_463_cov_3.561404:1-463 [pilon] NODE_603_length_506_cov_5.558442:1-506 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 60, Coverage: 14, minDepth: 5 [pilon] Confirmed 396 of 506 bases (78.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_603_length_506_cov_5.558442:1-506 [pilon] Processing NODE_176_length_794_cov_8.545319:1-794 [pilon] NODE_401_length_599_cov_3.085774:1-599 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 50, Coverage: 11, minDepth: 5 [pilon] Confirmed 419 of 599 bases (69.95%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_401_length_599_cov_3.085774:1-599 [pilon] Processing NODE_316_length_651_cov_6.639623:1-651 [pilon] NODE_670_length_482_cov_0.202216:1-482 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 14, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 482 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_670_length_482_cov_0.202216:1-482 [pilon] Processing NODE_265_length_692_cov_7.987741:1-692 [pilon] NODE_923_length_244_cov_169.414634:1-244 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 462, Coverage: 21, minDepth: 5 [pilon] Confirmed 217 of 244 bases (88.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_923_length_244_cov_169.414634:1-244 [pilon] Processing NODE_626_length_497_cov_6.694149:1-497 [pilon] NODE_338_length_641_cov_2.815385:1-641 log: [pilon] NODE_131_length_900_cov_0.893453:1-900 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 19, Coverage: 3, minDepth: 5 [pilon] Confirmed 203 of 900 bases (22.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_131_length_900_cov_0.893453:1-900 [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 36, Coverage: 7, minDepth: 5 [pilon] Confirmed 432 of 641 bases (67.39%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_338_length_641_cov_2.815385:1-641 [pilon] Processing NODE_162_length_819_cov_1.733524:1-819 [pilon] Processing NODE_130_length_907_cov_6.632316:1-907 [pilon] NODE_839_length_422_cov_2.694352:1-422 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 18, Coverage: 6, minDepth: 5 [pilon] Confirmed 222 of 422 bases (52.61%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_168_length_805_cov_6.302632:1-805 log: [pilon] frags shovill.bam: coverage 26 [pilon] Total Reads: 159, Coverage: 26, minDepth: 7 [pilon] Confirmed 579 of 805 bases (71.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_168_length_805_cov_6.302632:1-805 [pilon] Finished processing NODE_839_length_422_cov_2.694352:1-422 [pilon] Processing NODE_185_length_779_cov_5.962006:1-779 [pilon] Processing NODE_712_length_467_cov_0.942197:1-467 [pilon] NODE_531_length_537_cov_1.574519:1-537 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 152 of 537 bases (28.31%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_531_length_537_cov_1.574519:1-537 [pilon] Processing NODE_533_length_536_cov_3.684337:1-536 [pilon] NODE_720_length_463_cov_3.561404:1-463 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 41, Coverage: 12, minDepth: 5 [pilon] Confirmed 319 of 463 bases (68.90%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_720_length_463_cov_3.561404:1-463 [pilon] Processing NODE_217_length_740_cov_3.786753:1-740 [pilon] NODE_316_length_651_cov_6.639623:1-651 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 74, Coverage: 15, minDepth: 5 [pilon] Confirmed 470 of 651 bases (72.20%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_316_length_651_cov_6.639623:1-651 [pilon] Processing NODE_780_length_442_cov_0.872274:1-442 [pilon] NODE_176_length_794_cov_8.545319:1-794 log: [pilon] frags shovill.bam: coverage 28 [pilon] Total Reads: 173, Coverage: 28, minDepth: 7 [pilon] Confirmed 527 of 794 bases (66.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_176_length_794_cov_8.545319:1-794 [pilon] Processing NODE_478_length_561_cov_2.020455:1-561 [pilon] NODE_626_length_497_cov_6.694149:1-497 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 56, Coverage: 15, minDepth: 5 [pilon] Confirmed 386 of 497 bases (77.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_626_length_497_cov_6.694149:1-497 [pilon] Processing NODE_568_length_518_cov_18.236776:1-518 [pilon] NODE_265_length_692_cov_7.987741:1-692 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 101, Coverage: 18, minDepth: 5 [pilon] Confirmed 466 of 692 bases (67.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_265_length_692_cov_7.987741:1-692 [pilon] Processing NODE_867_length_413_cov_1.099315:1-413 [pilon] NODE_162_length_819_cov_1.733524:1-819 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 34, Coverage: 4, minDepth: 5 [pilon] Confirmed 247 of 819 bases (30.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_162_length_819_cov_1.733524:1-819 [pilon] Processing NODE_439_length_577_cov_1.967105:1-577 [pilon] NODE_130_length_907_cov_6.632316:1-907 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 127, Coverage: 18, minDepth: 5 [pilon] Confirmed 539 of 907 bases (59.43%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_130_length_907_cov_6.632316:1-907 [pilon] Processing NODE_667_length_482_cov_1.565097:1-482 [pilon] NODE_712_length_467_cov_0.942197:1-467 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 55 of 467 bases (11.78%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_712_length_467_cov_0.942197:1-467 [pilon] Processing NODE_452_length_572_cov_3.585366:1-572 [pilon] NODE_533_length_536_cov_3.684337:1-536 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 42, Coverage: 10, minDepth: 5 [pilon] Confirmed 329 of 536 bases (61.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_533_length_536_cov_3.684337:1-536 [pilon] NODE_185_length_779_cov_5.962006:1-779 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 91, Coverage: 15, minDepth: 5 [pilon] Confirmed 523 of 779 bases (67.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_185_length_779_cov_5.962006:1-779 [pilon] Processing NODE_104_length_1069_cov_3.148734:1-1069 [pilon] NODE_780_length_442_cov_0.872274:1-442 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 4, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 442 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_780_length_442_cov_0.872274:1-442 [pilon] Processing NODE_141_length_854_cov_13.597544:1-854 [pilon] Processing NODE_577_length_515_cov_1.951777:1-515 [pilon] NODE_867_length_413_cov_1.099315:1-413 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 13, Coverage: 4, minDepth: 5 [pilon] Confirmed 175 of 413 bases (42.37%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_867_length_413_cov_1.099315:1-413 [pilon] Processing NODE_768_length_445_cov_0.330247:1-445 [pilon] NODE_217_length_740_cov_3.786753:1-740 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 62, Coverage: 10, minDepth: 5 [pilon] Confirmed 605 of 740 bases (81.76%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_217_length_740_cov_3.786753:1-740 [pilon] Processing NODE_675_length_479_cov_1.821229:1-479 [pilon] NODE_478_length_561_cov_2.020455:1-561 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 20, Coverage: 5, minDepth: 5 [pilon] Confirmed 288 of 561 bases (51.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_478_length_561_cov_2.020455:1-561 [pilon] Processing NODE_89_length_1219_cov_6.331512:1-1219 [pilon] NODE_439_length_577_cov_1.967105:1-577 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 28, Coverage: 6, minDepth: 5 [pilon] Confirmed 308 of 577 bases (53.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_439_length_577_cov_1.967105:1-577 [pilon] Processing NODE_597_length_508_cov_1.573643:1-508 [pilon] NODE_667_length_482_cov_1.565097:1-482 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 18, Coverage: 5, minDepth: 5 [pilon] Confirmed 210 of 482 bases (43.57%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_568_length_518_cov_18.236776:1-518 log: [pilon] frags shovill.bam: coverage 72 [pilon] Total Reads: 307, Coverage: 72, minDepth: 18 [pilon] Confirmed 413 of 518 bases (79.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_667_length_482_cov_1.565097:1-482 [pilon] Finished processing NODE_568_length_518_cov_18.236776:1-518 [pilon] Processing NODE_484_length_557_cov_8.646789:1-557 [pilon] Processing NODE_758_length_447_cov_1.895706:1-447 [pilon] NODE_452_length_572_cov_3.585366:1-572 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 32, Coverage: 7, minDepth: 5 [pilon] Confirmed 340 of 572 bases (59.44%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_452_length_572_cov_3.585366:1-572 [pilon] Processing NODE_728_length_459_cov_1.073964:1-459 [pilon] NODE_104_length_1069_cov_3.148734:1-1069 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 93, Coverage: 11, minDepth: 5 [pilon] Confirmed 693 of 1069 bases (64.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_104_length_1069_cov_3.148734:1-1069 [pilon] Processing NODE_491_length_555_cov_2.361751:1-555 [pilon] NODE_577_length_515_cov_1.951777:1-515 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 21, Coverage: 5, minDepth: 5 [pilon] Confirmed 172 of 515 bases (33.40%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_577_length_515_cov_1.951777:1-515 [pilon] Processing NODE_872_length_411_cov_1.951724:1-411 [pilon] NODE_675_length_479_cov_1.821229:1-479 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 18, Coverage: 4, minDepth: 5 [pilon] Confirmed 189 of 479 bases (39.46%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_675_length_479_cov_1.821229:1-479 [pilon] Processing NODE_892_length_406_cov_0.407018:1-406 [pilon] NODE_141_length_854_cov_13.597544:1-854 log: [pilon] frags shovill.bam: coverage 34 [pilon] Total Reads: 231, Coverage: 34, minDepth: 9 [pilon] Confirmed 654 of 854 bases (76.58%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_141_length_854_cov_13.597544:1-854 [pilon] Processing NODE_753_length_448_cov_4.626911:1-448 [pilon] NODE_768_length_445_cov_0.330247:1-445 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 83 of 445 bases (18.65%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_768_length_445_cov_0.330247:1-445 [pilon] Processing NODE_190_length_769_cov_13.608025:1-769 [pilon] NODE_89_length_1219_cov_6.331512:1-1219 log: [pilon] frags shovill.bam: coverage 20 [pilon] Total Reads: 189, Coverage: 20, minDepth: 5 [pilon] Confirmed 940 of 1219 bases (77.11%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_89_length_1219_cov_6.331512:1-1219 [pilon] NODE_484_length_557_cov_8.646789:1-557 log: [pilon] frags shovill.bam: coverage 22 [pilon] Total Reads: 102, Coverage: 22, minDepth: 6 [pilon] Confirmed 444 of 557 bases (79.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_484_length_557_cov_8.646789:1-557 [pilon] Processing NODE_709_length_468_cov_0.446686:1-468 [pilon] Processing NODE_326_length_647_cov_2.990494:1-647 [pilon] NODE_597_length_508_cov_1.573643:1-508 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 19, Coverage: 5, minDepth: 5 [pilon] Confirmed 241 of 508 bases (47.44%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_597_length_508_cov_1.573643:1-508 [pilon] Processing NODE_136_length_881_cov_2.910526:1-881 [pilon] NODE_758_length_447_cov_1.895706:1-447 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 14, Coverage: 3, minDepth: 5 [pilon] Confirmed 147 of 447 bases (32.89%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_758_length_447_cov_1.895706:1-447 [pilon] Processing NODE_110_length_1041_cov_2.452174:1-1041 [pilon] NODE_491_length_555_cov_2.361751:1-555 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 31, Coverage: 7, minDepth: 5 [pilon] Confirmed 293 of 555 bases (52.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_491_length_555_cov_2.361751:1-555 [pilon] Processing NODE_300_length_662_cov_3.741220:1-662 [pilon] NODE_872_length_411_cov_1.951724:1-411 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 17, Coverage: 5, minDepth: 5 [pilon] Confirmed 234 of 411 bases (56.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_872_length_411_cov_1.951724:1-411 [pilon] Processing NODE_118_length_994_cov_4.241695:1-994 [pilon] NODE_728_length_459_cov_1.073964:1-459 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 87 of 459 bases (18.95%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_728_length_459_cov_1.073964:1-459 [pilon] Processing NODE_843_length_421_cov_1.720000:1-421 [pilon] NODE_892_length_406_cov_0.407018:1-406 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 4, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 406 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_892_length_406_cov_0.407018:1-406 [pilon] Processing NODE_612_length_503_cov_1.065445:1-503 [pilon] NODE_753_length_448_cov_4.626911:1-448 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 39, Coverage: 11, minDepth: 5 [pilon] Confirmed 313 of 448 bases (69.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_753_length_448_cov_4.626911:1-448 [pilon] Processing NODE_193_length_768_cov_4.341577:1-768 [pilon] NODE_709_length_468_cov_0.446686:1-468 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 468 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_709_length_468_cov_0.446686:1-468 [pilon] Processing NODE_202_length_753_cov_15.832278:1-753 [pilon] NODE_190_length_769_cov_13.608025:1-769 log: [pilon] frags shovill.bam: coverage 32 [pilon] Total Reads: 190, Coverage: 32, minDepth: 8 [pilon] Confirmed 528 of 769 bases (68.66%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_190_length_769_cov_13.608025:1-769 [pilon] Processing NODE_762_length_445_cov_4.845679:1-445 [pilon] NODE_326_length_647_cov_2.990494:1-647 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 38, Coverage: 8, minDepth: 5 [pilon] Confirmed 439 of 647 bases (67.85%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_326_length_647_cov_2.990494:1-647 [pilon] Processing NODE_565_length_519_cov_5.457286:1-519 [pilon] NODE_110_length_1041_cov_2.452174:1-1041 log: [pilon] NODE_300_length_662_cov_3.741220:1-662 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 72, Coverage: 12, minDepth: 5 [pilon] Confirmed 554 of 662 bases (83.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_300_length_662_cov_3.741220:1-662 [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 55, Coverage: 7, minDepth: 5 [pilon] Confirmed 465 of 1041 bases (44.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_110_length_1041_cov_2.452174:1-1041 [pilon] Processing NODE_879_length_408_cov_1.905923:1-408 [pilon] Processing NODE_473_length_563_cov_1.889140:1-563 [pilon] NODE_136_length_881_cov_2.910526:1-881 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 60, Coverage: 9, minDepth: 5 [pilon] Confirmed 512 of 881 bases (58.12%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_136_length_881_cov_2.910526:1-881 [pilon] Processing NODE_76_length_1464_cov_25.960536:1-1464 [pilon] NODE_612_length_503_cov_1.065445:1-503 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 20, Coverage: 5, minDepth: 5 [pilon] Confirmed 198 of 503 bases (39.36%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_612_length_503_cov_1.065445:1-503 [pilon] Processing NODE_620_length_500_cov_4.200528:1-500 [pilon] NODE_118_length_994_cov_4.241695:1-994 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 126, Coverage: 16, minDepth: 5 [pilon] Confirmed 647 of 994 bases (65.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_118_length_994_cov_4.241695:1-994 [pilon] Processing NODE_931_length_243_cov_33.811475:1-243 [pilon] NODE_193_length_768_cov_4.341577:1-768 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 83, Coverage: 14, minDepth: 5 [pilon] Confirmed 474 of 768 bases (61.72%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_193_length_768_cov_4.341577:1-768 [pilon] Processing NODE_535_length_536_cov_1.884337:1-536 [pilon] NODE_843_length_421_cov_1.720000:1-421 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 16, Coverage: 5, minDepth: 5 [pilon] Confirmed 165 of 421 bases (39.19%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_843_length_421_cov_1.720000:1-421 [pilon] Processing NODE_501_length_551_cov_1.011628:1-551 [pilon] NODE_762_length_445_cov_4.845679:1-445 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 34, Coverage: 10, minDepth: 5 [pilon] Confirmed 321 of 445 bases (72.13%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_762_length_445_cov_4.845679:1-445 [pilon] Processing NODE_49_length_3569_cov_33.689385:1-3569 [pilon] NODE_565_length_519_cov_5.457286:1-519 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 46, Coverage: 11, minDepth: 5 [pilon] Confirmed 345 of 519 bases (66.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_565_length_519_cov_5.457286:1-519 [pilon] Processing NODE_519_length_545_cov_0.896226:1-545 [pilon] NODE_473_length_563_cov_1.889140:1-563 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 31, Coverage: 7, minDepth: 5 [pilon] Confirmed 334 of 563 bases (59.33%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_473_length_563_cov_1.889140:1-563 [pilon] Processing NODE_797_length_436_cov_0.952381:1-436 [pilon] NODE_879_length_408_cov_1.905923:1-408 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 8, Coverage: 3, minDepth: 5 [pilon] Confirmed 55 of 408 bases (13.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_879_length_408_cov_1.905923:1-408 [pilon] Processing NODE_559_length_524_cov_2.161290:1-524 [pilon] NODE_202_length_753_cov_15.832278:1-753 log: [pilon] frags shovill.bam: coverage 42 [pilon] Total Reads: 313, Coverage: 42, minDepth: 11 [pilon] Confirmed 660 of 753 bases (87.65%) [pilon] Corrected 4 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_202_length_753_cov_15.832278:1-753 [pilon] Processing NODE_257_length_700_cov_3.290155:1-700 [pilon] NODE_620_length_500_cov_4.200528:1-500 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 37, Coverage: 9, minDepth: 5 [pilon] Confirmed 308 of 500 bases (61.60%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_620_length_500_cov_4.200528:1-500 [pilon] Processing NODE_786_length_439_cov_8.606918:1-439 [pilon] NODE_931_length_243_cov_33.811475:1-243 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 90, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 243 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_931_length_243_cov_33.811475:1-243 [pilon] Processing NODE_74_length_1493_cov_5.978863:1-1493 [pilon] NODE_535_length_536_cov_1.884337:1-536 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 26, Coverage: 6, minDepth: 5 [pilon] Confirmed 313 of 536 bases (58.40%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_535_length_536_cov_1.884337:1-536 [pilon] Processing NODE_254_length_702_cov_9.564544:1-702 [pilon] NODE_501_length_551_cov_1.011628:1-551 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 14, Coverage: 3, minDepth: 5 [pilon] Confirmed 129 of 551 bases (23.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_501_length_551_cov_1.011628:1-551 [pilon] Processing NODE_173_length_801_cov_2.636765:1-801 [pilon] NODE_519_length_545_cov_0.896226:1-545 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 9, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 545 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_519_length_545_cov_0.896226:1-545 [pilon] Processing NODE_443_length_577_cov_0.660088:1-577 [pilon] NODE_797_length_436_cov_0.952381:1-436 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 60 of 436 bases (13.76%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_797_length_436_cov_0.952381:1-436 [pilon] Processing NODE_115_length_1007_cov_6.306998:1-1007 [pilon] NODE_257_length_700_cov_3.290155:1-700 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 59, Coverage: 11, minDepth: 5 [pilon] Confirmed 504 of 700 bases (72.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_257_length_700_cov_3.290155:1-700 [pilon] Processing NODE_781_length_441_cov_1.575000:1-441 [pilon] NODE_559_length_524_cov_2.161290:1-524 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 22, Coverage: 5, minDepth: 5 [pilon] Confirmed 322 of 524 bases (61.45%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_559_length_524_cov_2.161290:1-524 [pilon] Processing NODE_135_length_884_cov_2.306684:1-884 [pilon] NODE_76_length_1464_cov_25.960536:1-1464 log: [pilon] frags shovill.bam: coverage 22 [pilon] Total Reads: 936, Coverage: 22, minDepth: 6 [pilon] Confirmed 1342 of 1464 bases (91.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_76_length_1464_cov_25.960536:1-1464 [pilon] Processing NODE_59_length_2348_cov_66.015267:1-2348 [pilon] NODE_443_length_577_cov_0.660088:1-577 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 11, Coverage: 2, minDepth: 5 [pilon] Confirmed 37 of 577 bases (6.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_443_length_577_cov_0.660088:1-577 [pilon] Processing NODE_28_length_36726_cov_35.802459:1-36726 [pilon] NODE_786_length_439_cov_8.606918:1-439 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 54, Coverage: 16, minDepth: 5 [pilon] Confirmed 301 of 439 bases (68.56%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_786_length_439_cov_8.606918:1-439 [pilon] Processing NODE_204_length_752_cov_0.689382:1-752 [pilon] NODE_173_length_801_cov_2.636765:1-801 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 46, Coverage: 7, minDepth: 5 [pilon] Confirmed 515 of 801 bases (64.29%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_173_length_801_cov_2.636765:1-801 [pilon] Processing NODE_26_length_42055_cov_41.688606:1-42055 [pilon] NODE_254_length_702_cov_9.564544:1-702 log: [pilon] frags shovill.bam: coverage 24 [pilon] Total Reads: 132, Coverage: 24, minDepth: 6 [pilon] Confirmed 472 of 702 bases (67.24%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_254_length_702_cov_9.564544:1-702 [pilon] Processing NODE_662_length_483_cov_1.417127:1-483 [pilon] NODE_781_length_441_cov_1.575000:1-441 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 18, Coverage: 5, minDepth: 5 [pilon] Confirmed 274 of 441 bases (62.13%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_781_length_441_cov_1.575000:1-441 [pilon] Processing NODE_600_length_508_cov_0.578811:1-508 [pilon] NODE_74_length_1493_cov_5.978863:1-1493 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 190, Coverage: 17, minDepth: 5 [pilon] Confirmed 989 of 1493 bases (66.24%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_74_length_1493_cov_5.978863:1-1493 [pilon] Processing NODE_737_length_456_cov_2.773134:1-456 [pilon] NODE_115_length_1007_cov_6.306998:1-1007 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 138, Coverage: 17, minDepth: 5 [pilon] Confirmed 685 of 1007 bases (68.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_115_length_1007_cov_6.306998:1-1007 [pilon] Processing NODE_165_length_812_cov_15.761216:1-812 [pilon] NODE_135_length_884_cov_2.306684:1-884 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 48, Coverage: 7, minDepth: 5 [pilon] Confirmed 564 of 884 bases (63.80%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_135_length_884_cov_2.306684:1-884 [pilon] Processing NODE_524_length_541_cov_2.733333:1-541 [pilon] NODE_49_length_3569_cov_33.689385:1-3569 log: [pilon] frags shovill.bam: coverage 100 [pilon] Total Reads: 2766, Coverage: 100, minDepth: 25 [pilon] Confirmed 3219 of 3569 bases (90.19%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_49_length_3569_cov_33.689385:1-3569 [pilon] Processing NODE_888_length_406_cov_3.042105:1-406 [pilon] NODE_600_length_508_cov_0.578811:1-508 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 6, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 508 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_600_length_508_cov_0.578811:1-508 [pilon] Processing NODE_123_length_954_cov_5.753902:1-954 [pilon] NODE_204_length_752_cov_0.689382:1-752 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 10, Coverage: 2, minDepth: 5 [pilon] Confirmed 4 of 752 bases (0.53%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_204_length_752_cov_0.689382:1-752 [pilon] Processing NODE_367_length_619_cov_4.359438:1-619 [pilon] NODE_662_length_483_cov_1.417127:1-483 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 18, Coverage: 4, minDepth: 5 [pilon] Confirmed 231 of 483 bases (47.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_662_length_483_cov_1.417127:1-483 [pilon] Processing NODE_106_length_1064_cov_6.551432:1-1064 [pilon] NODE_737_length_456_cov_2.773134:1-456 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 24, Coverage: 7, minDepth: 5 [pilon] Confirmed 325 of 456 bases (71.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_737_length_456_cov_2.773134:1-456 [pilon] Processing NODE_360_length_622_cov_2.205589:1-622 [pilon] NODE_888_length_406_cov_3.042105:1-406 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 18, Coverage: 6, minDepth: 5 [pilon] Confirmed 280 of 406 bases (68.97%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_888_length_406_cov_3.042105:1-406 [pilon] Processing NODE_922_length_249_cov_85.476562:1-249 [pilon] NODE_123_length_954_cov_5.753902:1-954 log: [pilon] frags shovill.bam: coverage 20 [pilon] Total Reads: 151, Coverage: 20, minDepth: 5 [pilon] Confirmed 863 of 954 bases (90.46%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_123_length_954_cov_5.753902:1-954 [pilon] Processing NODE_420_length_589_cov_2.865385:1-589 [pilon] NODE_524_length_541_cov_2.733333:1-541 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 44, Coverage: 10, minDepth: 5 [pilon] Confirmed 332 of 541 bases (61.37%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_524_length_541_cov_2.733333:1-541 [pilon] Processing NODE_592_length_510_cov_3.915167:1-510 [pilon] NODE_165_length_812_cov_15.761216:1-812 log: [pilon] frags shovill.bam: coverage 41 [pilon] Total Reads: 262, Coverage: 41, minDepth: 10 [pilon] Confirmed 571 of 812 bases (70.32%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_165_length_812_cov_15.761216:1-812 [pilon] Processing NODE_11_length_215661_cov_46.585335:1-215661 [pilon] NODE_367_length_619_cov_4.359438:1-619 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 48, Coverage: 10, minDepth: 5 [pilon] Confirmed 480 of 619 bases (77.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_367_length_619_cov_4.359438:1-619 [pilon] NODE_360_length_622_cov_2.205589:1-622 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 29, Coverage: 6, minDepth: 5 [pilon] Confirmed 328 of 622 bases (52.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_360_length_622_cov_2.205589:1-622 [pilon] Processing NODE_705_length_470_cov_1.094556:1-470 [pilon] NODE_106_length_1064_cov_6.551432:1-1064 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 126, Coverage: 15, minDepth: 5 [pilon] Confirmed 688 of 1064 bases (64.66%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_106_length_1064_cov_6.551432:1-1064 [pilon] Processing NODE_13_length_131029_cov_39.753338:1-131029 [pilon] NODE_22_length_72603_cov_36.721489:1-72603 log: [pilon] frags shovill.bam: coverage 113 [pilon] Total Reads: 63221, Coverage: 113, minDepth: 28 [pilon] Confirmed 71961 of 72603 bases (99.12%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_22_length_72603_cov_36.721489:1-72603 [pilon] Processing NODE_516_length_547_cov_1.326291:1-547 [pilon] NODE_420_length_589_cov_2.865385:1-589 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 34, Coverage: 8, minDepth: 5 [pilon] Confirmed 343 of 589 bases (58.23%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_420_length_589_cov_2.865385:1-589 [pilon] Processing NODE_180_length_790_cov_1.372197:1-790 [pilon] NODE_922_length_249_cov_85.476562:1-249 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 252, Coverage: 15, minDepth: 5 [pilon] Confirmed 214 of 249 bases (85.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_922_length_249_cov_85.476562:1-249 [pilon] Processing NODE_242_length_711_cov_13.779661:1-711 [pilon] NODE_592_length_510_cov_3.915167:1-510 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 52, Coverage: 9, minDepth: 5 [pilon] Confirmed 390 of 510 bases (76.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_592_length_510_cov_3.915167:1-510 [pilon] Processing NODE_144_length_849_cov_10.245879:1-849 [pilon] NODE_705_length_470_cov_1.094556:1-470 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 14 of 470 bases (2.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_705_length_470_cov_1.094556:1-470 [pilon] Processing NODE_799_length_435_cov_3.480892:1-435 [pilon] NODE_516_length_547_cov_1.326291:1-547 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 18, Coverage: 4, minDepth: 5 [pilon] Confirmed 216 of 547 bases (39.49%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_516_length_547_cov_1.326291:1-547 [pilon] NODE_180_length_790_cov_1.372197:1-790 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 29, Coverage: 5, minDepth: 5 [pilon] Confirmed 350 of 790 bases (44.30%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_180_length_790_cov_1.372197:1-790 [pilon] Processing NODE_461_length_568_cov_3.635347:1-568 [pilon] NODE_799_length_435_cov_3.480892:1-435 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 31, Coverage: 9, minDepth: 5 [pilon] Confirmed 320 of 435 bases (73.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_799_length_435_cov_3.480892:1-435 [pilon] Processing NODE_40_length_4928_cov_33.585604:1-4928 [pilon] NODE_242_length_711_cov_13.779661:1-711 log: [pilon] frags shovill.bam: coverage 36 [pilon] Total Reads: 197, Coverage: 36, minDepth: 9 [pilon] Confirmed 498 of 711 bases (70.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_242_length_711_cov_13.779661:1-711 [pilon] Processing NODE_88_length_1223_cov_8.430127:1-1223 [pilon] NODE_59_length_2348_cov_66.015267:1-2348 log: [pilon] frags shovill.bam: coverage 191 [pilon] Total Reads: 3478, Coverage: 191, minDepth: 48 [pilon] Confirmed 1878 of 2348 bases (79.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_59_length_2348_cov_66.015267:1-2348 [pilon] NODE_144_length_849_cov_10.245879:1-849 log: [pilon] frags shovill.bam: coverage 34 [pilon] Total Reads: 222, Coverage: 34, minDepth: 9 [pilon] Confirmed 552 of 849 bases (65.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_144_length_849_cov_10.245879:1-849 [pilon] Processing NODE_192_length_768_cov_9.409583:1-768 [pilon] NODE_25_length_46794_cov_38.082832:1-46794 log: [pilon] frags shovill.bam: coverage 116 [pilon] Total Reads: 42091, Coverage: 116, minDepth: 29 [pilon] Confirmed 46100 of 46794 bases (98.52%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_25_length_46794_cov_38.082832:1-46794 [pilon] NODE_461_length_568_cov_3.635347:1-568 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 39, Coverage: 9, minDepth: 5 [pilon] Confirmed 338 of 568 bases (59.51%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_461_length_568_cov_3.635347:1-568 [pilon] Processing NODE_802_length_435_cov_0.821656:1-435 [pilon] NODE_88_length_1223_cov_8.430127:1-1223 log: [pilon] frags shovill.bam: coverage 30 [pilon] Total Reads: 283, Coverage: 30, minDepth: 8 [pilon] Confirmed 860 of 1223 bases (70.32%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_88_length_1223_cov_8.430127:1-1223 [pilon] Processing NODE_112_length_1027_cov_23.616998:1-1027 [pilon] NODE_192_length_768_cov_9.409583:1-768 log: [pilon] frags shovill.bam: coverage 27 [pilon] Total Reads: 159, Coverage: 27, minDepth: 7 [pilon] Confirmed 527 of 768 bases (68.62%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_192_length_768_cov_9.409583:1-768 [pilon] Processing NODE_400_length_599_cov_3.847280:1-599 [pilon] NODE_802_length_435_cov_0.821656:1-435 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 4, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 435 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_802_length_435_cov_0.821656:1-435 [pilon] Processing NODE_332_length_643_cov_0.992337:1-643 [pilon] NODE_400_length_599_cov_3.847280:1-599 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 52, Coverage: 11, minDepth: 5 [pilon] Confirmed 374 of 599 bases (62.44%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_400_length_599_cov_3.847280:1-599 [pilon] Processing NODE_754_length_448_cov_2.688073:1-448 [pilon] NODE_332_length_643_cov_0.992337:1-643 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 20, Coverage: 4, minDepth: 5 [pilon] Confirmed 236 of 643 bases (36.70%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_332_length_643_cov_0.992337:1-643 [pilon] Processing NODE_120_length_964_cov_4.476868:1-964 [pilon] NODE_112_length_1027_cov_23.616998:1-1027 log: [pilon] frags shovill.bam: coverage 63 [pilon] Total Reads: 500, Coverage: 63, minDepth: 16 [pilon] Confirmed 591 of 1027 bases (57.55%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_112_length_1027_cov_23.616998:1-1027 [pilon] Processing NODE_24_length_58446_cov_40.223472:1-58446 [pilon] NODE_754_length_448_cov_2.688073:1-448 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 31, Coverage: 8, minDepth: 5 [pilon] Confirmed 308 of 448 bases (68.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_754_length_448_cov_2.688073:1-448 [pilon] Processing NODE_241_length_712_cov_3.707276:1-712 [pilon] NODE_120_length_964_cov_4.476868:1-964 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 107, Coverage: 14, minDepth: 5 [pilon] Confirmed 783 of 964 bases (81.22%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_120_length_964_cov_4.476868:1-964 [pilon] Processing NODE_402_length_599_cov_2.025105:1-599 [pilon] NODE_241_length_712_cov_3.707276:1-712 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 65, Coverage: 12, minDepth: 5 [pilon] Confirmed 411 of 712 bases (57.72%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_241_length_712_cov_3.707276:1-712 [pilon] Processing NODE_529_length_538_cov_0.671463:1-538 [pilon] NODE_40_length_4928_cov_33.585604:1-4928 log: [pilon] frags shovill.bam: coverage 102 [pilon] Total Reads: 3884, Coverage: 102, minDepth: 26 [pilon] Confirmed 4634 of 4928 bases (94.03%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_40_length_4928_cov_33.585604:1-4928 [pilon] Processing NODE_50_length_3332_cov_18.815634:1-3332 [pilon] NODE_402_length_599_cov_2.025105:1-599 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 28, Coverage: 6, minDepth: 5 [pilon] Confirmed 397 of 599 bases (66.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_402_length_599_cov_2.025105:1-599 [pilon] Processing NODE_496_length_552_cov_2.361949:1-552 [pilon] NODE_529_length_538_cov_0.671463:1-538 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 10, Coverage: 2, minDepth: 5 [pilon] Confirmed 36 of 538 bases (6.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_529_length_538_cov_0.671463:1-538 [pilon] Processing NODE_453_length_571_cov_2.268889:1-571 [pilon] NODE_453_length_571_cov_2.268889:1-571 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 29, Coverage: 7, minDepth: 5 [pilon] Confirmed 305 of 571 bases (53.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_453_length_571_cov_2.268889:1-571 [pilon] Processing NODE_561_length_521_cov_4.760000:1-521 [pilon] NODE_496_length_552_cov_2.361949:1-552 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 30, Coverage: 7, minDepth: 5 [pilon] Confirmed 301 of 552 bases (54.53%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_496_length_552_cov_2.361949:1-552 [pilon] Processing NODE_470_length_565_cov_3.094595:1-565 [pilon] NODE_561_length_521_cov_4.760000:1-521 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 51, Coverage: 11, minDepth: 5 [pilon] Confirmed 383 of 521 bases (73.51%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_561_length_521_cov_4.760000:1-521 [pilon] Processing NODE_588_length_512_cov_1.002558:1-512 [pilon] NODE_470_length_565_cov_3.094595:1-565 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 49, Coverage: 11, minDepth: 5 [pilon] Confirmed 411 of 565 bases (72.74%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_470_length_565_cov_3.094595:1-565 [pilon] NODE_588_length_512_cov_1.002558:1-512 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 71 of 512 bases (13.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_588_length_512_cov_1.002558:1-512 [pilon] Processing NODE_672_length_480_cov_1.114206:1-480 [pilon] Processing NODE_930_length_243_cov_43.418033:1-243 [pilon] NODE_50_length_3332_cov_18.815634:1-3332 log: [pilon] frags shovill.bam: coverage 56 [pilon] Total Reads: 1442, Coverage: 56, minDepth: 14 [pilon] Confirmed 2342 of 3332 bases (70.29%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_50_length_3332_cov_18.815634:1-3332 [pilon] Processing NODE_876_length_409_cov_0.697917:1-409 [pilon] Processing NODE_312_length_654_cov_7.894934:1-654 [pilon] Processing NODE_258_length_697_cov_6.779514:1-697 [pilon] NODE_672_length_480_cov_1.114206:1-480 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 480 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_672_length_480_cov_1.114206:1-480 [pilon] Processing NODE_693_length_472_cov_2.629630:1-472 [pilon] NODE_930_length_243_cov_43.418033:1-243 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 101, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 243 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_930_length_243_cov_43.418033:1-243 [pilon] Processing NODE_788_length_438_cov_1.712934:1-438 [pilon] NODE_876_length_409_cov_0.697917:1-409 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 2, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 409 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_876_length_409_cov_0.697917:1-409 [pilon] Processing NODE_566_length_519_cov_1.587940:1-519 [pilon] NODE_312_length_654_cov_7.894934:1-654 log: [pilon] frags shovill.bam: coverage 20 [pilon] Total Reads: 100, Coverage: 20, minDepth: 5 [pilon] Confirmed 518 of 654 bases (79.20%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_312_length_654_cov_7.894934:1-654 [pilon] Processing NODE_643_length_492_cov_1.210243:1-492 [pilon] NODE_693_length_472_cov_2.629630:1-472 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 24, Coverage: 6, minDepth: 5 [pilon] Confirmed 291 of 472 bases (61.65%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_693_length_472_cov_2.629630:1-472 [pilon] Processing NODE_824_length_427_cov_3.235294:1-427 [pilon] NODE_258_length_697_cov_6.779514:1-697 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 93, Coverage: 17, minDepth: 5 [pilon] Confirmed 536 of 697 bases (76.90%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_258_length_697_cov_6.779514:1-697 [pilon] Processing NODE_854_length_418_cov_0.653199:1-418 [pilon] NODE_788_length_438_cov_1.712934:1-438 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 17, Coverage: 4, minDepth: 5 [pilon] Confirmed 208 of 438 bases (47.49%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_788_length_438_cov_1.712934:1-438 [pilon] Processing NODE_818_length_429_cov_3.509740:1-429 [pilon] NODE_824_length_427_cov_3.235294:1-427 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 19, Coverage: 5, minDepth: 5 [pilon] Confirmed 237 of 427 bases (55.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_824_length_427_cov_3.235294:1-427 [pilon] Processing NODE_837_length_423_cov_4.079470:1-423 [pilon] NODE_566_length_519_cov_1.587940:1-519 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 98 of 519 bases (18.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_566_length_519_cov_1.587940:1-519 [pilon] Processing NODE_397_length_600_cov_1.826722:1-600 [pilon] NODE_643_length_492_cov_1.210243:1-492 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 201 of 492 bases (40.85%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_643_length_492_cov_1.210243:1-492 [pilon] Processing NODE_724_length_462_cov_0.718475:1-462 [pilon] NODE_837_length_423_cov_4.079470:1-423 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 25, Coverage: 5, minDepth: 5 [pilon] Confirmed 209 of 423 bases (49.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_837_length_423_cov_4.079470:1-423 [pilon] Processing NODE_853_length_418_cov_1.835017:1-418 [pilon] NODE_854_length_418_cov_0.653199:1-418 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 418 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_854_length_418_cov_0.653199:1-418 [pilon] Processing NODE_20_length_85280_cov_39.769913:1-85280 [pilon] NODE_818_length_429_cov_3.509740:1-429 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 42, Coverage: 7, minDepth: 5 [pilon] Confirmed 212 of 429 bases (49.42%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_818_length_429_cov_3.509740:1-429 [pilon] Processing NODE_7_length_261794_cov_36.956113:1-261794 [pilon] NODE_397_length_600_cov_1.826722:1-600 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 28, Coverage: 6, minDepth: 5 [pilon] Confirmed 308 of 600 bases (51.33%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_397_length_600_cov_1.826722:1-600 [pilon] Processing NODE_608_length_505_cov_2.986979:1-505 [pilon] NODE_724_length_462_cov_0.718475:1-462 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 14, Coverage: 3, minDepth: 5 [pilon] Confirmed 146 of 462 bases (31.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_724_length_462_cov_0.718475:1-462 [pilon] Processing NODE_315_length_652_cov_14.425612:1-652 [pilon] NODE_853_length_418_cov_1.835017:1-418 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 17, Coverage: 5, minDepth: 5 [pilon] Confirmed 264 of 418 bases (63.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_853_length_418_cov_1.835017:1-418 [pilon] Processing NODE_703_length_470_cov_1.630372:1-470 [pilon] NODE_608_length_505_cov_2.986979:1-505 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 34, Coverage: 9, minDepth: 5 [pilon] Confirmed 311 of 505 bases (61.58%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_608_length_505_cov_2.986979:1-505 [pilon] Processing NODE_476_length_561_cov_3.343182:1-561 [pilon] NODE_703_length_470_cov_1.630372:1-470 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 25, Coverage: 7, minDepth: 5 [pilon] Confirmed 237 of 470 bases (50.43%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_703_length_470_cov_1.630372:1-470 [pilon] Processing NODE_678_length_478_cov_1.873950:1-478 [pilon] NODE_678_length_478_cov_1.873950:1-478 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 24, Coverage: 5, minDepth: 5 [pilon] Confirmed 229 of 478 bases (47.91%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_678_length_478_cov_1.873950:1-478 [pilon] Processing NODE_585_length_513_cov_2.102041:1-513 [pilon] NODE_315_length_652_cov_14.425612:1-652 log: [pilon] frags shovill.bam: coverage 32 [pilon] Total Reads: 163, Coverage: 32, minDepth: 8 [pilon] Confirmed 538 of 652 bases (82.52%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_315_length_652_cov_14.425612:1-652 [pilon] Processing NODE_99_length_1136_cov_38.045320:1-1136 [pilon] NODE_476_length_561_cov_3.343182:1-561 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 38, Coverage: 9, minDepth: 5 [pilon] Confirmed 296 of 561 bases (52.76%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_476_length_561_cov_3.343182:1-561 [pilon] Processing NODE_119_length_983_cov_1.813225:1-983 [pilon] NODE_585_length_513_cov_2.102041:1-513 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 22, Coverage: 6, minDepth: 5 [pilon] Confirmed 282 of 513 bases (54.97%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_585_length_513_cov_2.102041:1-513 [pilon] Processing NODE_623_length_498_cov_5.785146:1-498 [pilon] NODE_623_length_498_cov_5.785146:1-498 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 58, Coverage: 15, minDepth: 5 [pilon] Confirmed 390 of 498 bases (78.31%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_623_length_498_cov_5.785146:1-498 [pilon] Processing NODE_665_length_482_cov_7.817175:1-482 [pilon] NODE_119_length_983_cov_1.813225:1-983 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 33, Coverage: 4, minDepth: 5 [pilon] Confirmed 403 of 983 bases (41.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_119_length_983_cov_1.813225:1-983 [pilon] Processing NODE_528_length_538_cov_1.446043:1-538 [pilon] NODE_99_length_1136_cov_38.045320:1-1136 log: [pilon] frags shovill.bam: coverage 96 [pilon] Total Reads: 837, Coverage: 96, minDepth: 24 [pilon] Confirmed 790 of 1136 bases (69.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_99_length_1136_cov_38.045320:1-1136 [pilon] Processing NODE_575_length_517_cov_1.606061:1-517 [pilon] NODE_665_length_482_cov_7.817175:1-482 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 64, Coverage: 14, minDepth: 5 [pilon] Confirmed 288 of 482 bases (59.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_665_length_482_cov_7.817175:1-482 [pilon] Processing NODE_840_length_422_cov_1.694352:1-422 [pilon] NODE_528_length_538_cov_1.446043:1-538 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 14, Coverage: 3, minDepth: 5 [pilon] Confirmed 158 of 538 bases (29.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_528_length_538_cov_1.446043:1-538 [pilon] Processing NODE_334_length_642_cov_2.654511:1-642 [pilon] NODE_575_length_517_cov_1.606061:1-517 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 21, Coverage: 3, minDepth: 5 [pilon] Confirmed 136 of 517 bases (26.31%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_575_length_517_cov_1.606061:1-517 [pilon] Processing NODE_391_length_604_cov_1.165631:1-604 [pilon] NODE_840_length_422_cov_1.694352:1-422 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 118 of 422 bases (27.96%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_840_length_422_cov_1.694352:1-422 [pilon] Processing NODE_311_length_655_cov_2.867041:1-655 [pilon] NODE_334_length_642_cov_2.654511:1-642 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 30, Coverage: 6, minDepth: 5 [pilon] Confirmed 355 of 642 bases (55.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_334_length_642_cov_2.654511:1-642 [pilon] Processing NODE_774_length_442_cov_1.616822:1-442 [pilon] NODE_391_length_604_cov_1.165631:1-604 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 18, Coverage: 3, minDepth: 5 [pilon] Confirmed 178 of 604 bases (29.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_391_length_604_cov_1.165631:1-604 [pilon] Processing NODE_935_length_124_cov_143.000000:1-124 [pilon] NODE_311_length_655_cov_2.867041:1-655 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 37, Coverage: 7, minDepth: 5 [pilon] Confirmed 466 of 655 bases (71.15%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_311_length_655_cov_2.867041:1-655 [pilon] Processing NODE_284_length_674_cov_0.871609:1-674 [pilon] NODE_935_length_124_cov_143.000000:1-124 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 0, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 124 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_935_length_124_cov_143.000000:1-124 [pilon] Processing NODE_62_length_2174_cov_30.686800:1-2174 [pilon] NODE_774_length_442_cov_1.616822:1-442 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 170 of 442 bases (38.46%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_774_length_442_cov_1.616822:1-442 [pilon] Processing NODE_398_length_600_cov_1.668058:1-600 [pilon] NODE_284_length_674_cov_0.871609:1-674 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 16, Coverage: 3, minDepth: 5 [pilon] Confirmed 218 of 674 bases (32.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_284_length_674_cov_0.871609:1-674 [pilon] Processing NODE_481_length_559_cov_3.180365:1-559 [pilon] NODE_398_length_600_cov_1.668058:1-600 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 23, Coverage: 5, minDepth: 5 [pilon] Confirmed 269 of 600 bases (44.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_398_length_600_cov_1.668058:1-600 [pilon] Processing NODE_83_length_1292_cov_5.887276:1-1292 [pilon] NODE_481_length_559_cov_3.180365:1-559 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 40, Coverage: 9, minDepth: 5 [pilon] Confirmed 342 of 559 bases (61.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_481_length_559_cov_3.180365:1-559 [pilon] Processing NODE_652_length_487_cov_7.292350:1-487 [pilon] NODE_83_length_1292_cov_5.887276:1-1292 log: [pilon] frags shovill.bam: coverage 23 [pilon] Total Reads: 232, Coverage: 23, minDepth: 6 [pilon] Confirmed 1082 of 1292 bases (83.75%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_83_length_1292_cov_5.887276:1-1292 [pilon] Processing NODE_919_length_293_cov_34.162791:1-293 [pilon] NODE_62_length_2174_cov_30.686800:1-2174 log: [pilon] frags shovill.bam: coverage 91 [pilon] Total Reads: 1523, Coverage: 91, minDepth: 23 [pilon] Confirmed 1782 of 2174 bases (81.97%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_62_length_2174_cov_30.686800:1-2174 [pilon] Processing NODE_314_length_653_cov_1.436090:1-653 [pilon] NODE_652_length_487_cov_7.292350:1-487 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 77, Coverage: 21, minDepth: 5 [pilon] Confirmed 405 of 487 bases (83.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_652_length_487_cov_7.292350:1-487 [pilon] Processing NODE_382_length_609_cov_3.040984:1-609 [pilon] NODE_382_length_609_cov_3.040984:1-609 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 50, Coverage: 11, minDepth: 5 [pilon] Confirmed 449 of 609 bases (73.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_382_length_609_cov_3.040984:1-609 [pilon] Processing NODE_687_length_474_cov_1.000000:1-474 [pilon] NODE_919_length_293_cov_34.162791:1-293 log: [pilon] frags shovill.bam: coverage 23 [pilon] Total Reads: 162, Coverage: 23, minDepth: 6 [pilon] Confirmed 235 of 293 bases (80.20%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_919_length_293_cov_34.162791:1-293 [pilon] Processing NODE_651_length_488_cov_0.828338:1-488 [pilon] NODE_314_length_653_cov_1.436090:1-653 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 18, Coverage: 2, minDepth: 5 [pilon] Confirmed 53 of 653 bases (8.12%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_314_length_653_cov_1.436090:1-653 [pilon] Processing NODE_195_length_763_cov_4.828660:1-763 [pilon] NODE_651_length_488_cov_0.828338:1-488 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 89 of 488 bases (18.24%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_651_length_488_cov_0.828338:1-488 [pilon] Processing NODE_352_length_628_cov_16.928994:1-628 [pilon] NODE_687_length_474_cov_1.000000:1-474 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 9, Coverage: 2, minDepth: 5 [pilon] Confirmed 32 of 474 bases (6.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_687_length_474_cov_1.000000:1-474 [pilon] Processing NODE_19_length_86850_cov_37.116951:1-86850 [pilon] NODE_195_length_763_cov_4.828660:1-763 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 68, Coverage: 12, minDepth: 5 [pilon] Confirmed 487 of 763 bases (63.83%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_195_length_763_cov_4.828660:1-763 [pilon] Processing NODE_21_length_80035_cov_40.956891:1-80035 [pilon] NODE_352_length_628_cov_16.928994:1-628 log: [pilon] frags shovill.bam: coverage 45 [pilon] Total Reads: 218, Coverage: 45, minDepth: 11 [pilon] Confirmed 524 of 628 bases (83.44%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_352_length_628_cov_16.928994:1-628 [pilon] Processing NODE_809_length_432_cov_4.299035:1-432 [pilon] NODE_809_length_432_cov_4.299035:1-432 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 30, Coverage: 9, minDepth: 5 [pilon] Confirmed 301 of 432 bases (69.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_809_length_432_cov_4.299035:1-432 [pilon] Processing NODE_671_length_481_cov_2.166667:1-481 [pilon] NODE_671_length_481_cov_2.166667:1-481 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 20, Coverage: 5, minDepth: 5 [pilon] Confirmed 259 of 481 bases (53.85%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_671_length_481_cov_2.166667:1-481 [pilon] Processing NODE_747_length_452_cov_1.981873:1-452 [pilon] NODE_747_length_452_cov_1.981873:1-452 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 163 of 452 bases (36.06%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_747_length_452_cov_1.981873:1-452 [pilon] Processing NODE_599_length_508_cov_1.232558:1-508 [pilon] NODE_599_length_508_cov_1.232558:1-508 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 26, Coverage: 5, minDepth: 5 [pilon] Confirmed 199 of 508 bases (39.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_599_length_508_cov_1.232558:1-508 [pilon] Processing NODE_865_length_414_cov_0.641638:1-414 [pilon] NODE_865_length_414_cov_0.641638:1-414 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 5, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 414 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_865_length_414_cov_0.641638:1-414 [pilon] Processing NODE_122_length_955_cov_0.471223:1-955 [pilon] NODE_122_length_955_cov_0.471223:1-955 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 17, Coverage: 2, minDepth: 5 [pilon] Confirmed 4 of 955 bases (0.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_122_length_955_cov_0.471223:1-955 [pilon] Processing NODE_291_length_671_cov_4.807273:1-671 [pilon] NODE_291_length_671_cov_4.807273:1-671 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 67, Coverage: 13, minDepth: 5 [pilon] Confirmed 551 of 671 bases (82.12%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_291_length_671_cov_4.807273:1-671 [pilon] Processing NODE_503_length_550_cov_3.997669:1-550 [pilon] NODE_28_length_36726_cov_35.802459:1-36726 log: [pilon] frags shovill.bam: coverage 109 [pilon] Total Reads: 31089, Coverage: 109, minDepth: 27 [pilon] Confirmed 35835 of 36726 bases (97.57%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_28_length_36726_cov_35.802459:1-36726 [pilon] Processing NODE_359_length_624_cov_2.216700:1-624 [pilon] NODE_503_length_550_cov_3.997669:1-550 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 40, Coverage: 9, minDepth: 5 [pilon] Confirmed 428 of 550 bases (77.82%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_503_length_550_cov_3.997669:1-550 [pilon] Processing NODE_432_length_582_cov_5.616052:1-582 [pilon] NODE_359_length_624_cov_2.216700:1-624 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 38, Coverage: 8, minDepth: 5 [pilon] Confirmed 419 of 624 bases (67.15%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_359_length_624_cov_2.216700:1-624 [pilon] Processing NODE_525_length_541_cov_1.269048:1-541 [pilon] NODE_26_length_42055_cov_41.688606:1-42055 log: [pilon] frags shovill.bam: coverage 127 [pilon] Total Reads: 41437, Coverage: 127, minDepth: 32 [pilon] Confirmed 41744 of 42055 bases (99.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_26_length_42055_cov_41.688606:1-42055 [pilon] Processing NODE_215_length_741_cov_5.527419:1-741 [pilon] NODE_432_length_582_cov_5.616052:1-582 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 70, Coverage: 16, minDepth: 5 [pilon] Confirmed 456 of 582 bases (78.35%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_432_length_582_cov_5.616052:1-582 [pilon] Processing NODE_220_length_739_cov_4.432039:1-739 [pilon] NODE_525_length_541_cov_1.269048:1-541 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 18, Coverage: 4, minDepth: 5 [pilon] Confirmed 184 of 541 bases (34.01%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_525_length_541_cov_1.269048:1-541 [pilon] Processing NODE_777_length_442_cov_1.336449:1-442 [pilon] NODE_23_length_65675_cov_40.839644:1-65675 log: [pilon] frags shovill.bam: coverage 125 [pilon] Total Reads: 63413, Coverage: 125, minDepth: 31 [pilon] Confirmed 64967 of 65675 bases (98.92%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_23_length_65675_cov_40.839644:1-65675 [pilon] Processing NODE_683_length_476_cov_3.591549:1-476 [pilon] NODE_215_length_741_cov_5.527419:1-741 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 106, Coverage: 18, minDepth: 5 [pilon] Confirmed 528 of 741 bases (71.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_215_length_741_cov_5.527419:1-741 [pilon] Processing NODE_584_length_513_cov_2.403061:1-513 [pilon] NODE_777_length_442_cov_1.336449:1-442 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 12, Coverage: 4, minDepth: 5 [pilon] Confirmed 148 of 442 bases (33.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_777_length_442_cov_1.336449:1-442 [pilon] Processing NODE_75_length_1476_cov_5.915867:1-1476 [pilon] NODE_220_length_739_cov_4.432039:1-739 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 74, Coverage: 11, minDepth: 5 [pilon] Confirmed 442 of 739 bases (59.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_220_length_739_cov_4.432039:1-739 [pilon] Processing NODE_860_length_415_cov_1.057823:1-415 [pilon] NODE_683_length_476_cov_3.591549:1-476 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 34, Coverage: 9, minDepth: 5 [pilon] Confirmed 339 of 476 bases (71.22%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_683_length_476_cov_3.591549:1-476 [pilon] Processing NODE_297_length_666_cov_8.636697:1-666 [pilon] NODE_584_length_513_cov_2.403061:1-513 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 29, Coverage: 7, minDepth: 5 [pilon] Confirmed 285 of 513 bases (55.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_584_length_513_cov_2.403061:1-513 [pilon] NODE_860_length_415_cov_1.057823:1-415 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 415 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_860_length_415_cov_1.057823:1-415 [pilon] Processing NODE_389_length_604_cov_4.391304:1-604 [pilon] NODE_75_length_1476_cov_5.915867:1-1476 log: [pilon] frags shovill.bam: coverage 23 [pilon] Total Reads: 269, Coverage: 23, minDepth: 6 [pilon] Confirmed 925 of 1476 bases (62.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_75_length_1476_cov_5.915867:1-1476 [pilon] Processing NODE_609_length_505_cov_1.932292:1-505 [pilon] NODE_389_length_604_cov_4.391304:1-604 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 48, Coverage: 10, minDepth: 5 [pilon] Confirmed 503 of 604 bases (83.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_389_length_604_cov_4.391304:1-604 [pilon] Processing NODE_850_length_419_cov_1.157718:1-419 [pilon] NODE_297_length_666_cov_8.636697:1-666 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 133, Coverage: 21, minDepth: 5 [pilon] Confirmed 560 of 666 bases (84.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_297_length_666_cov_8.636697:1-666 [pilon] Processing NODE_895_length_405_cov_0.510563:1-405 [pilon] NODE_609_length_505_cov_1.932292:1-505 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 18, Coverage: 5, minDepth: 5 [pilon] Confirmed 251 of 505 bases (49.70%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_609_length_505_cov_1.932292:1-505 [pilon] Processing NODE_855_length_417_cov_1.611486:1-417 [pilon] NODE_850_length_419_cov_1.157718:1-419 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 127 of 419 bases (30.31%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_850_length_419_cov_1.157718:1-419 [pilon] Processing NODE_417_length_592_cov_2.675159:1-592 [pilon] NODE_895_length_405_cov_0.510563:1-405 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 7, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 405 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_895_length_405_cov_0.510563:1-405 [pilon] Processing NODE_874_length_410_cov_2.944637:1-410 [pilon] NODE_855_length_417_cov_1.611486:1-417 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 122 of 417 bases (29.26%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_855_length_417_cov_1.611486:1-417 [pilon] NODE_417_length_592_cov_2.675159:1-592 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 28, Coverage: 6, minDepth: 5 [pilon] Confirmed 267 of 592 bases (45.10%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_417_length_592_cov_2.675159:1-592 [pilon] Processing NODE_77_length_1411_cov_3.496124:1-1411 [pilon] NODE_874_length_410_cov_2.944637:1-410 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 24, Coverage: 5, minDepth: 5 [pilon] Confirmed 195 of 410 bases (47.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_874_length_410_cov_2.944637:1-410 [pilon] Processing NODE_619_length_501_cov_2.636842:1-501 [pilon] NODE_18_length_88019_cov_41.386914:1-88019 log: [pilon] frags shovill.bam: coverage 127 [pilon] Total Reads: 86358, Coverage: 127, minDepth: 32 [pilon] Confirmed 87479 of 88019 bases (99.39%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_18_length_88019_cov_41.386914:1-88019 [pilon] Processing NODE_861_length_414_cov_2.470990:1-414 [pilon] NODE_17_length_89057_cov_42.425002:1-89057 log: [pilon] frags shovill.bam: coverage 130 [pilon] Total Reads: 89298, Coverage: 130, minDepth: 33 [pilon] Confirmed 87341 of 89057 bases (98.07%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_17_length_89057_cov_42.425002:1-89057 [pilon] Processing NODE_289_length_671_cov_7.592727:1-671 [pilon] NODE_16_length_93240_cov_43.502379:1-93240 log: [pilon] frags shovill.bam: coverage 133 [pilon] Total Reads: 96055, Coverage: 133, minDepth: 33 [pilon] Confirmed 92928 of 93240 bases (99.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_16_length_93240_cov_43.502379:1-93240 [pilon] Processing NODE_583_length_514_cov_1.720102:1-514 [pilon] NODE_77_length_1411_cov_3.496124:1-1411 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 113, Coverage: 10, minDepth: 5 [pilon] Confirmed 1006 of 1411 bases (71.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_77_length_1411_cov_3.496124:1-1411 [pilon] Processing NODE_91_length_1210_cov_1.355372:1-1210 [pilon] NODE_619_length_501_cov_2.636842:1-501 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 23, Coverage: 6, minDepth: 5 [pilon] Confirmed 241 of 501 bases (48.10%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_619_length_501_cov_2.636842:1-501 [pilon] Processing NODE_759_length_447_cov_0.871166:1-447 [pilon] NODE_861_length_414_cov_2.470990:1-414 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 16, Coverage: 5, minDepth: 5 [pilon] Confirmed 187 of 414 bases (45.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_861_length_414_cov_2.470990:1-414 [pilon] Processing NODE_610_length_505_cov_1.351562:1-505 [pilon] NODE_289_length_671_cov_7.592727:1-671 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 94, Coverage: 18, minDepth: 5 [pilon] Confirmed 515 of 671 bases (76.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_289_length_671_cov_7.592727:1-671 [pilon] Processing NODE_743_length_454_cov_0.693694:1-454 [pilon] NODE_583_length_514_cov_1.720102:1-514 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 18, Coverage: 5, minDepth: 5 [pilon] Confirmed 159 of 514 bases (30.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_583_length_514_cov_1.720102:1-514 [pilon] Processing NODE_405_length_597_cov_3.039916:1-597 [pilon] NODE_759_length_447_cov_0.871166:1-447 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 447 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_759_length_447_cov_0.871166:1-447 [pilon] Processing NODE_341_length_639_cov_4.073359:1-639 [pilon] NODE_91_length_1210_cov_1.355372:1-1210 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 39, Coverage: 4, minDepth: 5 [pilon] Confirmed 515 of 1210 bases (42.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_91_length_1210_cov_1.355372:1-1210 [pilon] Processing NODE_295_length_668_cov_2.533821:1-668 [pilon] Processing NODE_682_length_477_cov_1.047753:1-477 [pilon] NODE_610_length_505_cov_1.351562:1-505 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 146 of 505 bases (28.91%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_610_length_505_cov_1.351562:1-505 [pilon] Processing NODE_741_length_454_cov_3.621622:1-454 [pilon] NODE_743_length_454_cov_0.693694:1-454 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 454 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_743_length_454_cov_0.693694:1-454 [pilon] Processing NODE_214_length_741_cov_13.583871:1-741 [pilon] NODE_405_length_597_cov_3.039916:1-597 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 40, Coverage: 9, minDepth: 5 [pilon] Confirmed 433 of 597 bases (72.53%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_405_length_597_cov_3.039916:1-597 [pilon] Processing NODE_570_length_518_cov_4.511335:1-518 [pilon] NODE_24_length_58446_cov_40.223472:1-58446 log: [pilon] frags shovill.bam: coverage 123 [pilon] Total Reads: 55719, Coverage: 123, minDepth: 31 [pilon] Confirmed 56676 of 58446 bases (96.97%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_24_length_58446_cov_40.223472:1-58446 [pilon] NODE_295_length_668_cov_2.533821:1-668 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 52, Coverage: 10, minDepth: 5 [pilon] Confirmed 438 of 668 bases (65.57%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_295_length_668_cov_2.533821:1-668 [pilon] Processing NODE_431_length_583_cov_5.699134:1-583 [pilon] NODE_682_length_477_cov_1.047753:1-477 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 124 of 477 bases (26.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_682_length_477_cov_1.047753:1-477 [pilon] Processing NODE_294_length_668_cov_4.166362:1-668 [pilon] NODE_341_length_639_cov_4.073359:1-639 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 74, Coverage: 15, minDepth: 5 [pilon] Confirmed 507 of 639 bases (79.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_341_length_639_cov_4.073359:1-639 [pilon] NODE_741_length_454_cov_3.621622:1-454 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 23, Coverage: 7, minDepth: 5 [pilon] Confirmed 253 of 454 bases (55.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_741_length_454_cov_3.621622:1-454 [pilon] NODE_214_length_741_cov_13.583871:1-741 log: [pilon] frags shovill.bam: coverage 34 [pilon] Total Reads: 198, Coverage: 34, minDepth: 9 [pilon] Confirmed 572 of 741 bases (77.19%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_214_length_741_cov_13.583871:1-741 [pilon] Processing NODE_166_length_811_cov_9.781159:1-811 [pilon] NODE_570_length_518_cov_4.511335:1-518 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 61, Coverage: 15, minDepth: 5 [pilon] Confirmed 413 of 518 bases (79.73%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_570_length_518_cov_4.511335:1-518 [pilon] Processing NODE_103_length_1073_cov_3.695378:1-1073 [pilon] NODE_431_length_583_cov_5.699134:1-583 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 96, Coverage: 21, minDepth: 5 [pilon] Confirmed 494 of 583 bases (84.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_431_length_583_cov_5.699134:1-583 [pilon] Processing NODE_659_length_485_cov_1.793956:1-485 [pilon] NODE_294_length_668_cov_4.166362:1-668 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 57, Coverage: 9, minDepth: 5 [pilon] Confirmed 521 of 668 bases (77.99%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_294_length_668_cov_4.166362:1-668 [pilon] Processing NODE_556_length_526_cov_1.901235:1-526 [pilon] NODE_166_length_811_cov_9.781159:1-811 log: [pilon] frags shovill.bam: coverage 32 [pilon] Total Reads: 202, Coverage: 32, minDepth: 8 [pilon] Confirmed 536 of 811 bases (66.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_166_length_811_cov_9.781159:1-811 [pilon] Processing NODE_124_length_952_cov_5.531889:1-952 [pilon] NODE_103_length_1073_cov_3.695378:1-1073 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 106, Coverage: 13, minDepth: 5 [pilon] Confirmed 755 of 1073 bases (70.36%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_103_length_1073_cov_3.695378:1-1073 [pilon] Processing NODE_685_length_474_cov_1.252125:1-474 [pilon] NODE_556_length_526_cov_1.901235:1-526 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 28, Coverage: 7, minDepth: 5 [pilon] Confirmed 303 of 526 bases (57.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_556_length_526_cov_1.901235:1-526 [pilon] Processing NODE_918_length_294_cov_139.098266:1-294 [pilon] NODE_659_length_485_cov_1.793956:1-485 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 22, Coverage: 6, minDepth: 5 [pilon] Confirmed 276 of 485 bases (56.91%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_659_length_485_cov_1.793956:1-485 [pilon] Processing NODE_490_length_555_cov_3.237327:1-555 [pilon] NODE_124_length_952_cov_5.531889:1-952 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 148, Coverage: 18, minDepth: 5 [pilon] Confirmed 618 of 952 bases (64.92%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_124_length_952_cov_5.531889:1-952 [pilon] Processing NODE_832_length_425_cov_1.098684:1-425 [pilon] NODE_685_length_474_cov_1.252125:1-474 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 17, Coverage: 4, minDepth: 5 [pilon] Confirmed 201 of 474 bases (42.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_685_length_474_cov_1.252125:1-474 [pilon] Processing NODE_849_length_419_cov_2.194631:1-419 [pilon] NODE_15_length_107429_cov_46.392263:1-107429 log: [pilon] frags shovill.bam: coverage 142 [pilon] Total Reads: 118157, Coverage: 142, minDepth: 36 [pilon] Confirmed 106799 of 107429 bases (99.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_15_length_107429_cov_46.392263:1-107429 [pilon] NODE_918_length_294_cov_139.098266:1-294 log: [pilon] frags shovill.bam: coverage 47 [pilon] Total Reads: 560, Coverage: 47, minDepth: 12 [pilon] Confirmed 249 of 294 bases (84.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_918_length_294_cov_139.098266:1-294 [pilon] NODE_832_length_425_cov_1.098684:1-425 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 13, Coverage: 3, minDepth: 5 [pilon] Confirmed 83 of 425 bases (19.53%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_832_length_425_cov_1.098684:1-425 [pilon] Processing NODE_925_length_243_cov_51.655738:1-243 [pilon] NODE_490_length_555_cov_3.237327:1-555 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 33, Coverage: 8, minDepth: 5 [pilon] Confirmed 374 of 555 bases (67.39%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_490_length_555_cov_3.237327:1-555 [pilon] NODE_849_length_419_cov_2.194631:1-419 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 13, Coverage: 4, minDepth: 5 [pilon] Confirmed 203 of 419 bases (48.45%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_849_length_419_cov_2.194631:1-419 [pilon] Processing NODE_37_length_8057_cov_33.363911:1-8057 [pilon] NODE_925_length_243_cov_51.655738:1-243 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 152, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 243 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_925_length_243_cov_51.655738:1-243 [pilon] NODE_37_length_8057_cov_33.363911:1-8057 log: [pilon] frags shovill.bam: coverage 101 [pilon] Total Reads: 6315, Coverage: 101, minDepth: 25 [pilon] Confirmed 7350 of 8057 bases (91.23%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_37_length_8057_cov_33.363911:1-8057 [pilon] Processing NODE_515_length_547_cov_2.814554:1-547 [pilon] NODE_515_length_547_cov_2.814554:1-547 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 30, Coverage: 7, minDepth: 5 [pilon] Confirmed 406 of 547 bases (74.22%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_515_length_547_cov_2.814554:1-547 [pilon] Processing NODE_801_length_435_cov_0.898089:1-435 [pilon] NODE_801_length_435_cov_0.898089:1-435 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 11, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 435 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_801_length_435_cov_0.898089:1-435 [pilon] NODE_20_length_85280_cov_39.769913:1-85280 log: [pilon] frags shovill.bam: coverage 122 [pilon] Total Reads: 80200, Coverage: 122, minDepth: 31 [pilon] Confirmed 84709 of 85280 bases (99.33%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_20_length_85280_cov_39.769913:1-85280 [pilon] NODE_14_length_120159_cov_46.979490:1-120159 log: [pilon] frags shovill.bam: coverage 144 [pilon] Total Reads: 134422, Coverage: 144, minDepth: 36 [pilon] Confirmed 120018 of 120159 bases (99.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_14_length_120159_cov_46.979490:1-120159 [pilon] Processing NODE_928_length_243_cov_45.540984:1-243 [pilon] NODE_928_length_243_cov_45.540984:1-243 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 30, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 243 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_928_length_243_cov_45.540984:1-243 [pilon] Processing NODE_179_length_791_cov_7.877612:1-791 [pilon] NODE_179_length_791_cov_7.877612:1-791 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 128, Coverage: 21, minDepth: 5 [pilon] Confirmed 580 of 791 bases (73.32%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_179_length_791_cov_7.877612:1-791 [pilon] Processing NODE_244_length_708_cov_7.870528:1-708 [pilon] NODE_244_length_708_cov_7.870528:1-708 log: [pilon] frags shovill.bam: coverage 23 [pilon] Total Reads: 129, Coverage: 23, minDepth: 6 [pilon] Confirmed 522 of 708 bases (73.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_244_length_708_cov_7.870528:1-708 [pilon] Processing NODE_722_length_462_cov_4.020528:1-462 [pilon] NODE_722_length_462_cov_4.020528:1-462 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 36, Coverage: 9, minDepth: 5 [pilon] Confirmed 301 of 462 bases (65.15%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_722_length_462_cov_4.020528:1-462 [pilon] Processing NODE_744_length_453_cov_1.325301:1-453 [pilon] NODE_744_length_453_cov_1.325301:1-453 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 21, Coverage: 6, minDepth: 5 [pilon] Confirmed 225 of 453 bases (49.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_744_length_453_cov_1.325301:1-453 [pilon] NODE_19_length_86850_cov_37.116951:1-86850 log: [pilon] frags shovill.bam: coverage 114 [pilon] Total Reads: 76618, Coverage: 114, minDepth: 29 [pilon] Confirmed 85550 of 86850 bases (98.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_19_length_86850_cov_37.116951:1-86850 [pilon] Processing NODE_882_length_408_cov_0.658537:1-408 [pilon] NODE_882_length_408_cov_0.658537:1-408 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 408 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_882_length_408_cov_0.658537:1-408 [pilon] NODE_21_length_80035_cov_40.956891:1-80035 log: [pilon] frags shovill.bam: coverage 126 [pilon] Total Reads: 77869, Coverage: 126, minDepth: 32 [pilon] Confirmed 78767 of 80035 bases (98.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_21_length_80035_cov_40.956891:1-80035 [pilon] Processing NODE_172_length_802_cov_1.509545:1-802 [pilon] NODE_172_length_802_cov_1.509545:1-802 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 30, Coverage: 5, minDepth: 5 [pilon] Confirmed 396 of 802 bases (49.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_172_length_802_cov_1.509545:1-802 [pilon] Processing NODE_649_length_488_cov_2.272480:1-488 [pilon] NODE_649_length_488_cov_2.272480:1-488 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 18, Coverage: 5, minDepth: 5 [pilon] Confirmed 194 of 488 bases (39.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_649_length_488_cov_2.272480:1-488 [pilon] Processing NODE_691_length_473_cov_1.085227:1-473 [pilon] NODE_691_length_473_cov_1.085227:1-473 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 63 of 473 bases (13.32%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_691_length_473_cov_1.085227:1-473 [pilon] NODE_12_length_161867_cov_46.822283:1-161867 log: [pilon] frags shovill.bam: coverage 143 [pilon] Total Reads: 179685, Coverage: 143, minDepth: 36 [pilon] Confirmed 161592 of 161867 bases (99.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_12_length_161867_cov_46.822283:1-161867 [pilon] Processing NODE_655_length_486_cov_5.709589:1-486 [pilon] NODE_655_length_486_cov_5.709589:1-486 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 45, Coverage: 9, minDepth: 5 [pilon] Confirmed 327 of 486 bases (67.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_655_length_486_cov_5.709589:1-486 [pilon] Processing NODE_375_length_614_cov_8.077079:1-614 [pilon] NODE_375_length_614_cov_8.077079:1-614 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 105, Coverage: 21, minDepth: 5 [pilon] Confirmed 372 of 614 bases (60.59%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_375_length_614_cov_8.077079:1-614 [pilon] NODE_13_length_131029_cov_39.753338:1-131029 log: [pilon] frags shovill.bam: coverage 122 [pilon] Total Reads: 123890, Coverage: 122, minDepth: 31 [pilon] Confirmed 129976 of 131029 bases (99.20%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_13_length_131029_cov_39.753338:1-131029 [pilon] Processing NODE_885_length_407_cov_1.398601:1-407 [pilon] NODE_885_length_407_cov_1.398601:1-407 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 11, Coverage: 2, minDepth: 5 [pilon] Confirmed 35 of 407 bases (8.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_885_length_407_cov_1.398601:1-407 [pilon] Processing NODE_210_length_744_cov_11.926164:1-744 [pilon] NODE_210_length_744_cov_11.926164:1-744 log: [pilon] frags shovill.bam: coverage 37 [pilon] Total Reads: 214, Coverage: 37, minDepth: 9 [pilon] Confirmed 569 of 744 bases (76.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_210_length_744_cov_11.926164:1-744 [pilon] Processing NODE_183_length_781_cov_9.374242:1-781 [pilon] NODE_183_length_781_cov_9.374242:1-781 log: [pilon] frags shovill.bam: coverage 26 [pilon] Total Reads: 158, Coverage: 26, minDepth: 7 [pilon] Confirmed 566 of 781 bases (72.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_183_length_781_cov_9.374242:1-781 [pilon] Processing NODE_547_length_529_cov_2.970588:1-529 [pilon] NODE_547_length_529_cov_2.970588:1-529 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 35, Coverage: 8, minDepth: 5 [pilon] Confirmed 386 of 529 bases (72.97%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_547_length_529_cov_2.970588:1-529 [pilon] NODE_9_length_223393_cov_42.039651:1-223393 log: [pilon] frags shovill.bam: coverage 129 [pilon] Total Reads: 222267, Coverage: 129, minDepth: 32 [pilon] Confirmed 223025 of 223393 bases (99.84%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_9_length_223393_cov_42.039651:1-223393 [pilon] Processing NODE_413_length_594_cov_1.040169:1-594 [pilon] NODE_413_length_594_cov_1.040169:1-594 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 131 of 594 bases (22.05%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_413_length_594_cov_1.040169:1-594 [pilon] Processing NODE_611_length_503_cov_1.246073:1-503 [pilon] NODE_611_length_503_cov_1.246073:1-503 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 130 of 503 bases (25.84%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_611_length_503_cov_1.246073:1-503 [pilon] Processing NODE_718_length_464_cov_3.422741:1-464 [pilon] NODE_718_length_464_cov_3.422741:1-464 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 36, Coverage: 9, minDepth: 5 [pilon] Confirmed 259 of 464 bases (55.82%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_718_length_464_cov_3.422741:1-464 [pilon] Processing NODE_42_length_4672_cov_34.057570:1-4672 [pilon] NODE_42_length_4672_cov_34.057570:1-4672 log: [pilon] frags shovill.bam: coverage 100 [pilon] Total Reads: 3632, Coverage: 100, minDepth: 25 [pilon] Confirmed 4098 of 4672 bases (87.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_42_length_4672_cov_34.057570:1-4672 [pilon] Processing NODE_422_length_587_cov_4.302575:1-587 [pilon] NODE_422_length_587_cov_4.302575:1-587 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 62, Coverage: 14, minDepth: 5 [pilon] Confirmed 448 of 587 bases (76.32%) [pilon] Corrected 1 snps; 1 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_422_length_587_cov_4.302575:1-587 [pilon] NODE_8_length_244740_cov_43.085002:1-244740 log: [pilon] frags shovill.bam: coverage 132 [pilon] Total Reads: 249915, Coverage: 132, minDepth: 33 [pilon] Confirmed 244329 of 244740 bases (99.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_8_length_244740_cov_43.085002:1-244740 [pilon] NODE_10_length_218666_cov_45.518241:1-218666 log: [pilon] frags shovill.bam: coverage 140 [pilon] Total Reads: 236253, Coverage: 140, minDepth: 35 [pilon] Confirmed 218013 of 218666 bases (99.70%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_10_length_218666_cov_45.518241:1-218666 [pilon] Processing NODE_636_length_494_cov_2.922252:1-494 [pilon] NODE_636_length_494_cov_2.922252:1-494 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 28, Coverage: 7, minDepth: 5 [pilon] Confirmed 373 of 494 bases (75.51%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_636_length_494_cov_2.922252:1-494 [pilon] NODE_11_length_215661_cov_46.585335:1-215661 log: [pilon] frags shovill.bam: coverage 142 [pilon] Total Reads: 237556, Coverage: 142, minDepth: 36 [pilon] Confirmed 213951 of 215661 bases (99.21%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_11_length_215661_cov_46.585335:1-215661 [pilon] Processing NODE_323_length_648_cov_2.656546:1-648 [pilon] NODE_323_length_648_cov_2.656546:1-648 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 41, Coverage: 8, minDepth: 5 [pilon] Confirmed 453 of 648 bases (69.91%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_323_length_648_cov_2.656546:1-648 [pilon] Processing NODE_757_length_448_cov_1.134557:1-448 [pilon] NODE_757_length_448_cov_1.134557:1-448 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 104 of 448 bases (23.21%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_757_length_448_cov_1.134557:1-448 [pilon] Processing NODE_517_length_547_cov_1.286385:1-547 [pilon] NODE_517_length_547_cov_1.286385:1-547 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 18, Coverage: 4, minDepth: 5 [pilon] Confirmed 165 of 547 bases (30.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_517_length_547_cov_1.286385:1-547 [pilon] NODE_7_length_261794_cov_36.956113:1-261794 log: [pilon] frags shovill.bam: coverage 113 [pilon] Total Reads: 229153, Coverage: 113, minDepth: 28 [pilon] Confirmed 260470 of 261794 bases (99.49%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_7_length_261794_cov_36.956113:1-261794 [pilon] Processing NODE_614_length_503_cov_0.821990:1-503 [pilon] NODE_614_length_503_cov_0.821990:1-503 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 14, Coverage: 3, minDepth: 5 [pilon] Confirmed 108 of 503 bases (21.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_614_length_503_cov_0.821990:1-503 [pilon] Processing NODE_225_length_732_cov_6.176759:1-732 [pilon] NODE_225_length_732_cov_6.176759:1-732 log: [pilon] frags shovill.bam: coverage 19 [pilon] Total Reads: 109, Coverage: 19, minDepth: 5 [pilon] Confirmed 513 of 732 bases (70.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_225_length_732_cov_6.176759:1-732 [pilon] Processing NODE_373_length_616_cov_2.294949:1-616 [pilon] NODE_373_length_616_cov_2.294949:1-616 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 32, Coverage: 7, minDepth: 5 [pilon] Confirmed 331 of 616 bases (53.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_373_length_616_cov_2.294949:1-616 [pilon] NODE_3_length_343968_cov_36.406323:1-343968 log: [pilon] frags shovill.bam: coverage 111 [pilon] Total Reads: 296442, Coverage: 111, minDepth: 28 [pilon] Confirmed 343431 of 343968 bases (99.84%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_3_length_343968_cov_36.406323:1-343968 [pilon] Processing NODE_65_length_1936_cov_32.256198:1-1936 [pilon] NODE_4_length_326788_cov_39.039413:1-326788 log: [pilon] frags shovill.bam: coverage 119 [pilon] Total Reads: 302334, Coverage: 119, minDepth: 30 [pilon] Confirmed 324818 of 326788 bases (99.40%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_4_length_326788_cov_39.039413:1-326788 [pilon] Processing NODE_274_length_686_cov_1.407080:1-686 [pilon] NODE_274_length_686_cov_1.407080:1-686 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 22, Coverage: 4, minDepth: 5 [pilon] Confirmed 208 of 686 bases (30.32%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_274_length_686_cov_1.407080:1-686 [pilon] NODE_65_length_1936_cov_32.256198:1-1936 log: [pilon] frags shovill.bam: coverage 92 [pilon] Total Reads: 1377, Coverage: 92, minDepth: 23 [pilon] Confirmed 1599 of 1936 bases (82.59%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_65_length_1936_cov_32.256198:1-1936 [pilon] Processing NODE_414_length_593_cov_0.741525:1-593 [pilon] NODE_414_length_593_cov_0.741525:1-593 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 73 of 593 bases (12.31%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_414_length_593_cov_0.741525:1-593 [pilon] Processing NODE_488_length_556_cov_3.949425:1-556 [pilon] NODE_488_length_556_cov_3.949425:1-556 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 51, Coverage: 12, minDepth: 5 [pilon] Confirmed 303 of 556 bases (54.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_488_length_556_cov_3.949425:1-556 [pilon] Processing NODE_560_length_523_cov_3.296020:1-523 [pilon] NODE_560_length_523_cov_3.296020:1-523 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 37, Coverage: 9, minDepth: 5 [pilon] Confirmed 352 of 523 bases (67.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_560_length_523_cov_3.296020:1-523 [pilon] Processing NODE_676_length_479_cov_1.611732:1-479 [pilon] NODE_676_length_479_cov_1.611732:1-479 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 207 of 479 bases (43.22%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_676_length_479_cov_1.611732:1-479 [pilon] Processing NODE_674_length_479_cov_9.053073:1-479 [pilon] NODE_674_length_479_cov_9.053073:1-479 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 74, Coverage: 18, minDepth: 5 [pilon] Confirmed 368 of 479 bases (76.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_674_length_479_cov_9.053073:1-479 [pilon] Processing NODE_160_length_821_cov_8.034286:1-821 [pilon] NODE_160_length_821_cov_8.034286:1-821 log: [pilon] frags shovill.bam: coverage 31 [pilon] Total Reads: 196, Coverage: 31, minDepth: 8 [pilon] Confirmed 531 of 821 bases (64.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_160_length_821_cov_8.034286:1-821 [pilon] Processing NODE_463_length_568_cov_1.210291:1-568 [pilon] NODE_463_length_568_cov_1.210291:1-568 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 23 of 568 bases (4.05%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_463_length_568_cov_1.210291:1-568 [pilon] Processing NODE_377_length_613_cov_3.654472:1-613 [pilon] NODE_377_length_613_cov_3.654472:1-613 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 48, Coverage: 10, minDepth: 5 [pilon] Confirmed 436 of 613 bases (71.13%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_377_length_613_cov_3.654472:1-613 [pilon] Processing NODE_408_length_595_cov_3.504219:1-595 [pilon] NODE_408_length_595_cov_3.504219:1-595 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 37, Coverage: 8, minDepth: 5 [pilon] Confirmed 368 of 595 bases (61.85%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_408_length_595_cov_3.504219:1-595 [pilon] Processing NODE_263_length_693_cov_11.055944:1-693 [pilon] NODE_6_length_324215_cov_45.379603:1-324215 log: [pilon] frags shovill.bam: coverage 139 [pilon] Total Reads: 348856, Coverage: 139, minDepth: 35 [pilon] Confirmed 323210 of 324215 bases (99.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_6_length_324215_cov_45.379603:1-324215 [pilon] Processing NODE_618_length_501_cov_3.376316:1-501 [pilon] NODE_263_length_693_cov_11.055944:1-693 log: [pilon] frags shovill.bam: coverage 32 [pilon] Total Reads: 171, Coverage: 32, minDepth: 8 [pilon] Confirmed 542 of 693 bases (78.21%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_263_length_693_cov_11.055944:1-693 [pilon] Processing NODE_357_length_625_cov_1.605159:1-625 [pilon] NODE_618_length_501_cov_3.376316:1-501 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 37, Coverage: 9, minDepth: 5 [pilon] Confirmed 343 of 501 bases (68.46%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_618_length_501_cov_3.376316:1-501 [pilon] NODE_357_length_625_cov_1.605159:1-625 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 21, Coverage: 4, minDepth: 5 [pilon] Confirmed 270 of 625 bases (43.20%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_357_length_625_cov_1.605159:1-625 [pilon] Processing NODE_379_length_611_cov_1.889796:1-611 [pilon] NODE_379_length_611_cov_1.889796:1-611 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 25, Coverage: 5, minDepth: 5 [pilon] Confirmed 407 of 611 bases (66.61%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_379_length_611_cov_1.889796:1-611 [pilon] Processing NODE_749_length_451_cov_1.954545:1-451 [pilon] NODE_749_length_451_cov_1.954545:1-451 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 26, Coverage: 7, minDepth: 5 [pilon] Confirmed 282 of 451 bases (62.53%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_749_length_451_cov_1.954545:1-451 [pilon] NODE_5_length_326645_cov_43.335586:1-326645 log: [pilon] frags shovill.bam: coverage 133 [pilon] Total Reads: 335461, Coverage: 133, minDepth: 33 [pilon] Confirmed 324197 of 326645 bases (99.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_5_length_326645_cov_43.335586:1-326645 [pilon] Processing NODE_286_length_673_cov_2.041667:1-673 [pilon] NODE_286_length_673_cov_2.041667:1-673 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 34, Coverage: 6, minDepth: 5 [pilon] Confirmed 395 of 673 bases (58.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_286_length_673_cov_2.041667:1-673 [pilon] NODE_2_length_407886_cov_34.907846:1-407886 log: [pilon] frags shovill.bam: coverage 107 [pilon] Total Reads: 337518, Coverage: 107, minDepth: 27 [pilon] Confirmed 406538 of 407886 bases (99.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_2_length_407886_cov_34.907846:1-407886 [pilon] Processing NODE_235_length_716_cov_7.309244:1-716 [pilon] NODE_235_length_716_cov_7.309244:1-716 log: [pilon] frags shovill.bam: coverage 29 [pilon] Total Reads: 158, Coverage: 29, minDepth: 7 [pilon] Confirmed 478 of 716 bases (66.76%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_235_length_716_cov_7.309244:1-716 [pilon] Processing NODE_742_length_454_cov_0.879880:1-454 [pilon] NODE_742_length_454_cov_0.879880:1-454 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 6, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 454 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_742_length_454_cov_0.879880:1-454 [pilon] Processing NODE_668_length_482_cov_1.476454:1-482 [pilon] NODE_668_length_482_cov_1.476454:1-482 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 21, Coverage: 5, minDepth: 5 [pilon] Confirmed 202 of 482 bases (41.91%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_668_length_482_cov_1.476454:1-482 [pilon] Processing NODE_881_length_408_cov_1.121951:1-408 [pilon] NODE_881_length_408_cov_1.121951:1-408 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 408 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_881_length_408_cov_1.121951:1-408 [pilon] Processing NODE_181_length_788_cov_5.743628:1-788 [pilon] NODE_181_length_788_cov_5.743628:1-788 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 97, Coverage: 16, minDepth: 5 [pilon] Confirmed 536 of 788 bases (68.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_181_length_788_cov_5.743628:1-788 [pilon] Processing NODE_222_length_738_cov_1.311183:1-738 [pilon] NODE_222_length_738_cov_1.311183:1-738 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 38, Coverage: 7, minDepth: 5 [pilon] Confirmed 328 of 738 bases (44.44%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_222_length_738_cov_1.311183:1-738 [pilon] Processing NODE_814_length_430_cov_2.194175:1-430 [pilon] NODE_814_length_430_cov_2.194175:1-430 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 19, Coverage: 5, minDepth: 5 [pilon] Confirmed 213 of 430 bases (49.53%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_814_length_430_cov_2.194175:1-430 [pilon] Processing NODE_218_length_740_cov_3.093700:1-740 [pilon] NODE_218_length_740_cov_3.093700:1-740 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 50, Coverage: 9, minDepth: 5 [pilon] Confirmed 396 of 740 bases (53.51%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_218_length_740_cov_3.093700:1-740 [pilon] Processing NODE_29_length_30827_cov_46.041165:1-30827 [pilon] NODE_29_length_30827_cov_46.041165:1-30827 log: [pilon] frags shovill.bam: coverage 138 [pilon] Total Reads: 33288, Coverage: 138, minDepth: 35 [pilon] Confirmed 30553 of 30827 bases (99.11%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_29_length_30827_cov_46.041165:1-30827 [pilon] Processing NODE_97_length_1150_cov_19.428571:1-1150 [pilon] NODE_97_length_1150_cov_19.428571:1-1150 log: [pilon] frags shovill.bam: coverage 50 [pilon] Total Reads: 448, Coverage: 50, minDepth: 13 [pilon] Confirmed 864 of 1150 bases (75.13%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_97_length_1150_cov_19.428571:1-1150 [pilon] Processing NODE_163_length_816_cov_14.430216:1-816 [pilon] NODE_163_length_816_cov_14.430216:1-816 log: [pilon] frags shovill.bam: coverage 43 [pilon] Total Reads: 267, Coverage: 43, minDepth: 11 [pilon] Confirmed 571 of 816 bases (69.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_163_length_816_cov_14.430216:1-816 [pilon] Processing NODE_31_length_25176_cov_43.548593:1-25176 [pilon] NODE_1_length_490052_cov_33.720238:1-490052 log: [pilon] frags shovill.bam: coverage 103 [pilon] Total Reads: 391504, Coverage: 103, minDepth: 26 [pilon] Confirmed 488323 of 490052 bases (99.65%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_1_length_490052_cov_33.720238:1-490052 [pilon] NODE_31_length_25176_cov_43.548593:1-25176 log: [pilon] frags shovill.bam: coverage 133 [pilon] Total Reads: 25901, Coverage: 133, minDepth: 33 [pilon] Confirmed 24726 of 25176 bases (98.21%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_31_length_25176_cov_43.548593:1-25176 [pilon] Writing NODE_1_length_490052_cov_33.720238:1-490052 changes to pilon.changes [pilon] Writing updated NODE_1_length_490052_cov_33.720238_pilon to pilon.fasta [pilon] Writing NODE_2_length_407886_cov_34.907846:1-407886 changes to pilon.changes [pilon] Writing updated NODE_2_length_407886_cov_34.907846_pilon to pilon.fasta [pilon] Writing NODE_3_length_343968_cov_36.406323:1-343968 changes to pilon.changes [pilon] Writing updated NODE_3_length_343968_cov_36.406323_pilon to pilon.fasta [pilon] Writing NODE_4_length_326788_cov_39.039413:1-326788 changes to pilon.changes [pilon] Writing updated NODE_4_length_326788_cov_39.039413_pilon to pilon.fasta [pilon] Writing NODE_5_length_326645_cov_43.335586:1-326645 changes to pilon.changes [pilon] Writing updated NODE_5_length_326645_cov_43.335586_pilon to pilon.fasta [pilon] Writing NODE_6_length_324215_cov_45.379603:1-324215 changes to pilon.changes [pilon] Writing updated NODE_6_length_324215_cov_45.379603_pilon to pilon.fasta [pilon] Writing NODE_7_length_261794_cov_36.956113:1-261794 changes to pilon.changes [pilon] Writing updated NODE_7_length_261794_cov_36.956113_pilon to pilon.fasta [pilon] Writing NODE_8_length_244740_cov_43.085002:1-244740 changes to pilon.changes [pilon] Writing updated NODE_8_length_244740_cov_43.085002_pilon to pilon.fasta [pilon] Writing NODE_9_length_223393_cov_42.039651:1-223393 changes to pilon.changes [pilon] Writing updated NODE_9_length_223393_cov_42.039651_pilon to pilon.fasta [pilon] Writing NODE_10_length_218666_cov_45.518241:1-218666 changes to pilon.changes [pilon] Writing updated NODE_10_length_218666_cov_45.518241_pilon to pilon.fasta [pilon] Writing NODE_11_length_215661_cov_46.585335:1-215661 changes to pilon.changes [pilon] Writing updated NODE_11_length_215661_cov_46.585335_pilon to pilon.fasta [pilon] Writing NODE_12_length_161867_cov_46.822283:1-161867 changes to pilon.changes [pilon] Writing updated NODE_12_length_161867_cov_46.822283_pilon to pilon.fasta [pilon] Writing NODE_13_length_131029_cov_39.753338:1-131029 changes to pilon.changes [pilon] Writing updated NODE_13_length_131029_cov_39.753338_pilon to pilon.fasta [pilon] Writing NODE_14_length_120159_cov_46.979490:1-120159 changes to pilon.changes [pilon] Writing updated NODE_14_length_120159_cov_46.979490_pilon to pilon.fasta [pilon] Writing NODE_15_length_107429_cov_46.392263:1-107429 changes to pilon.changes [pilon] Writing updated NODE_15_length_107429_cov_46.392263_pilon to pilon.fasta [pilon] Writing NODE_16_length_93240_cov_43.502379:1-93240 changes to pilon.changes [pilon] Writing updated NODE_16_length_93240_cov_43.502379_pilon to pilon.fasta [pilon] Writing NODE_17_length_89057_cov_42.425002:1-89057 changes to pilon.changes [pilon] Writing updated NODE_17_length_89057_cov_42.425002_pilon to pilon.fasta [pilon] Writing NODE_18_length_88019_cov_41.386914:1-88019 changes to pilon.changes [pilon] Writing updated NODE_18_length_88019_cov_41.386914_pilon to pilon.fasta [pilon] Writing NODE_19_length_86850_cov_37.116951:1-86850 changes to pilon.changes [pilon] Writing updated NODE_19_length_86850_cov_37.116951_pilon to pilon.fasta [pilon] Writing NODE_20_length_85280_cov_39.769913:1-85280 changes to pilon.changes [pilon] Writing updated NODE_20_length_85280_cov_39.769913_pilon to pilon.fasta [pilon] Writing NODE_21_length_80035_cov_40.956891:1-80035 changes to pilon.changes [pilon] Writing updated NODE_21_length_80035_cov_40.956891_pilon to pilon.fasta [pilon] Writing NODE_22_length_72603_cov_36.721489:1-72603 changes to pilon.changes [pilon] Writing updated NODE_22_length_72603_cov_36.721489_pilon to pilon.fasta [pilon] Writing NODE_23_length_65675_cov_40.839644:1-65675 changes to pilon.changes [pilon] Writing updated NODE_23_length_65675_cov_40.839644_pilon to pilon.fasta [pilon] Writing NODE_24_length_58446_cov_40.223472:1-58446 changes to pilon.changes [pilon] Writing updated NODE_24_length_58446_cov_40.223472_pilon to pilon.fasta [pilon] Writing NODE_25_length_46794_cov_38.082832:1-46794 changes to pilon.changes [pilon] Writing updated NODE_25_length_46794_cov_38.082832_pilon to pilon.fasta [pilon] Writing NODE_26_length_42055_cov_41.688606:1-42055 changes to pilon.changes [pilon] Writing updated NODE_26_length_42055_cov_41.688606_pilon to pilon.fasta [pilon] Writing NODE_27_length_38554_cov_39.888481:1-38554 changes to pilon.changes [pilon] Writing updated NODE_27_length_38554_cov_39.888481_pilon to pilon.fasta [pilon] Writing NODE_28_length_36726_cov_35.802459:1-36726 changes to pilon.changes [pilon] Writing updated NODE_28_length_36726_cov_35.802459_pilon to pilon.fasta [pilon] Writing NODE_29_length_30827_cov_46.041165:1-30827 changes to pilon.changes [pilon] Writing updated NODE_29_length_30827_cov_46.041165_pilon to pilon.fasta [pilon] Writing NODE_30_length_25829_cov_44.046017:1-25829 changes to pilon.changes [pilon] Writing updated NODE_30_length_25829_cov_44.046017_pilon to pilon.fasta [pilon] Writing NODE_31_length_25176_cov_43.548593:1-25176 changes to pilon.changes [pilon] Writing updated NODE_31_length_25176_cov_43.548593_pilon to pilon.fasta [pilon] Writing NODE_32_length_23617_cov_34.984721:1-23617 changes to pilon.changes [pilon] Writing updated NODE_32_length_23617_cov_34.984721_pilon to pilon.fasta [pilon] Writing NODE_33_length_10685_cov_34.309447:1-10685 changes to pilon.changes [pilon] Writing updated NODE_33_length_10685_cov_34.309447_pilon to pilon.fasta [pilon] Writing NODE_34_length_9773_cov_31.265334:1-9773 changes to pilon.changes [pilon] Writing updated NODE_34_length_9773_cov_31.265334_pilon to pilon.fasta [pilon] Writing NODE_35_length_9076_cov_59.737353:1-9076 changes to pilon.changes [pilon] Writing updated NODE_35_length_9076_cov_59.737353_pilon to pilon.fasta [pilon] Writing NODE_36_length_8792_cov_31.574559:1-8792 changes to pilon.changes [pilon] Writing updated NODE_36_length_8792_cov_31.574559_pilon to pilon.fasta [pilon] Writing NODE_37_length_8057_cov_33.363911:1-8057 changes to pilon.changes [pilon] Writing updated NODE_37_length_8057_cov_33.363911_pilon to pilon.fasta [pilon] Writing NODE_38_length_5880_cov_24.816461:1-5880 changes to pilon.changes [pilon] Writing updated NODE_38_length_5880_cov_24.816461_pilon to pilon.fasta [pilon] Writing NODE_39_length_5426_cov_45.750236:1-5426 changes to pilon.changes [pilon] Writing updated NODE_39_length_5426_cov_45.750236_pilon to pilon.fasta [pilon] Writing NODE_40_length_4928_cov_33.585604:1-4928 changes to pilon.changes [pilon] Writing updated NODE_40_length_4928_cov_33.585604_pilon to pilon.fasta [pilon] Writing NODE_41_length_4807_cov_50.648314:1-4807 changes to pilon.changes [pilon] Writing updated NODE_41_length_4807_cov_50.648314_pilon to pilon.fasta [pilon] Writing NODE_42_length_4672_cov_34.057570:1-4672 changes to pilon.changes [pilon] Writing updated NODE_42_length_4672_cov_34.057570_pilon to pilon.fasta [pilon] Writing NODE_43_length_4199_cov_27.804316:1-4199 changes to pilon.changes [pilon] Writing updated NODE_43_length_4199_cov_27.804316_pilon to pilon.fasta [pilon] Writing NODE_44_length_4154_cov_17.558889:1-4154 changes to pilon.changes [pilon] Writing updated NODE_44_length_4154_cov_17.558889_pilon to pilon.fasta [pilon] Writing NODE_45_length_4048_cov_21.660300:1-4048 changes to pilon.changes [pilon] Writing updated NODE_45_length_4048_cov_21.660300_pilon to pilon.fasta [pilon] Writing NODE_46_length_3713_cov_27.868875:1-3713 changes to pilon.changes [pilon] Writing updated NODE_46_length_3713_cov_27.868875_pilon to pilon.fasta [pilon] Writing NODE_47_length_3711_cov_34.911699:1-3711 changes to pilon.changes [pilon] Writing updated NODE_47_length_3711_cov_34.911699_pilon to pilon.fasta [pilon] Writing NODE_48_length_3613_cov_14.987113:1-3613 changes to pilon.changes [pilon] Writing updated NODE_48_length_3613_cov_14.987113_pilon to pilon.fasta [pilon] Writing NODE_49_length_3569_cov_33.689385:1-3569 changes to pilon.changes [pilon] Writing updated NODE_49_length_3569_cov_33.689385_pilon to pilon.fasta [pilon] Writing NODE_50_length_3332_cov_18.815634:1-3332 changes to pilon.changes [pilon] Writing updated NODE_50_length_3332_cov_18.815634_pilon to pilon.fasta [pilon] Writing NODE_51_length_3042_cov_23.091065:1-3042 changes to pilon.changes [pilon] Writing updated NODE_51_length_3042_cov_23.091065_pilon to pilon.fasta [pilon] Writing NODE_52_length_2905_cov_24.298132:1-2905 changes to pilon.changes [pilon] Writing updated NODE_52_length_2905_cov_24.298132_pilon to pilon.fasta [pilon] Writing NODE_53_length_2821_cov_26.718519:1-2821 changes to pilon.changes [pilon] Writing updated NODE_53_length_2821_cov_26.718519_pilon to pilon.fasta [pilon] Writing NODE_54_length_2785_cov_55.135135:1-2785 changes to pilon.changes [pilon] Writing updated NODE_54_length_2785_cov_55.135135_pilon to pilon.fasta [pilon] Writing NODE_55_length_2727_cov_44.844973:1-2727 changes to pilon.changes [pilon] Writing updated NODE_55_length_2727_cov_44.844973_pilon to pilon.fasta [pilon] Writing NODE_56_length_2632_cov_23.807248:1-2632 changes to pilon.changes [pilon] Writing updated NODE_56_length_2632_cov_23.807248_pilon to pilon.fasta [pilon] Writing NODE_57_length_2590_cov_24.109356:1-2590 changes to pilon.changes [pilon] Writing updated NODE_57_length_2590_cov_24.109356_pilon to pilon.fasta [pilon] Writing NODE_58_length_2458_cov_28.578947:1-2458 changes to pilon.changes [pilon] Writing updated NODE_58_length_2458_cov_28.578947_pilon to pilon.fasta [pilon] Writing NODE_59_length_2348_cov_66.015267:1-2348 changes to pilon.changes [pilon] Writing updated NODE_59_length_2348_cov_66.015267_pilon to pilon.fasta [pilon] Writing NODE_60_length_2263_cov_6.024743:1-2263 changes to pilon.changes [pilon] Writing updated NODE_60_length_2263_cov_6.024743_pilon to pilon.fasta [pilon] Writing NODE_61_length_2178_cov_37.741857:1-2178 changes to pilon.changes [pilon] Writing updated NODE_61_length_2178_cov_37.741857_pilon to pilon.fasta [pilon] Writing NODE_62_length_2174_cov_30.686800:1-2174 changes to pilon.changes [pilon] Writing updated NODE_62_length_2174_cov_30.686800_pilon to pilon.fasta [pilon] Writing NODE_63_length_2135_cov_25.848560:1-2135 changes to pilon.changes [pilon] Writing updated NODE_63_length_2135_cov_25.848560_pilon to pilon.fasta [pilon] Writing NODE_64_length_2049_cov_28.913900:1-2049 changes to pilon.changes [pilon] Writing updated NODE_64_length_2049_cov_28.913900_pilon to pilon.fasta [pilon] Writing NODE_65_length_1936_cov_32.256198:1-1936 changes to pilon.changes [pilon] Writing updated NODE_65_length_1936_cov_32.256198_pilon to pilon.fasta [pilon] Writing NODE_66_length_1897_cov_28.582770:1-1897 changes to pilon.changes [pilon] Writing updated NODE_66_length_1897_cov_28.582770_pilon to pilon.fasta [pilon] Writing NODE_67_length_1824_cov_7.270112:1-1824 changes to pilon.changes [pilon] Writing updated NODE_67_length_1824_cov_7.270112_pilon to pilon.fasta [pilon] Writing NODE_68_length_1819_cov_5.074205:1-1819 changes to pilon.changes [pilon] Writing updated NODE_68_length_1819_cov_5.074205_pilon to pilon.fasta [pilon] Writing NODE_69_length_1792_cov_6.403351:1-1792 changes to pilon.changes [pilon] Writing updated NODE_69_length_1792_cov_6.403351_pilon to pilon.fasta [pilon] Writing NODE_70_length_1613_cov_190.256032:1-1613 changes to pilon.changes [pilon] Writing updated NODE_70_length_1613_cov_190.256032_pilon to pilon.fasta [pilon] Writing NODE_71_length_1564_cov_90.154539:1-1564 changes to pilon.changes [pilon] Writing updated NODE_71_length_1564_cov_90.154539_pilon to pilon.fasta [pilon] Writing NODE_72_length_1553_cov_5.699022:1-1553 changes to pilon.changes [pilon] Writing updated NODE_72_length_1553_cov_5.699022_pilon to pilon.fasta [pilon] Writing NODE_73_length_1546_cov_14.455439:1-1546 changes to pilon.changes [pilon] Writing updated NODE_73_length_1546_cov_14.455439_pilon to pilon.fasta [pilon] Writing NODE_74_length_1493_cov_5.978863:1-1493 changes to pilon.changes [pilon] Writing updated NODE_74_length_1493_cov_5.978863_pilon to pilon.fasta [pilon] Writing NODE_75_length_1476_cov_5.915867:1-1476 changes to pilon.changes [pilon] Writing updated NODE_75_length_1476_cov_5.915867_pilon to pilon.fasta [pilon] Writing NODE_76_length_1464_cov_25.960536:1-1464 changes to pilon.changes [pilon] Writing updated NODE_76_length_1464_cov_25.960536_pilon to pilon.fasta [pilon] Writing NODE_77_length_1411_cov_3.496124:1-1411 changes to pilon.changes [pilon] Writing updated NODE_77_length_1411_cov_3.496124_pilon to pilon.fasta [pilon] Writing NODE_78_length_1390_cov_5.759653:1-1390 changes to pilon.changes [pilon] Writing updated NODE_78_length_1390_cov_5.759653_pilon to pilon.fasta [pilon] Writing NODE_79_length_1387_cov_156.505529:1-1387 changes to pilon.changes [pilon] Writing updated NODE_79_length_1387_cov_156.505529_pilon to pilon.fasta [pilon] Writing NODE_80_length_1327_cov_10.440299:1-1327 changes to pilon.changes [pilon] Writing updated NODE_80_length_1327_cov_10.440299_pilon to pilon.fasta [pilon] Writing NODE_81_length_1306_cov_7.258228:1-1306 changes to pilon.changes [pilon] Writing updated NODE_81_length_1306_cov_7.258228_pilon to pilon.fasta [pilon] Writing NODE_82_length_1299_cov_12.027165:1-1299 changes to pilon.changes [pilon] Writing updated NODE_82_length_1299_cov_12.027165_pilon to pilon.fasta [pilon] Writing NODE_83_length_1292_cov_5.887276:1-1292 changes to pilon.changes [pilon] Writing updated NODE_83_length_1292_cov_5.887276_pilon to pilon.fasta [pilon] Writing NODE_84_length_1289_cov_7.542808:1-1289 changes to pilon.changes [pilon] Writing updated NODE_84_length_1289_cov_7.542808_pilon to pilon.fasta [pilon] Writing NODE_85_length_1260_cov_4.128183:1-1260 changes to pilon.changes [pilon] Writing updated NODE_85_length_1260_cov_4.128183_pilon to pilon.fasta [pilon] Writing NODE_86_length_1257_cov_11.625880:1-1257 changes to pilon.changes [pilon] Writing updated NODE_86_length_1257_cov_11.625880_pilon to pilon.fasta [pilon] Writing NODE_87_length_1232_cov_4.632763:1-1232 changes to pilon.changes [pilon] Writing updated NODE_87_length_1232_cov_4.632763_pilon to pilon.fasta [pilon] Writing NODE_88_length_1223_cov_8.430127:1-1223 changes to pilon.changes [pilon] Writing updated NODE_88_length_1223_cov_8.430127_pilon to pilon.fasta [pilon] Writing NODE_89_length_1219_cov_6.331512:1-1219 changes to pilon.changes [pilon] Writing updated NODE_89_length_1219_cov_6.331512_pilon to pilon.fasta [pilon] Writing NODE_90_length_1212_cov_6.421632:1-1212 changes to pilon.changes [pilon] Writing updated NODE_90_length_1212_cov_6.421632_pilon to pilon.fasta [pilon] Writing NODE_91_length_1210_cov_1.355372:1-1210 changes to pilon.changes [pilon] Writing updated NODE_91_length_1210_cov_1.355372_pilon to pilon.fasta [pilon] Writing NODE_92_length_1208_cov_7.812328:1-1208 changes to pilon.changes [pilon] Writing updated NODE_92_length_1208_cov_7.812328_pilon to pilon.fasta [pilon] Writing NODE_93_length_1188_cov_3.535145:1-1188 changes to pilon.changes [pilon] Writing updated NODE_93_length_1188_cov_3.535145_pilon to pilon.fasta [pilon] Writing NODE_94_length_1172_cov_6.336822:1-1172 changes to pilon.changes [pilon] Writing updated NODE_94_length_1172_cov_6.336822_pilon to pilon.fasta [pilon] Writing NODE_95_length_1170_cov_6.428980:1-1170 changes to pilon.changes [pilon] Writing updated NODE_95_length_1170_cov_6.428980_pilon to pilon.fasta [pilon] Writing NODE_96_length_1166_cov_18.626794:1-1166 changes to pilon.changes [pilon] Writing updated NODE_96_length_1166_cov_18.626794_pilon to pilon.fasta [pilon] Writing NODE_97_length_1150_cov_19.428571:1-1150 changes to pilon.changes [pilon] Writing updated NODE_97_length_1150_cov_19.428571_pilon to pilon.fasta [pilon] Writing NODE_98_length_1148_cov_0.789679:1-1148 changes to pilon.changes [pilon] Writing updated NODE_98_length_1148_cov_0.789679_pilon to pilon.fasta [pilon] Writing NODE_99_length_1136_cov_38.045320:1-1136 changes to pilon.changes [pilon] Writing updated NODE_99_length_1136_cov_38.045320_pilon to pilon.fasta [pilon] Writing NODE_100_length_1118_cov_11.091274:1-1118 changes to pilon.changes [pilon] Writing updated NODE_100_length_1118_cov_11.091274_pilon to pilon.fasta [pilon] Writing NODE_101_length_1100_cov_7.600613:1-1100 changes to pilon.changes [pilon] Writing updated NODE_101_length_1100_cov_7.600613_pilon to pilon.fasta [pilon] Writing NODE_102_length_1098_cov_3.344933:1-1098 changes to pilon.changes [pilon] Writing updated NODE_102_length_1098_cov_3.344933_pilon to pilon.fasta [pilon] Writing NODE_103_length_1073_cov_3.695378:1-1073 changes to pilon.changes [pilon] Writing updated NODE_103_length_1073_cov_3.695378_pilon to pilon.fasta [pilon] Writing NODE_104_length_1069_cov_3.148734:1-1069 changes to pilon.changes [pilon] Writing updated NODE_104_length_1069_cov_3.148734_pilon to pilon.fasta [pilon] Writing NODE_105_length_1066_cov_12.984127:1-1066 changes to pilon.changes [pilon] Writing updated NODE_105_length_1066_cov_12.984127_pilon to pilon.fasta [pilon] Writing NODE_106_length_1064_cov_6.551432:1-1064 changes to pilon.changes [pilon] Writing updated NODE_106_length_1064_cov_6.551432_pilon to pilon.fasta [pilon] Writing NODE_107_length_1063_cov_2.485138:1-1063 changes to pilon.changes [pilon] Writing updated NODE_107_length_1063_cov_2.485138_pilon to pilon.fasta [pilon] Writing NODE_108_length_1050_cov_11.834230:1-1050 changes to pilon.changes [pilon] Writing updated NODE_108_length_1050_cov_11.834230_pilon to pilon.fasta [pilon] Writing NODE_109_length_1044_cov_3.619718:1-1044 changes to pilon.changes [pilon] Writing updated NODE_109_length_1044_cov_3.619718_pilon to pilon.fasta [pilon] Writing NODE_110_length_1041_cov_2.452174:1-1041 changes to pilon.changes [pilon] Writing updated NODE_110_length_1041_cov_2.452174_pilon to pilon.fasta [pilon] Writing NODE_111_length_1038_cov_10.586696:1-1038 changes to pilon.changes [pilon] Writing updated NODE_111_length_1038_cov_10.586696_pilon to pilon.fasta [pilon] Writing NODE_112_length_1027_cov_23.616998:1-1027 changes to pilon.changes [pilon] Writing updated NODE_112_length_1027_cov_23.616998_pilon to pilon.fasta [pilon] Writing NODE_113_length_1014_cov_3.965286:1-1014 changes to pilon.changes [pilon] Writing updated NODE_113_length_1014_cov_3.965286_pilon to pilon.fasta [pilon] Writing NODE_114_length_1009_cov_11.805180:1-1009 changes to pilon.changes [pilon] Writing updated NODE_114_length_1009_cov_11.805180_pilon to pilon.fasta [pilon] Writing NODE_115_length_1007_cov_6.306998:1-1007 changes to pilon.changes [pilon] Writing updated NODE_115_length_1007_cov_6.306998_pilon to pilon.fasta [pilon] Writing NODE_116_length_1006_cov_1.476836:1-1006 changes to pilon.changes [pilon] Writing updated NODE_116_length_1006_cov_1.476836_pilon to pilon.fasta [pilon] Writing NODE_117_length_997_cov_4.005708:1-997 changes to pilon.changes [pilon] Writing updated NODE_117_length_997_cov_4.005708_pilon to pilon.fasta [pilon] Writing NODE_118_length_994_cov_4.241695:1-994 changes to pilon.changes [pilon] Writing updated NODE_118_length_994_cov_4.241695_pilon to pilon.fasta [pilon] Writing NODE_119_length_983_cov_1.813225:1-983 changes to pilon.changes [pilon] Writing updated NODE_119_length_983_cov_1.813225_pilon to pilon.fasta [pilon] Writing NODE_120_length_964_cov_4.476868:1-964 changes to pilon.changes [pilon] Writing updated NODE_120_length_964_cov_4.476868_pilon to pilon.fasta [pilon] Writing NODE_121_length_956_cov_2.796407:1-956 changes to pilon.changes [pilon] Writing updated NODE_121_length_956_cov_2.796407_pilon to pilon.fasta [pilon] Writing NODE_122_length_955_cov_0.471223:1-955 changes to pilon.changes [pilon] Writing updated NODE_122_length_955_cov_0.471223_pilon to pilon.fasta [pilon] Writing NODE_123_length_954_cov_5.753902:1-954 changes to pilon.changes [pilon] Writing updated NODE_123_length_954_cov_5.753902_pilon to pilon.fasta [pilon] Writing NODE_124_length_952_cov_5.531889:1-952 changes to pilon.changes [pilon] Writing updated NODE_124_length_952_cov_5.531889_pilon to pilon.fasta [pilon] Writing NODE_125_length_940_cov_17.301587:1-940 changes to pilon.changes [pilon] Writing updated NODE_125_length_940_cov_17.301587_pilon to pilon.fasta [pilon] Writing NODE_126_length_933_cov_4.070197:1-933 changes to pilon.changes [pilon] Writing updated NODE_126_length_933_cov_4.070197_pilon to pilon.fasta [pilon] Writing NODE_127_length_929_cov_1.813119:1-929 changes to pilon.changes [pilon] Writing updated NODE_127_length_929_cov_1.813119_pilon to pilon.fasta [pilon] Writing NODE_128_length_922_cov_10.159800:1-922 changes to pilon.changes [pilon] Writing updated NODE_128_length_922_cov_10.159800_pilon to pilon.fasta [pilon] Writing NODE_129_length_909_cov_2.441624:1-909 changes to pilon.changes [pilon] Writing updated NODE_129_length_909_cov_2.441624_pilon to pilon.fasta [pilon] Writing NODE_130_length_907_cov_6.632316:1-907 changes to pilon.changes [pilon] Writing updated NODE_130_length_907_cov_6.632316_pilon to pilon.fasta [pilon] Writing NODE_131_length_900_cov_0.893453:1-900 changes to pilon.changes [pilon] Writing updated NODE_131_length_900_cov_0.893453_pilon to pilon.fasta [pilon] Writing NODE_132_length_899_cov_8.776350:1-899 changes to pilon.changes [pilon] Writing updated NODE_132_length_899_cov_8.776350_pilon to pilon.fasta [pilon] Writing NODE_133_length_896_cov_12.440000:1-896 changes to pilon.changes [pilon] Writing updated NODE_133_length_896_cov_12.440000_pilon to pilon.fasta [pilon] Writing NODE_134_length_895_cov_1.293282:1-895 changes to pilon.changes [pilon] Writing updated NODE_134_length_895_cov_1.293282_pilon to pilon.fasta [pilon] Writing NODE_135_length_884_cov_2.306684:1-884 changes to pilon.changes [pilon] Writing updated NODE_135_length_884_cov_2.306684_pilon to pilon.fasta [pilon] Writing NODE_136_length_881_cov_2.910526:1-881 changes to pilon.changes [pilon] Writing updated NODE_136_length_881_cov_2.910526_pilon to pilon.fasta [pilon] Writing NODE_137_length_877_cov_3.000000:1-877 changes to pilon.changes [pilon] Writing updated NODE_137_length_877_cov_3.000000_pilon to pilon.fasta [pilon] Writing NODE_138_length_876_cov_1.023841:1-876 changes to pilon.changes [pilon] Writing updated NODE_138_length_876_cov_1.023841_pilon to pilon.fasta [pilon] Writing NODE_139_length_869_cov_15.966578:1-869 changes to pilon.changes [pilon] Writing updated NODE_139_length_869_cov_15.966578_pilon to pilon.fasta [pilon] Writing NODE_140_length_858_cov_24.404342:1-858 changes to pilon.changes [pilon] Writing updated NODE_140_length_858_cov_24.404342_pilon to pilon.fasta [pilon] Writing NODE_141_length_854_cov_13.597544:1-854 changes to pilon.changes [pilon] Writing updated NODE_141_length_854_cov_13.597544_pilon to pilon.fasta [pilon] Writing NODE_142_length_852_cov_1.573187:1-852 changes to pilon.changes [pilon] Writing updated NODE_142_length_852_cov_1.573187_pilon to pilon.fasta [pilon] Writing NODE_143_length_849_cov_11.251374:1-849 changes to pilon.changes [pilon] Writing updated NODE_143_length_849_cov_11.251374_pilon to pilon.fasta [pilon] Writing NODE_144_length_849_cov_10.245879:1-849 changes to pilon.changes [pilon] Writing updated NODE_144_length_849_cov_10.245879_pilon to pilon.fasta [pilon] Writing NODE_145_length_846_cov_11.144828:1-846 changes to pilon.changes [pilon] Writing updated NODE_145_length_846_cov_11.144828_pilon to pilon.fasta [pilon] Writing NODE_146_length_846_cov_4.600000:1-846 changes to pilon.changes [pilon] Writing updated NODE_146_length_846_cov_4.600000_pilon to pilon.fasta [pilon] Writing NODE_147_length_842_cov_10.613037:1-842 changes to pilon.changes [pilon] Writing updated NODE_147_length_842_cov_10.613037_pilon to pilon.fasta [pilon] Writing NODE_148_length_838_cov_5.747559:1-838 changes to pilon.changes [pilon] Writing updated NODE_148_length_838_cov_5.747559_pilon to pilon.fasta [pilon] Writing NODE_149_length_838_cov_0.669456:1-838 changes to pilon.changes [pilon] Writing updated NODE_149_length_838_cov_0.669456_pilon to pilon.fasta [pilon] Writing NODE_150_length_836_cov_9.173427:1-836 changes to pilon.changes [pilon] Writing updated NODE_150_length_836_cov_9.173427_pilon to pilon.fasta [pilon] Writing NODE_151_length_836_cov_7.868531:1-836 changes to pilon.changes [pilon] Writing updated NODE_151_length_836_cov_7.868531_pilon to pilon.fasta [pilon] Writing NODE_152_length_836_cov_4.925874:1-836 changes to pilon.changes [pilon] Writing updated NODE_152_length_836_cov_4.925874_pilon to pilon.fasta [pilon] Writing NODE_153_length_834_cov_11.768583:1-834 changes to pilon.changes [pilon] Writing updated NODE_153_length_834_cov_11.768583_pilon to pilon.fasta [pilon] Writing NODE_154_length_832_cov_1.753868:1-832 changes to pilon.changes [pilon] Writing updated NODE_154_length_832_cov_1.753868_pilon to pilon.fasta [pilon] Writing NODE_155_length_831_cov_32.573239:1-831 changes to pilon.changes [pilon] Writing updated NODE_155_length_831_cov_32.573239_pilon to pilon.fasta [pilon] Writing NODE_156_length_826_cov_13.026950:1-826 changes to pilon.changes [pilon] Writing updated NODE_156_length_826_cov_13.026950_pilon to pilon.fasta [pilon] Writing NODE_157_length_825_cov_4.169034:1-825 changes to pilon.changes [pilon] Writing updated NODE_157_length_825_cov_4.169034_pilon to pilon.fasta [pilon] Writing NODE_158_length_824_cov_2.116643:1-824 changes to pilon.changes [pilon] Writing updated NODE_158_length_824_cov_2.116643_pilon to pilon.fasta [pilon] Writing NODE_159_length_822_cov_2.813124:1-822 changes to pilon.changes [pilon] Writing updated NODE_159_length_822_cov_2.813124_pilon to pilon.fasta [pilon] Writing NODE_160_length_821_cov_8.034286:1-821 changes to pilon.changes [pilon] Writing updated NODE_160_length_821_cov_8.034286_pilon to pilon.fasta [pilon] Writing NODE_161_length_819_cov_2.855301:1-819 changes to pilon.changes [pilon] Writing updated NODE_161_length_819_cov_2.855301_pilon to pilon.fasta [pilon] Writing NODE_162_length_819_cov_1.733524:1-819 changes to pilon.changes [pilon] Writing updated NODE_162_length_819_cov_1.733524_pilon to pilon.fasta [pilon] Writing NODE_163_length_816_cov_14.430216:1-816 changes to pilon.changes [pilon] Writing updated NODE_163_length_816_cov_14.430216_pilon to pilon.fasta [pilon] Writing NODE_164_length_816_cov_5.598561:1-816 changes to pilon.changes [pilon] Writing updated NODE_164_length_816_cov_5.598561_pilon to pilon.fasta [pilon] Writing NODE_165_length_812_cov_15.761216:1-812 changes to pilon.changes [pilon] Writing updated NODE_165_length_812_cov_15.761216_pilon to pilon.fasta [pilon] Writing NODE_166_length_811_cov_9.781159:1-811 changes to pilon.changes [pilon] Writing updated NODE_166_length_811_cov_9.781159_pilon to pilon.fasta [pilon] Writing NODE_167_length_809_cov_20.085756:1-809 changes to pilon.changes [pilon] Writing updated NODE_167_length_809_cov_20.085756_pilon to pilon.fasta [pilon] Writing NODE_168_length_805_cov_6.302632:1-805 changes to pilon.changes [pilon] Writing updated NODE_168_length_805_cov_6.302632_pilon to pilon.fasta [pilon] Writing NODE_169_length_805_cov_0.739766:1-805 changes to pilon.changes [pilon] Writing updated NODE_169_length_805_cov_0.739766_pilon to pilon.fasta [pilon] Writing NODE_170_length_803_cov_5.054252:1-803 changes to pilon.changes [pilon] Writing updated NODE_170_length_803_cov_5.054252_pilon to pilon.fasta [pilon] Writing NODE_171_length_802_cov_1.945668:1-802 changes to pilon.changes [pilon] Writing updated NODE_171_length_802_cov_1.945668_pilon to pilon.fasta [pilon] Writing NODE_172_length_802_cov_1.509545:1-802 changes to pilon.changes [pilon] Writing updated NODE_172_length_802_cov_1.509545_pilon to pilon.fasta [pilon] Writing NODE_173_length_801_cov_2.636765:1-801 changes to pilon.changes [pilon] Writing updated NODE_173_length_801_cov_2.636765_pilon to pilon.fasta [pilon] Writing NODE_174_length_799_cov_7.619469:1-799 changes to pilon.changes [pilon] Writing updated NODE_174_length_799_cov_7.619469_pilon to pilon.fasta [pilon] Writing NODE_175_length_799_cov_4.877581:1-799 changes to pilon.changes [pilon] Writing updated NODE_175_length_799_cov_4.877581_pilon to pilon.fasta [pilon] Writing NODE_176_length_794_cov_8.545319:1-794 changes to pilon.changes [pilon] Writing updated NODE_176_length_794_cov_8.545319_pilon to pilon.fasta [pilon] Writing NODE_177_length_794_cov_4.732541:1-794 changes to pilon.changes [pilon] Writing updated NODE_177_length_794_cov_4.732541_pilon to pilon.fasta [pilon] Writing NODE_178_length_792_cov_11.068554:1-792 changes to pilon.changes [pilon] Writing updated NODE_178_length_792_cov_11.068554_pilon to pilon.fasta [pilon] Writing NODE_179_length_791_cov_7.877612:1-791 changes to pilon.changes [pilon] Writing updated NODE_179_length_791_cov_7.877612_pilon to pilon.fasta [pilon] Writing NODE_180_length_790_cov_1.372197:1-790 changes to pilon.changes [pilon] Writing updated NODE_180_length_790_cov_1.372197_pilon to pilon.fasta [pilon] Writing NODE_181_length_788_cov_5.743628:1-788 changes to pilon.changes [pilon] Writing updated NODE_181_length_788_cov_5.743628_pilon to pilon.fasta [pilon] Writing NODE_182_length_784_cov_6.437406:1-784 changes to pilon.changes [pilon] Writing updated NODE_182_length_784_cov_6.437406_pilon to pilon.fasta [pilon] Writing NODE_183_length_781_cov_9.374242:1-781 changes to pilon.changes [pilon] Writing updated NODE_183_length_781_cov_9.374242_pilon to pilon.fasta [pilon] Writing NODE_184_length_780_cov_8.930197:1-780 changes to pilon.changes [pilon] Writing updated NODE_184_length_780_cov_8.930197_pilon to pilon.fasta [pilon] Writing NODE_185_length_779_cov_5.962006:1-779 changes to pilon.changes [pilon] Writing updated NODE_185_length_779_cov_5.962006_pilon to pilon.fasta [pilon] Writing NODE_186_length_778_cov_2.202435:1-778 changes to pilon.changes [pilon] Writing updated NODE_186_length_778_cov_2.202435_pilon to pilon.fasta [pilon] Writing NODE_187_length_777_cov_18.288110:1-777 changes to pilon.changes [pilon] Writing updated NODE_187_length_777_cov_18.288110_pilon to pilon.fasta [pilon] Writing NODE_188_length_773_cov_15.803681:1-773 changes to pilon.changes [pilon] Writing updated NODE_188_length_773_cov_15.803681_pilon to pilon.fasta [pilon] Writing NODE_189_length_770_cov_1.961479:1-770 changes to pilon.changes [pilon] Writing updated NODE_189_length_770_cov_1.961479_pilon to pilon.fasta [pilon] Writing NODE_190_length_769_cov_13.608025:1-769 changes to pilon.changes [pilon] Writing updated NODE_190_length_769_cov_13.608025_pilon to pilon.fasta [pilon] Writing NODE_191_length_769_cov_3.649691:1-769 changes to pilon.changes [pilon] Writing updated NODE_191_length_769_cov_3.649691_pilon to pilon.fasta [pilon] Writing NODE_192_length_768_cov_9.409583:1-768 changes to pilon.changes [pilon] Writing updated NODE_192_length_768_cov_9.409583_pilon to pilon.fasta [pilon] Writing NODE_193_length_768_cov_4.341577:1-768 changes to pilon.changes [pilon] Writing updated NODE_193_length_768_cov_4.341577_pilon to pilon.fasta [pilon] Writing NODE_194_length_767_cov_3.058824:1-767 changes to pilon.changes [pilon] Writing updated NODE_194_length_767_cov_3.058824_pilon to pilon.fasta [pilon] Writing NODE_195_length_763_cov_4.828660:1-763 changes to pilon.changes [pilon] Writing updated NODE_195_length_763_cov_4.828660_pilon to pilon.fasta [pilon] Writing NODE_196_length_761_cov_8.310937:1-761 changes to pilon.changes [pilon] Writing updated NODE_196_length_761_cov_8.310937_pilon to pilon.fasta [pilon] Writing NODE_197_length_761_cov_7.173438:1-761 changes to pilon.changes [pilon] Writing updated NODE_197_length_761_cov_7.173438_pilon to pilon.fasta [pilon] Writing NODE_198_length_760_cov_9.341158:1-760 changes to pilon.changes [pilon] Writing updated NODE_198_length_760_cov_9.341158_pilon to pilon.fasta [pilon] Writing NODE_199_length_758_cov_12.158556:1-758 changes to pilon.changes [pilon] Writing updated NODE_199_length_758_cov_12.158556_pilon to pilon.fasta [pilon] Writing NODE_200_length_758_cov_3.084772:1-758 changes to pilon.changes [pilon] Writing updated NODE_200_length_758_cov_3.084772_pilon to pilon.fasta [pilon] Writing NODE_201_length_756_cov_8.740157:1-756 changes to pilon.changes [pilon] Writing updated NODE_201_length_756_cov_8.740157_pilon to pilon.fasta [pilon] Writing NODE_202_length_753_cov_15.832278:1-753 changes to pilon.changes [pilon] Writing updated NODE_202_length_753_cov_15.832278_pilon to pilon.fasta [pilon] Writing NODE_203_length_753_cov_3.724684:1-753 changes to pilon.changes [pilon] Writing updated NODE_203_length_753_cov_3.724684_pilon to pilon.fasta [pilon] Writing NODE_204_length_752_cov_0.689382:1-752 changes to pilon.changes [pilon] Writing updated NODE_204_length_752_cov_0.689382_pilon to pilon.fasta [pilon] Writing NODE_205_length_750_cov_16.674086:1-750 changes to pilon.changes [pilon] Writing updated NODE_205_length_750_cov_16.674086_pilon to pilon.fasta [pilon] Writing NODE_206_length_750_cov_12.383148:1-750 changes to pilon.changes [pilon] Writing updated NODE_206_length_750_cov_12.383148_pilon to pilon.fasta [pilon] Writing NODE_207_length_750_cov_6.608903:1-750 changes to pilon.changes [pilon] Writing updated NODE_207_length_750_cov_6.608903_pilon to pilon.fasta [pilon] Writing NODE_208_length_748_cov_9.604466:1-748 changes to pilon.changes [pilon] Writing updated NODE_208_length_748_cov_9.604466_pilon to pilon.fasta [pilon] Writing NODE_209_length_748_cov_4.261563:1-748 changes to pilon.changes [pilon] Writing updated NODE_209_length_748_cov_4.261563_pilon to pilon.fasta [pilon] Writing NODE_210_length_744_cov_11.926164:1-744 changes to pilon.changes [pilon] Writing updated NODE_210_length_744_cov_11.926164_pilon to pilon.fasta [pilon] Writing NODE_211_length_743_cov_8.315113:1-743 changes to pilon.changes [pilon] Writing updated NODE_211_length_743_cov_8.315113_pilon to pilon.fasta [pilon] Writing NODE_212_length_743_cov_0.860129:1-743 changes to pilon.changes [pilon] Writing updated NODE_212_length_743_cov_0.860129_pilon to pilon.fasta [pilon] Writing NODE_213_length_742_cov_0.743961:1-742 changes to pilon.changes [pilon] Writing updated NODE_213_length_742_cov_0.743961_pilon to pilon.fasta [pilon] Writing NODE_214_length_741_cov_13.583871:1-741 changes to pilon.changes [pilon] Writing updated NODE_214_length_741_cov_13.583871_pilon to pilon.fasta [pilon] Writing NODE_215_length_741_cov_5.527419:1-741 changes to pilon.changes [pilon] Writing updated NODE_215_length_741_cov_5.527419_pilon to pilon.fasta [pilon] Writing NODE_216_length_740_cov_13.583199:1-740 changes to pilon.changes [pilon] Writing updated NODE_216_length_740_cov_13.583199_pilon to pilon.fasta [pilon] Writing NODE_217_length_740_cov_3.786753:1-740 changes to pilon.changes [pilon] Writing updated NODE_217_length_740_cov_3.786753_pilon to pilon.fasta [pilon] Writing NODE_218_length_740_cov_3.093700:1-740 changes to pilon.changes [pilon] Writing updated NODE_218_length_740_cov_3.093700_pilon to pilon.fasta [pilon] Writing NODE_219_length_739_cov_13.367314:1-739 changes to pilon.changes [pilon] Writing updated NODE_219_length_739_cov_13.367314_pilon to pilon.fasta [pilon] Writing NODE_220_length_739_cov_4.432039:1-739 changes to pilon.changes [pilon] Writing updated NODE_220_length_739_cov_4.432039_pilon to pilon.fasta [pilon] Writing NODE_221_length_739_cov_2.076052:1-739 changes to pilon.changes [pilon] Writing updated NODE_221_length_739_cov_2.076052_pilon to pilon.fasta [pilon] Writing NODE_222_length_738_cov_1.311183:1-738 changes to pilon.changes [pilon] Writing updated NODE_222_length_738_cov_1.311183_pilon to pilon.fasta [pilon] Writing NODE_223_length_735_cov_17.998371:1-735 changes to pilon.changes [pilon] Writing updated NODE_223_length_735_cov_17.998371_pilon to pilon.fasta [pilon] Writing NODE_224_length_735_cov_2.224756:1-735 changes to pilon.changes [pilon] Writing updated NODE_224_length_735_cov_2.224756_pilon to pilon.fasta [pilon] Writing NODE_225_length_732_cov_6.176759:1-732 changes to pilon.changes [pilon] Writing updated NODE_225_length_732_cov_6.176759_pilon to pilon.fasta [pilon] Writing NODE_226_length_731_cov_4.532787:1-731 changes to pilon.changes [pilon] Writing updated NODE_226_length_731_cov_4.532787_pilon to pilon.fasta [pilon] Writing NODE_227_length_727_cov_3.968647:1-727 changes to pilon.changes [pilon] Writing updated NODE_227_length_727_cov_3.968647_pilon to pilon.fasta [pilon] Writing NODE_228_length_726_cov_13.768595:1-726 changes to pilon.changes [pilon] Writing updated NODE_228_length_726_cov_13.768595_pilon to pilon.fasta [pilon] Writing NODE_229_length_726_cov_1.993388:1-726 changes to pilon.changes [pilon] Writing updated NODE_229_length_726_cov_1.993388_pilon to pilon.fasta [pilon] Writing NODE_230_length_724_cov_4.943615:1-724 changes to pilon.changes [pilon] Writing updated NODE_230_length_724_cov_4.943615_pilon to pilon.fasta [pilon] Writing NODE_231_length_721_cov_3.973333:1-721 changes to pilon.changes [pilon] Writing updated NODE_231_length_721_cov_3.973333_pilon to pilon.fasta [pilon] Writing NODE_232_length_721_cov_1.846667:1-721 changes to pilon.changes [pilon] Writing updated NODE_232_length_721_cov_1.846667_pilon to pilon.fasta [pilon] Writing NODE_233_length_720_cov_2.071786:1-720 changes to pilon.changes [pilon] Writing updated NODE_233_length_720_cov_2.071786_pilon to pilon.fasta [pilon] Writing NODE_234_length_718_cov_4.132328:1-718 changes to pilon.changes [pilon] Writing updated NODE_234_length_718_cov_4.132328_pilon to pilon.fasta [pilon] Writing NODE_235_length_716_cov_7.309244:1-716 changes to pilon.changes [pilon] Writing updated NODE_235_length_716_cov_7.309244_pilon to pilon.fasta [pilon] Writing NODE_236_length_716_cov_3.312605:1-716 changes to pilon.changes [pilon] Writing updated NODE_236_length_716_cov_3.312605_pilon to pilon.fasta [pilon] Writing NODE_237_length_715_cov_10.309764:1-715 changes to pilon.changes [pilon] Writing updated NODE_237_length_715_cov_10.309764_pilon to pilon.fasta [pilon] Writing NODE_238_length_714_cov_11.553120:1-714 changes to pilon.changes [pilon] Writing updated NODE_238_length_714_cov_11.553120_pilon to pilon.fasta [pilon] Writing NODE_239_length_714_cov_4.460371:1-714 changes to pilon.changes [pilon] Writing updated NODE_239_length_714_cov_4.460371_pilon to pilon.fasta [pilon] Writing NODE_240_length_714_cov_0.691400:1-714 changes to pilon.changes [pilon] Writing updated NODE_240_length_714_cov_0.691400_pilon to pilon.fasta [pilon] Writing NODE_241_length_712_cov_3.707276:1-712 changes to pilon.changes [pilon] Writing updated NODE_241_length_712_cov_3.707276_pilon to pilon.fasta [pilon] Writing NODE_242_length_711_cov_13.779661:1-711 changes to pilon.changes [pilon] Writing updated NODE_242_length_711_cov_13.779661_pilon to pilon.fasta [pilon] Writing NODE_243_length_710_cov_9.393888:1-710 changes to pilon.changes [pilon] Writing updated NODE_243_length_710_cov_9.393888_pilon to pilon.fasta [pilon] Writing NODE_244_length_708_cov_7.870528:1-708 changes to pilon.changes [pilon] Writing updated NODE_244_length_708_cov_7.870528_pilon to pilon.fasta [pilon] Writing NODE_245_length_708_cov_2.270869:1-708 changes to pilon.changes [pilon] Writing updated NODE_245_length_708_cov_2.270869_pilon to pilon.fasta [pilon] Writing NODE_246_length_706_cov_12.011966:1-706 changes to pilon.changes [pilon] Writing updated NODE_246_length_706_cov_12.011966_pilon to pilon.fasta [pilon] Writing NODE_247_length_706_cov_7.126496:1-706 changes to pilon.changes [pilon] Writing updated NODE_247_length_706_cov_7.126496_pilon to pilon.fasta [pilon] Writing NODE_248_length_706_cov_4.246154:1-706 changes to pilon.changes [pilon] Writing updated NODE_248_length_706_cov_4.246154_pilon to pilon.fasta [pilon] Writing NODE_249_length_705_cov_10.506849:1-705 changes to pilon.changes [pilon] Writing updated NODE_249_length_705_cov_10.506849_pilon to pilon.fasta [pilon] Writing NODE_250_length_703_cov_13.702749:1-703 changes to pilon.changes [pilon] Writing updated NODE_250_length_703_cov_13.702749_pilon to pilon.fasta [pilon] Writing NODE_251_length_703_cov_2.912371:1-703 changes to pilon.changes [pilon] Writing updated NODE_251_length_703_cov_2.912371_pilon to pilon.fasta [pilon] Writing NODE_252_length_703_cov_2.020619:1-703 changes to pilon.changes [pilon] Writing updated NODE_252_length_703_cov_2.020619_pilon to pilon.fasta [pilon] Writing NODE_253_length_702_cov_10.481928:1-702 changes to pilon.changes [pilon] Writing updated NODE_253_length_702_cov_10.481928_pilon to pilon.fasta [pilon] Writing NODE_254_length_702_cov_9.564544:1-702 changes to pilon.changes [pilon] Writing updated NODE_254_length_702_cov_9.564544_pilon to pilon.fasta [pilon] Writing NODE_255_length_702_cov_1.733219:1-702 changes to pilon.changes [pilon] Writing updated NODE_255_length_702_cov_1.733219_pilon to pilon.fasta [pilon] Writing NODE_256_length_700_cov_10.943005:1-700 changes to pilon.changes [pilon] Writing updated NODE_256_length_700_cov_10.943005_pilon to pilon.fasta [pilon] Writing NODE_257_length_700_cov_3.290155:1-700 changes to pilon.changes [pilon] Writing updated NODE_257_length_700_cov_3.290155_pilon to pilon.fasta [pilon] Writing NODE_258_length_697_cov_6.779514:1-697 changes to pilon.changes [pilon] Writing updated NODE_258_length_697_cov_6.779514_pilon to pilon.fasta [pilon] Writing NODE_259_length_697_cov_2.095486:1-697 changes to pilon.changes [pilon] Writing updated NODE_259_length_697_cov_2.095486_pilon to pilon.fasta [pilon] Writing NODE_260_length_696_cov_4.808696:1-696 changes to pilon.changes [pilon] Writing updated NODE_260_length_696_cov_4.808696_pilon to pilon.fasta [pilon] Writing NODE_261_length_694_cov_5.057592:1-694 changes to pilon.changes [pilon] Writing updated NODE_261_length_694_cov_5.057592_pilon to pilon.fasta [pilon] Writing NODE_262_length_693_cov_18.087413:1-693 changes to pilon.changes [pilon] Writing updated NODE_262_length_693_cov_18.087413_pilon to pilon.fasta [pilon] Writing NODE_263_length_693_cov_11.055944:1-693 changes to pilon.changes [pilon] Writing updated NODE_263_length_693_cov_11.055944_pilon to pilon.fasta [pilon] Writing NODE_264_length_693_cov_5.673077:1-693 changes to pilon.changes [pilon] Writing updated NODE_264_length_693_cov_5.673077_pilon to pilon.fasta [pilon] Writing NODE_265_length_692_cov_7.987741:1-692 changes to pilon.changes [pilon] Writing updated NODE_265_length_692_cov_7.987741_pilon to pilon.fasta [pilon] Writing NODE_266_length_690_cov_13.720562:1-690 changes to pilon.changes [pilon] Writing updated NODE_266_length_690_cov_13.720562_pilon to pilon.fasta [pilon] Writing NODE_267_length_690_cov_8.441125:1-690 changes to pilon.changes [pilon] Writing updated NODE_267_length_690_cov_8.441125_pilon to pilon.fasta [pilon] Writing NODE_268_length_689_cov_5.595070:1-689 changes to pilon.changes [pilon] Writing updated NODE_268_length_689_cov_5.595070_pilon to pilon.fasta [pilon] Writing NODE_269_length_689_cov_2.417254:1-689 changes to pilon.changes [pilon] Writing updated NODE_269_length_689_cov_2.417254_pilon to pilon.fasta [pilon] Writing NODE_270_length_688_cov_2.793651:1-688 changes to pilon.changes [pilon] Writing updated NODE_270_length_688_cov_2.793651_pilon to pilon.fasta [pilon] Writing NODE_271_length_687_cov_9.517668:1-687 changes to pilon.changes [pilon] Writing updated NODE_271_length_687_cov_9.517668_pilon to pilon.fasta [pilon] Writing NODE_272_length_687_cov_9.204947:1-687 changes to pilon.changes [pilon] Writing updated NODE_272_length_687_cov_9.204947_pilon to pilon.fasta [pilon] Writing NODE_273_length_686_cov_4.472566:1-686 changes to pilon.changes [pilon] Writing updated NODE_273_length_686_cov_4.472566_pilon to pilon.fasta [pilon] Writing NODE_274_length_686_cov_1.407080:1-686 changes to pilon.changes [pilon] Writing updated NODE_274_length_686_cov_1.407080_pilon to pilon.fasta [pilon] Writing NODE_275_length_685_cov_5.287234:1-685 changes to pilon.changes [pilon] Writing updated NODE_275_length_685_cov_5.287234_pilon to pilon.fasta [pilon] Writing NODE_276_length_684_cov_5.488455:1-684 changes to pilon.changes [pilon] Writing updated NODE_276_length_684_cov_5.488455_pilon to pilon.fasta [pilon] Writing NODE_277_length_682_cov_6.190731:1-682 changes to pilon.changes [pilon] Writing updated NODE_277_length_682_cov_6.190731_pilon to pilon.fasta [pilon] Writing NODE_278_length_682_cov_5.737968:1-682 changes to pilon.changes [pilon] Writing updated NODE_278_length_682_cov_5.737968_pilon to pilon.fasta [pilon] Writing NODE_279_length_680_cov_8.694097:1-680 changes to pilon.changes [pilon] Writing updated NODE_279_length_680_cov_8.694097_pilon to pilon.fasta [pilon] Writing NODE_280_length_680_cov_6.016100:1-680 changes to pilon.changes [pilon] Writing updated NODE_280_length_680_cov_6.016100_pilon to pilon.fasta [pilon] Writing NODE_281_length_678_cov_15.633752:1-678 changes to pilon.changes [pilon] Writing updated NODE_281_length_678_cov_15.633752_pilon to pilon.fasta [pilon] Writing NODE_282_length_675_cov_3.539711:1-675 changes to pilon.changes [pilon] Writing updated NODE_282_length_675_cov_3.539711_pilon to pilon.fasta [pilon] Writing NODE_283_length_674_cov_4.443038:1-674 changes to pilon.changes [pilon] Writing updated NODE_283_length_674_cov_4.443038_pilon to pilon.fasta [pilon] Writing NODE_284_length_674_cov_0.871609:1-674 changes to pilon.changes [pilon] Writing updated NODE_284_length_674_cov_0.871609_pilon to pilon.fasta [pilon] Writing NODE_285_length_673_cov_6.056159:1-673 changes to pilon.changes [pilon] Writing updated NODE_285_length_673_cov_6.056159_pilon to pilon.fasta [pilon] Writing NODE_286_length_673_cov_2.041667:1-673 changes to pilon.changes [pilon] Writing updated NODE_286_length_673_cov_2.041667_pilon to pilon.fasta [pilon] Writing NODE_287_length_672_cov_135.872958:1-672 changes to pilon.changes [pilon] Writing updated NODE_287_length_672_cov_135.872958_pilon to pilon.fasta [pilon] Writing NODE_288_length_672_cov_5.842105:1-672 changes to pilon.changes [pilon] Writing updated NODE_288_length_672_cov_5.842105_pilon to pilon.fasta [pilon] Writing NODE_289_length_671_cov_7.592727:1-671 changes to pilon.changes [pilon] Writing updated NODE_289_length_671_cov_7.592727_pilon to pilon.fasta [pilon] Writing NODE_290_length_671_cov_5.743636:1-671 changes to pilon.changes [pilon] Writing updated NODE_290_length_671_cov_5.743636_pilon to pilon.fasta [pilon] Writing NODE_291_length_671_cov_4.807273:1-671 changes to pilon.changes [pilon] Writing updated NODE_291_length_671_cov_4.807273_pilon to pilon.fasta [pilon] Writing NODE_292_length_671_cov_1.358182:1-671 changes to pilon.changes [pilon] Writing updated NODE_292_length_671_cov_1.358182_pilon to pilon.fasta [pilon] Writing NODE_293_length_671_cov_1.327273:1-671 changes to pilon.changes [pilon] Writing updated NODE_293_length_671_cov_1.327273_pilon to pilon.fasta [pilon] Writing NODE_294_length_668_cov_4.166362:1-668 changes to pilon.changes [pilon] Writing updated NODE_294_length_668_cov_4.166362_pilon to pilon.fasta [pilon] Writing NODE_295_length_668_cov_2.533821:1-668 changes to pilon.changes [pilon] Writing updated NODE_295_length_668_cov_2.533821_pilon to pilon.fasta [pilon] Writing NODE_296_length_667_cov_2.014652:1-667 changes to pilon.changes [pilon] Writing updated NODE_296_length_667_cov_2.014652_pilon to pilon.fasta [pilon] Writing NODE_297_length_666_cov_8.636697:1-666 changes to pilon.changes [pilon] Writing updated NODE_297_length_666_cov_8.636697_pilon to pilon.fasta [pilon] Writing NODE_298_length_666_cov_2.227523:1-666 changes to pilon.changes [pilon] Writing updated NODE_298_length_666_cov_2.227523_pilon to pilon.fasta [pilon] Writing NODE_299_length_666_cov_0.715596:1-666 changes to pilon.changes [pilon] Writing updated NODE_299_length_666_cov_0.715596_pilon to pilon.fasta [pilon] Writing NODE_300_length_662_cov_3.741220:1-662 changes to pilon.changes [pilon] Writing updated NODE_300_length_662_cov_3.741220_pilon to pilon.fasta [pilon] Writing NODE_301_length_662_cov_1.837338:1-662 changes to pilon.changes [pilon] Writing updated NODE_301_length_662_cov_1.837338_pilon to pilon.fasta [pilon] Writing NODE_302_length_661_cov_12.557407:1-661 changes to pilon.changes [pilon] Writing updated NODE_302_length_661_cov_12.557407_pilon to pilon.fasta [pilon] Writing NODE_303_length_661_cov_10.912963:1-661 changes to pilon.changes [pilon] Writing updated NODE_303_length_661_cov_10.912963_pilon to pilon.fasta [pilon] Writing NODE_304_length_661_cov_3.374074:1-661 changes to pilon.changes [pilon] Writing updated NODE_304_length_661_cov_3.374074_pilon to pilon.fasta [pilon] Writing NODE_305_length_661_cov_1.529630:1-661 changes to pilon.changes [pilon] Writing updated NODE_305_length_661_cov_1.529630_pilon to pilon.fasta [pilon] Writing NODE_306_length_660_cov_4.077922:1-660 changes to pilon.changes [pilon] Writing updated NODE_306_length_660_cov_4.077922_pilon to pilon.fasta [pilon] Writing NODE_307_length_658_cov_2.163873:1-658 changes to pilon.changes [pilon] Writing updated NODE_307_length_658_cov_2.163873_pilon to pilon.fasta [pilon] Writing NODE_308_length_657_cov_3.386194:1-657 changes to pilon.changes [pilon] Writing updated NODE_308_length_657_cov_3.386194_pilon to pilon.fasta [pilon] Writing NODE_309_length_656_cov_4.977570:1-656 changes to pilon.changes [pilon] Writing updated NODE_309_length_656_cov_4.977570_pilon to pilon.fasta [pilon] Writing NODE_310_length_656_cov_1.218692:1-656 changes to pilon.changes [pilon] Writing updated NODE_310_length_656_cov_1.218692_pilon to pilon.fasta [pilon] Writing NODE_311_length_655_cov_2.867041:1-655 changes to pilon.changes [pilon] Writing updated NODE_311_length_655_cov_2.867041_pilon to pilon.fasta [pilon] Writing NODE_312_length_654_cov_7.894934:1-654 changes to pilon.changes [pilon] Writing updated NODE_312_length_654_cov_7.894934_pilon to pilon.fasta [pilon] Writing NODE_313_length_654_cov_2.236398:1-654 changes to pilon.changes [pilon] Writing updated NODE_313_length_654_cov_2.236398_pilon to pilon.fasta [pilon] Writing NODE_314_length_653_cov_1.436090:1-653 changes to pilon.changes [pilon] Writing updated NODE_314_length_653_cov_1.436090_pilon to pilon.fasta [pilon] Writing NODE_315_length_652_cov_14.425612:1-652 changes to pilon.changes [pilon] Writing updated NODE_315_length_652_cov_14.425612_pilon to pilon.fasta [pilon] Writing NODE_316_length_651_cov_6.639623:1-651 changes to pilon.changes [pilon] Writing updated NODE_316_length_651_cov_6.639623_pilon to pilon.fasta [pilon] Writing NODE_317_length_651_cov_2.745283:1-651 changes to pilon.changes [pilon] Writing updated NODE_317_length_651_cov_2.745283_pilon to pilon.fasta [pilon] Writing NODE_318_length_650_cov_4.098299:1-650 changes to pilon.changes [pilon] Writing updated NODE_318_length_650_cov_4.098299_pilon to pilon.fasta [pilon] Writing NODE_319_length_650_cov_4.007561:1-650 changes to pilon.changes [pilon] Writing updated NODE_319_length_650_cov_4.007561_pilon to pilon.fasta [pilon] Writing NODE_320_length_649_cov_4.556818:1-649 changes to pilon.changes [pilon] Writing updated NODE_320_length_649_cov_4.556818_pilon to pilon.fasta [pilon] Writing NODE_321_length_649_cov_2.943182:1-649 changes to pilon.changes [pilon] Writing updated NODE_321_length_649_cov_2.943182_pilon to pilon.fasta [pilon] Writing NODE_322_length_648_cov_5.081594:1-648 changes to pilon.changes [pilon] Writing updated NODE_322_length_648_cov_5.081594_pilon to pilon.fasta [pilon] Writing NODE_323_length_648_cov_2.656546:1-648 changes to pilon.changes [pilon] Writing updated NODE_323_length_648_cov_2.656546_pilon to pilon.fasta [pilon] Writing NODE_324_length_647_cov_13.633080:1-647 changes to pilon.changes [pilon] Writing updated NODE_324_length_647_cov_13.633080_pilon to pilon.fasta [pilon] Writing NODE_325_length_647_cov_6.089354:1-647 changes to pilon.changes [pilon] Writing updated NODE_325_length_647_cov_6.089354_pilon to pilon.fasta [pilon] Writing NODE_326_length_647_cov_2.990494:1-647 changes to pilon.changes [pilon] Writing updated NODE_326_length_647_cov_2.990494_pilon to pilon.fasta [pilon] Writing NODE_327_length_646_cov_3.708571:1-646 changes to pilon.changes [pilon] Writing updated NODE_327_length_646_cov_3.708571_pilon to pilon.fasta [pilon] Writing NODE_328_length_646_cov_0.775238:1-646 changes to pilon.changes [pilon] Writing updated NODE_328_length_646_cov_0.775238_pilon to pilon.fasta [pilon] Writing NODE_329_length_646_cov_0.761905:1-646 changes to pilon.changes [pilon] Writing updated NODE_329_length_646_cov_0.761905_pilon to pilon.fasta [pilon] Writing NODE_330_length_644_cov_7.353728:1-644 changes to pilon.changes [pilon] Writing updated NODE_330_length_644_cov_7.353728_pilon to pilon.fasta [pilon] Writing NODE_331_length_643_cov_3.398467:1-643 changes to pilon.changes [pilon] Writing updated NODE_331_length_643_cov_3.398467_pilon to pilon.fasta [pilon] Writing NODE_332_length_643_cov_0.992337:1-643 changes to pilon.changes [pilon] Writing updated NODE_332_length_643_cov_0.992337_pilon to pilon.fasta [pilon] Writing NODE_333_length_642_cov_4.161228:1-642 changes to pilon.changes [pilon] Writing updated NODE_333_length_642_cov_4.161228_pilon to pilon.fasta [pilon] Writing NODE_334_length_642_cov_2.654511:1-642 changes to pilon.changes [pilon] Writing updated NODE_334_length_642_cov_2.654511_pilon to pilon.fasta [pilon] Writing NODE_335_length_642_cov_1.644914:1-642 changes to pilon.changes [pilon] Writing updated NODE_335_length_642_cov_1.644914_pilon to pilon.fasta [pilon] Writing NODE_336_length_642_cov_0.660269:1-642 changes to pilon.changes [pilon] Writing updated NODE_336_length_642_cov_0.660269_pilon to pilon.fasta [pilon] Writing NODE_337_length_641_cov_20.051923:1-641 changes to pilon.changes [pilon] Writing updated NODE_337_length_641_cov_20.051923_pilon to pilon.fasta [pilon] Writing NODE_338_length_641_cov_2.815385:1-641 changes to pilon.changes [pilon] Writing updated NODE_338_length_641_cov_2.815385_pilon to pilon.fasta [pilon] Writing NODE_339_length_641_cov_0.930769:1-641 changes to pilon.changes [pilon] Writing updated NODE_339_length_641_cov_0.930769_pilon to pilon.fasta [pilon] Writing NODE_340_length_640_cov_2.533719:1-640 changes to pilon.changes [pilon] Writing updated NODE_340_length_640_cov_2.533719_pilon to pilon.fasta [pilon] Writing NODE_341_length_639_cov_4.073359:1-639 changes to pilon.changes [pilon] Writing updated NODE_341_length_639_cov_4.073359_pilon to pilon.fasta [pilon] Writing NODE_342_length_637_cov_19.019380:1-637 changes to pilon.changes [pilon] Writing updated NODE_342_length_637_cov_19.019380_pilon to pilon.fasta [pilon] Writing NODE_343_length_637_cov_10.397287:1-637 changes to pilon.changes [pilon] Writing updated NODE_343_length_637_cov_10.397287_pilon to pilon.fasta [pilon] Writing NODE_344_length_636_cov_4.460194:1-636 changes to pilon.changes [pilon] Writing updated NODE_344_length_636_cov_4.460194_pilon to pilon.fasta [pilon] Writing NODE_345_length_634_cov_2.976608:1-634 changes to pilon.changes [pilon] Writing updated NODE_345_length_634_cov_2.976608_pilon to pilon.fasta [pilon] Writing NODE_346_length_632_cov_1.418787:1-632 changes to pilon.changes [pilon] Writing updated NODE_346_length_632_cov_1.418787_pilon to pilon.fasta [pilon] Writing NODE_347_length_631_cov_7.131373:1-631 changes to pilon.changes [pilon] Writing updated NODE_347_length_631_cov_7.131373_pilon to pilon.fasta [pilon] Writing NODE_348_length_630_cov_6.960707:1-630 changes to pilon.changes [pilon] Writing updated NODE_348_length_630_cov_6.960707_pilon to pilon.fasta [pilon] Writing NODE_349_length_629_cov_12.068898:1-629 changes to pilon.changes [pilon] Writing updated NODE_349_length_629_cov_12.068898_pilon to pilon.fasta [pilon] Writing NODE_350_length_629_cov_3.021654:1-629 changes to pilon.changes [pilon] Writing updated NODE_350_length_629_cov_3.021654_pilon to pilon.fasta [pilon] Writing NODE_351_length_629_cov_0.990157:1-629 changes to pilon.changes [pilon] Writing updated NODE_351_length_629_cov_0.990157_pilon to pilon.fasta [pilon] Writing NODE_352_length_628_cov_16.928994:1-628 changes to pilon.changes [pilon] Writing updated NODE_352_length_628_cov_16.928994_pilon to pilon.fasta [pilon] Writing NODE_353_length_628_cov_1.211045:1-628 changes to pilon.changes [pilon] Writing updated NODE_353_length_628_cov_1.211045_pilon to pilon.fasta [pilon] Writing NODE_354_length_627_cov_0.901186:1-627 changes to pilon.changes [pilon] Writing updated NODE_354_length_627_cov_0.901186_pilon to pilon.fasta [pilon] Writing NODE_355_length_627_cov_0.723320:1-627 changes to pilon.changes [pilon] Writing updated NODE_355_length_627_cov_0.723320_pilon to pilon.fasta [pilon] Writing NODE_356_length_626_cov_2.227723:1-626 changes to pilon.changes [pilon] Writing updated NODE_356_length_626_cov_2.227723_pilon to pilon.fasta [pilon] Writing NODE_357_length_625_cov_1.605159:1-625 changes to pilon.changes [pilon] Writing updated NODE_357_length_625_cov_1.605159_pilon to pilon.fasta [pilon] Writing NODE_358_length_624_cov_6.866799:1-624 changes to pilon.changes [pilon] Writing updated NODE_358_length_624_cov_6.866799_pilon to pilon.fasta [pilon] Writing NODE_359_length_624_cov_2.216700:1-624 changes to pilon.changes [pilon] Writing updated NODE_359_length_624_cov_2.216700_pilon to pilon.fasta [pilon] Writing NODE_360_length_622_cov_2.205589:1-622 changes to pilon.changes [pilon] Writing updated NODE_360_length_622_cov_2.205589_pilon to pilon.fasta [pilon] Writing NODE_361_length_622_cov_1.826347:1-622 changes to pilon.changes [pilon] Writing updated NODE_361_length_622_cov_1.826347_pilon to pilon.fasta [pilon] Writing NODE_362_length_622_cov_0.612774:1-622 changes to pilon.changes [pilon] Writing updated NODE_362_length_622_cov_0.612774_pilon to pilon.fasta [pilon] Writing NODE_363_length_621_cov_1.536000:1-621 changes to pilon.changes [pilon] Writing updated NODE_363_length_621_cov_1.536000_pilon to pilon.fasta [pilon] Writing NODE_364_length_620_cov_3.044088:1-620 changes to pilon.changes [pilon] Writing updated NODE_364_length_620_cov_3.044088_pilon to pilon.fasta [pilon] Writing NODE_365_length_620_cov_1.148297:1-620 changes to pilon.changes [pilon] Writing updated NODE_365_length_620_cov_1.148297_pilon to pilon.fasta [pilon] Writing NODE_366_length_619_cov_9.184739:1-619 changes to pilon.changes [pilon] Writing updated NODE_366_length_619_cov_9.184739_pilon to pilon.fasta [pilon] Writing NODE_367_length_619_cov_4.359438:1-619 changes to pilon.changes [pilon] Writing updated NODE_367_length_619_cov_4.359438_pilon to pilon.fasta [pilon] Writing NODE_368_length_618_cov_3.501006:1-618 changes to pilon.changes [pilon] Writing updated NODE_368_length_618_cov_3.501006_pilon to pilon.fasta [pilon] Writing NODE_369_length_618_cov_2.336016:1-618 changes to pilon.changes [pilon] Writing updated NODE_369_length_618_cov_2.336016_pilon to pilon.fasta [pilon] Writing NODE_370_length_617_cov_0.774194:1-617 changes to pilon.changes [pilon] Writing updated NODE_370_length_617_cov_0.774194_pilon to pilon.fasta [pilon] Writing NODE_371_length_616_cov_2.884848:1-616 changes to pilon.changes [pilon] Writing updated NODE_371_length_616_cov_2.884848_pilon to pilon.fasta [pilon] Writing NODE_372_length_616_cov_2.371717:1-616 changes to pilon.changes [pilon] Writing updated NODE_372_length_616_cov_2.371717_pilon to pilon.fasta [pilon] Writing NODE_373_length_616_cov_2.294949:1-616 changes to pilon.changes [pilon] Writing updated NODE_373_length_616_cov_2.294949_pilon to pilon.fasta [pilon] Writing NODE_374_length_615_cov_1.866397:1-615 changes to pilon.changes [pilon] Writing updated NODE_374_length_615_cov_1.866397_pilon to pilon.fasta [pilon] Writing NODE_375_length_614_cov_8.077079:1-614 changes to pilon.changes [pilon] Writing updated NODE_375_length_614_cov_8.077079_pilon to pilon.fasta [pilon] Writing NODE_376_length_614_cov_1.245436:1-614 changes to pilon.changes [pilon] Writing updated NODE_376_length_614_cov_1.245436_pilon to pilon.fasta [pilon] Writing NODE_377_length_613_cov_3.654472:1-613 changes to pilon.changes [pilon] Writing updated NODE_377_length_613_cov_3.654472_pilon to pilon.fasta [pilon] Writing NODE_378_length_613_cov_1.747967:1-613 changes to pilon.changes [pilon] Writing updated NODE_378_length_613_cov_1.747967_pilon to pilon.fasta [pilon] Writing NODE_379_length_611_cov_1.889796:1-611 changes to pilon.changes [pilon] Writing updated NODE_379_length_611_cov_1.889796_pilon to pilon.fasta [pilon] Writing NODE_380_length_610_cov_3.396728:1-610 changes to pilon.changes [pilon] Writing updated NODE_380_length_610_cov_3.396728_pilon to pilon.fasta [pilon] Writing NODE_381_length_609_cov_3.153689:1-609 changes to pilon.changes [pilon] Writing updated NODE_381_length_609_cov_3.153689_pilon to pilon.fasta [pilon] Writing NODE_382_length_609_cov_3.040984:1-609 changes to pilon.changes [pilon] Writing updated NODE_382_length_609_cov_3.040984_pilon to pilon.fasta [pilon] Writing NODE_383_length_608_cov_2.195072:1-608 changes to pilon.changes [pilon] Writing updated NODE_383_length_608_cov_2.195072_pilon to pilon.fasta [pilon] Writing NODE_384_length_607_cov_3.839506:1-607 changes to pilon.changes [pilon] Writing updated NODE_384_length_607_cov_3.839506_pilon to pilon.fasta [pilon] Writing NODE_385_length_607_cov_2.683128:1-607 changes to pilon.changes [pilon] Writing updated NODE_385_length_607_cov_2.683128_pilon to pilon.fasta [pilon] Writing NODE_386_length_607_cov_0.742798:1-607 changes to pilon.changes [pilon] Writing updated NODE_386_length_607_cov_0.742798_pilon to pilon.fasta [pilon] Writing NODE_387_length_606_cov_1.863918:1-606 changes to pilon.changes [pilon] Writing updated NODE_387_length_606_cov_1.863918_pilon to pilon.fasta [pilon] Writing NODE_388_length_604_cov_4.625259:1-604 changes to pilon.changes [pilon] Writing updated NODE_388_length_604_cov_4.625259_pilon to pilon.fasta [pilon] Writing NODE_389_length_604_cov_4.391304:1-604 changes to pilon.changes [pilon] Writing updated NODE_389_length_604_cov_4.391304_pilon to pilon.fasta [pilon] Writing NODE_390_length_604_cov_1.343685:1-604 changes to pilon.changes [pilon] Writing updated NODE_390_length_604_cov_1.343685_pilon to pilon.fasta [pilon] Writing NODE_391_length_604_cov_1.165631:1-604 changes to pilon.changes [pilon] Writing updated NODE_391_length_604_cov_1.165631_pilon to pilon.fasta [pilon] Writing NODE_392_length_603_cov_1.765560:1-603 changes to pilon.changes [pilon] Writing updated NODE_392_length_603_cov_1.765560_pilon to pilon.fasta [pilon] Writing NODE_393_length_602_cov_7.295218:1-602 changes to pilon.changes [pilon] Writing updated NODE_393_length_602_cov_7.295218_pilon to pilon.fasta [pilon] Writing NODE_394_length_602_cov_1.147609:1-602 changes to pilon.changes [pilon] Writing updated NODE_394_length_602_cov_1.147609_pilon to pilon.fasta [pilon] Writing NODE_395_length_601_cov_1.741667:1-601 changes to pilon.changes [pilon] Writing updated NODE_395_length_601_cov_1.741667_pilon to pilon.fasta [pilon] Writing NODE_396_length_600_cov_13.361169:1-600 changes to pilon.changes [pilon] Writing updated NODE_396_length_600_cov_13.361169_pilon to pilon.fasta [pilon] Writing NODE_397_length_600_cov_1.826722:1-600 changes to pilon.changes [pilon] Writing updated NODE_397_length_600_cov_1.826722_pilon to pilon.fasta [pilon] Writing NODE_398_length_600_cov_1.668058:1-600 changes to pilon.changes [pilon] Writing updated NODE_398_length_600_cov_1.668058_pilon to pilon.fasta [pilon] Writing NODE_399_length_599_cov_11.370293:1-599 changes to pilon.changes [pilon] Writing updated NODE_399_length_599_cov_11.370293_pilon to pilon.fasta [pilon] Writing NODE_400_length_599_cov_3.847280:1-599 changes to pilon.changes [pilon] Writing updated NODE_400_length_599_cov_3.847280_pilon to pilon.fasta [pilon] Writing NODE_401_length_599_cov_3.085774:1-599 changes to pilon.changes [pilon] Writing updated NODE_401_length_599_cov_3.085774_pilon to pilon.fasta [pilon] Writing NODE_402_length_599_cov_2.025105:1-599 changes to pilon.changes [pilon] Writing updated NODE_402_length_599_cov_2.025105_pilon to pilon.fasta [pilon] Writing NODE_403_length_597_cov_5.792017:1-597 changes to pilon.changes [pilon] Writing updated NODE_403_length_597_cov_5.792017_pilon to pilon.fasta [pilon] Writing NODE_404_length_597_cov_3.235294:1-597 changes to pilon.changes [pilon] Writing updated NODE_404_length_597_cov_3.235294_pilon to pilon.fasta [pilon] Writing NODE_405_length_597_cov_3.039916:1-597 changes to pilon.changes [pilon] Writing updated NODE_405_length_597_cov_3.039916_pilon to pilon.fasta [pilon] Writing NODE_406_length_597_cov_2.689076:1-597 changes to pilon.changes [pilon] Writing updated NODE_406_length_597_cov_2.689076_pilon to pilon.fasta [pilon] Writing NODE_407_length_597_cov_2.407563:1-597 changes to pilon.changes [pilon] Writing updated NODE_407_length_597_cov_2.407563_pilon to pilon.fasta [pilon] Writing NODE_408_length_595_cov_3.504219:1-595 changes to pilon.changes [pilon] Writing updated NODE_408_length_595_cov_3.504219_pilon to pilon.fasta [pilon] Writing NODE_409_length_595_cov_2.453586:1-595 changes to pilon.changes [pilon] Writing updated NODE_409_length_595_cov_2.453586_pilon to pilon.fasta [pilon] Writing NODE_410_length_595_cov_2.067511:1-595 changes to pilon.changes [pilon] Writing updated NODE_410_length_595_cov_2.067511_pilon to pilon.fasta [pilon] Writing NODE_411_length_595_cov_2.040084:1-595 changes to pilon.changes [pilon] Writing updated NODE_411_length_595_cov_2.040084_pilon to pilon.fasta [pilon] Writing NODE_412_length_594_cov_16.319239:1-594 changes to pilon.changes [pilon] Writing updated NODE_412_length_594_cov_16.319239_pilon to pilon.fasta [pilon] Writing NODE_413_length_594_cov_1.040169:1-594 changes to pilon.changes [pilon] Writing updated NODE_413_length_594_cov_1.040169_pilon to pilon.fasta [pilon] Writing NODE_414_length_593_cov_0.741525:1-593 changes to pilon.changes [pilon] Writing updated NODE_414_length_593_cov_0.741525_pilon to pilon.fasta [pilon] Writing NODE_415_length_592_cov_8.649682:1-592 changes to pilon.changes [pilon] Writing updated NODE_415_length_592_cov_8.649682_pilon to pilon.fasta [pilon] Writing NODE_416_length_592_cov_4.552017:1-592 changes to pilon.changes [pilon] Writing updated NODE_416_length_592_cov_4.552017_pilon to pilon.fasta [pilon] Writing NODE_417_length_592_cov_2.675159:1-592 changes to pilon.changes [pilon] Writing updated NODE_417_length_592_cov_2.675159_pilon to pilon.fasta [pilon] Writing NODE_418_length_592_cov_2.409766:1-592 changes to pilon.changes [pilon] Writing updated NODE_418_length_592_cov_2.409766_pilon to pilon.fasta [pilon] Writing NODE_419_length_591_cov_3.208511:1-591 changes to pilon.changes [pilon] Writing updated NODE_419_length_591_cov_3.208511_pilon to pilon.fasta [pilon] Writing NODE_420_length_589_cov_2.865385:1-589 changes to pilon.changes [pilon] Writing updated NODE_420_length_589_cov_2.865385_pilon to pilon.fasta [pilon] Writing NODE_421_length_587_cov_11.553648:1-587 changes to pilon.changes [pilon] Writing updated NODE_421_length_587_cov_11.553648_pilon to pilon.fasta [pilon] Writing NODE_422_length_587_cov_4.302575:1-587 changes to pilon.changes [pilon] Writing updated NODE_422_length_587_cov_4.302575_pilon to pilon.fasta [pilon] Writing NODE_423_length_587_cov_3.555794:1-587 changes to pilon.changes [pilon] Writing updated NODE_423_length_587_cov_3.555794_pilon to pilon.fasta [pilon] Writing NODE_424_length_587_cov_2.729614:1-587 changes to pilon.changes [pilon] Writing updated NODE_424_length_587_cov_2.729614_pilon to pilon.fasta [pilon] Writing NODE_425_length_585_cov_7.530172:1-585 changes to pilon.changes [pilon] Writing updated NODE_425_length_585_cov_7.530172_pilon to pilon.fasta [pilon] Writing NODE_426_length_585_cov_3.517241:1-585 changes to pilon.changes [pilon] Writing updated NODE_426_length_585_cov_3.517241_pilon to pilon.fasta [pilon] Writing NODE_427_length_584_cov_4.844492:1-584 changes to pilon.changes [pilon] Writing updated NODE_427_length_584_cov_4.844492_pilon to pilon.fasta [pilon] Writing NODE_428_length_584_cov_2.097192:1-584 changes to pilon.changes [pilon] Writing updated NODE_428_length_584_cov_2.097192_pilon to pilon.fasta [pilon] Writing NODE_429_length_584_cov_1.611231:1-584 changes to pilon.changes [pilon] Writing updated NODE_429_length_584_cov_1.611231_pilon to pilon.fasta [pilon] Writing NODE_430_length_584_cov_0.552916:1-584 changes to pilon.changes [pilon] Writing updated NODE_430_length_584_cov_0.552916_pilon to pilon.fasta [pilon] Writing NODE_431_length_583_cov_5.699134:1-583 changes to pilon.changes [pilon] Writing updated NODE_431_length_583_cov_5.699134_pilon to pilon.fasta [pilon] Writing NODE_432_length_582_cov_5.616052:1-582 changes to pilon.changes [pilon] Writing updated NODE_432_length_582_cov_5.616052_pilon to pilon.fasta [pilon] Writing NODE_433_length_582_cov_2.464208:1-582 changes to pilon.changes [pilon] Writing updated NODE_433_length_582_cov_2.464208_pilon to pilon.fasta [pilon] Writing NODE_434_length_581_cov_1.110870:1-581 changes to pilon.changes [pilon] Writing updated NODE_434_length_581_cov_1.110870_pilon to pilon.fasta [pilon] Writing NODE_435_length_581_cov_0.717391:1-581 changes to pilon.changes [pilon] Writing updated NODE_435_length_581_cov_0.717391_pilon to pilon.fasta [pilon] Writing NODE_436_length_579_cov_9.914847:1-579 changes to pilon.changes [pilon] Writing updated NODE_436_length_579_cov_9.914847_pilon to pilon.fasta [pilon] Writing NODE_437_length_578_cov_1.682713:1-578 changes to pilon.changes [pilon] Writing updated NODE_437_length_578_cov_1.682713_pilon to pilon.fasta [pilon] Writing NODE_438_length_578_cov_1.271335:1-578 changes to pilon.changes [pilon] Writing updated NODE_438_length_578_cov_1.271335_pilon to pilon.fasta [pilon] Writing NODE_439_length_577_cov_1.967105:1-577 changes to pilon.changes [pilon] Writing updated NODE_439_length_577_cov_1.967105_pilon to pilon.fasta [pilon] Writing NODE_440_length_577_cov_1.548246:1-577 changes to pilon.changes [pilon] Writing updated NODE_440_length_577_cov_1.548246_pilon to pilon.fasta [pilon] Writing NODE_441_length_577_cov_1.447368:1-577 changes to pilon.changes [pilon] Writing updated NODE_441_length_577_cov_1.447368_pilon to pilon.fasta [pilon] Writing NODE_442_length_577_cov_1.396930:1-577 changes to pilon.changes [pilon] Writing updated NODE_442_length_577_cov_1.396930_pilon to pilon.fasta [pilon] Writing NODE_443_length_577_cov_0.660088:1-577 changes to pilon.changes [pilon] Writing updated NODE_443_length_577_cov_0.660088_pilon to pilon.fasta [pilon] Writing NODE_444_length_576_cov_2.457143:1-576 changes to pilon.changes [pilon] Writing updated NODE_444_length_576_cov_2.457143_pilon to pilon.fasta [pilon] Writing NODE_445_length_576_cov_1.593407:1-576 changes to pilon.changes [pilon] Writing updated NODE_445_length_576_cov_1.593407_pilon to pilon.fasta [pilon] Writing NODE_446_length_576_cov_1.351648:1-576 changes to pilon.changes [pilon] Writing updated NODE_446_length_576_cov_1.351648_pilon to pilon.fasta [pilon] Writing NODE_447_length_575_cov_4.718062:1-575 changes to pilon.changes [pilon] Writing updated NODE_447_length_575_cov_4.718062_pilon to pilon.fasta [pilon] Writing NODE_448_length_575_cov_4.389868:1-575 changes to pilon.changes [pilon] Writing updated NODE_448_length_575_cov_4.389868_pilon to pilon.fasta [pilon] Writing NODE_449_length_574_cov_1.578366:1-574 changes to pilon.changes [pilon] Writing updated NODE_449_length_574_cov_1.578366_pilon to pilon.fasta [pilon] Writing NODE_450_length_573_cov_4.059735:1-573 changes to pilon.changes [pilon] Writing updated NODE_450_length_573_cov_4.059735_pilon to pilon.fasta [pilon] Writing NODE_451_length_573_cov_0.865044:1-573 changes to pilon.changes [pilon] Writing updated NODE_451_length_573_cov_0.865044_pilon to pilon.fasta [pilon] Writing NODE_452_length_572_cov_3.585366:1-572 changes to pilon.changes [pilon] Writing updated NODE_452_length_572_cov_3.585366_pilon to pilon.fasta [pilon] Writing NODE_453_length_571_cov_2.268889:1-571 changes to pilon.changes [pilon] Writing updated NODE_453_length_571_cov_2.268889_pilon to pilon.fasta [pilon] Writing NODE_454_length_570_cov_0.556793:1-570 changes to pilon.changes [pilon] Writing updated NODE_454_length_570_cov_0.556793_pilon to pilon.fasta [pilon] Writing NODE_455_length_569_cov_4.328125:1-569 changes to pilon.changes [pilon] Writing updated NODE_455_length_569_cov_4.328125_pilon to pilon.fasta [pilon] Writing NODE_456_length_569_cov_4.133929:1-569 changes to pilon.changes [pilon] Writing updated NODE_456_length_569_cov_4.133929_pilon to pilon.fasta [pilon] Writing NODE_457_length_569_cov_3.955357:1-569 changes to pilon.changes [pilon] Writing updated NODE_457_length_569_cov_3.955357_pilon to pilon.fasta [pilon] Writing NODE_458_length_569_cov_1.357143:1-569 changes to pilon.changes [pilon] Writing updated NODE_458_length_569_cov_1.357143_pilon to pilon.fasta [pilon] Writing NODE_459_length_569_cov_0.763393:1-569 changes to pilon.changes [pilon] Writing updated NODE_459_length_569_cov_0.763393_pilon to pilon.fasta [pilon] Writing NODE_460_length_568_cov_10.100671:1-568 changes to pilon.changes [pilon] Writing updated NODE_460_length_568_cov_10.100671_pilon to pilon.fasta [pilon] Writing NODE_461_length_568_cov_3.635347:1-568 changes to pilon.changes [pilon] Writing updated NODE_461_length_568_cov_3.635347_pilon to pilon.fasta [pilon] Writing NODE_462_length_568_cov_1.662192:1-568 changes to pilon.changes [pilon] Writing updated NODE_462_length_568_cov_1.662192_pilon to pilon.fasta [pilon] Writing NODE_463_length_568_cov_1.210291:1-568 changes to pilon.changes [pilon] Writing updated NODE_463_length_568_cov_1.210291_pilon to pilon.fasta [pilon] Writing NODE_464_length_566_cov_4.561798:1-566 changes to pilon.changes [pilon] Writing updated NODE_464_length_566_cov_4.561798_pilon to pilon.fasta [pilon] Writing NODE_465_length_566_cov_3.964045:1-566 changes to pilon.changes [pilon] Writing updated NODE_465_length_566_cov_3.964045_pilon to pilon.fasta [pilon] Writing NODE_466_length_566_cov_3.494382:1-566 changes to pilon.changes [pilon] Writing updated NODE_466_length_566_cov_3.494382_pilon to pilon.fasta [pilon] Writing NODE_467_length_566_cov_0.833708:1-566 changes to pilon.changes [pilon] Writing updated NODE_467_length_566_cov_0.833708_pilon to pilon.fasta [pilon] Writing NODE_468_length_565_cov_6.135135:1-565 changes to pilon.changes [pilon] Writing updated NODE_468_length_565_cov_6.135135_pilon to pilon.fasta [pilon] Writing NODE_469_length_565_cov_6.002252:1-565 changes to pilon.changes [pilon] Writing updated NODE_469_length_565_cov_6.002252_pilon to pilon.fasta [pilon] Writing NODE_470_length_565_cov_3.094595:1-565 changes to pilon.changes [pilon] Writing updated NODE_470_length_565_cov_3.094595_pilon to pilon.fasta [pilon] Writing NODE_471_length_564_cov_4.591422:1-564 changes to pilon.changes [pilon] Writing updated NODE_471_length_564_cov_4.591422_pilon to pilon.fasta [pilon] Writing NODE_472_length_563_cov_7.088235:1-563 changes to pilon.changes [pilon] Writing updated NODE_472_length_563_cov_7.088235_pilon to pilon.fasta [pilon] Writing NODE_473_length_563_cov_1.889140:1-563 changes to pilon.changes [pilon] Writing updated NODE_473_length_563_cov_1.889140_pilon to pilon.fasta [pilon] Writing NODE_474_length_563_cov_1.601810:1-563 changes to pilon.changes [pilon] Writing updated NODE_474_length_563_cov_1.601810_pilon to pilon.fasta [pilon] Writing NODE_475_length_562_cov_2.623583:1-562 changes to pilon.changes [pilon] Writing updated NODE_475_length_562_cov_2.623583_pilon to pilon.fasta [pilon] Writing NODE_476_length_561_cov_3.343182:1-561 changes to pilon.changes [pilon] Writing updated NODE_476_length_561_cov_3.343182_pilon to pilon.fasta [pilon] Writing NODE_477_length_561_cov_2.334091:1-561 changes to pilon.changes [pilon] Writing updated NODE_477_length_561_cov_2.334091_pilon to pilon.fasta [pilon] Writing NODE_478_length_561_cov_2.020455:1-561 changes to pilon.changes [pilon] Writing updated NODE_478_length_561_cov_2.020455_pilon to pilon.fasta [pilon] Writing NODE_479_length_561_cov_1.650000:1-561 changes to pilon.changes [pilon] Writing updated NODE_479_length_561_cov_1.650000_pilon to pilon.fasta [pilon] Writing NODE_480_length_561_cov_1.459091:1-561 changes to pilon.changes [pilon] Writing updated NODE_480_length_561_cov_1.459091_pilon to pilon.fasta [pilon] Writing NODE_481_length_559_cov_3.180365:1-559 changes to pilon.changes [pilon] Writing updated NODE_481_length_559_cov_3.180365_pilon to pilon.fasta [pilon] Writing NODE_482_length_559_cov_0.958904:1-559 changes to pilon.changes [pilon] Writing updated NODE_482_length_559_cov_0.958904_pilon to pilon.fasta [pilon] Writing NODE_483_length_558_cov_2.189931:1-558 changes to pilon.changes [pilon] Writing updated NODE_483_length_558_cov_2.189931_pilon to pilon.fasta [pilon] Writing NODE_484_length_557_cov_8.646789:1-557 changes to pilon.changes [pilon] Writing updated NODE_484_length_557_cov_8.646789_pilon to pilon.fasta [pilon] Writing NODE_485_length_557_cov_5.697248:1-557 changes to pilon.changes [pilon] Writing updated NODE_485_length_557_cov_5.697248_pilon to pilon.fasta [pilon] Writing NODE_486_length_557_cov_3.717890:1-557 changes to pilon.changes [pilon] Writing updated NODE_486_length_557_cov_3.717890_pilon to pilon.fasta [pilon] Writing NODE_487_length_557_cov_0.983945:1-557 changes to pilon.changes [pilon] Writing updated NODE_487_length_557_cov_0.983945_pilon to pilon.fasta [pilon] Writing NODE_488_length_556_cov_3.949425:1-556 changes to pilon.changes [pilon] Writing updated NODE_488_length_556_cov_3.949425_pilon to pilon.fasta [pilon] Writing NODE_489_length_555_cov_5.700461:1-555 changes to pilon.changes [pilon] Writing updated NODE_489_length_555_cov_5.700461_pilon to pilon.fasta [pilon] Writing NODE_490_length_555_cov_3.237327:1-555 changes to pilon.changes [pilon] Writing updated NODE_490_length_555_cov_3.237327_pilon to pilon.fasta [pilon] Writing NODE_491_length_555_cov_2.361751:1-555 changes to pilon.changes [pilon] Writing updated NODE_491_length_555_cov_2.361751_pilon to pilon.fasta [pilon] Writing NODE_492_length_555_cov_1.419355:1-555 changes to pilon.changes [pilon] Writing updated NODE_492_length_555_cov_1.419355_pilon to pilon.fasta [pilon] Writing NODE_493_length_554_cov_1.586605:1-554 changes to pilon.changes [pilon] Writing updated NODE_493_length_554_cov_1.586605_pilon to pilon.fasta [pilon] Writing NODE_494_length_554_cov_1.124711:1-554 changes to pilon.changes [pilon] Writing updated NODE_494_length_554_cov_1.124711_pilon to pilon.fasta [pilon] Writing NODE_495_length_553_cov_1.171296:1-553 changes to pilon.changes [pilon] Writing updated NODE_495_length_553_cov_1.171296_pilon to pilon.fasta [pilon] Writing NODE_496_length_552_cov_2.361949:1-552 changes to pilon.changes [pilon] Writing updated NODE_496_length_552_cov_2.361949_pilon to pilon.fasta [pilon] Writing NODE_497_length_552_cov_2.109049:1-552 changes to pilon.changes [pilon] Writing updated NODE_497_length_552_cov_2.109049_pilon to pilon.fasta [pilon] Writing NODE_498_length_552_cov_1.018561:1-552 changes to pilon.changes [pilon] Writing updated NODE_498_length_552_cov_1.018561_pilon to pilon.fasta [pilon] Writing NODE_499_length_551_cov_2.186047:1-551 changes to pilon.changes [pilon] Writing updated NODE_499_length_551_cov_2.186047_pilon to pilon.fasta [pilon] Writing NODE_500_length_551_cov_1.555814:1-551 changes to pilon.changes [pilon] Writing updated NODE_500_length_551_cov_1.555814_pilon to pilon.fasta [pilon] Writing NODE_501_length_551_cov_1.011628:1-551 changes to pilon.changes [pilon] Writing updated NODE_501_length_551_cov_1.011628_pilon to pilon.fasta [pilon] Writing NODE_502_length_550_cov_7.286713:1-550 changes to pilon.changes [pilon] Writing updated NODE_502_length_550_cov_7.286713_pilon to pilon.fasta [pilon] Writing NODE_503_length_550_cov_3.997669:1-550 changes to pilon.changes [pilon] Writing updated NODE_503_length_550_cov_3.997669_pilon to pilon.fasta [pilon] Writing NODE_504_length_550_cov_3.918415:1-550 changes to pilon.changes [pilon] Writing updated NODE_504_length_550_cov_3.918415_pilon to pilon.fasta [pilon] Writing NODE_505_length_550_cov_3.151515:1-550 changes to pilon.changes [pilon] Writing updated NODE_505_length_550_cov_3.151515_pilon to pilon.fasta [pilon] Writing NODE_506_length_550_cov_2.547786:1-550 changes to pilon.changes [pilon] Writing updated NODE_506_length_550_cov_2.547786_pilon to pilon.fasta [pilon] Writing NODE_507_length_550_cov_1.172494:1-550 changes to pilon.changes [pilon] Writing updated NODE_507_length_550_cov_1.172494_pilon to pilon.fasta [pilon] Writing NODE_508_length_549_cov_7.191589:1-549 changes to pilon.changes [pilon] Writing updated NODE_508_length_549_cov_7.191589_pilon to pilon.fasta [pilon] Writing NODE_509_length_549_cov_1.934579:1-549 changes to pilon.changes [pilon] Writing updated NODE_509_length_549_cov_1.934579_pilon to pilon.fasta [pilon] Writing NODE_510_length_549_cov_1.546729:1-549 changes to pilon.changes [pilon] Writing updated NODE_510_length_549_cov_1.546729_pilon to pilon.fasta [pilon] Writing NODE_511_length_548_cov_2.377049:1-548 changes to pilon.changes [pilon] Writing updated NODE_511_length_548_cov_2.377049_pilon to pilon.fasta [pilon] Writing NODE_512_length_548_cov_1.957845:1-548 changes to pilon.changes [pilon] Writing updated NODE_512_length_548_cov_1.957845_pilon to pilon.fasta [pilon] Writing NODE_513_length_548_cov_1.515222:1-548 changes to pilon.changes [pilon] Writing updated NODE_513_length_548_cov_1.515222_pilon to pilon.fasta [pilon] Writing NODE_514_length_547_cov_5.532864:1-547 changes to pilon.changes [pilon] Writing updated NODE_514_length_547_cov_5.532864_pilon to pilon.fasta [pilon] Writing NODE_515_length_547_cov_2.814554:1-547 changes to pilon.changes [pilon] Writing updated NODE_515_length_547_cov_2.814554_pilon to pilon.fasta [pilon] Writing NODE_516_length_547_cov_1.326291:1-547 changes to pilon.changes [pilon] Writing updated NODE_516_length_547_cov_1.326291_pilon to pilon.fasta [pilon] Writing NODE_517_length_547_cov_1.286385:1-547 changes to pilon.changes [pilon] Writing updated NODE_517_length_547_cov_1.286385_pilon to pilon.fasta [pilon] Writing NODE_518_length_546_cov_2.468235:1-546 changes to pilon.changes [pilon] Writing updated NODE_518_length_546_cov_2.468235_pilon to pilon.fasta [pilon] Writing NODE_519_length_545_cov_0.896226:1-545 changes to pilon.changes [pilon] Writing updated NODE_519_length_545_cov_0.896226_pilon to pilon.fasta [pilon] Writing NODE_520_length_544_cov_9.387707:1-544 changes to pilon.changes [pilon] Writing updated NODE_520_length_544_cov_9.387707_pilon to pilon.fasta [pilon] Writing NODE_521_length_544_cov_3.744681:1-544 changes to pilon.changes [pilon] Writing updated NODE_521_length_544_cov_3.744681_pilon to pilon.fasta [pilon] Writing NODE_522_length_544_cov_1.345154:1-544 changes to pilon.changes [pilon] Writing updated NODE_522_length_544_cov_1.345154_pilon to pilon.fasta [pilon] Writing NODE_523_length_543_cov_0.696682:1-543 changes to pilon.changes [pilon] Writing updated NODE_523_length_543_cov_0.696682_pilon to pilon.fasta [pilon] Writing NODE_524_length_541_cov_2.733333:1-541 changes to pilon.changes [pilon] Writing updated NODE_524_length_541_cov_2.733333_pilon to pilon.fasta [pilon] Writing NODE_525_length_541_cov_1.269048:1-541 changes to pilon.changes [pilon] Writing updated NODE_525_length_541_cov_1.269048_pilon to pilon.fasta [pilon] Writing NODE_526_length_539_cov_0.894737:1-539 changes to pilon.changes [pilon] Writing updated NODE_526_length_539_cov_0.894737_pilon to pilon.fasta [pilon] Writing NODE_527_length_538_cov_1.733813:1-538 changes to pilon.changes [pilon] Writing updated NODE_527_length_538_cov_1.733813_pilon to pilon.fasta [pilon] Writing NODE_528_length_538_cov_1.446043:1-538 changes to pilon.changes [pilon] Writing updated NODE_528_length_538_cov_1.446043_pilon to pilon.fasta [pilon] Writing NODE_529_length_538_cov_0.671463:1-538 changes to pilon.changes [pilon] Writing updated NODE_529_length_538_cov_0.671463_pilon to pilon.fasta [pilon] Writing NODE_530_length_537_cov_13.817308:1-537 changes to pilon.changes [pilon] Writing updated NODE_530_length_537_cov_13.817308_pilon to pilon.fasta [pilon] Writing NODE_531_length_537_cov_1.574519:1-537 changes to pilon.changes [pilon] Writing updated NODE_531_length_537_cov_1.574519_pilon to pilon.fasta [pilon] Writing NODE_532_length_536_cov_4.913253:1-536 changes to pilon.changes [pilon] Writing updated NODE_532_length_536_cov_4.913253_pilon to pilon.fasta [pilon] Writing NODE_533_length_536_cov_3.684337:1-536 changes to pilon.changes [pilon] Writing updated NODE_533_length_536_cov_3.684337_pilon to pilon.fasta [pilon] Writing NODE_534_length_536_cov_2.457831:1-536 changes to pilon.changes [pilon] Writing updated NODE_534_length_536_cov_2.457831_pilon to pilon.fasta [pilon] Writing NODE_535_length_536_cov_1.884337:1-536 changes to pilon.changes [pilon] Writing updated NODE_535_length_536_cov_1.884337_pilon to pilon.fasta [pilon] Writing NODE_536_length_536_cov_1.077108:1-536 changes to pilon.changes [pilon] Writing updated NODE_536_length_536_cov_1.077108_pilon to pilon.fasta [pilon] Writing NODE_537_length_535_cov_3.253623:1-535 changes to pilon.changes [pilon] Writing updated NODE_537_length_535_cov_3.253623_pilon to pilon.fasta [pilon] Writing NODE_538_length_535_cov_2.850242:1-535 changes to pilon.changes [pilon] Writing updated NODE_538_length_535_cov_2.850242_pilon to pilon.fasta [pilon] Writing NODE_539_length_535_cov_2.376812:1-535 changes to pilon.changes [pilon] Writing updated NODE_539_length_535_cov_2.376812_pilon to pilon.fasta [pilon] Writing NODE_540_length_535_cov_2.193237:1-535 changes to pilon.changes [pilon] Writing updated NODE_540_length_535_cov_2.193237_pilon to pilon.fasta [pilon] Writing NODE_541_length_534_cov_3.578692:1-534 changes to pilon.changes [pilon] Writing updated NODE_541_length_534_cov_3.578692_pilon to pilon.fasta [pilon] Writing NODE_542_length_534_cov_1.515738:1-534 changes to pilon.changes [pilon] Writing updated NODE_542_length_534_cov_1.515738_pilon to pilon.fasta [pilon] Writing NODE_543_length_533_cov_4.640777:1-533 changes to pilon.changes [pilon] Writing updated NODE_543_length_533_cov_4.640777_pilon to pilon.fasta [pilon] Writing NODE_544_length_533_cov_1.235437:1-533 changes to pilon.changes [pilon] Writing updated NODE_544_length_533_cov_1.235437_pilon to pilon.fasta [pilon] Writing NODE_545_length_530_cov_109.266504:1-530 changes to pilon.changes [pilon] Writing updated NODE_545_length_530_cov_109.266504_pilon to pilon.fasta [pilon] Writing NODE_546_length_529_cov_5.019608:1-529 changes to pilon.changes [pilon] Writing updated NODE_546_length_529_cov_5.019608_pilon to pilon.fasta [pilon] Writing NODE_547_length_529_cov_2.970588:1-529 changes to pilon.changes [pilon] Writing updated NODE_547_length_529_cov_2.970588_pilon to pilon.fasta [pilon] Writing NODE_548_length_529_cov_1.431373:1-529 changes to pilon.changes [pilon] Writing updated NODE_548_length_529_cov_1.431373_pilon to pilon.fasta [pilon] Writing NODE_549_length_528_cov_1.393120:1-528 changes to pilon.changes [pilon] Writing updated NODE_549_length_528_cov_1.393120_pilon to pilon.fasta [pilon] Writing NODE_550_length_527_cov_7.167488:1-527 changes to pilon.changes [pilon] Writing updated NODE_550_length_527_cov_7.167488_pilon to pilon.fasta [pilon] Writing NODE_551_length_527_cov_4.490148:1-527 changes to pilon.changes [pilon] Writing updated NODE_551_length_527_cov_4.490148_pilon to pilon.fasta [pilon] Writing NODE_552_length_527_cov_3.625616:1-527 changes to pilon.changes [pilon] Writing updated NODE_552_length_527_cov_3.625616_pilon to pilon.fasta [pilon] Writing NODE_553_length_527_cov_1.901478:1-527 changes to pilon.changes [pilon] Writing updated NODE_553_length_527_cov_1.901478_pilon to pilon.fasta [pilon] Writing NODE_554_length_526_cov_2.827160:1-526 changes to pilon.changes [pilon] Writing updated NODE_554_length_526_cov_2.827160_pilon to pilon.fasta [pilon] Writing NODE_555_length_526_cov_2.797531:1-526 changes to pilon.changes [pilon] Writing updated NODE_555_length_526_cov_2.797531_pilon to pilon.fasta [pilon] Writing NODE_556_length_526_cov_1.901235:1-526 changes to pilon.changes [pilon] Writing updated NODE_556_length_526_cov_1.901235_pilon to pilon.fasta [pilon] Writing NODE_557_length_526_cov_0.708642:1-526 changes to pilon.changes [pilon] Writing updated NODE_557_length_526_cov_0.708642_pilon to pilon.fasta [pilon] Writing NODE_558_length_525_cov_1.509901:1-525 changes to pilon.changes [pilon] Writing updated NODE_558_length_525_cov_1.509901_pilon to pilon.fasta [pilon] Writing NODE_559_length_524_cov_2.161290:1-524 changes to pilon.changes [pilon] Writing updated NODE_559_length_524_cov_2.161290_pilon to pilon.fasta [pilon] Writing NODE_560_length_523_cov_3.296020:1-523 changes to pilon.changes [pilon] Writing updated NODE_560_length_523_cov_3.296020_pilon to pilon.fasta [pilon] Writing NODE_561_length_521_cov_4.760000:1-521 changes to pilon.changes [pilon] Writing updated NODE_561_length_521_cov_4.760000_pilon to pilon.fasta [pilon] Writing NODE_562_length_521_cov_3.597500:1-521 changes to pilon.changes [pilon] Writing updated NODE_562_length_521_cov_3.597500_pilon to pilon.fasta [pilon] Writing NODE_563_length_521_cov_3.055000:1-521 changes to pilon.changes [pilon] Writing updated NODE_563_length_521_cov_3.055000_pilon to pilon.fasta [pilon] Writing NODE_564_length_520_cov_3.781955:1-520 changes to pilon.changes [pilon] Writing updated NODE_564_length_520_cov_3.781955_pilon to pilon.fasta [pilon] Writing NODE_565_length_519_cov_5.457286:1-519 changes to pilon.changes [pilon] Writing updated NODE_565_length_519_cov_5.457286_pilon to pilon.fasta [pilon] Writing NODE_566_length_519_cov_1.587940:1-519 changes to pilon.changes [pilon] Writing updated NODE_566_length_519_cov_1.587940_pilon to pilon.fasta [pilon] Writing NODE_567_length_519_cov_0.748744:1-519 changes to pilon.changes [pilon] Writing updated NODE_567_length_519_cov_0.748744_pilon to pilon.fasta [pilon] Writing NODE_568_length_518_cov_18.236776:1-518 changes to pilon.changes [pilon] Writing updated NODE_568_length_518_cov_18.236776_pilon to pilon.fasta [pilon] Writing NODE_569_length_518_cov_6.191436:1-518 changes to pilon.changes [pilon] Writing updated NODE_569_length_518_cov_6.191436_pilon to pilon.fasta [pilon] Writing NODE_570_length_518_cov_4.511335:1-518 changes to pilon.changes [pilon] Writing updated NODE_570_length_518_cov_4.511335_pilon to pilon.fasta [pilon] Writing NODE_571_length_518_cov_4.347607:1-518 changes to pilon.changes [pilon] Writing updated NODE_571_length_518_cov_4.347607_pilon to pilon.fasta [pilon] Writing NODE_572_length_518_cov_2.743073:1-518 changes to pilon.changes [pilon] Writing updated NODE_572_length_518_cov_2.743073_pilon to pilon.fasta [pilon] Writing NODE_573_length_517_cov_6.219697:1-517 changes to pilon.changes [pilon] Writing updated NODE_573_length_517_cov_6.219697_pilon to pilon.fasta [pilon] Writing NODE_574_length_517_cov_2.780303:1-517 changes to pilon.changes [pilon] Writing updated NODE_574_length_517_cov_2.780303_pilon to pilon.fasta [pilon] Writing NODE_575_length_517_cov_1.606061:1-517 changes to pilon.changes [pilon] Writing updated NODE_575_length_517_cov_1.606061_pilon to pilon.fasta [pilon] Writing NODE_576_length_516_cov_4.445570:1-516 changes to pilon.changes [pilon] Writing updated NODE_576_length_516_cov_4.445570_pilon to pilon.fasta [pilon] Writing NODE_577_length_515_cov_1.951777:1-515 changes to pilon.changes [pilon] Writing updated NODE_577_length_515_cov_1.951777_pilon to pilon.fasta [pilon] Writing NODE_578_length_515_cov_1.868020:1-515 changes to pilon.changes [pilon] Writing updated NODE_578_length_515_cov_1.868020_pilon to pilon.fasta [pilon] Writing NODE_579_length_515_cov_1.614213:1-515 changes to pilon.changes [pilon] Writing updated NODE_579_length_515_cov_1.614213_pilon to pilon.fasta [pilon] Writing NODE_580_length_515_cov_0.791878:1-515 changes to pilon.changes [pilon] Writing updated NODE_580_length_515_cov_0.791878_pilon to pilon.fasta [pilon] Writing NODE_581_length_514_cov_4.358779:1-514 changes to pilon.changes [pilon] Writing updated NODE_581_length_514_cov_4.358779_pilon to pilon.fasta [pilon] Writing NODE_582_length_514_cov_2.391858:1-514 changes to pilon.changes [pilon] Writing updated NODE_582_length_514_cov_2.391858_pilon to pilon.fasta [pilon] Writing NODE_583_length_514_cov_1.720102:1-514 changes to pilon.changes [pilon] Writing updated NODE_583_length_514_cov_1.720102_pilon to pilon.fasta [pilon] Writing NODE_584_length_513_cov_2.403061:1-513 changes to pilon.changes [pilon] Writing updated NODE_584_length_513_cov_2.403061_pilon to pilon.fasta [pilon] Writing NODE_585_length_513_cov_2.102041:1-513 changes to pilon.changes [pilon] Writing updated NODE_585_length_513_cov_2.102041_pilon to pilon.fasta [pilon] Writing NODE_586_length_513_cov_2.084184:1-513 changes to pilon.changes [pilon] Writing updated NODE_586_length_513_cov_2.084184_pilon to pilon.fasta [pilon] Writing NODE_587_length_513_cov_1.696429:1-513 changes to pilon.changes [pilon] Writing updated NODE_587_length_513_cov_1.696429_pilon to pilon.fasta [pilon] Writing NODE_588_length_512_cov_1.002558:1-512 changes to pilon.changes [pilon] Writing updated NODE_588_length_512_cov_1.002558_pilon to pilon.fasta [pilon] Writing NODE_589_length_512_cov_0.864450:1-512 changes to pilon.changes [pilon] Writing updated NODE_589_length_512_cov_0.864450_pilon to pilon.fasta [pilon] Writing NODE_590_length_511_cov_2.210256:1-511 changes to pilon.changes [pilon] Writing updated NODE_590_length_511_cov_2.210256_pilon to pilon.fasta [pilon] Writing NODE_591_length_511_cov_0.435897:1-511 changes to pilon.changes [pilon] Writing updated NODE_591_length_511_cov_0.435897_pilon to pilon.fasta [pilon] Writing NODE_592_length_510_cov_3.915167:1-510 changes to pilon.changes [pilon] Writing updated NODE_592_length_510_cov_3.915167_pilon to pilon.fasta [pilon] Writing NODE_593_length_510_cov_3.740360:1-510 changes to pilon.changes [pilon] Writing updated NODE_593_length_510_cov_3.740360_pilon to pilon.fasta [pilon] Writing NODE_594_length_510_cov_1.971722:1-510 changes to pilon.changes [pilon] Writing updated NODE_594_length_510_cov_1.971722_pilon to pilon.fasta [pilon] Writing NODE_595_length_509_cov_1.961340:1-509 changes to pilon.changes [pilon] Writing updated NODE_595_length_509_cov_1.961340_pilon to pilon.fasta [pilon] Writing NODE_596_length_508_cov_1.614987:1-508 changes to pilon.changes [pilon] Writing updated NODE_596_length_508_cov_1.614987_pilon to pilon.fasta [pilon] Writing NODE_597_length_508_cov_1.573643:1-508 changes to pilon.changes [pilon] Writing updated NODE_597_length_508_cov_1.573643_pilon to pilon.fasta [pilon] Writing NODE_598_length_508_cov_1.550388:1-508 changes to pilon.changes [pilon] Writing updated NODE_598_length_508_cov_1.550388_pilon to pilon.fasta [pilon] Writing NODE_599_length_508_cov_1.232558:1-508 changes to pilon.changes [pilon] Writing updated NODE_599_length_508_cov_1.232558_pilon to pilon.fasta [pilon] Writing NODE_600_length_508_cov_0.578811:1-508 changes to pilon.changes [pilon] Writing updated NODE_600_length_508_cov_0.578811_pilon to pilon.fasta [pilon] Writing NODE_601_length_507_cov_0.917098:1-507 changes to pilon.changes [pilon] Writing updated NODE_601_length_507_cov_0.917098_pilon to pilon.fasta [pilon] Writing NODE_602_length_507_cov_0.505181:1-507 changes to pilon.changes [pilon] Writing updated NODE_602_length_507_cov_0.505181_pilon to pilon.fasta [pilon] Writing NODE_603_length_506_cov_5.558442:1-506 changes to pilon.changes [pilon] Writing updated NODE_603_length_506_cov_5.558442_pilon to pilon.fasta [pilon] Writing NODE_604_length_506_cov_3.267532:1-506 changes to pilon.changes [pilon] Writing updated NODE_604_length_506_cov_3.267532_pilon to pilon.fasta [pilon] Writing NODE_605_length_506_cov_1.724675:1-506 changes to pilon.changes [pilon] Writing updated NODE_605_length_506_cov_1.724675_pilon to pilon.fasta [pilon] Writing NODE_606_length_505_cov_7.375000:1-505 changes to pilon.changes [pilon] Writing updated NODE_606_length_505_cov_7.375000_pilon to pilon.fasta [pilon] Writing NODE_607_length_505_cov_5.414062:1-505 changes to pilon.changes [pilon] Writing updated NODE_607_length_505_cov_5.414062_pilon to pilon.fasta [pilon] Writing NODE_608_length_505_cov_2.986979:1-505 changes to pilon.changes [pilon] Writing updated NODE_608_length_505_cov_2.986979_pilon to pilon.fasta [pilon] Writing NODE_609_length_505_cov_1.932292:1-505 changes to pilon.changes [pilon] Writing updated NODE_609_length_505_cov_1.932292_pilon to pilon.fasta [pilon] Writing NODE_610_length_505_cov_1.351562:1-505 changes to pilon.changes [pilon] Writing updated NODE_610_length_505_cov_1.351562_pilon to pilon.fasta [pilon] Writing NODE_611_length_503_cov_1.246073:1-503 changes to pilon.changes [pilon] Writing updated NODE_611_length_503_cov_1.246073_pilon to pilon.fasta [pilon] Writing NODE_612_length_503_cov_1.065445:1-503 changes to pilon.changes [pilon] Writing updated NODE_612_length_503_cov_1.065445_pilon to pilon.fasta [pilon] Writing NODE_613_length_503_cov_0.960733:1-503 changes to pilon.changes [pilon] Writing updated NODE_613_length_503_cov_0.960733_pilon to pilon.fasta [pilon] Writing NODE_614_length_503_cov_0.821990:1-503 changes to pilon.changes [pilon] Writing updated NODE_614_length_503_cov_0.821990_pilon to pilon.fasta [pilon] Writing NODE_615_length_502_cov_3.490814:1-502 changes to pilon.changes [pilon] Writing updated NODE_615_length_502_cov_3.490814_pilon to pilon.fasta [pilon] Writing NODE_616_length_502_cov_3.451444:1-502 changes to pilon.changes [pilon] Writing updated NODE_616_length_502_cov_3.451444_pilon to pilon.fasta [pilon] Writing NODE_617_length_502_cov_1.545932:1-502 changes to pilon.changes [pilon] Writing updated NODE_617_length_502_cov_1.545932_pilon to pilon.fasta [pilon] Writing NODE_618_length_501_cov_3.376316:1-501 changes to pilon.changes [pilon] Writing updated NODE_618_length_501_cov_3.376316_pilon to pilon.fasta [pilon] Writing NODE_619_length_501_cov_2.636842:1-501 changes to pilon.changes [pilon] Writing updated NODE_619_length_501_cov_2.636842_pilon to pilon.fasta [pilon] Writing NODE_620_length_500_cov_4.200528:1-500 changes to pilon.changes [pilon] Writing updated NODE_620_length_500_cov_4.200528_pilon to pilon.fasta [pilon] Writing NODE_621_length_500_cov_2.366755:1-500 changes to pilon.changes [pilon] Writing updated NODE_621_length_500_cov_2.366755_pilon to pilon.fasta [pilon] Writing NODE_622_length_499_cov_2.269841:1-499 changes to pilon.changes [pilon] Writing updated NODE_622_length_499_cov_2.269841_pilon to pilon.fasta [pilon] Writing NODE_623_length_498_cov_5.785146:1-498 changes to pilon.changes [pilon] Writing updated NODE_623_length_498_cov_5.785146_pilon to pilon.fasta [pilon] Writing NODE_624_length_498_cov_3.225464:1-498 changes to pilon.changes [pilon] Writing updated NODE_624_length_498_cov_3.225464_pilon to pilon.fasta [pilon] Writing NODE_625_length_498_cov_0.941645:1-498 changes to pilon.changes [pilon] Writing updated NODE_625_length_498_cov_0.941645_pilon to pilon.fasta [pilon] Writing NODE_626_length_497_cov_6.694149:1-497 changes to pilon.changes [pilon] Writing updated NODE_626_length_497_cov_6.694149_pilon to pilon.fasta [pilon] Writing NODE_627_length_497_cov_2.901596:1-497 changes to pilon.changes [pilon] Writing updated NODE_627_length_497_cov_2.901596_pilon to pilon.fasta [pilon] Writing NODE_628_length_496_cov_15.306667:1-496 changes to pilon.changes [pilon] Writing updated NODE_628_length_496_cov_15.306667_pilon to pilon.fasta [pilon] Writing NODE_629_length_495_cov_4.328877:1-495 changes to pilon.changes [pilon] Writing updated NODE_629_length_495_cov_4.328877_pilon to pilon.fasta [pilon] Writing NODE_630_length_495_cov_3.577540:1-495 changes to pilon.changes [pilon] Writing updated NODE_630_length_495_cov_3.577540_pilon to pilon.fasta [pilon] Writing NODE_631_length_495_cov_2.147059:1-495 changes to pilon.changes [pilon] Writing updated NODE_631_length_495_cov_2.147059_pilon to pilon.fasta [pilon] Writing NODE_632_length_495_cov_1.462567:1-495 changes to pilon.changes [pilon] Writing updated NODE_632_length_495_cov_1.462567_pilon to pilon.fasta [pilon] Writing NODE_633_length_495_cov_1.304813:1-495 changes to pilon.changes [pilon] Writing updated NODE_633_length_495_cov_1.304813_pilon to pilon.fasta [pilon] Writing NODE_634_length_495_cov_1.278075:1-495 changes to pilon.changes [pilon] Writing updated NODE_634_length_495_cov_1.278075_pilon to pilon.fasta [pilon] Writing NODE_635_length_494_cov_9.292225:1-494 changes to pilon.changes [pilon] Writing updated NODE_635_length_494_cov_9.292225_pilon to pilon.fasta [pilon] Writing NODE_636_length_494_cov_2.922252:1-494 changes to pilon.changes [pilon] Writing updated NODE_636_length_494_cov_2.922252_pilon to pilon.fasta [pilon] Writing NODE_637_length_494_cov_1.126005:1-494 changes to pilon.changes [pilon] Writing updated NODE_637_length_494_cov_1.126005_pilon to pilon.fasta [pilon] Writing NODE_638_length_494_cov_1.048257:1-494 changes to pilon.changes [pilon] Writing updated NODE_638_length_494_cov_1.048257_pilon to pilon.fasta [pilon] Writing NODE_639_length_493_cov_2.107527:1-493 changes to pilon.changes [pilon] Writing updated NODE_639_length_493_cov_2.107527_pilon to pilon.fasta [pilon] Writing NODE_640_length_493_cov_1.413978:1-493 changes to pilon.changes [pilon] Writing updated NODE_640_length_493_cov_1.413978_pilon to pilon.fasta [pilon] Writing NODE_641_length_492_cov_7.970350:1-492 changes to pilon.changes [pilon] Writing updated NODE_641_length_492_cov_7.970350_pilon to pilon.fasta [pilon] Writing NODE_642_length_492_cov_1.908356:1-492 changes to pilon.changes [pilon] Writing updated NODE_642_length_492_cov_1.908356_pilon to pilon.fasta [pilon] Writing NODE_643_length_492_cov_1.210243:1-492 changes to pilon.changes [pilon] Writing updated NODE_643_length_492_cov_1.210243_pilon to pilon.fasta [pilon] Writing NODE_644_length_491_cov_3.045946:1-491 changes to pilon.changes [pilon] Writing updated NODE_644_length_491_cov_3.045946_pilon to pilon.fasta [pilon] Writing NODE_645_length_491_cov_0.581081:1-491 changes to pilon.changes [pilon] Writing updated NODE_645_length_491_cov_0.581081_pilon to pilon.fasta [pilon] Writing NODE_646_length_490_cov_1.785908:1-490 changes to pilon.changes [pilon] Writing updated NODE_646_length_490_cov_1.785908_pilon to pilon.fasta [pilon] Writing NODE_647_length_490_cov_1.132791:1-490 changes to pilon.changes [pilon] Writing updated NODE_647_length_490_cov_1.132791_pilon to pilon.fasta [pilon] Writing NODE_648_length_489_cov_4.967391:1-489 changes to pilon.changes [pilon] Writing updated NODE_648_length_489_cov_4.967391_pilon to pilon.fasta [pilon] Writing NODE_649_length_488_cov_2.272480:1-488 changes to pilon.changes [pilon] Writing updated NODE_649_length_488_cov_2.272480_pilon to pilon.fasta [pilon] Writing NODE_650_length_488_cov_0.945504:1-488 changes to pilon.changes [pilon] Writing updated NODE_650_length_488_cov_0.945504_pilon to pilon.fasta [pilon] Writing NODE_651_length_488_cov_0.828338:1-488 changes to pilon.changes [pilon] Writing updated NODE_651_length_488_cov_0.828338_pilon to pilon.fasta [pilon] Writing NODE_652_length_487_cov_7.292350:1-487 changes to pilon.changes [pilon] Writing updated NODE_652_length_487_cov_7.292350_pilon to pilon.fasta [pilon] Writing NODE_653_length_487_cov_2.789617:1-487 changes to pilon.changes [pilon] Writing updated NODE_653_length_487_cov_2.789617_pilon to pilon.fasta [pilon] Writing NODE_654_length_487_cov_1.333333:1-487 changes to pilon.changes [pilon] Writing updated NODE_654_length_487_cov_1.333333_pilon to pilon.fasta [pilon] Writing NODE_655_length_486_cov_5.709589:1-486 changes to pilon.changes [pilon] Writing updated NODE_655_length_486_cov_5.709589_pilon to pilon.fasta [pilon] Writing NODE_656_length_486_cov_3.769863:1-486 changes to pilon.changes [pilon] Writing updated NODE_656_length_486_cov_3.769863_pilon to pilon.fasta [pilon] Writing NODE_657_length_485_cov_11.313187:1-485 changes to pilon.changes [pilon] Writing updated NODE_657_length_485_cov_11.313187_pilon to pilon.fasta [pilon] Writing NODE_658_length_485_cov_2.060440:1-485 changes to pilon.changes [pilon] Writing updated NODE_658_length_485_cov_2.060440_pilon to pilon.fasta [pilon] Writing NODE_659_length_485_cov_1.793956:1-485 changes to pilon.changes [pilon] Writing updated NODE_659_length_485_cov_1.793956_pilon to pilon.fasta [pilon] Writing NODE_660_length_484_cov_14.564738:1-484 changes to pilon.changes [pilon] Writing updated NODE_660_length_484_cov_14.564738_pilon to pilon.fasta [pilon] Writing NODE_661_length_483_cov_1.726519:1-483 changes to pilon.changes [pilon] Writing updated NODE_661_length_483_cov_1.726519_pilon to pilon.fasta [pilon] Writing NODE_662_length_483_cov_1.417127:1-483 changes to pilon.changes [pilon] Writing updated NODE_662_length_483_cov_1.417127_pilon to pilon.fasta [pilon] Writing NODE_663_length_483_cov_1.342541:1-483 changes to pilon.changes [pilon] Writing updated NODE_663_length_483_cov_1.342541_pilon to pilon.fasta [pilon] Writing NODE_664_length_483_cov_1.215470:1-483 changes to pilon.changes [pilon] Writing updated NODE_664_length_483_cov_1.215470_pilon to pilon.fasta [pilon] Writing NODE_665_length_482_cov_7.817175:1-482 changes to pilon.changes [pilon] Writing updated NODE_665_length_482_cov_7.817175_pilon to pilon.fasta [pilon] Writing NODE_666_length_482_cov_4.121884:1-482 changes to pilon.changes [pilon] Writing updated NODE_666_length_482_cov_4.121884_pilon to pilon.fasta [pilon] Writing NODE_667_length_482_cov_1.565097:1-482 changes to pilon.changes [pilon] Writing updated NODE_667_length_482_cov_1.565097_pilon to pilon.fasta [pilon] Writing NODE_668_length_482_cov_1.476454:1-482 changes to pilon.changes [pilon] Writing updated NODE_668_length_482_cov_1.476454_pilon to pilon.fasta [pilon] Writing NODE_669_length_482_cov_0.850416:1-482 changes to pilon.changes [pilon] Writing updated NODE_669_length_482_cov_0.850416_pilon to pilon.fasta [pilon] Writing NODE_670_length_482_cov_0.202216:1-482 changes to pilon.changes [pilon] Writing updated NODE_670_length_482_cov_0.202216_pilon to pilon.fasta [pilon] Writing NODE_671_length_481_cov_2.166667:1-481 changes to pilon.changes [pilon] Writing updated NODE_671_length_481_cov_2.166667_pilon to pilon.fasta [pilon] Writing NODE_672_length_480_cov_1.114206:1-480 changes to pilon.changes [pilon] Writing updated NODE_672_length_480_cov_1.114206_pilon to pilon.fasta [pilon] Writing NODE_673_length_479_cov_9.251397:1-479 changes to pilon.changes [pilon] Writing updated NODE_673_length_479_cov_9.251397_pilon to pilon.fasta [pilon] Writing NODE_674_length_479_cov_9.053073:1-479 changes to pilon.changes [pilon] Writing updated NODE_674_length_479_cov_9.053073_pilon to pilon.fasta [pilon] Writing NODE_675_length_479_cov_1.821229:1-479 changes to pilon.changes [pilon] Writing updated NODE_675_length_479_cov_1.821229_pilon to pilon.fasta [pilon] Writing NODE_676_length_479_cov_1.611732:1-479 changes to pilon.changes [pilon] Writing updated NODE_676_length_479_cov_1.611732_pilon to pilon.fasta [pilon] Writing NODE_677_length_478_cov_4.187675:1-478 changes to pilon.changes [pilon] Writing updated NODE_677_length_478_cov_4.187675_pilon to pilon.fasta [pilon] Writing NODE_678_length_478_cov_1.873950:1-478 changes to pilon.changes [pilon] Writing updated NODE_678_length_478_cov_1.873950_pilon to pilon.fasta [pilon] Writing NODE_679_length_478_cov_1.364146:1-478 changes to pilon.changes [pilon] Writing updated NODE_679_length_478_cov_1.364146_pilon to pilon.fasta [pilon] Writing NODE_680_length_478_cov_0.591036:1-478 changes to pilon.changes [pilon] Writing updated NODE_680_length_478_cov_0.591036_pilon to pilon.fasta [pilon] Writing NODE_681_length_477_cov_2.002809:1-477 changes to pilon.changes [pilon] Writing updated NODE_681_length_477_cov_2.002809_pilon to pilon.fasta [pilon] Writing NODE_682_length_477_cov_1.047753:1-477 changes to pilon.changes [pilon] Writing updated NODE_682_length_477_cov_1.047753_pilon to pilon.fasta [pilon] Writing NODE_683_length_476_cov_3.591549:1-476 changes to pilon.changes [pilon] Writing updated NODE_683_length_476_cov_3.591549_pilon to pilon.fasta [pilon] Writing NODE_684_length_474_cov_2.334278:1-474 changes to pilon.changes [pilon] Writing updated NODE_684_length_474_cov_2.334278_pilon to pilon.fasta [pilon] Writing NODE_685_length_474_cov_1.252125:1-474 changes to pilon.changes [pilon] Writing updated NODE_685_length_474_cov_1.252125_pilon to pilon.fasta [pilon] Writing NODE_686_length_474_cov_1.118980:1-474 changes to pilon.changes [pilon] Writing updated NODE_686_length_474_cov_1.118980_pilon to pilon.fasta [pilon] Writing NODE_687_length_474_cov_1.000000:1-474 changes to pilon.changes [pilon] Writing updated NODE_687_length_474_cov_1.000000_pilon to pilon.fasta [pilon] Writing NODE_688_length_473_cov_2.355114:1-473 changes to pilon.changes [pilon] Writing updated NODE_688_length_473_cov_2.355114_pilon to pilon.fasta [pilon] Writing NODE_689_length_473_cov_1.911932:1-473 changes to pilon.changes [pilon] Writing updated NODE_689_length_473_cov_1.911932_pilon to pilon.fasta [pilon] Writing NODE_690_length_473_cov_1.758523:1-473 changes to pilon.changes [pilon] Writing updated NODE_690_length_473_cov_1.758523_pilon to pilon.fasta [pilon] Writing NODE_691_length_473_cov_1.085227:1-473 changes to pilon.changes [pilon] Writing updated NODE_691_length_473_cov_1.085227_pilon to pilon.fasta [pilon] Writing NODE_692_length_473_cov_0.417614:1-473 changes to pilon.changes [pilon] Writing updated NODE_692_length_473_cov_0.417614_pilon to pilon.fasta [pilon] Writing NODE_693_length_472_cov_2.629630:1-472 changes to pilon.changes [pilon] Writing updated NODE_693_length_472_cov_2.629630_pilon to pilon.fasta [pilon] Writing NODE_694_length_471_cov_18.674286:1-471 changes to pilon.changes [pilon] Writing updated NODE_694_length_471_cov_18.674286_pilon to pilon.fasta [pilon] Writing NODE_695_length_471_cov_10.322857:1-471 changes to pilon.changes [pilon] Writing updated NODE_695_length_471_cov_10.322857_pilon to pilon.fasta [pilon] Writing NODE_696_length_471_cov_1.554286:1-471 changes to pilon.changes [pilon] Writing updated NODE_696_length_471_cov_1.554286_pilon to pilon.fasta [pilon] Writing NODE_697_length_471_cov_1.057143:1-471 changes to pilon.changes [pilon] Writing updated NODE_697_length_471_cov_1.057143_pilon to pilon.fasta [pilon] Writing NODE_698_length_471_cov_0.974286:1-471 changes to pilon.changes [pilon] Writing updated NODE_698_length_471_cov_0.974286_pilon to pilon.fasta [pilon] Writing NODE_699_length_471_cov_0.662857:1-471 changes to pilon.changes [pilon] Writing updated NODE_699_length_471_cov_0.662857_pilon to pilon.fasta [pilon] Writing NODE_700_length_470_cov_3.160458:1-470 changes to pilon.changes [pilon] Writing updated NODE_700_length_470_cov_3.160458_pilon to pilon.fasta [pilon] Writing NODE_701_length_470_cov_2.902579:1-470 changes to pilon.changes [pilon] Writing updated NODE_701_length_470_cov_2.902579_pilon to pilon.fasta [pilon] Writing NODE_702_length_470_cov_1.716332:1-470 changes to pilon.changes [pilon] Writing updated NODE_702_length_470_cov_1.716332_pilon to pilon.fasta [pilon] Writing NODE_703_length_470_cov_1.630372:1-470 changes to pilon.changes [pilon] Writing updated NODE_703_length_470_cov_1.630372_pilon to pilon.fasta [pilon] Writing NODE_704_length_470_cov_1.512894:1-470 changes to pilon.changes [pilon] Writing updated NODE_704_length_470_cov_1.512894_pilon to pilon.fasta [pilon] Writing NODE_705_length_470_cov_1.094556:1-470 changes to pilon.changes [pilon] Writing updated NODE_705_length_470_cov_1.094556_pilon to pilon.fasta [pilon] Writing NODE_706_length_469_cov_5.272989:1-469 changes to pilon.changes [pilon] Writing updated NODE_706_length_469_cov_5.272989_pilon to pilon.fasta [pilon] Writing NODE_707_length_469_cov_1.566092:1-469 changes to pilon.changes [pilon] Writing updated NODE_707_length_469_cov_1.566092_pilon to pilon.fasta [pilon] Writing NODE_708_length_468_cov_3.763689:1-468 changes to pilon.changes [pilon] Writing updated NODE_708_length_468_cov_3.763689_pilon to pilon.fasta [pilon] Writing NODE_709_length_468_cov_0.446686:1-468 changes to pilon.changes [pilon] Writing updated NODE_709_length_468_cov_0.446686_pilon to pilon.fasta [pilon] Writing NODE_710_length_467_cov_2.164740:1-467 changes to pilon.changes [pilon] Writing updated NODE_710_length_467_cov_2.164740_pilon to pilon.fasta [pilon] Writing NODE_711_length_467_cov_1.242775:1-467 changes to pilon.changes [pilon] Writing updated NODE_711_length_467_cov_1.242775_pilon to pilon.fasta [pilon] Writing NODE_712_length_467_cov_0.942197:1-467 changes to pilon.changes [pilon] Writing updated NODE_712_length_467_cov_0.942197_pilon to pilon.fasta [pilon] Writing NODE_713_length_467_cov_0.624277:1-467 changes to pilon.changes [pilon] Writing updated NODE_713_length_467_cov_0.624277_pilon to pilon.fasta [pilon] Writing NODE_714_length_466_cov_0.820290:1-466 changes to pilon.changes [pilon] Writing updated NODE_714_length_466_cov_0.820290_pilon to pilon.fasta [pilon] Writing NODE_715_length_466_cov_0.753623:1-466 changes to pilon.changes [pilon] Writing updated NODE_715_length_466_cov_0.753623_pilon to pilon.fasta [pilon] Writing NODE_716_length_465_cov_2.866279:1-465 changes to pilon.changes [pilon] Writing updated NODE_716_length_465_cov_2.866279_pilon to pilon.fasta [pilon] Writing NODE_717_length_465_cov_1.183140:1-465 changes to pilon.changes [pilon] Writing updated NODE_717_length_465_cov_1.183140_pilon to pilon.fasta [pilon] Writing NODE_718_length_464_cov_3.422741:1-464 changes to pilon.changes [pilon] Writing updated NODE_718_length_464_cov_3.422741_pilon to pilon.fasta [pilon] Writing NODE_719_length_464_cov_1.702624:1-464 changes to pilon.changes [pilon] Writing updated NODE_719_length_464_cov_1.702624_pilon to pilon.fasta [pilon] Writing NODE_720_length_463_cov_3.561404:1-463 changes to pilon.changes [pilon] Writing updated NODE_720_length_463_cov_3.561404_pilon to pilon.fasta [pilon] Writing NODE_721_length_463_cov_1.137427:1-463 changes to pilon.changes [pilon] Writing updated NODE_721_length_463_cov_1.137427_pilon to pilon.fasta [pilon] Writing NODE_722_length_462_cov_4.020528:1-462 changes to pilon.changes [pilon] Writing updated NODE_722_length_462_cov_4.020528_pilon to pilon.fasta [pilon] Writing NODE_723_length_462_cov_1.307918:1-462 changes to pilon.changes [pilon] Writing updated NODE_723_length_462_cov_1.307918_pilon to pilon.fasta [pilon] Writing NODE_724_length_462_cov_0.718475:1-462 changes to pilon.changes [pilon] Writing updated NODE_724_length_462_cov_0.718475_pilon to pilon.fasta [pilon] Writing NODE_725_length_461_cov_2.061765:1-461 changes to pilon.changes [pilon] Writing updated NODE_725_length_461_cov_2.061765_pilon to pilon.fasta [pilon] Writing NODE_726_length_460_cov_3.766962:1-460 changes to pilon.changes [pilon] Writing updated NODE_726_length_460_cov_3.766962_pilon to pilon.fasta [pilon] Writing NODE_727_length_460_cov_3.401180:1-460 changes to pilon.changes [pilon] Writing updated NODE_727_length_460_cov_3.401180_pilon to pilon.fasta [pilon] Writing NODE_728_length_459_cov_1.073964:1-459 changes to pilon.changes [pilon] Writing updated NODE_728_length_459_cov_1.073964_pilon to pilon.fasta [pilon] Writing NODE_729_length_458_cov_7.721068:1-458 changes to pilon.changes [pilon] Writing updated NODE_729_length_458_cov_7.721068_pilon to pilon.fasta [pilon] Writing NODE_730_length_458_cov_7.433234:1-458 changes to pilon.changes [pilon] Writing updated NODE_730_length_458_cov_7.433234_pilon to pilon.fasta [pilon] Writing NODE_731_length_458_cov_1.655786:1-458 changes to pilon.changes [pilon] Writing updated NODE_731_length_458_cov_1.655786_pilon to pilon.fasta [pilon] Writing NODE_732_length_458_cov_1.370920:1-458 changes to pilon.changes [pilon] Writing updated NODE_732_length_458_cov_1.370920_pilon to pilon.fasta [pilon] Writing NODE_733_length_457_cov_3.083333:1-457 changes to pilon.changes [pilon] Writing updated NODE_733_length_457_cov_3.083333_pilon to pilon.fasta [pilon] Writing NODE_734_length_457_cov_1.136905:1-457 changes to pilon.changes [pilon] Writing updated NODE_734_length_457_cov_1.136905_pilon to pilon.fasta [pilon] Writing NODE_735_length_456_cov_4.352239:1-456 changes to pilon.changes [pilon] Writing updated NODE_735_length_456_cov_4.352239_pilon to pilon.fasta [pilon] Writing NODE_736_length_456_cov_3.922388:1-456 changes to pilon.changes [pilon] Writing updated NODE_736_length_456_cov_3.922388_pilon to pilon.fasta [pilon] Writing NODE_737_length_456_cov_2.773134:1-456 changes to pilon.changes [pilon] Writing updated NODE_737_length_456_cov_2.773134_pilon to pilon.fasta [pilon] Writing NODE_738_length_455_cov_8.790419:1-455 changes to pilon.changes [pilon] Writing updated NODE_738_length_455_cov_8.790419_pilon to pilon.fasta [pilon] Writing NODE_739_length_454_cov_9.126126:1-454 changes to pilon.changes [pilon] Writing updated NODE_739_length_454_cov_9.126126_pilon to pilon.fasta [pilon] Writing NODE_740_length_454_cov_5.174174:1-454 changes to pilon.changes [pilon] Writing updated NODE_740_length_454_cov_5.174174_pilon to pilon.fasta [pilon] Writing NODE_741_length_454_cov_3.621622:1-454 changes to pilon.changes [pilon] Writing updated NODE_741_length_454_cov_3.621622_pilon to pilon.fasta [pilon] Writing NODE_742_length_454_cov_0.879880:1-454 changes to pilon.changes [pilon] Writing updated NODE_742_length_454_cov_0.879880_pilon to pilon.fasta [pilon] Writing NODE_743_length_454_cov_0.693694:1-454 changes to pilon.changes [pilon] Writing updated NODE_743_length_454_cov_0.693694_pilon to pilon.fasta [pilon] Writing NODE_744_length_453_cov_1.325301:1-453 changes to pilon.changes [pilon] Writing updated NODE_744_length_453_cov_1.325301_pilon to pilon.fasta [pilon] Writing NODE_745_length_452_cov_87.323263:1-452 changes to pilon.changes [pilon] Writing updated NODE_745_length_452_cov_87.323263_pilon to pilon.fasta [pilon] Writing NODE_746_length_452_cov_2.232628:1-452 changes to pilon.changes [pilon] Writing updated NODE_746_length_452_cov_2.232628_pilon to pilon.fasta [pilon] Writing NODE_747_length_452_cov_1.981873:1-452 changes to pilon.changes [pilon] Writing updated NODE_747_length_452_cov_1.981873_pilon to pilon.fasta [pilon] Writing NODE_748_length_451_cov_2.118182:1-451 changes to pilon.changes [pilon] Writing updated NODE_748_length_451_cov_2.118182_pilon to pilon.fasta [pilon] Writing NODE_749_length_451_cov_1.954545:1-451 changes to pilon.changes [pilon] Writing updated NODE_749_length_451_cov_1.954545_pilon to pilon.fasta [pilon] Writing NODE_750_length_451_cov_1.569697:1-451 changes to pilon.changes [pilon] Writing updated NODE_750_length_451_cov_1.569697_pilon to pilon.fasta [pilon] Writing NODE_751_length_451_cov_0.939394:1-451 changes to pilon.changes [pilon] Writing updated NODE_751_length_451_cov_0.939394_pilon to pilon.fasta [pilon] Writing NODE_752_length_450_cov_1.425532:1-450 changes to pilon.changes [pilon] Writing updated NODE_752_length_450_cov_1.425532_pilon to pilon.fasta [pilon] Writing NODE_753_length_448_cov_4.626911:1-448 changes to pilon.changes [pilon] Writing updated NODE_753_length_448_cov_4.626911_pilon to pilon.fasta [pilon] Writing NODE_754_length_448_cov_2.688073:1-448 changes to pilon.changes [pilon] Writing updated NODE_754_length_448_cov_2.688073_pilon to pilon.fasta [pilon] Writing NODE_755_length_448_cov_2.556575:1-448 changes to pilon.changes [pilon] Writing updated NODE_755_length_448_cov_2.556575_pilon to pilon.fasta [pilon] Writing NODE_756_length_448_cov_2.027523:1-448 changes to pilon.changes [pilon] Writing updated NODE_756_length_448_cov_2.027523_pilon to pilon.fasta [pilon] Writing NODE_757_length_448_cov_1.134557:1-448 changes to pilon.changes [pilon] Writing updated NODE_757_length_448_cov_1.134557_pilon to pilon.fasta [pilon] Writing NODE_758_length_447_cov_1.895706:1-447 changes to pilon.changes [pilon] Writing updated NODE_758_length_447_cov_1.895706_pilon to pilon.fasta [pilon] Writing NODE_759_length_447_cov_0.871166:1-447 changes to pilon.changes [pilon] Writing updated NODE_759_length_447_cov_0.871166_pilon to pilon.fasta [pilon] Writing NODE_760_length_446_cov_0.907692:1-446 changes to pilon.changes [pilon] Writing updated NODE_760_length_446_cov_0.907692_pilon to pilon.fasta [pilon] Writing NODE_761_length_445_cov_5.623457:1-445 changes to pilon.changes [pilon] Writing updated NODE_761_length_445_cov_5.623457_pilon to pilon.fasta [pilon] Writing NODE_762_length_445_cov_4.845679:1-445 changes to pilon.changes [pilon] Writing updated NODE_762_length_445_cov_4.845679_pilon to pilon.fasta [pilon] Writing NODE_763_length_445_cov_2.472222:1-445 changes to pilon.changes [pilon] Writing updated NODE_763_length_445_cov_2.472222_pilon to pilon.fasta [pilon] Writing NODE_764_length_445_cov_2.015432:1-445 changes to pilon.changes [pilon] Writing updated NODE_764_length_445_cov_2.015432_pilon to pilon.fasta [pilon] Writing NODE_765_length_445_cov_1.546296:1-445 changes to pilon.changes [pilon] Writing updated NODE_765_length_445_cov_1.546296_pilon to pilon.fasta [pilon] Writing NODE_766_length_445_cov_1.274691:1-445 changes to pilon.changes [pilon] Writing updated NODE_766_length_445_cov_1.274691_pilon to pilon.fasta [pilon] Writing NODE_767_length_445_cov_0.580247:1-445 changes to pilon.changes [pilon] Writing updated NODE_767_length_445_cov_0.580247_pilon to pilon.fasta [pilon] Writing NODE_768_length_445_cov_0.330247:1-445 changes to pilon.changes [pilon] Writing updated NODE_768_length_445_cov_0.330247_pilon to pilon.fasta [pilon] Writing NODE_769_length_444_cov_1.272446:1-444 changes to pilon.changes [pilon] Writing updated NODE_769_length_444_cov_1.272446_pilon to pilon.fasta [pilon] Writing NODE_770_length_443_cov_1.981366:1-443 changes to pilon.changes [pilon] Writing updated NODE_770_length_443_cov_1.981366_pilon to pilon.fasta [pilon] Writing NODE_771_length_443_cov_1.807453:1-443 changes to pilon.changes [pilon] Writing updated NODE_771_length_443_cov_1.807453_pilon to pilon.fasta [pilon] Writing NODE_772_length_443_cov_1.645963:1-443 changes to pilon.changes [pilon] Writing updated NODE_772_length_443_cov_1.645963_pilon to pilon.fasta [pilon] Writing NODE_773_length_443_cov_1.043478:1-443 changes to pilon.changes [pilon] Writing updated NODE_773_length_443_cov_1.043478_pilon to pilon.fasta [pilon] Writing NODE_774_length_442_cov_1.616822:1-442 changes to pilon.changes [pilon] Writing updated NODE_774_length_442_cov_1.616822_pilon to pilon.fasta [pilon] Writing NODE_775_length_442_cov_1.545171:1-442 changes to pilon.changes [pilon] Writing updated NODE_775_length_442_cov_1.545171_pilon to pilon.fasta [pilon] Writing NODE_776_length_442_cov_1.417445:1-442 changes to pilon.changes [pilon] Writing updated NODE_776_length_442_cov_1.417445_pilon to pilon.fasta [pilon] Writing NODE_777_length_442_cov_1.336449:1-442 changes to pilon.changes [pilon] Writing updated NODE_777_length_442_cov_1.336449_pilon to pilon.fasta [pilon] Writing NODE_778_length_442_cov_1.221184:1-442 changes to pilon.changes [pilon] Writing updated NODE_778_length_442_cov_1.221184_pilon to pilon.fasta [pilon] Writing NODE_779_length_442_cov_1.180685:1-442 changes to pilon.changes [pilon] Writing updated NODE_779_length_442_cov_1.180685_pilon to pilon.fasta [pilon] Writing NODE_780_length_442_cov_0.872274:1-442 changes to pilon.changes [pilon] Writing updated NODE_780_length_442_cov_0.872274_pilon to pilon.fasta [pilon] Writing NODE_781_length_441_cov_1.575000:1-441 changes to pilon.changes [pilon] Writing updated NODE_781_length_441_cov_1.575000_pilon to pilon.fasta [pilon] Writing NODE_782_length_441_cov_1.571875:1-441 changes to pilon.changes [pilon] Writing updated NODE_782_length_441_cov_1.571875_pilon to pilon.fasta [pilon] Writing NODE_783_length_441_cov_1.387500:1-441 changes to pilon.changes [pilon] Writing updated NODE_783_length_441_cov_1.387500_pilon to pilon.fasta [pilon] Writing NODE_784_length_440_cov_2.858934:1-440 changes to pilon.changes [pilon] Writing updated NODE_784_length_440_cov_2.858934_pilon to pilon.fasta [pilon] Writing NODE_785_length_440_cov_1.241379:1-440 changes to pilon.changes [pilon] Writing updated NODE_785_length_440_cov_1.241379_pilon to pilon.fasta [pilon] Writing NODE_786_length_439_cov_8.606918:1-439 changes to pilon.changes [pilon] Writing updated NODE_786_length_439_cov_8.606918_pilon to pilon.fasta [pilon] Writing NODE_787_length_439_cov_0.468553:1-439 changes to pilon.changes [pilon] Writing updated NODE_787_length_439_cov_0.468553_pilon to pilon.fasta [pilon] Writing NODE_788_length_438_cov_1.712934:1-438 changes to pilon.changes [pilon] Writing updated NODE_788_length_438_cov_1.712934_pilon to pilon.fasta [pilon] Writing NODE_789_length_438_cov_1.056782:1-438 changes to pilon.changes [pilon] Writing updated NODE_789_length_438_cov_1.056782_pilon to pilon.fasta [pilon] Writing NODE_790_length_437_cov_2.594937:1-437 changes to pilon.changes [pilon] Writing updated NODE_790_length_437_cov_2.594937_pilon to pilon.fasta [pilon] Writing NODE_791_length_437_cov_1.363924:1-437 changes to pilon.changes [pilon] Writing updated NODE_791_length_437_cov_1.363924_pilon to pilon.fasta [pilon] Writing NODE_792_length_437_cov_1.060127:1-437 changes to pilon.changes [pilon] Writing updated NODE_792_length_437_cov_1.060127_pilon to pilon.fasta [pilon] Writing NODE_793_length_437_cov_0.787975:1-437 changes to pilon.changes [pilon] Writing updated NODE_793_length_437_cov_0.787975_pilon to pilon.fasta [pilon] Writing NODE_794_length_436_cov_4.212698:1-436 changes to pilon.changes [pilon] Writing updated NODE_794_length_436_cov_4.212698_pilon to pilon.fasta [pilon] Writing NODE_795_length_436_cov_2.041270:1-436 changes to pilon.changes [pilon] Writing updated NODE_795_length_436_cov_2.041270_pilon to pilon.fasta [pilon] Writing NODE_796_length_436_cov_1.904762:1-436 changes to pilon.changes [pilon] Writing updated NODE_796_length_436_cov_1.904762_pilon to pilon.fasta [pilon] Writing NODE_797_length_436_cov_0.952381:1-436 changes to pilon.changes [pilon] Writing updated NODE_797_length_436_cov_0.952381_pilon to pilon.fasta [pilon] Writing NODE_798_length_436_cov_0.701587:1-436 changes to pilon.changes [pilon] Writing updated NODE_798_length_436_cov_0.701587_pilon to pilon.fasta [pilon] Writing NODE_799_length_435_cov_3.480892:1-435 changes to pilon.changes [pilon] Writing updated NODE_799_length_435_cov_3.480892_pilon to pilon.fasta [pilon] Writing NODE_800_length_435_cov_2.630573:1-435 changes to pilon.changes [pilon] Writing updated NODE_800_length_435_cov_2.630573_pilon to pilon.fasta [pilon] Writing NODE_801_length_435_cov_0.898089:1-435 changes to pilon.changes [pilon] Writing updated NODE_801_length_435_cov_0.898089_pilon to pilon.fasta [pilon] Writing NODE_802_length_435_cov_0.821656:1-435 changes to pilon.changes [pilon] Writing updated NODE_802_length_435_cov_0.821656_pilon to pilon.fasta [pilon] Writing NODE_803_length_434_cov_2.204473:1-434 changes to pilon.changes [pilon] Writing updated NODE_803_length_434_cov_2.204473_pilon to pilon.fasta [pilon] Writing NODE_804_length_434_cov_1.642173:1-434 changes to pilon.changes [pilon] Writing updated NODE_804_length_434_cov_1.642173_pilon to pilon.fasta [pilon] Writing NODE_805_length_434_cov_1.562300:1-434 changes to pilon.changes [pilon] Writing updated NODE_805_length_434_cov_1.562300_pilon to pilon.fasta [pilon] Writing NODE_806_length_434_cov_1.172524:1-434 changes to pilon.changes [pilon] Writing updated NODE_806_length_434_cov_1.172524_pilon to pilon.fasta [pilon] Writing NODE_807_length_434_cov_0.463259:1-434 changes to pilon.changes [pilon] Writing updated NODE_807_length_434_cov_0.463259_pilon to pilon.fasta [pilon] Writing NODE_808_length_433_cov_6.464744:1-433 changes to pilon.changes [pilon] Writing updated NODE_808_length_433_cov_6.464744_pilon to pilon.fasta [pilon] Writing NODE_809_length_432_cov_4.299035:1-432 changes to pilon.changes [pilon] Writing updated NODE_809_length_432_cov_4.299035_pilon to pilon.fasta [pilon] Writing NODE_810_length_432_cov_3.016077:1-432 changes to pilon.changes [pilon] Writing updated NODE_810_length_432_cov_3.016077_pilon to pilon.fasta [pilon] Writing NODE_811_length_432_cov_1.360129:1-432 changes to pilon.changes [pilon] Writing updated NODE_811_length_432_cov_1.360129_pilon to pilon.fasta [pilon] Writing NODE_812_length_431_cov_1.306452:1-431 changes to pilon.changes [pilon] Writing updated NODE_812_length_431_cov_1.306452_pilon to pilon.fasta [pilon] Writing NODE_813_length_431_cov_1.167742:1-431 changes to pilon.changes [pilon] Writing updated NODE_813_length_431_cov_1.167742_pilon to pilon.fasta [pilon] Writing NODE_814_length_430_cov_2.194175:1-430 changes to pilon.changes [pilon] Writing updated NODE_814_length_430_cov_2.194175_pilon to pilon.fasta [pilon] Writing NODE_815_length_430_cov_1.165049:1-430 changes to pilon.changes [pilon] Writing updated NODE_815_length_430_cov_1.165049_pilon to pilon.fasta [pilon] Writing NODE_816_length_430_cov_0.708738:1-430 changes to pilon.changes [pilon] Writing updated NODE_816_length_430_cov_0.708738_pilon to pilon.fasta [pilon] Writing NODE_817_length_429_cov_4.000000:1-429 changes to pilon.changes [pilon] Writing updated NODE_817_length_429_cov_4.000000_pilon to pilon.fasta [pilon] Writing NODE_818_length_429_cov_3.509740:1-429 changes to pilon.changes [pilon] Writing updated NODE_818_length_429_cov_3.509740_pilon to pilon.fasta [pilon] Writing NODE_819_length_428_cov_5.026059:1-428 changes to pilon.changes [pilon] Writing updated NODE_819_length_428_cov_5.026059_pilon to pilon.fasta [pilon] Writing NODE_820_length_428_cov_3.618893:1-428 changes to pilon.changes [pilon] Writing updated NODE_820_length_428_cov_3.618893_pilon to pilon.fasta [pilon] Writing NODE_821_length_428_cov_2.817590:1-428 changes to pilon.changes [pilon] Writing updated NODE_821_length_428_cov_2.817590_pilon to pilon.fasta [pilon] Writing NODE_822_length_428_cov_1.267101:1-428 changes to pilon.changes [pilon] Writing updated NODE_822_length_428_cov_1.267101_pilon to pilon.fasta [pilon] Writing NODE_823_length_428_cov_0.716612:1-428 changes to pilon.changes [pilon] Writing updated NODE_823_length_428_cov_0.716612_pilon to pilon.fasta [pilon] Writing NODE_824_length_427_cov_3.235294:1-427 changes to pilon.changes [pilon] Writing updated NODE_824_length_427_cov_3.235294_pilon to pilon.fasta [pilon] Writing NODE_825_length_427_cov_0.901961:1-427 changes to pilon.changes [pilon] Writing updated NODE_825_length_427_cov_0.901961_pilon to pilon.fasta [pilon] Writing NODE_826_length_426_cov_5.003279:1-426 changes to pilon.changes [pilon] Writing updated NODE_826_length_426_cov_5.003279_pilon to pilon.fasta [pilon] Writing NODE_827_length_426_cov_1.180328:1-426 changes to pilon.changes [pilon] Writing updated NODE_827_length_426_cov_1.180328_pilon to pilon.fasta [pilon] Writing NODE_828_length_426_cov_0.645902:1-426 changes to pilon.changes [pilon] Writing updated NODE_828_length_426_cov_0.645902_pilon to pilon.fasta [pilon] Writing NODE_829_length_426_cov_0.570492:1-426 changes to pilon.changes [pilon] Writing updated NODE_829_length_426_cov_0.570492_pilon to pilon.fasta [pilon] Writing NODE_830_length_426_cov_0.413115:1-426 changes to pilon.changes [pilon] Writing updated NODE_830_length_426_cov_0.413115_pilon to pilon.fasta [pilon] Writing NODE_831_length_425_cov_1.289474:1-425 changes to pilon.changes [pilon] Writing updated NODE_831_length_425_cov_1.289474_pilon to pilon.fasta [pilon] Writing NODE_832_length_425_cov_1.098684:1-425 changes to pilon.changes [pilon] Writing updated NODE_832_length_425_cov_1.098684_pilon to pilon.fasta [pilon] Writing NODE_833_length_424_cov_1.283828:1-424 changes to pilon.changes [pilon] Writing updated NODE_833_length_424_cov_1.283828_pilon to pilon.fasta [pilon] Writing NODE_834_length_424_cov_1.237624:1-424 changes to pilon.changes [pilon] Writing updated NODE_834_length_424_cov_1.237624_pilon to pilon.fasta [pilon] Writing NODE_835_length_424_cov_0.689769:1-424 changes to pilon.changes [pilon] Writing updated NODE_835_length_424_cov_0.689769_pilon to pilon.fasta [pilon] Writing NODE_836_length_423_cov_5.794702:1-423 changes to pilon.changes [pilon] Writing updated NODE_836_length_423_cov_5.794702_pilon to pilon.fasta [pilon] Writing NODE_837_length_423_cov_4.079470:1-423 changes to pilon.changes [pilon] Writing updated NODE_837_length_423_cov_4.079470_pilon to pilon.fasta [pilon] Writing NODE_838_length_423_cov_2.384106:1-423 changes to pilon.changes [pilon] Writing updated NODE_838_length_423_cov_2.384106_pilon to pilon.fasta [pilon] Writing NODE_839_length_422_cov_2.694352:1-422 changes to pilon.changes [pilon] Writing updated NODE_839_length_422_cov_2.694352_pilon to pilon.fasta [pilon] Writing NODE_840_length_422_cov_1.694352:1-422 changes to pilon.changes [pilon] Writing updated NODE_840_length_422_cov_1.694352_pilon to pilon.fasta [pilon] Writing NODE_841_length_422_cov_0.710963:1-422 changes to pilon.changes [pilon] Writing updated NODE_841_length_422_cov_0.710963_pilon to pilon.fasta [pilon] Writing NODE_842_length_421_cov_2.793333:1-421 changes to pilon.changes [pilon] Writing updated NODE_842_length_421_cov_2.793333_pilon to pilon.fasta [pilon] Writing NODE_843_length_421_cov_1.720000:1-421 changes to pilon.changes [pilon] Writing updated NODE_843_length_421_cov_1.720000_pilon to pilon.fasta [pilon] Writing NODE_844_length_421_cov_1.536667:1-421 changes to pilon.changes [pilon] Writing updated NODE_844_length_421_cov_1.536667_pilon to pilon.fasta [pilon] Writing NODE_845_length_421_cov_0.993333:1-421 changes to pilon.changes [pilon] Writing updated NODE_845_length_421_cov_0.993333_pilon to pilon.fasta [pilon] Writing NODE_846_length_421_cov_0.366667:1-421 changes to pilon.changes [pilon] Writing updated NODE_846_length_421_cov_0.366667_pilon to pilon.fasta [pilon] Writing NODE_847_length_420_cov_0.959866:1-420 changes to pilon.changes [pilon] Writing updated NODE_847_length_420_cov_0.959866_pilon to pilon.fasta [pilon] Writing NODE_848_length_419_cov_2.550336:1-419 changes to pilon.changes [pilon] Writing updated NODE_848_length_419_cov_2.550336_pilon to pilon.fasta [pilon] Writing NODE_849_length_419_cov_2.194631:1-419 changes to pilon.changes [pilon] Writing updated NODE_849_length_419_cov_2.194631_pilon to pilon.fasta [pilon] Writing NODE_850_length_419_cov_1.157718:1-419 changes to pilon.changes [pilon] Writing updated NODE_850_length_419_cov_1.157718_pilon to pilon.fasta [pilon] Writing NODE_851_length_419_cov_0.617450:1-419 changes to pilon.changes [pilon] Writing updated NODE_851_length_419_cov_0.617450_pilon to pilon.fasta [pilon] Writing NODE_852_length_418_cov_3.343434:1-418 changes to pilon.changes [pilon] Writing updated NODE_852_length_418_cov_3.343434_pilon to pilon.fasta [pilon] Writing NODE_853_length_418_cov_1.835017:1-418 changes to pilon.changes [pilon] Writing updated NODE_853_length_418_cov_1.835017_pilon to pilon.fasta [pilon] Writing NODE_854_length_418_cov_0.653199:1-418 changes to pilon.changes [pilon] Writing updated NODE_854_length_418_cov_0.653199_pilon to pilon.fasta [pilon] Writing NODE_855_length_417_cov_1.611486:1-417 changes to pilon.changes [pilon] Writing updated NODE_855_length_417_cov_1.611486_pilon to pilon.fasta [pilon] Writing NODE_856_length_416_cov_1.623729:1-416 changes to pilon.changes [pilon] Writing updated NODE_856_length_416_cov_1.623729_pilon to pilon.fasta [pilon] Writing NODE_857_length_416_cov_1.081356:1-416 changes to pilon.changes [pilon] Writing updated NODE_857_length_416_cov_1.081356_pilon to pilon.fasta [pilon] Writing NODE_858_length_416_cov_0.461017:1-416 changes to pilon.changes [pilon] Writing updated NODE_858_length_416_cov_0.461017_pilon to pilon.fasta [pilon] Writing NODE_859_length_416_cov_0.294915:1-416 changes to pilon.changes [pilon] Writing updated NODE_859_length_416_cov_0.294915_pilon to pilon.fasta [pilon] Writing NODE_860_length_415_cov_1.057823:1-415 changes to pilon.changes [pilon] Writing updated NODE_860_length_415_cov_1.057823_pilon to pilon.fasta [pilon] Writing NODE_861_length_414_cov_2.470990:1-414 changes to pilon.changes [pilon] Writing updated NODE_861_length_414_cov_2.470990_pilon to pilon.fasta [pilon] Writing NODE_862_length_414_cov_1.331058:1-414 changes to pilon.changes [pilon] Writing updated NODE_862_length_414_cov_1.331058_pilon to pilon.fasta [pilon] Writing NODE_863_length_414_cov_1.262799:1-414 changes to pilon.changes [pilon] Writing updated NODE_863_length_414_cov_1.262799_pilon to pilon.fasta [pilon] Writing NODE_864_length_414_cov_1.255973:1-414 changes to pilon.changes [pilon] Writing updated NODE_864_length_414_cov_1.255973_pilon to pilon.fasta [pilon] Writing NODE_865_length_414_cov_0.641638:1-414 changes to pilon.changes [pilon] Writing updated NODE_865_length_414_cov_0.641638_pilon to pilon.fasta [pilon] Writing NODE_866_length_413_cov_2.428082:1-413 changes to pilon.changes [pilon] Writing updated NODE_866_length_413_cov_2.428082_pilon to pilon.fasta [pilon] Writing NODE_867_length_413_cov_1.099315:1-413 changes to pilon.changes [pilon] Writing updated NODE_867_length_413_cov_1.099315_pilon to pilon.fasta [pilon] Writing NODE_868_length_412_cov_1.797251:1-412 changes to pilon.changes [pilon] Writing updated NODE_868_length_412_cov_1.797251_pilon to pilon.fasta [pilon] Writing NODE_869_length_412_cov_1.501718:1-412 changes to pilon.changes [pilon] Writing updated NODE_869_length_412_cov_1.501718_pilon to pilon.fasta [pilon] Writing NODE_870_length_412_cov_1.364261:1-412 changes to pilon.changes [pilon] Writing updated NODE_870_length_412_cov_1.364261_pilon to pilon.fasta [pilon] Writing NODE_871_length_411_cov_2.048276:1-411 changes to pilon.changes [pilon] Writing updated NODE_871_length_411_cov_2.048276_pilon to pilon.fasta [pilon] Writing NODE_872_length_411_cov_1.951724:1-411 changes to pilon.changes [pilon] Writing updated NODE_872_length_411_cov_1.951724_pilon to pilon.fasta [pilon] Writing NODE_873_length_411_cov_1.644828:1-411 changes to pilon.changes [pilon] Writing updated NODE_873_length_411_cov_1.644828_pilon to pilon.fasta [pilon] Writing NODE_874_length_410_cov_2.944637:1-410 changes to pilon.changes [pilon] Writing updated NODE_874_length_410_cov_2.944637_pilon to pilon.fasta [pilon] Writing NODE_875_length_409_cov_2.204861:1-409 changes to pilon.changes [pilon] Writing updated NODE_875_length_409_cov_2.204861_pilon to pilon.fasta [pilon] Writing NODE_876_length_409_cov_0.697917:1-409 changes to pilon.changes [pilon] Writing updated NODE_876_length_409_cov_0.697917_pilon to pilon.fasta [pilon] Writing NODE_877_length_408_cov_4.003484:1-408 changes to pilon.changes [pilon] Writing updated NODE_877_length_408_cov_4.003484_pilon to pilon.fasta [pilon] Writing NODE_878_length_408_cov_3.770035:1-408 changes to pilon.changes [pilon] Writing updated NODE_878_length_408_cov_3.770035_pilon to pilon.fasta [pilon] Writing NODE_879_length_408_cov_1.905923:1-408 changes to pilon.changes [pilon] Writing updated NODE_879_length_408_cov_1.905923_pilon to pilon.fasta [pilon] Writing NODE_880_length_408_cov_1.236934:1-408 changes to pilon.changes [pilon] Writing updated NODE_880_length_408_cov_1.236934_pilon to pilon.fasta [pilon] Writing NODE_881_length_408_cov_1.121951:1-408 changes to pilon.changes [pilon] Writing updated NODE_881_length_408_cov_1.121951_pilon to pilon.fasta [pilon] Writing NODE_882_length_408_cov_0.658537:1-408 changes to pilon.changes [pilon] Writing updated NODE_882_length_408_cov_0.658537_pilon to pilon.fasta [pilon] Writing NODE_883_length_408_cov_0.404181:1-408 changes to pilon.changes [pilon] Writing updated NODE_883_length_408_cov_0.404181_pilon to pilon.fasta [pilon] Writing NODE_884_length_408_cov_0.202091:1-408 changes to pilon.changes [pilon] Writing updated NODE_884_length_408_cov_0.202091_pilon to pilon.fasta [pilon] Writing NODE_885_length_407_cov_1.398601:1-407 changes to pilon.changes [pilon] Writing updated NODE_885_length_407_cov_1.398601_pilon to pilon.fasta [pilon] Writing NODE_886_length_407_cov_0.944056:1-407 changes to pilon.changes [pilon] Writing updated NODE_886_length_407_cov_0.944056_pilon to pilon.fasta [pilon] Writing NODE_887_length_407_cov_0.916084:1-407 changes to pilon.changes [pilon] Writing updated NODE_887_length_407_cov_0.916084_pilon to pilon.fasta [pilon] Writing NODE_888_length_406_cov_3.042105:1-406 changes to pilon.changes [pilon] Writing updated NODE_888_length_406_cov_3.042105_pilon to pilon.fasta [pilon] Writing NODE_889_length_406_cov_1.396491:1-406 changes to pilon.changes [pilon] Writing updated NODE_889_length_406_cov_1.396491_pilon to pilon.fasta [pilon] Writing NODE_890_length_406_cov_1.101754:1-406 changes to pilon.changes [pilon] Writing updated NODE_890_length_406_cov_1.101754_pilon to pilon.fasta [pilon] Writing NODE_891_length_406_cov_0.757895:1-406 changes to pilon.changes [pilon] Writing updated NODE_891_length_406_cov_0.757895_pilon to pilon.fasta [pilon] Writing NODE_892_length_406_cov_0.407018:1-406 changes to pilon.changes [pilon] Writing updated NODE_892_length_406_cov_0.407018_pilon to pilon.fasta [pilon] Writing NODE_893_length_405_cov_2.873239:1-405 changes to pilon.changes [pilon] Writing updated NODE_893_length_405_cov_2.873239_pilon to pilon.fasta [pilon] Writing NODE_894_length_405_cov_1.165493:1-405 changes to pilon.changes [pilon] Writing updated NODE_894_length_405_cov_1.165493_pilon to pilon.fasta [pilon] Writing NODE_895_length_405_cov_0.510563:1-405 changes to pilon.changes [pilon] Writing updated NODE_895_length_405_cov_0.510563_pilon to pilon.fasta [pilon] Writing NODE_896_length_404_cov_90.671378:1-404 changes to pilon.changes [pilon] Writing updated NODE_896_length_404_cov_90.671378_pilon to pilon.fasta [pilon] Writing NODE_897_length_404_cov_2.787986:1-404 changes to pilon.changes [pilon] Writing updated NODE_897_length_404_cov_2.787986_pilon to pilon.fasta [pilon] Writing NODE_898_length_404_cov_1.795053:1-404 changes to pilon.changes [pilon] Writing updated NODE_898_length_404_cov_1.795053_pilon to pilon.fasta [pilon] Writing NODE_899_length_404_cov_1.544170:1-404 changes to pilon.changes [pilon] Writing updated NODE_899_length_404_cov_1.544170_pilon to pilon.fasta [pilon] Writing NODE_900_length_404_cov_0.621908:1-404 changes to pilon.changes [pilon] Writing updated NODE_900_length_404_cov_0.621908_pilon to pilon.fasta [pilon] Writing NODE_901_length_403_cov_3.290780:1-403 changes to pilon.changes [pilon] Writing updated NODE_901_length_403_cov_3.290780_pilon to pilon.fasta [pilon] Writing NODE_902_length_403_cov_1.453901:1-403 changes to pilon.changes [pilon] Writing updated NODE_902_length_403_cov_1.453901_pilon to pilon.fasta [pilon] Writing NODE_903_length_403_cov_0.929078:1-403 changes to pilon.changes [pilon] Writing updated NODE_903_length_403_cov_0.929078_pilon to pilon.fasta [pilon] Writing NODE_904_length_403_cov_0.882979:1-403 changes to pilon.changes [pilon] Writing updated NODE_904_length_403_cov_0.882979_pilon to pilon.fasta [pilon] Writing NODE_905_length_403_cov_0.500000:1-403 changes to pilon.changes [pilon] Writing updated NODE_905_length_403_cov_0.500000_pilon to pilon.fasta [pilon] Writing NODE_906_length_402_cov_91.327402:1-402 changes to pilon.changes [pilon] Writing updated NODE_906_length_402_cov_91.327402_pilon to pilon.fasta [pilon] Writing NODE_907_length_402_cov_2.704626:1-402 changes to pilon.changes [pilon] Writing updated NODE_907_length_402_cov_2.704626_pilon to pilon.fasta [pilon] Writing NODE_908_length_402_cov_2.448399:1-402 changes to pilon.changes [pilon] Writing updated NODE_908_length_402_cov_2.448399_pilon to pilon.fasta [pilon] Writing NODE_909_length_402_cov_2.437722:1-402 changes to pilon.changes [pilon] Writing updated NODE_909_length_402_cov_2.437722_pilon to pilon.fasta [pilon] Writing NODE_910_length_402_cov_2.049822:1-402 changes to pilon.changes [pilon] Writing updated NODE_910_length_402_cov_2.049822_pilon to pilon.fasta [pilon] Writing NODE_911_length_402_cov_1.007117:1-402 changes to pilon.changes [pilon] Writing updated NODE_911_length_402_cov_1.007117_pilon to pilon.fasta [pilon] Writing NODE_912_length_402_cov_0.523132:1-402 changes to pilon.changes [pilon] Writing updated NODE_912_length_402_cov_0.523132_pilon to pilon.fasta [pilon] Writing NODE_913_length_399_cov_99.758993:1-399 changes to pilon.changes [pilon] Writing updated NODE_913_length_399_cov_99.758993_pilon to pilon.fasta [pilon] Writing NODE_914_length_345_cov_42.709821:1-345 changes to pilon.changes [pilon] Writing updated NODE_914_length_345_cov_42.709821_pilon to pilon.fasta [pilon] Writing NODE_915_length_328_cov_30.048309:1-328 changes to pilon.changes [pilon] Writing updated NODE_915_length_328_cov_30.048309_pilon to pilon.fasta [pilon] Writing NODE_916_length_308_cov_40.363636:1-308 changes to pilon.changes [pilon] Writing updated NODE_916_length_308_cov_40.363636_pilon to pilon.fasta [pilon] Writing NODE_917_length_297_cov_40.056818:1-297 changes to pilon.changes [pilon] Writing updated NODE_917_length_297_cov_40.056818_pilon to pilon.fasta [pilon] Writing NODE_918_length_294_cov_139.098266:1-294 changes to pilon.changes [pilon] Writing updated NODE_918_length_294_cov_139.098266_pilon to pilon.fasta [pilon] Writing NODE_919_length_293_cov_34.162791:1-293 changes to pilon.changes [pilon] Writing updated NODE_919_length_293_cov_34.162791_pilon to pilon.fasta [pilon] Writing NODE_920_length_273_cov_36.506579:1-273 changes to pilon.changes [pilon] Writing updated NODE_920_length_273_cov_36.506579_pilon to pilon.fasta [pilon] Writing NODE_921_length_270_cov_27.093960:1-270 changes to pilon.changes [pilon] Writing updated NODE_921_length_270_cov_27.093960_pilon to pilon.fasta [pilon] Writing NODE_922_length_249_cov_85.476562:1-249 changes to pilon.changes [pilon] Writing updated NODE_922_length_249_cov_85.476562_pilon to pilon.fasta [pilon] Writing NODE_923_length_244_cov_169.414634:1-244 changes to pilon.changes [pilon] Writing updated NODE_923_length_244_cov_169.414634_pilon to pilon.fasta [pilon] Writing NODE_924_length_244_cov_85.203252:1-244 changes to pilon.changes [pilon] Writing updated NODE_924_length_244_cov_85.203252_pilon to pilon.fasta [pilon] Writing NODE_925_length_243_cov_51.655738:1-243 changes to pilon.changes [pilon] Writing updated NODE_925_length_243_cov_51.655738_pilon to pilon.fasta [pilon] Writing NODE_926_length_243_cov_50.122951:1-243 changes to pilon.changes [pilon] Writing updated NODE_926_length_243_cov_50.122951_pilon to pilon.fasta [pilon] Writing NODE_927_length_243_cov_45.827869:1-243 changes to pilon.changes [pilon] Writing updated NODE_927_length_243_cov_45.827869_pilon to pilon.fasta [pilon] Writing NODE_928_length_243_cov_45.540984:1-243 changes to pilon.changes [pilon] Writing updated NODE_928_length_243_cov_45.540984_pilon to pilon.fasta [pilon] Writing NODE_929_length_243_cov_44.868852:1-243 changes to pilon.changes [pilon] Writing updated NODE_929_length_243_cov_44.868852_pilon to pilon.fasta [pilon] Writing NODE_930_length_243_cov_43.418033:1-243 changes to pilon.changes [pilon] Writing updated NODE_930_length_243_cov_43.418033_pilon to pilon.fasta [pilon] Writing NODE_931_length_243_cov_33.811475:1-243 changes to pilon.changes [pilon] Writing updated NODE_931_length_243_cov_33.811475_pilon to pilon.fasta [pilon] Writing NODE_932_length_241_cov_38.241667:1-241 changes to pilon.changes [pilon] Writing updated NODE_932_length_241_cov_38.241667_pilon to pilon.fasta [pilon] Writing NODE_933_length_240_cov_55.739496:1-240 changes to pilon.changes [pilon] Writing updated NODE_933_length_240_cov_55.739496_pilon to pilon.fasta [pilon] Writing NODE_934_length_134_cov_36.384615:1-134 changes to pilon.changes [pilon] Writing updated NODE_934_length_134_cov_36.384615_pilon to pilon.fasta [pilon] Writing NODE_935_length_124_cov_143.000000:1-124 changes to pilon.changes [pilon] Writing updated NODE_935_length_124_cov_143.000000_pilon to pilon.fasta [pilon] Writing NODE_936_length_122_cov_4573.000000:1-122 changes to pilon.changes [pilon] Writing updated NODE_936_length_122_cov_4573.000000_pilon to pilon.fasta [pilon] Writing NODE_937_length_122_cov_58.000000:1-122 changes to pilon.changes [pilon] Writing updated NODE_937_length_122_cov_58.000000_pilon to pilon.fasta [pilon] Mean frags coverage: 113 [pilon] Mean total coverage: 113 [shovill] Repaired 72 contigs from spades.fasta at 95 positions. [shovill] Removing low coverage contig (< 2 x): NODE_91_length_1210_cov_1.355372_pilon [shovill] Removing low coverage contig (< 2 x): NODE_98_length_1148_cov_0.789679_pilon [shovill] Removing low coverage contig (< 2 x): NODE_116_length_1006_cov_1.476836_pilon [shovill] Removing low coverage contig (< 2 x): NODE_119_length_983_cov_1.813225_pilon [shovill] Removing low coverage contig (< 2 x): NODE_122_length_955_cov_0.471223_pilon [shovill] Removing low coverage contig (< 2 x): NODE_127_length_929_cov_1.813119_pilon [shovill] Removing low coverage contig (< 2 x): NODE_131_length_900_cov_0.893453_pilon [shovill] Removing low coverage contig (< 2 x): NODE_134_length_895_cov_1.293282_pilon [shovill] Removing low coverage contig (< 2 x): NODE_138_length_876_cov_1.023841_pilon [shovill] Removing low coverage contig (< 2 x): NODE_142_length_852_cov_1.573187_pilon [shovill] Removing low coverage contig (< 2 x): NODE_149_length_838_cov_0.669456_pilon [shovill] Removing low coverage contig (< 2 x): NODE_154_length_832_cov_1.753868_pilon [shovill] Removing low coverage contig (< 2 x): NODE_162_length_819_cov_1.733524_pilon [shovill] Removing low coverage contig (< 2 x): NODE_169_length_805_cov_0.739766_pilon [shovill] Removing low coverage contig (< 2 x): NODE_171_length_802_cov_1.945668_pilon [shovill] Removing low coverage contig (< 2 x): NODE_172_length_802_cov_1.509545_pilon [shovill] Removing low coverage contig (< 2 x): NODE_180_length_790_cov_1.372197_pilon [shovill] Removing low coverage contig (< 2 x): NODE_189_length_770_cov_1.961479_pilon [shovill] Removing low coverage contig (< 2 x): NODE_204_length_752_cov_0.689382_pilon [shovill] Removing low coverage contig (< 2 x): NODE_212_length_743_cov_0.860129_pilon [shovill] Removing low coverage contig (< 2 x): NODE_213_length_742_cov_0.743961_pilon [shovill] Removing low coverage contig (< 2 x): NODE_222_length_738_cov_1.311183_pilon [shovill] Removing low coverage contig (< 2 x): NODE_229_length_726_cov_1.993388_pilon [shovill] Removing low coverage contig (< 2 x): NODE_232_length_721_cov_1.846667_pilon [shovill] Removing low coverage contig (< 2 x): NODE_240_length_714_cov_0.691400_pilon [shovill] Removing low coverage contig (< 2 x): NODE_255_length_702_cov_1.733219_pilon [shovill] Removing low coverage contig (< 2 x): NODE_274_length_686_cov_1.407080_pilon [shovill] Removing low coverage contig (< 2 x): NODE_284_length_674_cov_0.871609_pilon [shovill] Removing low coverage contig (< 2 x): NODE_292_length_671_cov_1.358182_pilon [shovill] Removing low coverage contig (< 2 x): NODE_293_length_671_cov_1.327273_pilon [shovill] Removing low coverage contig (< 2 x): NODE_299_length_666_cov_0.715596_pilon [shovill] Removing low coverage contig (< 2 x): NODE_301_length_662_cov_1.837338_pilon [shovill] Removing low coverage contig (< 2 x): NODE_305_length_661_cov_1.529630_pilon [shovill] Removing low coverage contig (< 2 x): NODE_310_length_656_cov_1.218692_pilon [shovill] Removing low coverage contig (< 2 x): NODE_314_length_653_cov_1.436090_pilon [shovill] Removing low coverage contig (< 2 x): NODE_328_length_646_cov_0.775238_pilon [shovill] Removing low coverage contig (< 2 x): NODE_329_length_646_cov_0.761905_pilon [shovill] Removing low coverage contig (< 2 x): NODE_332_length_643_cov_0.992337_pilon [shovill] Removing low coverage contig (< 2 x): NODE_336_length_642_cov_0.660269_pilon [shovill] Removing low coverage contig (< 2 x): NODE_335_length_642_cov_1.644914_pilon [shovill] Removing low coverage contig (< 2 x): NODE_339_length_641_cov_0.930769_pilon [shovill] Removing low coverage contig (< 2 x): NODE_346_length_632_cov_1.418787_pilon [shovill] Removing low coverage contig (< 2 x): NODE_351_length_629_cov_0.990157_pilon [shovill] Removing low coverage contig (< 2 x): NODE_353_length_628_cov_1.211045_pilon [shovill] Removing low coverage contig (< 2 x): NODE_354_length_627_cov_0.901186_pilon [shovill] Removing low coverage contig (< 2 x): NODE_355_length_627_cov_0.723320_pilon [shovill] Removing low coverage contig (< 2 x): NODE_357_length_625_cov_1.605159_pilon [shovill] Removing low coverage contig (< 2 x): NODE_361_length_622_cov_1.826347_pilon [shovill] Removing low coverage contig (< 2 x): NODE_362_length_622_cov_0.612774_pilon [shovill] Removing low coverage contig (< 2 x): NODE_363_length_621_cov_1.536000_pilon [shovill] Removing low coverage contig (< 2 x): NODE_365_length_620_cov_1.148297_pilon [shovill] Removing low coverage contig (< 2 x): NODE_370_length_617_cov_0.774194_pilon [shovill] Removing low coverage contig (< 2 x): NODE_374_length_615_cov_1.866397_pilon [shovill] Removing low coverage contig (< 2 x): NODE_376_length_614_cov_1.245436_pilon [shovill] Removing low coverage contig (< 2 x): NODE_378_length_613_cov_1.747967_pilon [shovill] Removing low coverage contig (< 2 x): NODE_379_length_611_cov_1.889796_pilon [shovill] Removing low coverage contig (< 2 x): NODE_386_length_607_cov_0.742798_pilon [shovill] Removing low coverage contig (< 2 x): NODE_387_length_606_cov_1.863918_pilon [shovill] Removing low coverage contig (< 2 x): NODE_391_length_604_cov_1.165631_pilon [shovill] Removing low coverage contig (< 2 x): NODE_390_length_604_cov_1.343685_pilon [shovill] Removing low coverage contig (< 2 x): NODE_392_length_603_cov_1.765560_pilon [shovill] Removing low coverage contig (< 2 x): NODE_394_length_602_cov_1.147609_pilon [shovill] Removing low coverage contig (< 2 x): NODE_395_length_601_cov_1.741667_pilon [shovill] Removing low coverage contig (< 2 x): NODE_398_length_600_cov_1.668058_pilon [shovill] Removing low coverage contig (< 2 x): NODE_397_length_600_cov_1.826722_pilon [shovill] Removing low coverage contig (< 2 x): NODE_413_length_594_cov_1.040169_pilon [shovill] Removing low coverage contig (< 2 x): NODE_414_length_593_cov_0.741525_pilon [shovill] Removing low coverage contig (< 2 x): NODE_430_length_584_cov_0.552916_pilon [shovill] Removing low coverage contig (< 2 x): NODE_429_length_584_cov_1.611231_pilon [shovill] Removing low coverage contig (< 2 x): NODE_434_length_581_cov_1.110870_pilon [shovill] Removing low coverage contig (< 2 x): NODE_435_length_581_cov_0.717391_pilon [shovill] Removing low coverage contig (< 2 x): NODE_438_length_578_cov_1.271335_pilon [shovill] Removing low coverage contig (< 2 x): NODE_437_length_578_cov_1.682713_pilon [shovill] Removing low coverage contig (< 2 x): NODE_439_length_577_cov_1.967105_pilon [shovill] Removing low coverage contig (< 2 x): NODE_443_length_577_cov_0.660088_pilon [shovill] Removing low coverage contig (< 2 x): NODE_442_length_577_cov_1.396930_pilon [shovill] Removing low coverage contig (< 2 x): NODE_441_length_577_cov_1.447368_pilon [shovill] Removing low coverage contig (< 2 x): NODE_440_length_577_cov_1.548246_pilon [shovill] Removing low coverage contig (< 2 x): NODE_445_length_576_cov_1.593407_pilon [shovill] Removing low coverage contig (< 2 x): NODE_446_length_576_cov_1.351648_pilon [shovill] Removing low coverage contig (< 2 x): NODE_449_length_574_cov_1.578366_pilon [shovill] Removing low coverage contig (< 2 x): NODE_451_length_573_cov_0.865044_pilon [shovill] Removing low coverage contig (< 2 x): NODE_454_length_570_cov_0.556793_pilon [shovill] Removing low coverage contig (< 2 x): NODE_458_length_569_cov_1.357143_pilon [shovill] Removing low coverage contig (< 2 x): NODE_459_length_569_cov_0.763393_pilon [shovill] Removing low coverage contig (< 2 x): NODE_462_length_568_cov_1.662192_pilon [shovill] Removing low coverage contig (< 2 x): NODE_463_length_568_cov_1.210291_pilon [shovill] Removing low coverage contig (< 2 x): NODE_467_length_566_cov_0.833708_pilon [shovill] Removing low coverage contig (< 2 x): NODE_473_length_563_cov_1.889140_pilon [shovill] Removing low coverage contig (< 2 x): NODE_474_length_563_cov_1.601810_pilon [shovill] Removing low coverage contig (< 2 x): NODE_480_length_561_cov_1.459091_pilon [shovill] Removing low coverage contig (< 2 x): NODE_479_length_561_cov_1.650000_pilon [shovill] Removing low coverage contig (< 2 x): NODE_482_length_559_cov_0.958904_pilon [shovill] Removing low coverage contig (< 2 x): NODE_487_length_557_cov_0.983945_pilon [shovill] Removing low coverage contig (< 2 x): NODE_492_length_555_cov_1.419355_pilon [shovill] Removing low coverage contig (< 2 x): NODE_493_length_554_cov_1.586605_pilon [shovill] Removing low coverage contig (< 2 x): NODE_494_length_554_cov_1.124711_pilon [shovill] Removing low coverage contig (< 2 x): NODE_495_length_553_cov_1.171296_pilon [shovill] Removing low coverage contig (< 2 x): NODE_498_length_552_cov_1.018561_pilon [shovill] Removing low coverage contig (< 2 x): NODE_500_length_551_cov_1.555814_pilon [shovill] Removing low coverage contig (< 2 x): NODE_501_length_551_cov_1.011628_pilon [shovill] Removing low coverage contig (< 2 x): NODE_507_length_550_cov_1.172494_pilon [shovill] Removing low coverage contig (< 2 x): NODE_509_length_549_cov_1.934579_pilon [shovill] Removing low coverage contig (< 2 x): NODE_510_length_549_cov_1.546729_pilon [shovill] Removing low coverage contig (< 2 x): NODE_513_length_548_cov_1.515222_pilon [shovill] Removing low coverage contig (< 2 x): NODE_512_length_548_cov_1.957845_pilon [shovill] Removing low coverage contig (< 2 x): NODE_517_length_547_cov_1.286385_pilon [shovill] Removing low coverage contig (< 2 x): NODE_516_length_547_cov_1.326291_pilon [shovill] Removing low coverage contig (< 2 x): NODE_519_length_545_cov_0.896226_pilon [shovill] Removing low coverage contig (< 2 x): NODE_522_length_544_cov_1.345154_pilon [shovill] Removing low coverage contig (< 2 x): NODE_523_length_543_cov_0.696682_pilon [shovill] Removing low coverage contig (< 2 x): NODE_525_length_541_cov_1.269048_pilon [shovill] Removing low coverage contig (< 2 x): NODE_526_length_539_cov_0.894737_pilon [shovill] Removing low coverage contig (< 2 x): NODE_529_length_538_cov_0.671463_pilon [shovill] Removing low coverage contig (< 2 x): NODE_528_length_538_cov_1.446043_pilon [shovill] Removing low coverage contig (< 2 x): NODE_527_length_538_cov_1.733813_pilon [shovill] Removing low coverage contig (< 2 x): NODE_531_length_537_cov_1.574519_pilon [shovill] Removing low coverage contig (< 2 x): NODE_535_length_536_cov_1.884337_pilon [shovill] Removing low coverage contig (< 2 x): NODE_536_length_536_cov_1.077108_pilon [shovill] Removing low coverage contig (< 2 x): NODE_542_length_534_cov_1.515738_pilon [shovill] Removing low coverage contig (< 2 x): NODE_544_length_533_cov_1.235437_pilon [shovill] Removing low coverage contig (< 2 x): NODE_548_length_529_cov_1.431373_pilon [shovill] Removing low coverage contig (< 2 x): NODE_549_length_528_cov_1.393120_pilon [shovill] Removing low coverage contig (< 2 x): NODE_553_length_527_cov_1.901478_pilon [shovill] Removing low coverage contig (< 2 x): NODE_557_length_526_cov_0.708642_pilon [shovill] Removing low coverage contig (< 2 x): NODE_556_length_526_cov_1.901235_pilon [shovill] Removing low coverage contig (< 2 x): NODE_558_length_525_cov_1.509901_pilon [shovill] Removing low coverage contig (< 2 x): NODE_566_length_519_cov_1.587940_pilon [shovill] Removing low coverage contig (< 2 x): NODE_567_length_519_cov_0.748744_pilon [shovill] Removing low coverage contig (< 2 x): NODE_575_length_517_cov_1.606061_pilon [shovill] Removing low coverage contig (< 2 x): NODE_579_length_515_cov_1.614213_pilon [shovill] Removing low coverage contig (< 2 x): NODE_578_length_515_cov_1.868020_pilon [shovill] Removing low coverage contig (< 2 x): NODE_577_length_515_cov_1.951777_pilon [shovill] Removing low coverage contig (< 2 x): NODE_580_length_515_cov_0.791878_pilon [shovill] Removing low coverage contig (< 2 x): NODE_583_length_514_cov_1.720102_pilon [shovill] Removing low coverage contig (< 2 x): NODE_587_length_513_cov_1.696429_pilon [shovill] Removing low coverage contig (< 2 x): NODE_589_length_512_cov_0.864450_pilon [shovill] Removing low coverage contig (< 2 x): NODE_588_length_512_cov_1.002558_pilon [shovill] Removing low coverage contig (< 2 x): NODE_591_length_511_cov_0.435897_pilon [shovill] Removing low coverage contig (< 2 x): NODE_594_length_510_cov_1.971722_pilon [shovill] Removing low coverage contig (< 2 x): NODE_595_length_509_cov_1.961340_pilon [shovill] Removing low coverage contig (< 2 x): NODE_598_length_508_cov_1.550388_pilon [shovill] Removing low coverage contig (< 2 x): NODE_599_length_508_cov_1.232558_pilon [shovill] Removing low coverage contig (< 2 x): NODE_596_length_508_cov_1.614987_pilon [shovill] Removing low coverage contig (< 2 x): NODE_600_length_508_cov_0.578811_pilon [shovill] Removing low coverage contig (< 2 x): NODE_597_length_508_cov_1.573643_pilon [shovill] Removing low coverage contig (< 2 x): NODE_602_length_507_cov_0.505181_pilon [shovill] Removing low coverage contig (< 2 x): NODE_601_length_507_cov_0.917098_pilon [shovill] Removing low coverage contig (< 2 x): NODE_605_length_506_cov_1.724675_pilon [shovill] Removing low coverage contig (< 2 x): NODE_610_length_505_cov_1.351562_pilon [shovill] Removing low coverage contig (< 2 x): NODE_609_length_505_cov_1.932292_pilon [shovill] Removing low coverage contig (< 2 x): NODE_612_length_503_cov_1.065445_pilon [shovill] Removing low coverage contig (< 2 x): NODE_614_length_503_cov_0.821990_pilon [shovill] Removing low coverage contig (< 2 x): NODE_611_length_503_cov_1.246073_pilon [shovill] Removing low coverage contig (< 2 x): NODE_613_length_503_cov_0.960733_pilon [shovill] Removing low coverage contig (< 2 x): NODE_617_length_502_cov_1.545932_pilon [shovill] Removing low coverage contig (< 2 x): NODE_625_length_498_cov_0.941645_pilon [shovill] Removing low coverage contig (< 2 x): NODE_634_length_495_cov_1.278075_pilon [shovill] Removing low coverage contig (< 2 x): NODE_633_length_495_cov_1.304813_pilon [shovill] Removing low coverage contig (< 2 x): NODE_632_length_495_cov_1.462567_pilon [shovill] Removing low coverage contig (< 2 x): NODE_638_length_494_cov_1.048257_pilon [shovill] Removing low coverage contig (< 2 x): NODE_637_length_494_cov_1.126005_pilon [shovill] Removing low coverage contig (< 2 x): NODE_640_length_493_cov_1.413978_pilon [shovill] Removing low coverage contig (< 2 x): NODE_643_length_492_cov_1.210243_pilon [shovill] Removing low coverage contig (< 2 x): NODE_642_length_492_cov_1.908356_pilon [shovill] Removing low coverage contig (< 2 x): NODE_645_length_491_cov_0.581081_pilon [shovill] Removing low coverage contig (< 2 x): NODE_646_length_490_cov_1.785908_pilon [shovill] Removing low coverage contig (< 2 x): NODE_647_length_490_cov_1.132791_pilon [shovill] Removing low coverage contig (< 2 x): NODE_651_length_488_cov_0.828338_pilon [shovill] Removing low coverage contig (< 2 x): NODE_650_length_488_cov_0.945504_pilon [shovill] Removing low coverage contig (< 2 x): NODE_654_length_487_cov_1.333333_pilon [shovill] Removing low coverage contig (< 2 x): NODE_659_length_485_cov_1.793956_pilon [shovill] Removing low coverage contig (< 2 x): NODE_662_length_483_cov_1.417127_pilon [shovill] Removing low coverage contig (< 2 x): NODE_663_length_483_cov_1.342541_pilon [shovill] Removing low coverage contig (< 2 x): NODE_661_length_483_cov_1.726519_pilon [shovill] Removing low coverage contig (< 2 x): NODE_664_length_483_cov_1.215470_pilon [shovill] Removing low coverage contig (< 2 x): NODE_668_length_482_cov_1.476454_pilon [shovill] Removing low coverage contig (< 2 x): NODE_670_length_482_cov_0.202216_pilon [shovill] Removing low coverage contig (< 2 x): NODE_669_length_482_cov_0.850416_pilon [shovill] Removing low coverage contig (< 2 x): NODE_667_length_482_cov_1.565097_pilon [shovill] Removing low coverage contig (< 2 x): NODE_672_length_480_cov_1.114206_pilon [shovill] Removing low coverage contig (< 2 x): NODE_675_length_479_cov_1.821229_pilon [shovill] Removing low coverage contig (< 2 x): NODE_676_length_479_cov_1.611732_pilon [shovill] Removing low coverage contig (< 2 x): NODE_679_length_478_cov_1.364146_pilon [shovill] Removing low coverage contig (< 2 x): NODE_678_length_478_cov_1.873950_pilon [shovill] Removing low coverage contig (< 2 x): NODE_680_length_478_cov_0.591036_pilon [shovill] Removing low coverage contig (< 2 x): NODE_682_length_477_cov_1.047753_pilon [shovill] Removing low coverage contig (< 2 x): NODE_687_length_474_cov_1.000000_pilon [shovill] Removing low coverage contig (< 2 x): NODE_686_length_474_cov_1.118980_pilon [shovill] Removing low coverage contig (< 2 x): NODE_685_length_474_cov_1.252125_pilon [shovill] Removing low coverage contig (< 2 x): NODE_692_length_473_cov_0.417614_pilon [shovill] Removing low coverage contig (< 2 x): NODE_690_length_473_cov_1.758523_pilon [shovill] Removing low coverage contig (< 2 x): NODE_689_length_473_cov_1.911932_pilon [shovill] Removing low coverage contig (< 2 x): NODE_691_length_473_cov_1.085227_pilon [shovill] Removing low coverage contig (< 2 x): NODE_697_length_471_cov_1.057143_pilon [shovill] Removing low coverage contig (< 2 x): NODE_699_length_471_cov_0.662857_pilon [shovill] Removing low coverage contig (< 2 x): NODE_698_length_471_cov_0.974286_pilon [shovill] Removing low coverage contig (< 2 x): NODE_696_length_471_cov_1.554286_pilon [shovill] Removing low coverage contig (< 2 x): NODE_704_length_470_cov_1.512894_pilon [shovill] Removing low coverage contig (< 2 x): NODE_705_length_470_cov_1.094556_pilon [shovill] Removing low coverage contig (< 2 x): NODE_702_length_470_cov_1.716332_pilon [shovill] Removing low coverage contig (< 2 x): NODE_703_length_470_cov_1.630372_pilon [shovill] Removing low coverage contig (< 2 x): NODE_707_length_469_cov_1.566092_pilon [shovill] Removing low coverage contig (< 2 x): NODE_709_length_468_cov_0.446686_pilon [shovill] Removing low coverage contig (< 2 x): NODE_711_length_467_cov_1.242775_pilon [shovill] Removing low coverage contig (< 2 x): NODE_712_length_467_cov_0.942197_pilon [shovill] Removing low coverage contig (< 2 x): NODE_713_length_467_cov_0.624277_pilon [shovill] Removing low coverage contig (< 2 x): NODE_715_length_466_cov_0.753623_pilon [shovill] Removing low coverage contig (< 2 x): NODE_714_length_466_cov_0.820290_pilon [shovill] Removing low coverage contig (< 2 x): NODE_717_length_465_cov_1.183140_pilon [shovill] Removing low coverage contig (< 2 x): NODE_719_length_464_cov_1.702624_pilon [shovill] Removing low coverage contig (< 2 x): NODE_721_length_463_cov_1.137427_pilon [shovill] Removing low coverage contig (< 2 x): NODE_723_length_462_cov_1.307918_pilon [shovill] Removing low coverage contig (< 2 x): NODE_724_length_462_cov_0.718475_pilon [shovill] Removing low coverage contig (< 2 x): NODE_728_length_459_cov_1.073964_pilon [shovill] Removing low coverage contig (< 2 x): NODE_732_length_458_cov_1.370920_pilon [shovill] Removing low coverage contig (< 2 x): NODE_731_length_458_cov_1.655786_pilon [shovill] Removing low coverage contig (< 2 x): NODE_734_length_457_cov_1.136905_pilon [shovill] Removing low coverage contig (< 2 x): NODE_742_length_454_cov_0.879880_pilon [shovill] Removing low coverage contig (< 2 x): NODE_743_length_454_cov_0.693694_pilon [shovill] Removing low coverage contig (< 2 x): NODE_744_length_453_cov_1.325301_pilon [shovill] Removing low coverage contig (< 2 x): NODE_747_length_452_cov_1.981873_pilon [shovill] Removing low coverage contig (< 2 x): NODE_750_length_451_cov_1.569697_pilon [shovill] Removing low coverage contig (< 2 x): NODE_749_length_451_cov_1.954545_pilon [shovill] Removing low coverage contig (< 2 x): NODE_751_length_451_cov_0.939394_pilon [shovill] Removing low coverage contig (< 2 x): NODE_752_length_450_cov_1.425532_pilon [shovill] Removing low coverage contig (< 2 x): NODE_757_length_448_cov_1.134557_pilon [shovill] Removing low coverage contig (< 2 x): NODE_758_length_447_cov_1.895706_pilon [shovill] Removing low coverage contig (< 2 x): NODE_759_length_447_cov_0.871166_pilon [shovill] Removing low coverage contig (< 2 x): NODE_760_length_446_cov_0.907692_pilon [shovill] Removing low coverage contig (< 2 x): NODE_766_length_445_cov_1.274691_pilon [shovill] Removing low coverage contig (< 2 x): NODE_768_length_445_cov_0.330247_pilon [shovill] Removing low coverage contig (< 2 x): NODE_767_length_445_cov_0.580247_pilon [shovill] Removing low coverage contig (< 2 x): NODE_765_length_445_cov_1.546296_pilon [shovill] Removing low coverage contig (< 2 x): NODE_769_length_444_cov_1.272446_pilon [shovill] Removing low coverage contig (< 2 x): NODE_773_length_443_cov_1.043478_pilon [shovill] Removing low coverage contig (< 2 x): NODE_770_length_443_cov_1.981366_pilon [shovill] Removing low coverage contig (< 2 x): NODE_772_length_443_cov_1.645963_pilon [shovill] Removing low coverage contig (< 2 x): NODE_771_length_443_cov_1.807453_pilon [shovill] Removing low coverage contig (< 2 x): NODE_776_length_442_cov_1.417445_pilon [shovill] Removing low coverage contig (< 2 x): NODE_774_length_442_cov_1.616822_pilon [shovill] Removing low coverage contig (< 2 x): NODE_777_length_442_cov_1.336449_pilon [shovill] Removing low coverage contig (< 2 x): NODE_780_length_442_cov_0.872274_pilon [shovill] Removing low coverage contig (< 2 x): NODE_778_length_442_cov_1.221184_pilon [shovill] Removing low coverage contig (< 2 x): NODE_779_length_442_cov_1.180685_pilon [shovill] Removing low coverage contig (< 2 x): NODE_775_length_442_cov_1.545171_pilon [shovill] Removing low coverage contig (< 2 x): NODE_783_length_441_cov_1.387500_pilon [shovill] Removing low coverage contig (< 2 x): NODE_781_length_441_cov_1.575000_pilon [shovill] Removing low coverage contig (< 2 x): NODE_782_length_441_cov_1.571875_pilon [shovill] Removing low coverage contig (< 2 x): NODE_785_length_440_cov_1.241379_pilon [shovill] Removing low coverage contig (< 2 x): NODE_787_length_439_cov_0.468553_pilon [shovill] Removing low coverage contig (< 2 x): NODE_789_length_438_cov_1.056782_pilon [shovill] Removing low coverage contig (< 2 x): NODE_788_length_438_cov_1.712934_pilon [shovill] Removing low coverage contig (< 2 x): NODE_793_length_437_cov_0.787975_pilon [shovill] Removing low coverage contig (< 2 x): NODE_791_length_437_cov_1.363924_pilon [shovill] Removing low coverage contig (< 2 x): NODE_792_length_437_cov_1.060127_pilon [shovill] Removing low coverage contig (< 2 x): NODE_798_length_436_cov_0.701587_pilon [shovill] Removing low coverage contig (< 2 x): NODE_796_length_436_cov_1.904762_pilon [shovill] Removing low coverage contig (< 2 x): NODE_797_length_436_cov_0.952381_pilon [shovill] Removing low coverage contig (< 2 x): NODE_801_length_435_cov_0.898089_pilon [shovill] Removing low coverage contig (< 2 x): NODE_802_length_435_cov_0.821656_pilon [shovill] Removing low coverage contig (< 2 x): NODE_806_length_434_cov_1.172524_pilon [shovill] Removing low coverage contig (< 2 x): NODE_807_length_434_cov_0.463259_pilon [shovill] Removing low coverage contig (< 2 x): NODE_805_length_434_cov_1.562300_pilon [shovill] Removing low coverage contig (< 2 x): NODE_804_length_434_cov_1.642173_pilon [shovill] Removing low coverage contig (< 2 x): NODE_811_length_432_cov_1.360129_pilon [shovill] Removing low coverage contig (< 2 x): NODE_812_length_431_cov_1.306452_pilon [shovill] Removing low coverage contig (< 2 x): NODE_813_length_431_cov_1.167742_pilon [shovill] Removing low coverage contig (< 2 x): NODE_815_length_430_cov_1.165049_pilon [shovill] Removing low coverage contig (< 2 x): NODE_816_length_430_cov_0.708738_pilon [shovill] Removing low coverage contig (< 2 x): NODE_822_length_428_cov_1.267101_pilon [shovill] Removing low coverage contig (< 2 x): NODE_823_length_428_cov_0.716612_pilon [shovill] Removing low coverage contig (< 2 x): NODE_825_length_427_cov_0.901961_pilon [shovill] Removing low coverage contig (< 2 x): NODE_829_length_426_cov_0.570492_pilon [shovill] Removing low coverage contig (< 2 x): NODE_830_length_426_cov_0.413115_pilon [shovill] Removing low coverage contig (< 2 x): NODE_828_length_426_cov_0.645902_pilon [shovill] Removing low coverage contig (< 2 x): NODE_827_length_426_cov_1.180328_pilon [shovill] Removing low coverage contig (< 2 x): NODE_832_length_425_cov_1.098684_pilon [shovill] Removing low coverage contig (< 2 x): NODE_831_length_425_cov_1.289474_pilon [shovill] Removing low coverage contig (< 2 x): NODE_835_length_424_cov_0.689769_pilon [shovill] Removing low coverage contig (< 2 x): NODE_833_length_424_cov_1.283828_pilon [shovill] Removing low coverage contig (< 2 x): NODE_834_length_424_cov_1.237624_pilon [shovill] Removing low coverage contig (< 2 x): NODE_841_length_422_cov_0.710963_pilon [shovill] Removing low coverage contig (< 2 x): NODE_840_length_422_cov_1.694352_pilon [shovill] Removing low coverage contig (< 2 x): NODE_846_length_421_cov_0.366667_pilon [shovill] Removing low coverage contig (< 2 x): NODE_844_length_421_cov_1.536667_pilon [shovill] Removing low coverage contig (< 2 x): NODE_845_length_421_cov_0.993333_pilon [shovill] Removing low coverage contig (< 2 x): NODE_843_length_421_cov_1.720000_pilon [shovill] Removing low coverage contig (< 2 x): NODE_847_length_420_cov_0.959866_pilon [shovill] Removing low coverage contig (< 2 x): NODE_850_length_419_cov_1.157718_pilon [shovill] Removing low coverage contig (< 2 x): NODE_851_length_419_cov_0.617450_pilon [shovill] Removing low coverage contig (< 2 x): NODE_854_length_418_cov_0.653199_pilon [shovill] Removing low coverage contig (< 2 x): NODE_853_length_418_cov_1.835017_pilon [shovill] Removing low coverage contig (< 2 x): NODE_855_length_417_cov_1.611486_pilon [shovill] Removing low coverage contig (< 2 x): NODE_857_length_416_cov_1.081356_pilon [shovill] Removing low coverage contig (< 2 x): NODE_859_length_416_cov_0.294915_pilon [shovill] Removing low coverage contig (< 2 x): NODE_856_length_416_cov_1.623729_pilon [shovill] Removing low coverage contig (< 2 x): NODE_858_length_416_cov_0.461017_pilon [shovill] Removing low coverage contig (< 2 x): NODE_860_length_415_cov_1.057823_pilon [shovill] Removing low coverage contig (< 2 x): NODE_864_length_414_cov_1.255973_pilon [shovill] Removing low coverage contig (< 2 x): NODE_863_length_414_cov_1.262799_pilon [shovill] Removing low coverage contig (< 2 x): NODE_862_length_414_cov_1.331058_pilon [shovill] Removing low coverage contig (< 2 x): NODE_865_length_414_cov_0.641638_pilon [shovill] Removing low coverage contig (< 2 x): NODE_867_length_413_cov_1.099315_pilon [shovill] Removing low coverage contig (< 2 x): NODE_870_length_412_cov_1.364261_pilon [shovill] Removing low coverage contig (< 2 x): NODE_868_length_412_cov_1.797251_pilon [shovill] Removing low coverage contig (< 2 x): NODE_869_length_412_cov_1.501718_pilon [shovill] Removing low coverage contig (< 2 x): NODE_873_length_411_cov_1.644828_pilon [shovill] Removing low coverage contig (< 2 x): NODE_872_length_411_cov_1.951724_pilon [shovill] Removing low coverage contig (< 2 x): NODE_876_length_409_cov_0.697917_pilon [shovill] Removing low coverage contig (< 2 x): NODE_880_length_408_cov_1.236934_pilon [shovill] Removing low coverage contig (< 2 x): NODE_884_length_408_cov_0.202091_pilon [shovill] Removing low coverage contig (< 2 x): NODE_882_length_408_cov_0.658537_pilon [shovill] Removing low coverage contig (< 2 x): NODE_881_length_408_cov_1.121951_pilon [shovill] Removing low coverage contig (< 2 x): NODE_883_length_408_cov_0.404181_pilon [shovill] Removing low coverage contig (< 2 x): NODE_879_length_408_cov_1.905923_pilon [shovill] Removing low coverage contig (< 2 x): NODE_885_length_407_cov_1.398601_pilon [shovill] Removing low coverage contig (< 2 x): NODE_887_length_407_cov_0.916084_pilon [shovill] Removing low coverage contig (< 2 x): NODE_886_length_407_cov_0.944056_pilon [shovill] Removing low coverage contig (< 2 x): NODE_890_length_406_cov_1.101754_pilon [shovill] Removing low coverage contig (< 2 x): NODE_889_length_406_cov_1.396491_pilon [shovill] Removing low coverage contig (< 2 x): NODE_891_length_406_cov_0.757895_pilon [shovill] Removing low coverage contig (< 2 x): NODE_892_length_406_cov_0.407018_pilon [shovill] Removing low coverage contig (< 2 x): NODE_894_length_405_cov_1.165493_pilon [shovill] Removing low coverage contig (< 2 x): NODE_895_length_405_cov_0.510563_pilon [shovill] Removing low coverage contig (< 2 x): NODE_899_length_404_cov_1.544170_pilon [shovill] Removing low coverage contig (< 2 x): NODE_898_length_404_cov_1.795053_pilon [shovill] Removing low coverage contig (< 2 x): NODE_900_length_404_cov_0.621908_pilon [shovill] Removing low coverage contig (< 2 x): NODE_903_length_403_cov_0.929078_pilon [shovill] Removing low coverage contig (< 2 x): NODE_905_length_403_cov_0.500000_pilon [shovill] Removing low coverage contig (< 2 x): NODE_904_length_403_cov_0.882979_pilon [shovill] Removing low coverage contig (< 2 x): NODE_902_length_403_cov_1.453901_pilon [shovill] Removing low coverage contig (< 2 x): NODE_911_length_402_cov_1.007117_pilon [shovill] Removing low coverage contig (< 2 x): NODE_912_length_402_cov_0.523132_pilon [shovill] Removing short contig (< 200 bp): NODE_934_length_134_cov_36.384615_pilon [shovill] Removing short contig (< 200 bp): NODE_935_length_124_cov_143.000000_pilon [shovill] Removing short contig (< 200 bp): NODE_936_length_122_cov_4573.000000_pilon [shovill] Removing short contig (< 200 bp): NODE_937_length_122_cov_58.000000_pilon [shovill] Assembly is 5382784, estimated genome size was 5000000 (+7.66%) [shovill] Using genome graph file 'spades/assembly_graph_with_scaffolds.gfa' => 'contigs.gfa' [shovill] Walltime used: 10 min 54 sec [shovill] Results in: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia [shovill] Final assembly graph: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/contigs.gfa [shovill] Final assembly contigs: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Serratia/contigs.fa [shovill] It contains 599 (min=200) contigs totalling 5382784 bp. [shovill] Remember, genomic repeats > ~800bp will be collapsed into single contigs. [shovill] Done.
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Created: 12th Nov 2021 at 23:21
Last updated: 12th Nov 2021 at 23:21
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Version 1 (earliest) Created 12th Nov 2021 at 23:21 by Marko Petek
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https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
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National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
Advanced Projects list for this Document with search and filtering
This project’s main objective was to identify novel Colorado potato beetle gene targets for the development of specific RNAi insecticides and further validate prospective targets using transcriptomics. The work included gene selection, establishment of double-stranded RNA (dsRNA) production methodology and the evaluation of dsRNAs’ insecticidal potential in CPB feeding laboratory and field trials.
Programme: NIBSys
Public web page: http://projects.nib.si/rnainval/
Start date: 1st Nov 2014
End date: 31st Oct 2017
Advanced Investigations list for this Document with search and filtering
Short Name: 03_Omics Title: Omics analysis of RNAi response in CPB Description: Transcriptomics and metagenome changes upon feeding CPB larvae with dsRNA Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_01_ns-dsRNA_trans, _S_02_metagenome_resp
Assays: _A_01-DNAisol, _A_01_RNA-Seq_dsEGFP-NGS, _A_02-DNASeq, _A_02_CLC-RNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _I_03_Omics-files, _S_01_ns-dsRNA_trans-files, _S_02_metagenome_resp-files
Advanced Studies list for this Document with search and filtering
Short Name: 02_metagenome_resp Title: CPB gut microbiome response to dsRNA feeding Description: Response of CPB gut microbiome to dsRNA feeding on the level of microbe abundance Raw Data: pISA Study creation date: 2021-01-15 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_03_Omics
Assays: _A_01-DNAisol, _A_02-DNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _S_02_metagenome_resp-files
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Short Name: 06_extr_bact-assembly Assay Class: DRY Assay Type: assembly Title: De novo genome assembly of bacteria Description: De novo genome assembly of bacteria from rcf-extracted shotgun metagenomics reads pISA Assay creation date: 2021-01-16 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_03_Omics
Study: _S_02_metagenome_resp
