[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.