output/shovill/Enterococcus/shovill.log Version 1
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
SEEK ID: https://fairdomhub.org/documents/2568?version=1
Filename:
output/shovill/Enterococcus/shovill.log
Format: Plain text document
Size: 544 KB
[shovill] Hello administrator [shovill] You ran: /home/administrator/conda2/envs/shovill/bin/shovill --force --outdir ./shovill/Enterococcus/ --R1 ./fq/incl1353_R1.fastq --R2 ./fq/incl1353_R2.fastq --gsize 3M --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/Enterococcus/ [shovill] Using tempdir: /tmp/K1KwOhehG5 [shovill] Changing into folder: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus [shovill] Collecting raw read statistics with 'seqtk' [shovill] Running: seqtk fqchk -q3 \/DATB\/markop\/CPB\/CPB_rcf_DNAseq\/fq\/incl1353_R1\.fastq >/tmp/hDg5bXWiW4 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log [shovill] Read stats: min_len = 150 [shovill] Read stats: avg_len = 150 [shovill] Read stats: max_len = 150 [shovill] Read stats: total_bp = 6300630600 [shovill] Using genome size 3000000 bp [shovill] Estimated sequencing depth: 2100 x [shovill] Subsampling reads by factor 0.071 to get from 2100x to 150x [shovill] Running: seqtk sample \/DATB\/markop\/CPB\/CPB_rcf_DNAseq\/fq\/incl1353_R1\.fastq 0.071 | 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\/incl1353_R2\.fastq 0.071 | 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 3000000 -t 30 -maxcor 1 2>&1 | sed 's/^/[lighter] /' | tee -a shovill.log [lighter] [2021-01-23 11:53:32] =============Start==================== [lighter] [2021-01-23 11:53:32] Scanning the input files to infer alpha(sampling rate) [lighter] [2021-01-23 11:53:37] Average coverage is 149.164 and alpha is 0.047 [lighter] [2021-01-23 11:53:39] Bad quality threshold is ";" [lighter] [2021-01-23 11:54:01] Finish sampling kmers [lighter] [2021-01-23 11:54:01] Bloom filter A's false positive rate: 0.007526 [lighter] [2021-01-23 11:54:13] Finish storing trusted kmers [lighter] [2021-01-23 11:54:37] Finish error correction [lighter] Processed 2983284 reads: [lighter] 2483826 are error-free [lighter] Corrected 795388 bases(1.592502 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 1491642 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 1491642 [FLASH] Combined pairs: 700795 [FLASH] Uncombined pairs: 790847 [FLASH] Percent combined: 46.98% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v1.2.11 complete! [FLASH] 54.706 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/K1KwOhehG5 -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/Enterococcus/flash.notCombined_1.fastq.gz -2 /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/flash.notCombined_2.fastq.gz --isolate --threads 30 --memory 240 -o /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades --tmp-dir /tmp/K1KwOhehG5 -k 31,41,51,61,71,81,91,101,111,121 --merged /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/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/Enterococcus/flash.notCombined_1.fastq.gz'] [spades] right reads: ['/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/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/K1KwOhehG5 [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/Enterococcus/spades/spades.log [spades] [spades] /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/flash.notCombined_1.fastq.gz: max reads length: 150 [spades] /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/spades/K31/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/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/Enterococcus/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/Enterococcus/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] 0:00:01.296 203M / 203M INFO General (binary_converter.cpp : 96) 16384 reads processed [spades] 0:00:01.370 222M / 222M INFO General (binary_converter.cpp : 96) 32768 reads processed [spades] 0:00:01.518 260M / 260M INFO General (binary_converter.cpp : 96) 65536 reads processed [spades] 0:00:01.819 300M / 300M INFO General (binary_converter.cpp : 96) 131072 reads processed [spades] 0:00:02.493 385M / 385M INFO General (binary_converter.cpp : 96) 262144 reads processed [spades] 0:00:03.938 556M / 556M INFO General (binary_converter.cpp : 96) 524288 reads processed [spades] 0:00:05.368 674M / 677M INFO General (binary_converter.cpp : 111) 790847 reads written [spades] 0:00:05.372 650M / 677M INFO General (read_converter.cpp : 81) Converting single reads [spades] 0:00:05.373 660M / 677M INFO General (binary_converter.cpp : 111) 0 reads written [spades] 0:00:05.374 650M / 677M INFO General (read_converter.cpp : 87) Converting merged reads [spades] 0:00:06.031 732M / 732M INFO General (binary_converter.cpp : 96) 16384 reads processed [spades] 0:00:06.073 736M / 736M INFO General (binary_converter.cpp : 96) 32768 reads processed [spades] 0:00:06.159 744M / 744M INFO General (binary_converter.cpp : 96) 65536 reads processed [spades] 0:00:06.671 779M / 779M INFO General (binary_converter.cpp : 96) 131072 reads processed [spades] 0:00:07.407 831M / 831M INFO General (binary_converter.cpp : 96) 262144 reads processed [spades] 0:00:09.116 915M / 924M INFO General (binary_converter.cpp : 96) 524288 reads processed [spades] 0:00:10.169 924M / 928M INFO General (binary_converter.cpp : 111) 700795 reads written [spades] 0:00:10.205 94M / 928M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:10.213 94M / 928M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:10.214 94M / 928M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:10.215 94M / 928M INFO General (construction.cpp : 156) Average read length 178.524 [spades] 0:00:10.215 94M / 928M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:10.216 94M / 928M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:10.227 93M / 928M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:10.229 93M / 928M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66664 Gb [spades] 0:00:10.229 93M / 928M INFO General (kmer_splitters.hpp : 97) Using cell size of 74565 [spades] 0:00:13.972 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4564978 reads [spades] 0:00:14.210 254M / 3G INFO General (kmer_splitters.hpp : 293) Used 4564978 reads [spades] 0:00:14.210 254M / 3G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:14.486 251M / 3G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7607124 kmers in total. [spades] 0:00:14.487 251M / 3G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:14.588 245M / 3G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:14.589 245M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:14.590 245M / 3G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:14.590 245M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:14.591 245M / 3G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:14.591 245M / 3G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 [spades] 0:00:14.956 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 7607124 kmers [spades] 0:00:14.957 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 7607124 kmers. [spades] 0:00:15.016 256M / 3G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:15.219 228M / 3G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7603762 kmers in total. [spades] 0:00:15.221 228M / 3G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:15.307 228M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:15.492 237M / 3G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:15.590 237M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3534216 bytes occupied (3.71839 bits per kmer). [spades] 0:00:15.608 245M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:15.852 245M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:15.854 241M / 3G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping [spades] 0:00:15.856 241M / 3G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) [spades] 0:00:15.856 241M / 3G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping [spades] 0:00:16.097 249M / 3G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 42164 [spades] 0:00:16.100 249M / 3G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 42312 [spades] 0:00:16.108 249M / 3G INFO Early tip clipping (early_simplification.hpp : 30) 1926968 32-mers were removed by early tip clipper [spades] 0:00:16.109 249M / 3G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:16.112 245M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:16.344 223M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 62764 sequences extracted [spades] 0:00:16.501 223M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:16.574 223M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 5 loops collected [spades] 0:00:16.846 216M / 3G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:16.847 216M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:16.848 216M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:16.984 225M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3542648 bytes occupied (3.72561 bits per kmer). [spades] 0:00:17.015 257M / 3G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:21.614 255M / 3G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:21.782 255M / 3G INFO General (construction.cpp : 505) Processed 125496 edges [spades] 0:00:21.819 139M / 3G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:21.821 139M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 18 [spades] 0:00:21.822 139M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 111 [spades] 0:00:21.823 139M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 111. Coverage mad: 20.7564 [spades] 0:00:21.823 139M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:21.907 139M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:22.137 139M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:22.871 139M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:24.374 139M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:25.235 139M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 110.213. Fitted coverage std. dev: 20.2328 [spades] 0:00:25.240 139M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.988632 [spades] 0:00:25.240 139M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 71 [spades] 0:00:25.241 139M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 64 [spades] 0:00:25.241 139M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2850376 [spades] 0:00:25.242 139M / 3G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 110.213 [spades] 0:00:25.243 139M / 3G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 64 [spades] 0:00:25.243 139M / 3G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:25.244 139M / 3G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:25.251 139M / 3G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:25.253 139M / 3G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:25.254 139M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:25.259 139M / 3G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:25.260 139M / 3G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:25.261 139M / 3G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:25.261 139M / 3G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:25.262 139M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:25.263 139M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.277 139M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 313 times [spades] 0:00:25.277 139M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.707 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 13795 times [spades] 0:00:25.708 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:25.794 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2457 times [spades] 0:00:25.795 108M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:25.795 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.808 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 174 times [spades] 0:00:25.808 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.811 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 19 times [spades] 0:00:25.811 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:25.820 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 86 times [spades] 0:00:25.820 108M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:25.821 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.821 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:25.822 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.823 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:25.823 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:25.825 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 13 times [spades] 0:00:25.825 108M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:25.826 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.826 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:25.827 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.828 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:25.828 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:25.830 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times [spades] 0:00:25.831 108M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:25.831 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.832 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:25.832 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.833 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:25.833 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:25.834 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:25.835 108M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:25.835 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.836 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:25.836 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.837 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:25.837 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:25.838 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:25.838 108M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:25.839 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.840 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:25.840 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.841 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:25.841 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:25.842 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:25.842 108M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:25.843 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.844 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:25.844 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.845 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:25.846 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:25.846 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:25.847 108M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:25.848 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.848 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:25.849 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.849 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:25.850 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:25.851 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:25.851 108M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:25.852 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.852 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:25.853 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.853 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:25.854 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:25.855 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:25.855 108M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:25.856 108M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.860 109M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 3 times [spades] 0:00:25.861 109M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.864 109M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:25.865 109M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:25.868 109M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:25.869 109M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 [spades] 0:00:25.870 109M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.871 109M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:25.872 109M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.872 109M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:25.873 109M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:25.874 109M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:25.877 109M / 3G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:25.878 109M / 3G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:25.878 109M / 3G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:25.879 109M / 3G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:25.880 109M / 3G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:25.881 109M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.884 109M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:25.885 109M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.888 109M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:25.889 109M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:25.892 109M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:25.893 109M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:25.896 109M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:25.897 109M / 3G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:25.907 109M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:25.943 108M / 3G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 12875 times [spades] 0:00:25.944 108M / 3G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:25.945 108M / 3G INFO General (simplification.cpp : 502) Average coverage = 101.061 [spades] 0:00:25.946 108M / 3G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:25.952 108M / 3G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K31/simplified_contigs [spades] 0:00:25.958 112M / 3G INFO General (binary_converter.cpp : 111) 665 reads written [spades] 0:00:25.962 112M / 3G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:25.967 112M / 3G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 25 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/Enterococcus/spades/K41/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/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/Enterococcus/spades/K41/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/Enterococcus/spades/K41/configs/isolate_mode.info [spades] 0:00:00.000 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.001 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/Enterococcus/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/Enterococcus/spades/K31/simplified_contigs [spades] 0:00:00.009 9M / 10M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.009 9M / 10M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.009 9M / 10M INFO General (construction.cpp : 156) Average read length 178.524 [spades] 0:00:00.009 9M / 10M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.009 9M / 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 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 37282 [spades] 0:00:04.174 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4566308 reads [spades] 0:00:04.586 401M / 6G INFO General (kmer_splitters.hpp : 293) Used 4566308 reads [spades] 0:00:04.587 401M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.931 403M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7603060 kmers in total. [spades] 0:00:04.933 403M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:05.079 398M / 6G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:05.080 398M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:05.080 398M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:05.081 398M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:05.081 398M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:05.082 398M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:05.485 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 7603060 kmers [spades] 0:00:05.485 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 7603060 kmers. [spades] 0:00:05.557 428M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:05.782 428M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7606058 kmers in total. [spades] 0:00:05.784 428M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:05.917 428M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:06.114 432M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:06.314 432M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3535328 bytes occupied (3.71843 bits per kmer). [spades] 0:00:06.331 440M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:06.573 440M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:06.576 432M / 6G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping [spades] 0:00:06.577 432M / 6G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) [spades] 0:00:06.578 432M / 6G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping [spades] 0:00:06.831 442M / 6G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 41461 [spades] 0:00:06.834 442M / 6G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 41594 [spades] 0:00:06.845 442M / 6G INFO Early tip clipping (early_simplification.hpp : 30) 1847626 42-mers were removed by early tip clipper [spades] 0:00:06.846 442M / 6G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:06.849 442M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:07.094 305M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 53598 sequences extracted [spades] 0:00:07.246 305M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:07.317 305M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 4 loops collected [spades] 0:00:07.562 258M / 6G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:07.563 258M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:07.564 258M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:07.695 267M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3540856 bytes occupied (3.72572 bits per kmer). [spades] 0:00:07.717 299M / 6G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:12.014 299M / 6G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:12.181 299M / 6G INFO General (construction.cpp : 505) Processed 107181 edges [spades] 0:00:12.227 122M / 6G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:12.228 122M / 6G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 16 [spades] 0:00:12.229 122M / 6G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 103 [spades] 0:00:12.230 122M / 6G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 103. Coverage mad: 19.2738 [spades] 0:00:12.231 122M / 6G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:12.312 122M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:12.525 122M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:13.298 122M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:14.635 122M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:15.457 122M / 6G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 102.725. Fitted coverage std. dev: 19.0358 [spades] 0:00:15.462 122M / 6G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.990161 [spades] 0:00:15.462 122M / 6G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 66 [spades] 0:00:15.463 122M / 6G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 59 [spades] 0:00:15.464 122M / 6G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2853142 [spades] 0:00:15.464 122M / 6G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 102.725 [spades] 0:00:15.465 122M / 6G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 59 [spades] 0:00:15.466 122M / 6G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:15.466 122M / 6G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:15.467 122M / 6G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:15.468 122M / 6G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:15.468 122M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:15.472 122M / 6G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:15.473 122M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:15.474 122M / 6G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:15.475 122M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:15.476 122M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:15.477 122M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.489 122M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 390 times [spades] 0:00:15.490 122M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.840 89M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 10712 times [spades] 0:00:15.841 89M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.920 90M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1585 times [spades] 0:00:15.921 90M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:15.922 90M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.935 90M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 167 times [spades] 0:00:15.936 90M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.939 90M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 13 times [spades] 0:00:15.939 90M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.949 90M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 66 times [spades] 0:00:15.950 90M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:15.951 90M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.951 90M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.952 90M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.953 90M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:15.953 90M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.955 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times [spades] 0:00:15.956 91M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:15.957 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.957 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.958 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.958 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.959 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.960 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:15.961 91M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:15.961 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.962 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.963 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.963 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.964 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.965 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:15.965 91M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:15.966 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.966 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.967 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.968 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.968 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.969 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:15.969 91M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:15.970 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.971 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.971 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.972 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.972 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.973 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:15.974 91M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:15.974 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.975 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.976 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.976 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.977 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.978 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:15.978 91M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:15.979 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.979 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.980 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.981 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.981 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.982 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:15.983 91M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:15.983 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.984 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.985 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.985 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.986 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.986 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:15.987 91M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:15.988 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.993 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:15.994 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.998 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.999 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.002 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.003 91M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 [spades] 0:00:16.004 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.004 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.005 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.006 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.007 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.008 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.010 91M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:16.011 91M / 6G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:16.012 91M / 6G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:16.013 91M / 6G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:16.014 91M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:16.014 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.017 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.018 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.022 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.022 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.026 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.026 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.030 91M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.031 91M / 6G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:16.042 91M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:16.082 90M / 6G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 15209 times [spades] 0:00:16.083 90M / 6G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:16.084 90M / 6G INFO General (simplification.cpp : 502) Average coverage = 94.0423 [spades] 0:00:16.085 90M / 6G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:16.086 90M / 6G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K41/simplified_contigs [spades] 0:00:16.091 94M / 6G INFO General (binary_converter.cpp : 111) 578 reads written [spades] 0:00:16.093 94M / 6G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:16.095 94M / 6G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 16 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/Enterococcus/spades/K51/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/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/Enterococcus/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/Enterococcus/spades/K51/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/Enterococcus/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] 0:00:00.005 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K41/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] 0:00:00.008 9M / 9M INFO General (construction.cpp : 156) Average read length 178.524 [spades] 0:00:00.008 9M / 9M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.008 9M / 9M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.009 9M / 9M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.009 9M / 9M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.010 9M / 9M INFO General (kmer_splitters.hpp : 97) Using cell size of 37282 [spades] 0:00:03.909 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4566134 reads [spades] 0:00:04.294 475M / 5G INFO General (kmer_splitters.hpp : 293) Used 4566134 reads [spades] 0:00:04.295 475M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.642 477M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7547719 kmers in total. [spades] 0:00:04.644 477M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.791 470M / 5G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:04.792 470M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:04.792 470M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:04.793 470M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:04.793 470M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:04.794 470M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:05.223 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 7547719 kmers [spades] 0:00:05.225 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 7547719 kmers. [spades] 0:00:05.294 491M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:05.518 491M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7555047 kmers in total. [spades] 0:00:05.520 491M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:05.650 491M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:05.831 495M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:06.027 495M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3518912 bytes occupied (3.72616 bits per kmer). [spades] 0:00:06.045 503M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:06.277 503M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:06.279 496M / 5G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping [spades] 0:00:06.280 496M / 5G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) [spades] 0:00:06.281 496M / 5G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping [spades] 0:00:06.534 507M / 5G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 41253 [spades] 0:00:06.537 507M / 5G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 41387 [spades] 0:00:06.548 507M / 5G INFO Early tip clipping (early_simplification.hpp : 30) 1812107 52-mers were removed by early tip clipper [spades] 0:00:06.549 507M / 5G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:06.552 502M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:06.793 361M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 47876 sequences extracted [spades] 0:00:06.945 356M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:07.016 356M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 2 loops collected [spades] 0:00:07.254 325M / 5G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:07.258 325M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:07.259 325M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:07.390 326M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3515360 bytes occupied (3.72601 bits per kmer). [spades] 0:00:07.412 358M / 5G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:11.491 350M / 5G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:11.671 350M / 5G INFO General (construction.cpp : 505) Processed 95745 edges [spades] 0:00:11.712 310M / 5G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:11.713 310M / 5G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 16 [spades] 0:00:11.714 310M / 5G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 95 [spades] 0:00:11.715 310M / 5G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 96. Coverage mad: 17.7912 [spades] 0:00:11.715 310M / 5G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:11.788 310M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:11.984 310M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:12.609 310M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:13.825 310M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:14.257 310M / 5G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 95.2392. Fitted coverage std. dev: 17.8523 [spades] 0:00:14.261 310M / 5G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.985995 [spades] 0:00:14.262 310M / 5G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 61 [spades] 0:00:14.262 310M / 5G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 55 [spades] 0:00:14.263 310M / 5G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2850136 [spades] 0:00:14.263 310M / 5G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 95.2392 [spades] 0:00:14.264 310M / 5G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 55 [spades] 0:00:14.265 310M / 5G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:14.265 310M / 5G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:14.266 310M / 5G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:14.266 310M / 5G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:14.267 310M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:14.271 310M / 5G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:14.271 310M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:14.272 310M / 5G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:14.273 310M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:14.274 310M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:14.274 310M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.292 184M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 457 times [spades] 0:00:14.293 184M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.571 88M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 8617 times [spades] 0:00:14.572 88M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.625 88M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1108 times [spades] 0:00:14.626 88M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:14.627 88M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.640 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 142 times [spades] 0:00:14.641 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.644 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 15 times [spades] 0:00:14.644 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.653 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 60 times [spades] 0:00:14.654 89M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:14.654 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.655 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.655 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.656 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.657 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.659 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times [spades] 0:00:14.659 89M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:14.660 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.661 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.661 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.662 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:14.662 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.663 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:14.664 89M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:14.664 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.665 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.665 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.666 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.667 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.667 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:14.668 89M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:14.669 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.669 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.670 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.670 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.671 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.671 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.672 89M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:14.673 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.673 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.674 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.674 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.675 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.675 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.676 89M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:14.677 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.677 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.678 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.678 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.679 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.679 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:14.680 89M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:14.681 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.681 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.682 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.682 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.683 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.683 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.684 89M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:14.685 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.685 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.686 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.686 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.687 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.688 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.688 89M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:14.689 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.692 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.692 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.698 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.698 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.701 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.705 89M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:14.705 89M / 5G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:14.706 89M / 5G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:14.707 89M / 5G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:14.708 89M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:14.708 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.711 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.712 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.715 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.716 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.719 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.720 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.723 89M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.724 89M / 5G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:14.733 89M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:14.773 88M / 5G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 16942 times [spades] 0:00:14.774 88M / 5G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:14.775 88M / 5G INFO General (simplification.cpp : 502) Average coverage = 87.066 [spades] 0:00:14.776 88M / 5G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:14.777 88M / 5G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K51/simplified_contigs [spades] 0:00:14.780 92M / 5G INFO General (binary_converter.cpp : 111) 517 reads written [spades] 0:00:14.782 92M / 5G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:14.784 92M / 5G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 14 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/Enterococcus/spades/K61/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/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/Enterococcus/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/Enterococcus/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/Enterococcus/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] 0:00:00.005 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/Enterococcus/spades/K51/simplified_contigs [spades] 0:00:00.010 9M / 10M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.010 9M / 10M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.010 9M / 10M INFO General (construction.cpp : 156) Average read length 178.524 [spades] 0:00:00.011 9M / 10M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.011 9M / 10M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.012 9M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.013 9M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.013 9M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 37282 [spades] 0:00:03.661 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4566012 reads [spades] 0:00:04.033 366M / 5G INFO General (kmer_splitters.hpp : 293) Used 4566012 reads [spades] 0:00:04.034 366M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.382 368M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7454984 kmers in total. [spades] 0:00:04.383 368M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.531 363M / 5G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:04.531 363M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:04.532 363M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:04.533 363M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:04.533 363M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:04.534 363M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:04.952 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 7454984 kmers [spades] 0:00:04.953 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 7454984 kmers. [spades] 0:00:05.022 388M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:05.245 388M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7465847 kmers in total. [spades] 0:00:05.246 388M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:05.373 388M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:05.550 386M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:05.758 386M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3470288 bytes occupied (3.71857 bits per kmer). [spades] 0:00:05.773 394M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:06.046 394M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:06.050 384M / 5G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:06.055 384M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:06.339 275M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 125630 sequences extracted [spades] 0:00:06.535 275M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:06.607 275M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:07.199 277M / 5G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:07.203 277M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:07.204 277M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:07.330 277M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3472520 bytes occupied (3.72639 bits per kmer). [spades] 0:00:07.351 309M / 5G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:11.113 309M / 5G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:11.332 309M / 5G INFO General (construction.cpp : 505) Processed 251257 edges [spades] 0:00:11.376 156M / 5G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:11.377 156M / 5G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 16 [spades] 0:00:11.378 156M / 5G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 87 [spades] 0:00:11.379 156M / 5G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 88. Coverage mad: 17.7912 [spades] 0:00:11.380 156M / 5G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:11.448 156M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:11.615 156M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:11.939 156M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:12.209 156M / 5G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 88.5804. Fitted coverage std. dev: 15.7623 [spades] 0:00:12.212 156M / 5G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.999471 [spades] 0:00:12.212 156M / 5G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 59 [spades] 0:00:12.213 156M / 5G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 52 [spades] 0:00:12.213 156M / 5G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2839503 [spades] 0:00:12.214 156M / 5G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 88.5804 [spades] 0:00:12.215 156M / 5G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 52 [spades] 0:00:12.215 156M / 5G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:12.216 156M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:12.216 156M / 5G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:12.217 156M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:12.218 156M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:12.219 156M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:12.220 156M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66615 Gb [spades] 0:00:12.220 156M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:12.451 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 251257 edges [spades] 0:00:12.453 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 251257 sequences. [spades] 0:00:12.510 212M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:12.733 209M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7454984 kmers in total. [spades] 0:00:12.735 209M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:12.860 209M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:13.044 203M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:13.231 203M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3465240 bytes occupied (3.71858 bits per kmer). [spades] 0:00:13.313 331M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:13.463 331M / 5G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:13.466 331M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:13.612 336M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:14.121 314M / 5G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:14.122 314M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:14.154 314M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:14.261 310M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 49 gaps after checking 346 candidates [spades] 0:00:14.292 310M / 5G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:14.300 182M / 5G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:14.301 182M / 5G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:14.302 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:14.309 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:14.310 182M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:14.311 182M / 5G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:14.312 182M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:14.313 182M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:14.314 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.720 179M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 41344 times [spades] 0:00:14.721 179M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.968 208M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7182 times [spades] 0:00:15.969 208M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.019 208M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 816 times [spades] 0:00:16.020 208M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:16.021 208M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.032 208M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 116 times [spades] 0:00:16.033 208M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.039 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 14 times [spades] 0:00:16.040 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.047 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 46 times [spades] 0:00:16.048 209M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:16.048 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.049 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:16.049 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.050 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:16.051 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.054 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times [spades] 0:00:16.054 209M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:16.055 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.055 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.056 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.056 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.057 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.058 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:16.058 209M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:16.059 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.060 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.061 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.061 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.062 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.063 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:16.064 209M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:16.064 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.065 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.065 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.066 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.067 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.067 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.068 209M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:16.068 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.069 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.070 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.070 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.071 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.072 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:16.073 209M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:16.073 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.074 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.075 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.075 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.076 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.077 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:16.078 209M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:16.078 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.079 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.080 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.080 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.081 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.081 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.082 209M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:16.083 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.083 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.084 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.084 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.085 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.086 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:16.086 209M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:16.087 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.091 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.092 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.097 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.098 209M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.102 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.106 209M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:16.107 209M / 5G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:16.108 209M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:16.109 209M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:16.110 209M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:16.112 209M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66553 Gb [spades] 0:00:16.112 209M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:16.271 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 38284 edges [spades] 0:00:16.272 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 38284 sequences. [spades] 0:00:16.325 225M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:16.491 225M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4981368 kmers in total. [spades] 0:00:16.494 225M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:16.583 225M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:16.718 220M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:16.853 220M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2318136 bytes occupied (3.72289 bits per kmer). [spades] 0:00:16.933 300M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:17.056 295M / 5G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:17.058 295M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:17.105 295M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:17.649 287M / 5G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:17.651 287M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:17.694 288M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:17.726 288M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 6 gaps after checking 344 candidates [spades] 0:00:17.752 287M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:17.753 287M / 5G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:17.754 287M / 5G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:17.755 287M / 5G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:17.756 287M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:17.757 287M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.780 287M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.782 287M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.812 288M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.813 288M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.844 288M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.845 288M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.876 288M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.877 288M / 5G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:17.893 281M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:18.936 265M / 5G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 18673 times [spades] 0:00:18.937 265M / 5G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:18.939 265M / 5G INFO General (simplification.cpp : 502) Average coverage = 80.0545 [spades] 0:00:18.940 265M / 5G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:18.951 265M / 5G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K61/simplified_contigs [spades] 0:00:18.960 265M / 5G INFO General (binary_converter.cpp : 111) 463 reads written [spades] 0:00:18.964 266M / 5G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:19.097 173M / 5G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 19 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/Enterococcus/spades/K71/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/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/Enterococcus/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/Enterococcus/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/Enterococcus/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] 0:00:00.003 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/Enterococcus/spades/K61/simplified_contigs [spades] 0:00:00.008 8M / 10M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.008 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 178.524 [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 24855 [spades] 0:00:03.722 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4565904 reads [spades] 0:00:04.215 425M / 6G INFO General (kmer_splitters.hpp : 293) Used 4565904 reads [spades] 0:00:04.216 425M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.565 426M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7329061 kmers in total. [spades] 0:00:04.567 426M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.764 420M / 6G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:04.764 420M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:04.765 420M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:04.765 420M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:04.766 420M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:04.766 420M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:05.256 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 7329061 kmers [spades] 0:00:05.257 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 7329061 kmers. [spades] 0:00:05.335 446M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:05.581 446M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7343296 kmers in total. [spades] 0:00:05.582 446M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:05.757 446M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:05.954 445M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:06.236 445M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3413552 bytes occupied (3.71882 bits per kmer). [spades] 0:00:06.255 453M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:06.555 453M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:06.559 438M / 6G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:06.562 438M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:06.851 313M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 121836 sequences extracted [spades] 0:00:07.059 313M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:07.138 306M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected [spades] 0:00:07.708 264M / 6G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:07.712 264M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:07.713 264M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:07.840 264M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3414256 bytes occupied (3.72681 bits per kmer). [spades] 0:00:07.862 292M / 6G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:11.398 292M / 6G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:11.623 292M / 6G INFO General (construction.cpp : 505) Processed 243670 edges [spades] 0:00:11.675 144M / 6G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:11.677 144M / 6G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 14 [spades] 0:00:11.678 144M / 6G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 81 [spades] 0:00:11.678 144M / 6G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 81. Coverage mad: 16.3086 [spades] 0:00:11.679 144M / 6G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:11.742 144M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:11.899 144M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:12.275 144M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:12.525 144M / 6G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 80.9794. Fitted coverage std. dev: 14.7181 [spades] 0:00:12.528 144M / 6G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.999372 [spades] 0:00:12.528 144M / 6G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 54 [spades] 0:00:12.529 144M / 6G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 47 [spades] 0:00:12.530 144M / 6G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2842511 [spades] 0:00:12.530 144M / 6G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 80.9794 [spades] 0:00:12.531 144M / 6G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 47 [spades] 0:00:12.531 144M / 6G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:12.532 144M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:12.533 144M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:12.533 144M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:12.534 144M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:12.535 144M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:12.536 144M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66616 Gb [spades] 0:00:12.537 144M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:12.822 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 243670 edges [spades] 0:00:12.823 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 243670 sequences. [spades] 0:00:12.884 187M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:13.124 187M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7329061 kmers in total. [spades] 0:00:13.127 187M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:13.304 187M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:13.500 181M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:13.773 181M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3406776 bytes occupied (3.71865 bits per kmer). [spades] 0:00:13.853 293M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:14.001 293M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:14.003 293M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:14.152 297M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:14.636 281M / 6G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:14.637 281M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:14.670 280M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:14.775 273M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 33 gaps after checking 338 candidates [spades] 0:00:14.805 271M / 6G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:14.814 159M / 6G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:14.815 159M / 6G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:14.816 159M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:14.824 159M / 6G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:14.825 159M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:14.826 159M / 6G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:14.827 159M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:14.827 159M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:14.828 159M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.244 155M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 40846 times [spades] 0:00:15.245 155M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.471 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5831 times [spades] 0:00:16.472 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.517 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 624 times [spades] 0:00:16.518 209M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:16.518 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.528 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 97 times [spades] 0:00:16.529 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.535 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 11 times [spades] 0:00:16.535 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.543 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 48 times [spades] 0:00:16.543 210M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:16.544 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.545 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:16.545 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.546 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.547 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.549 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8 times [spades] 0:00:16.549 210M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:16.550 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.551 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.551 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.552 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.553 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.553 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:16.554 210M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:16.555 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.555 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.556 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.557 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.557 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.558 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:16.559 210M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:16.560 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.560 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.561 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.561 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.562 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.563 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:16.564 210M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:16.565 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.565 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.566 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.566 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.567 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.568 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.568 210M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:16.569 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.570 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.570 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.571 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.571 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.573 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:16.573 210M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:16.574 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.574 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.575 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.576 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.577 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.577 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.578 210M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:16.578 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.579 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.580 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.580 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.581 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.582 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.582 210M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:16.583 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.588 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.588 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.594 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.594 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.599 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.604 210M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:16.605 210M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:16.606 210M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:16.607 210M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:16.608 210M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:16.609 210M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66532 Gb [spades] 0:00:16.610 210M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:16.826 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 41894 edges [spades] 0:00:16.827 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 41894 sequences. [spades] 0:00:16.883 213M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:17.061 213M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4945006 kmers in total. [spades] 0:00:17.064 213M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:17.190 213M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:17.321 214M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:17.514 214M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2301320 bytes occupied (3.72306 bits per kmer). [spades] 0:00:17.594 294M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:17.713 294M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:17.716 294M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:17.769 296M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:18.316 294M / 6G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:18.324 294M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:18.376 295M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:18.411 295M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 1 gaps after checking 323 candidates [spades] 0:00:18.424 295M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:18.425 295M / 6G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:18.426 295M / 6G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:18.427 295M / 6G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:18.427 295M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:18.428 295M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:18.433 295M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:18.434 295M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:18.439 295M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:18.440 295M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:18.444 295M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:18.445 295M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:18.450 295M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:18.451 295M / 6G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:18.470 295M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:19.490 282M / 6G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 20508 times [spades] 0:00:19.492 282M / 6G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:19.494 282M / 6G INFO General (simplification.cpp : 502) Average coverage = 73.2148 [spades] 0:00:19.494 282M / 6G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:19.495 282M / 6G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K71/simplified_contigs [spades] 0:00:19.501 282M / 6G INFO General (binary_converter.cpp : 111) 438 reads written [spades] 0:00:19.505 283M / 6G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:19.660 196M / 6G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 19 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/Enterococcus/spades/K81/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/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/Enterococcus/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/Enterococcus/spades/K81/configs/isolate_mode.info [spades] 0:00:00.000 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.001 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/Enterococcus/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] 0:00:00.005 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K71/simplified_contigs [spades] 0:00:00.010 10M / 10M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.010 10M / 10M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.010 10M / 10M INFO General (construction.cpp : 156) Average read length 178.524 [spades] 0:00:00.010 10M / 10M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.011 10M / 10M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.012 10M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.012 10M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.013 10M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 24855 [spades] 0:00:03.350 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4565854 reads [spades] 0:00:03.785 424M / 6G INFO General (kmer_splitters.hpp : 293) Used 4565854 reads [spades] 0:00:03.785 424M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.137 426M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7167624 kmers in total. [spades] 0:00:04.139 426M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.327 421M / 6G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:04.328 421M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:04.328 421M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:04.329 421M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:04.330 421M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:04.330 421M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:04.791 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 7167624 kmers [spades] 0:00:04.791 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 7167624 kmers. [spades] 0:00:04.875 432M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:05.126 432M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7185255 kmers in total. [spades] 0:00:05.128 432M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:05.300 432M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:05.492 439M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:05.766 439M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3340208 bytes occupied (3.71896 bits per kmer). [spades] 0:00:05.780 439M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:06.041 439M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:06.044 439M / 6G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:06.049 439M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:06.327 305M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 118139 sequences extracted [spades] 0:00:06.524 305M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:06.599 305M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected [spades] 0:00:07.138 281M / 6G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:07.142 281M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:07.143 281M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:07.267 284M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3338960 bytes occupied (3.72671 bits per kmer). [spades] 0:00:07.289 312M / 6G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:10.517 312M / 6G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:10.746 312M / 6G INFO General (construction.cpp : 505) Processed 236277 edges [spades] 0:00:10.795 284M / 6G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:10.796 284M / 6G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 12 [spades] 0:00:10.797 284M / 6G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 73 [spades] 0:00:10.798 284M / 6G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 73. Coverage mad: 14.826 [spades] 0:00:10.798 284M / 6G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:10.855 284M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:11.004 284M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:11.467 284M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:12.422 152M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:12.845 152M / 6G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 72.8032. Fitted coverage std. dev: 14.3181 [spades] 0:00:12.849 152M / 6G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.982441 [spades] 0:00:12.849 152M / 6G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 46 [spades] 0:00:12.850 152M / 6G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 42 [spades] 0:00:12.850 152M / 6G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2845791 [spades] 0:00:12.851 152M / 6G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 72.8032 [spades] 0:00:12.852 152M / 6G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 42 [spades] 0:00:12.852 152M / 6G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:12.853 152M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:12.853 152M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:12.854 152M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:12.855 152M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:12.856 152M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:12.857 152M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.6662 Gb [spades] 0:00:12.857 152M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:13.119 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 236277 edges [spades] 0:00:13.121 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 236277 sequences. [spades] 0:00:13.183 206M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:13.437 202M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7167624 kmers in total. [spades] 0:00:13.439 202M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:13.605 202M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:13.788 200M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:14.062 200M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3332064 bytes occupied (3.71902 bits per kmer). [spades] 0:00:14.141 312M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:14.301 312M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:14.303 312M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:14.451 318M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:14.906 274M / 6G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:14.907 274M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:14.941 274M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:15.045 266M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 39 gaps after checking 355 candidates [spades] 0:00:15.077 265M / 6G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:15.084 153M / 6G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:15.085 153M / 6G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:15.086 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:15.094 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:15.095 153M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:15.095 153M / 6G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:15.096 153M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:15.097 153M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:15.098 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.506 151M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 39717 times [spades] 0:00:15.507 151M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.604 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4756 times [spades] 0:00:16.605 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.647 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 487 times [spades] 0:00:16.648 200M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:16.648 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.659 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 106 times [spades] 0:00:16.659 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.664 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 8 times [spades] 0:00:16.664 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.670 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 37 times [spades] 0:00:16.671 200M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:16.671 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.672 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.673 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.673 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.674 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.677 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 12 times [spades] 0:00:16.677 200M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:16.678 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.678 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.679 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.680 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.680 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.681 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:16.682 200M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:16.682 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.683 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.684 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.684 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.685 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.686 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:16.687 200M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:16.687 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.688 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.689 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.689 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.690 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.691 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:16.692 200M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:16.692 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.693 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.694 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.694 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.695 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.696 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.696 200M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:16.697 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.697 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.698 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.699 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.699 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.701 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:16.701 200M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:16.702 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.702 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.703 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.704 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.704 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.705 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.706 200M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:16.706 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.707 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.707 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.708 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.709 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.709 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.710 200M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:16.710 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.715 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.716 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.721 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.722 200M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.727 200M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.732 200M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:16.733 200M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:16.734 200M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:16.735 200M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:16.736 200M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:16.737 200M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.6654 Gb [spades] 0:00:16.738 200M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:16.942 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 46084 edges [spades] 0:00:16.943 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 46084 sequences. [spades] 0:00:16.999 197M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:17.176 199M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4899007 kmers in total. [spades] 0:00:17.179 199M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:17.299 199M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:17.436 201M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:17.615 201M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2279816 bytes occupied (3.7229 bits per kmer). [spades] 0:00:17.697 281M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:17.828 281M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:17.830 281M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:17.882 284M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:18.379 283M / 6G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:18.381 283M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:18.434 284M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:18.474 284M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 1 gaps after checking 362 candidates [spades] 0:00:18.487 284M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:18.488 284M / 6G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:18.489 284M / 6G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:18.490 284M / 6G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:18.491 284M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:18.492 284M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:18.497 284M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:18.498 284M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:18.503 284M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:18.504 284M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:18.508 284M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:18.509 284M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:18.514 284M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:18.515 284M / 6G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:18.535 284M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:19.554 273M / 6G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 22657 times [spades] 0:00:19.555 273M / 6G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:19.557 273M / 6G INFO General (simplification.cpp : 502) Average coverage = 66.3846 [spades] 0:00:19.558 273M / 6G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:19.559 273M / 6G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K81/simplified_contigs [spades] 0:00:19.567 275M / 6G INFO General (binary_converter.cpp : 111) 384 reads written [spades] 0:00:19.571 275M / 6G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:19.703 186M / 6G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 19 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/Enterococcus/spades/K91/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/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/Enterococcus/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/Enterococcus/spades/K91/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/Enterococcus/spades/dataset.info) with K=91 [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] 0:00:00.005 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K81/simplified_contigs [spades] 0:00:00.008 9M / 10M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.008 9M / 10M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.008 9M / 10M INFO General (construction.cpp : 156) Average read length 178.524 [spades] 0:00:00.008 9M / 10M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.008 9M / 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 9M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.009 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] 0:00:03.081 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4565746 reads [spades] 0:00:03.488 401M / 5G INFO General (kmer_splitters.hpp : 293) Used 4565746 reads [spades] 0:00:03.489 401M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:03.819 401M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 6968607 kmers in total. [spades] 0:00:03.820 401M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.006 395M / 5G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:04.007 395M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:04.008 395M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:04.008 395M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:04.009 395M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:04.009 395M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:04.450 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 6968607 kmers [spades] 0:00:04.451 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 6968607 kmers. [spades] 0:00:04.529 421M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.763 421M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 6990350 kmers in total. [spades] 0:00:04.765 421M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.941 421M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:05.129 420M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:05.374 420M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3249752 bytes occupied (3.71913 bits per kmer). [spades] 0:00:05.384 420M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:05.651 420M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:05.653 420M / 5G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:05.656 420M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:05.931 310M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 114023 sequences extracted [spades] 0:00:06.130 310M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:06.200 310M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected [spades] 0:00:06.749 267M / 5G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:06.751 267M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:06.752 267M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:06.885 268M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3246792 bytes occupied (3.72734 bits per kmer). [spades] 0:00:06.904 296M / 5G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:09.812 296M / 5G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:10.033 296M / 5G INFO General (construction.cpp : 505) Processed 228046 edges [spades] 0:00:10.082 174M / 5G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:10.083 174M / 5G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 12 [spades] 0:00:10.085 174M / 5G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 66 [spades] 0:00:10.085 174M / 5G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 66. Coverage mad: 14.826 [spades] 0:00:10.086 174M / 5G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:10.140 174M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:10.270 174M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:10.653 174M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:11.104 174M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:11.183 174M / 5G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 65.809. Fitted coverage std. dev: 12.5993 [spades] 0:00:11.185 174M / 5G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.997687 [spades] 0:00:11.185 174M / 5G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 43 [spades] 0:00:11.186 174M / 5G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 38 [spades] 0:00:11.186 174M / 5G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2840458 [spades] 0:00:11.187 174M / 5G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 65.809 [spades] 0:00:11.188 174M / 5G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 38 [spades] 0:00:11.188 174M / 5G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:11.189 174M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:11.190 174M / 5G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:11.190 174M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:11.191 174M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:11.192 174M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:11.193 174M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66618 Gb [spades] 0:00:11.194 174M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:11.451 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 228046 edges [spades] 0:00:11.452 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 228046 sequences. [spades] 0:00:11.511 215M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:11.737 215M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 6968607 kmers in total. [spades] 0:00:11.740 215M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:11.912 215M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:12.095 197M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:12.373 197M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3239648 bytes occupied (3.71913 bits per kmer). [spades] 0:00:12.447 309M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:12.586 309M / 5G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:12.588 309M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:12.738 307M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:13.155 286M / 5G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:13.156 286M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:13.193 286M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:13.297 286M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 51 gaps after checking 403 candidates [spades] 0:00:13.333 285M / 5G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:13.341 173M / 5G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:13.342 173M / 5G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:13.343 173M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:13.350 173M / 5G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:13.351 173M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:13.352 173M / 5G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:13.352 173M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:13.353 173M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:13.354 173M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.750 160M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 37813 times [spades] 0:00:13.751 160M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.721 205M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3768 times [spades] 0:00:14.722 205M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.761 205M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 376 times [spades] 0:00:14.762 205M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:14.763 205M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.772 205M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 85 times [spades] 0:00:14.773 205M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.777 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7 times [spades] 0:00:14.778 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.784 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 33 times [spades] 0:00:14.784 206M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:14.785 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.785 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.786 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.787 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.787 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.791 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times [spades] 0:00:14.791 206M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:14.792 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.793 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.793 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.794 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.794 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.796 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:14.796 206M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:14.797 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.798 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.799 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.799 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.800 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.801 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.801 206M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:14.802 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.802 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.803 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.804 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.804 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.806 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:14.806 206M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:14.807 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.807 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.808 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.809 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.809 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.810 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:14.811 206M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:14.811 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.812 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.813 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.813 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.814 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.815 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:14.816 206M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:14.817 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.817 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.818 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.818 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.819 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.820 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.820 206M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:14.821 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.822 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.822 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.823 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.823 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.824 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.825 206M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:14.825 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.830 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.831 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.837 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.838 206M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.843 206M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.850 206M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:14.851 206M / 5G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:14.852 206M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:14.852 206M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:14.854 206M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:14.855 206M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66551 Gb [spades] 0:00:14.856 206M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:15.060 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 52022 edges [spades] 0:00:15.061 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 52022 sequences. [spades] 0:00:15.121 199M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:15.294 199M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4867390 kmers in total. [spades] 0:00:15.298 199M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:15.423 199M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:15.551 200M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:15.727 200M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2265240 bytes occupied (3.72313 bits per kmer). [spades] 0:00:15.805 280M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:15.917 280M / 5G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:15.919 280M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:15.979 283M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:16.432 279M / 5G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:16.433 279M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:16.492 280M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:16.539 280M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 2 gaps after checking 412 candidates [spades] 0:00:16.558 280M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:16.559 280M / 5G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:16.560 280M / 5G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:16.561 280M / 5G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:16.562 280M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:16.563 280M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.568 280M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.569 280M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.574 280M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.575 280M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.580 280M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.581 280M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.586 280M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.587 280M / 5G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:16.610 280M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:17.657 264M / 5G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 25644 times [spades] 0:00:17.658 264M / 5G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:17.660 264M / 5G INFO General (simplification.cpp : 502) Average coverage = 59.54 [spades] 0:00:17.660 264M / 5G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:17.661 264M / 5G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K91/simplified_contigs [spades] 0:00:17.666 264M / 5G INFO General (binary_converter.cpp : 111) 365 reads written [spades] 0:00:17.668 264M / 5G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:17.775 180M / 5G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 17 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/Enterococcus/spades/K101/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/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/Enterococcus/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/Enterococcus/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/Enterococcus/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] 0:00:00.005 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/Enterococcus/spades/K91/simplified_contigs [spades] 0:00:00.009 9M / 10M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.009 9M / 10M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.009 9M / 10M INFO General (construction.cpp : 156) Average read length 178.524 [spades] 0:00:00.009 9M / 10M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.009 9M / 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 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 18641 [spades] 0:00:03.091 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4565708 reads [spades] 0:00:03.554 441M / 6G INFO General (kmer_splitters.hpp : 293) Used 4565708 reads [spades] 0:00:03.555 441M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:03.909 443M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 6725884 kmers in total. [spades] 0:00:03.910 443M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.134 439M / 6G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:04.135 439M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:04.135 439M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:04.136 439M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:04.137 439M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:04.137 439M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:04.621 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 6725884 kmers [spades] 0:00:04.623 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 6725884 kmers. [spades] 0:00:04.713 459M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.980 459M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 6752228 kmers in total. [spades] 0:00:04.981 459M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:05.188 459M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:05.372 465M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:05.727 465M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3139328 bytes occupied (3.71946 bits per kmer). [spades] 0:00:05.740 465M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:06.009 465M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:06.028 465M / 6G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:06.033 465M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:06.306 322M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 109421 sequences extracted [spades] 0:00:06.506 322M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:06.573 322M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected [spades] 0:00:07.092 274M / 6G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:07.093 274M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:07.093 274M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:07.220 288M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3134664 bytes occupied (3.72848 bits per kmer). [spades] 0:00:07.238 316M / 6G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:09.885 316M / 6G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:10.099 316M / 6G INFO General (construction.cpp : 505) Processed 218842 edges [spades] 0:00:10.154 189M / 6G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:10.155 189M / 6G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 12 [spades] 0:00:10.156 189M / 6G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 57 [spades] 0:00:10.156 189M / 6G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 58. Coverage mad: 13.3434 [spades] 0:00:10.157 189M / 6G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:10.203 189M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:10.319 189M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:10.637 189M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:10.940 189M / 6G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 58.2408. Fitted coverage std. dev: 11.5106 [spades] 0:00:10.942 189M / 6G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.992099 [spades] 0:00:10.942 189M / 6G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 37 [spades] 0:00:10.943 189M / 6G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 35 [spades] 0:00:10.943 189M / 6G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2822286 [spades] 0:00:10.944 189M / 6G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 58.2408 [spades] 0:00:10.945 189M / 6G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 35 [spades] 0:00:10.945 189M / 6G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:10.946 189M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:10.946 189M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:10.947 189M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:10.948 189M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:10.949 189M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:10.950 189M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66617 Gb [spades] 0:00:10.950 189M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:11.258 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 218842 edges [spades] 0:00:11.259 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 218842 sequences. [spades] 0:00:11.323 234M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:11.559 234M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 6725884 kmers in total. [spades] 0:00:11.562 234M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:11.773 234M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:11.952 214M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:12.309 214M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3127168 bytes occupied (3.71956 bits per kmer). [spades] 0:00:12.385 326M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:12.521 326M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:12.523 326M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:12.672 332M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:13.066 304M / 6G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:13.067 304M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:13.103 303M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:13.206 295M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 52 gaps after checking 394 candidates [spades] 0:00:13.242 294M / 6G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:13.249 182M / 6G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:13.250 182M / 6G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:13.250 182M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:13.257 182M / 6G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:13.258 182M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:13.259 182M / 6G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:13.260 182M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:13.261 182M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:13.262 182M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.645 175M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 35381 times [spades] 0:00:13.646 175M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.502 210M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2773 times [spades] 0:00:14.503 210M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.548 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 290 times [spades] 0:00:14.549 209M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:14.550 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.559 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 67 times [spades] 0:00:14.560 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.563 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times [spades] 0:00:14.563 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.570 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 37 times [spades] 0:00:14.570 209M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:14.571 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.571 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.572 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.573 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.573 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.575 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times [spades] 0:00:14.576 209M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:14.576 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.577 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.578 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.579 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:14.579 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.580 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:14.581 209M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:14.582 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.582 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.583 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.584 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.584 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.585 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.586 209M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:14.586 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.587 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.587 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.588 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.589 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.590 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:14.590 209M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:14.591 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.591 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.592 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.593 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.593 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.594 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:14.595 209M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:14.595 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.596 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.596 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.597 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.598 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.598 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.599 209M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:14.600 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.600 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.601 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.601 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.602 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.603 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:14.604 209M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:14.605 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.605 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.606 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.606 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.607 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.608 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.608 209M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:14.609 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.628 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:14.628 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.660 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.660 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.691 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.692 209M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 [spades] 0:00:14.693 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.694 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.695 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.695 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.696 209M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:14.697 209M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:14.723 209M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:14.724 209M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:14.725 209M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:14.726 209M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:14.727 209M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:14.729 209M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66556 Gb [spades] 0:00:14.729 209M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:14.962 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 59028 edges [spades] 0:00:14.964 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 59028 sequences. [spades] 0:00:15.022 224M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:15.233 224M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4811451 kmers in total. [spades] 0:00:15.236 224M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:15.387 224M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:15.526 218M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:15.759 218M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2239360 bytes occupied (3.72338 bits per kmer). [spades] 0:00:15.844 298M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:15.992 298M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:15.996 298M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:16.072 301M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:16.500 295M / 6G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:16.502 295M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:16.572 288M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:16.629 288M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 1 gaps after checking 492 candidates [spades] 0:00:16.645 282M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:16.646 282M / 6G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:16.647 282M / 6G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:16.648 282M / 6G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:16.649 282M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:16.650 282M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.656 282M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.657 282M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.663 282M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.664 282M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.670 282M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.671 282M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.677 282M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.679 282M / 6G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:16.703 282M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:17.865 264M / 6G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 29148 times [spades] 0:00:17.866 264M / 6G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:17.868 264M / 6G INFO General (simplification.cpp : 502) Average coverage = 52.6868 [spades] 0:00:17.868 264M / 6G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:17.869 264M / 6G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K101/simplified_contigs [spades] 0:00:17.874 264M / 6G INFO General (binary_converter.cpp : 111) 365 reads written [spades] 0:00:17.877 264M / 6G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:17.992 177M / 6G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 17 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/Enterococcus/spades/K111/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/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/Enterococcus/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/Enterococcus/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/Enterococcus/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] 0:00:00.004 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/Enterococcus/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 178.524 [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 / 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] 0:00:02.767 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4565708 reads [spades] 0:00:03.167 397M / 6G INFO General (kmer_splitters.hpp : 293) Used 4565708 reads [spades] 0:00:03.168 397M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:03.522 397M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 6433583 kmers in total. [spades] 0:00:03.524 397M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:03.733 397M / 6G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:03.733 397M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:03.734 397M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:03.734 397M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:03.735 397M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:03.735 397M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:04.210 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 6433583 kmers [spades] 0:00:04.210 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 6433583 kmers. [spades] 0:00:04.295 405M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.527 405M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 6465141 kmers in total. [spades] 0:00:04.529 405M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.734 405M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:04.922 410M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:05.265 410M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 3006176 bytes occupied (3.71986 bits per kmer). [spades] 0:00:05.278 410M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:05.537 410M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:05.541 410M / 6G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:05.547 410M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:05.802 330M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 104619 sequences extracted [spades] 0:00:05.990 330M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:06.054 330M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected [spades] 0:00:06.597 259M / 6G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:06.603 259M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:06.604 259M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:06.739 261M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2999024 bytes occupied (3.72921 bits per kmer). [spades] 0:00:06.758 289M / 6G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:09.101 289M / 6G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:09.317 289M / 6G INFO General (construction.cpp : 505) Processed 209238 edges [spades] 0:00:09.370 184M / 6G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:09.371 184M / 6G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 11 [spades] 0:00:09.372 184M / 6G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 50 [spades] 0:00:09.373 184M / 6G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 50. Coverage mad: 11.8608 [spades] 0:00:09.374 184M / 6G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:09.414 184M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:09.516 184M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:09.848 184M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:10.091 184M / 6G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 50.6954. Fitted coverage std. dev: 10.396 [spades] 0:00:10.093 184M / 6G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.981439 [spades] 0:00:10.093 184M / 6G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 32 [spades] 0:00:10.094 184M / 6G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 30 [spades] 0:00:10.095 184M / 6G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2824718 [spades] 0:00:10.095 184M / 6G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 50.6954 [spades] 0:00:10.096 184M / 6G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 30 [spades] 0:00:10.096 184M / 6G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:10.097 184M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:10.098 184M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:10.098 184M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:10.099 184M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:10.100 184M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:10.101 184M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66619 Gb [spades] 0:00:10.102 184M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:10.396 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 209238 edges [spades] 0:00:10.398 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 209238 sequences. [spades] 0:00:10.464 198M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:10.699 198M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 6433583 kmers in total. [spades] 0:00:10.703 198M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:10.897 198M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:11.084 185M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:11.414 185M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2991496 bytes occupied (3.71985 bits per kmer). [spades] 0:00:11.490 297M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:11.665 289M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:11.669 289M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:11.836 294M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:12.197 276M / 6G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:12.199 276M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:12.242 276M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:12.347 274M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 77 gaps after checking 434 candidates [spades] 0:00:12.390 273M / 6G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:12.397 161M / 6G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:12.398 161M / 6G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:12.399 161M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:12.406 161M / 6G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:12.407 161M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:12.408 161M / 6G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:12.409 161M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:12.410 161M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:12.411 161M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.778 152M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 32496 times [spades] 0:00:12.780 152M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.359 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1752 times [spades] 0:00:13.360 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.392 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 234 times [spades] 0:00:13.393 172M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:13.394 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.403 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 58 times [spades] 0:00:13.403 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.407 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4 times [spades] 0:00:13.407 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.412 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 26 times [spades] 0:00:13.413 172M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:13.413 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.414 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.415 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.415 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.416 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.418 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 9 times [spades] 0:00:13.418 172M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:13.419 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.420 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.420 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.421 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:13.422 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.423 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:13.423 172M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:13.424 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.425 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.425 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.426 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.426 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.427 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:13.428 172M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:13.428 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.429 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.429 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.430 172M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.430 172M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.431 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:13.432 171M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:13.432 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.433 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.434 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.434 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.435 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.436 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:13.436 171M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:13.437 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.437 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.438 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.438 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.439 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.440 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:13.440 171M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:13.441 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.441 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.442 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.443 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.443 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.444 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:13.445 171M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:13.445 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.446 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.446 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.447 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.448 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.448 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:13.449 171M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:13.449 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.455 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:13.456 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.463 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.464 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.470 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:13.471 171M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 [spades] 0:00:13.472 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.473 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.474 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.475 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.476 171M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.477 171M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:13.482 171M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:13.483 171M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:13.484 171M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:13.485 171M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:13.486 171M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:13.488 171M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66579 Gb [spades] 0:00:13.489 171M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:13.727 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 67224 edges [spades] 0:00:13.728 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 67224 sequences. [spades] 0:00:13.786 178M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:13.984 177M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4719623 kmers in total. [spades] 0:00:13.987 177M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:14.141 177M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:14.277 178M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:14.533 178M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2196776 bytes occupied (3.72365 bits per kmer). [spades] 0:00:14.622 258M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:14.751 258M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:14.753 258M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:14.834 262M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:15.233 251M / 6G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:15.235 251M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:15.302 253M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:15.369 253M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 5 gaps after checking 539 candidates [spades] 0:00:15.391 253M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:15.393 253M / 6G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:15.393 253M / 6G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:15.394 253M / 6G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:15.395 253M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:15.396 253M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.402 253M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.403 253M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.409 253M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.410 253M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.416 253M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.417 253M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.423 253M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.424 253M / 6G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:15.450 246M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:16.528 235M / 6G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 33243 times [spades] 0:00:16.529 235M / 6G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:16.531 235M / 6G INFO General (simplification.cpp : 502) Average coverage = 45.8343 [spades] 0:00:16.531 235M / 6G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:16.532 235M / 6G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K111/simplified_contigs [spades] 0:00:16.541 237M / 6G INFO General (binary_converter.cpp : 111) 364 reads written [spades] 0:00:16.545 237M / 6G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:16.623 156M / 6G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 16 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/Enterococcus/spades/K121/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/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/Enterococcus/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/Enterococcus/spades/K121/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] 0:00:00.001 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/Enterococcus/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] 0:00:00.004 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/Enterococcus/spades/K111/simplified_contigs [spades] 0:00:00.008 9M / 10M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.009 9M / 10M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.009 9M / 10M INFO General (construction.cpp : 156) Average read length 178.524 [spades] 0:00:00.009 9M / 10M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.009 9M / 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 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 18641 [spades] 0:00:02.453 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4565706 reads [spades] 0:00:02.806 371M / 5G INFO General (kmer_splitters.hpp : 293) Used 4565706 reads [spades] 0:00:02.807 371M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:03.154 373M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 6085153 kmers in total. [spades] 0:00:03.156 373M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:03.358 369M / 5G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:03.358 369M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:03.359 369M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:03.359 369M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:03.360 369M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:03.360 369M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:03.803 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 6085153 kmers [spades] 0:00:03.804 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 6085153 kmers. [spades] 0:00:03.887 396M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.131 396M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 6122741 kmers in total. [spades] 0:00:04.133 396M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.326 396M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:04.486 401M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:04.802 401M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2847400 bytes occupied (3.72043 bits per kmer). [spades] 0:00:04.816 401M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:05.060 401M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:05.062 391M / 5G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:05.065 391M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:05.309 338M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 98896 sequences extracted [spades] 0:00:05.489 338M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:05.551 338M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected [spades] 0:00:06.056 269M / 5G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:06.058 269M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:06.059 269M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:06.175 282M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2837576 bytes occupied (3.73049 bits per kmer). [spades] 0:00:06.196 306M / 5G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:08.217 306M / 5G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:08.405 306M / 5G INFO General (construction.cpp : 505) Processed 197792 edges [spades] 0:00:08.455 282M / 5G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:08.456 282M / 5G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 9 [spades] 0:00:08.457 282M / 5G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 43 [spades] 0:00:08.458 282M / 5G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 43. Coverage mad: 10.3782 [spades] 0:00:08.458 282M / 5G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:08.493 282M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:08.580 282M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:08.863 282M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:09.123 282M / 5G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 43.1752. Fitted coverage std. dev: 9.25787 [spades] 0:00:09.124 282M / 5G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.971857 [spades] 0:00:09.125 282M / 5G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 27 [spades] 0:00:09.125 282M / 5G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 26 [spades] 0:00:09.126 282M / 5G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2810331 [spades] 0:00:09.127 282M / 5G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 43.1752 [spades] 0:00:09.127 282M / 5G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 26 [spades] 0:00:09.128 282M / 5G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:09.128 282M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:09.129 282M / 5G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:09.130 282M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:09.130 282M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:09.132 174M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:09.133 174M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66621 Gb [spades] 0:00:09.134 174M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:09.425 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 197792 edges [spades] 0:00:09.428 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 197792 sequences. [spades] 0:00:09.491 202M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:09.738 202M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 6085153 kmers in total. [spades] 0:00:09.741 202M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:09.931 202M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:10.100 182M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:10.397 182M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2830032 bytes occupied (3.72057 bits per kmer). [spades] 0:00:10.463 278M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:10.645 267M / 5G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:10.649 267M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:10.805 273M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:11.135 255M / 5G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:11.136 255M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:11.175 255M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:11.277 247M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 72 gaps after checking 435 candidates [spades] 0:00:11.318 247M / 5G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:11.323 151M / 5G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:11.324 151M / 5G INFO General (simplification.cpp : 63) Most init cleaning disabled on main iteration [spades] 0:00:11.325 151M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:11.332 151M / 5G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:11.333 151M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:11.333 151M / 5G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:11.334 151M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:11.335 151M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:11.336 151M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:11.672 149M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 28533 times [spades] 0:00:11.673 149M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.001 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 884 times [spades] 0:00:12.002 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:12.031 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 153 times [spades] 0:00:12.032 153M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:12.033 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.039 152M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 31 times [spades] 0:00:12.040 152M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.043 152M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times [spades] 0:00:12.043 152M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:12.048 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 22 times [spades] 0:00:12.049 153M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:12.050 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.050 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:12.051 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.051 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:12.052 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:12.054 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times [spades] 0:00:12.054 153M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:12.055 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.056 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:12.056 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.057 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:12.058 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:12.058 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:12.059 153M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:12.060 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.060 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:12.061 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.061 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:12.062 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:12.063 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:12.063 153M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:12.064 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.064 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:12.065 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.065 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:12.066 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:12.067 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:12.067 153M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:12.068 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.068 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:12.069 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.070 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:12.070 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:12.071 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:12.072 153M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:12.072 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.073 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:12.073 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.074 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:12.074 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:12.075 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:12.076 153M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:12.076 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.077 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:12.078 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.078 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:12.079 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:12.079 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:12.080 153M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:12.081 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.081 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:12.082 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.082 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:12.083 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:12.084 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:12.084 153M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:12.085 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.091 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:12.093 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.099 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:12.100 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:12.107 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:12.107 153M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 [spades] 0:00:12.108 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.109 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:12.110 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.111 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:12.111 153M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:12.112 153M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:12.118 153M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:12.118 153M / 5G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:12.119 153M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:12.120 153M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:12.121 153M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:12.123 153M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66599 Gb [spades] 0:00:12.124 153M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:12.353 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 77354 edges [spades] 0:00:12.354 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 77354 sequences. [spades] 0:00:12.409 197M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:12.612 195M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4606960 kmers in total. [spades] 0:00:12.614 195M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:12.763 195M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:12.897 188M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:13.142 188M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2144664 bytes occupied (3.72422 bits per kmer). [spades] 0:00:13.233 268M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:13.366 268M / 5G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:13.371 268M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:13.472 273M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:13.835 259M / 5G INFO General (gap_closer.cpp : 126) Used 790847 paired reads [spades] 0:00:13.837 259M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:13.919 261M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:14.000 253M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 5 gaps after checking 610 candidates [spades] 0:00:14.024 253M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:14.026 253M / 5G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:14.027 253M / 5G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:14.028 253M / 5G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:14.029 253M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:14.030 253M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.037 253M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.038 253M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.045 253M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.046 253M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.052 253M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:14.053 253M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.060 253M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:14.061 253M / 5G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:14.089 253M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:15.202 241M / 5G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 38310 times [spades] 0:00:15.203 241M / 5G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:15.205 241M / 5G INFO General (simplification.cpp : 502) Average coverage = 38.9859 [spades] 0:00:15.205 241M / 5G INFO StageManager (stage.cpp : 166) STAGE == Mismatch Correction [spades] 0:00:15.206 241M / 5G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 240536 kmers to process [spades] 0:00:15.266 241M / 5G INFO General (graph_pack.hpp : 115) Normalizing done [spades] 0:00:18.418 253M / 5G INFO General (mismatch_shall_not_pass.hp: 195) Finished collecting potential mismatches positions [spades] 0:00:18.467 248M / 5G INFO General (mismatch_shall_not_pass.hp: 310) All edges processed [spades] 0:00:18.468 248M / 5G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides [spades] 0:00:18.469 248M / 5G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:18.470 248M / 5G INFO General (contig_output.hpp : 21) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/before_rr.fasta [spades] 0:00:18.526 248M / 5G INFO General (contig_output_stage.cpp : 146) Writing GFA graph to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/assembly_graph_after_simplification.gfa [spades] 0:00:18.556 248M / 5G INFO StageManager (stage.cpp : 166) STAGE == Paired Information Counting [spades] 0:00:18.559 244M / 5G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 240536 kmers to process [spades] 0:00:18.560 244M / 5G INFO General (graph_pack.hpp : 115) Normalizing done [spades] 0:00:18.561 244M / 5G INFO General (pair_info_count.cpp : 322) Min edge length for estimation: 41245 [spades] 0:00:18.562 244M / 5G INFO General (pair_info_count.cpp : 333) Estimating insert size for library #0 [spades] 0:00:18.563 244M / 5G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) [spades] 0:00:18.833 740M / 5G INFO General (pair_info_count.cpp : 39) Selecting usual mapper [spades] 0:00:20.115 712M / 5G INFO General (sequence_mapper_notifier.h: 94) Total 1491642 reads processed [spades] 0:00:20.201 712M / 5G INFO General (pair_info_count.cpp : 208) Edge pairs: 1280 [spades] 0:00:20.202 712M / 5G INFO General (pair_info_count.cpp : 212) 790045 paired reads (52.9648% of all) aligned to long edges [spades] 0:00:20.228 216M / 5G INFO General (pair_info_count.cpp : 356) Insert size = 286.172, deviation = 53.8064, left quantile = 220, right quantile = 355, read length = 150 [spades] 0:00:20.229 216M / 5G INFO General (pair_info_count.cpp : 373) Filtering data for library #0 [spades] 0:00:20.230 216M / 5G INFO General (pair_info_count.cpp : 39) Selecting usual mapper [spades] 0:00:20.896 213M / 5G INFO General (sequence_mapper_notifier.h: 94) Total 1491642 reads processed [spades] 0:00:20.898 213M / 5G INFO General (pair_info_count.cpp : 385) Mapping library #0 [spades] 0:00:20.899 213M / 5G INFO General (pair_info_count.cpp : 387) Mapping paired reads (takes a while) [spades] 0:00:20.900 213M / 5G INFO General (pair_info_count.cpp : 288) Left insert size quantile 220, right insert size quantile 355, filtering threshold 2, rounding threshold 0 [spades] 0:00:20.910 218M / 5G INFO General (pair_info_count.cpp : 39) Selecting usual mapper [spades] 0:00:21.680 217M / 5G INFO General (sequence_mapper_notifier.h: 94) Total 1491642 reads processed [spades] 0:00:21.687 217M / 5G INFO StageManager (stage.cpp : 166) STAGE == Distance Estimation [spades] 0:00:21.688 217M / 5G INFO General (distance_estimation.cpp : 174) Processing library #0 [spades] 0:00:21.689 217M / 5G INFO General (distance_estimation.cpp : 150) Weight Filter Done [spades] 0:00:21.690 217M / 5G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator [spades] 0:00:21.693 217M / 5G INFO General (distance_estimation.cpp : 35) Filtering info [spades] 0:00:21.694 217M / 5G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 1004 [spades] 0:00:21.696 217M / 5G INFO General (pair_info_filters.hpp : 263) Done filtering [spades] 0:00:21.697 217M / 5G INFO General (distance_estimation.cpp : 157) Refining clustered pair information [spades] 0:00:21.698 217M / 5G INFO General (distance_estimation.cpp : 159) The refining of clustered pair information has been finished [spades] 0:00:21.699 217M / 5G INFO General (distance_estimation.cpp : 161) Improving paired information [spades] 0:00:21.703 217M / 5G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 9; contradictional = 2 [spades] 0:00:21.707 217M / 5G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 [spades] 0:00:21.708 217M / 5G INFO General (distance_estimation.cpp : 104) Filling scaffolding index [spades] 0:00:21.709 217M / 5G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator [spades] 0:00:21.712 219M / 5G INFO General (distance_estimation.cpp : 35) Filtering info [spades] 0:00:21.713 219M / 5G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 754 [spades] 0:00:21.714 219M / 5G INFO General (pair_info_filters.hpp : 263) Done filtering [spades] 0:00:21.715 219M / 5G INFO General (distance_estimation.cpp : 183) Clearing raw paired index [spades] 0:00:21.717 219M / 5G INFO StageManager (stage.cpp : 166) STAGE == Repeat Resolving [spades] 0:00:21.718 219M / 5G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving [spades] 0:00:21.719 219M / 5G INFO General (launcher.cpp : 538) ExSPAnder repeat resolving tool started [spades] 0:00:21.723 219M / 5G INFO General (launcher.cpp : 404) Creating main extenders, unique edge length = 2000 [spades] 0:00:21.728 219M / 5G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #0 is 38.9859 [spades] 0:00:21.730 219M / 5G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #0 is 38.9859 [spades] 0:00:21.733 219M / 5G INFO General (extenders_logic.cpp : 519) Using 1 paired-end library [spades] 0:00:21.734 219M / 5G INFO General (extenders_logic.cpp : 520) Using 1 paired-end scaffolding library [spades] 0:00:21.734 219M / 5G INFO General (extenders_logic.cpp : 521) Using 0 single read libraries [spades] 0:00:21.735 219M / 5G INFO General (launcher.cpp : 432) Total number of extenders is 3 [spades] 0:00:21.736 219M / 5G INFO General (path_extender.hpp : 894) Processed 0 paths from 353 (0%) [spades] 0:00:21.746 219M / 5G INFO General (path_extender.hpp : 894) Processed 36 paths from 353 (10%) [spades] 0:00:21.750 219M / 5G INFO General (path_extender.hpp : 894) Processed 72 paths from 353 (20%) [spades] 0:00:21.756 219M / 5G INFO General (path_extender.hpp : 894) Processed 108 paths from 353 (30%) [spades] 0:00:21.758 219M / 5G INFO General (path_extender.hpp : 892) Processed 128 paths from 353 (36%) [spades] 0:00:21.761 219M / 5G INFO General (path_extender.hpp : 894) Processed 144 paths from 353 (40%) [spades] 0:00:21.764 219M / 5G INFO General (path_extender.hpp : 894) Processed 180 paths from 353 (50%) [spades] 0:00:21.767 219M / 5G INFO General (path_extender.hpp : 894) Processed 216 paths from 353 (61%) [spades] 0:00:21.770 219M / 5G INFO General (path_extender.hpp : 894) Processed 252 paths from 353 (71%) [spades] 0:00:21.771 219M / 5G INFO General (path_extender.hpp : 892) Processed 256 paths from 353 (72%) [spades] 0:00:21.774 219M / 5G INFO General (path_extender.hpp : 894) Processed 288 paths from 353 (81%) [spades] 0:00:21.776 219M / 5G INFO General (path_extender.hpp : 894) Processed 324 paths from 353 (91%) [spades] 0:00:21.779 219M / 5G INFO General (launcher.cpp : 244) Finalizing paths [spades] 0:00:21.780 219M / 5G INFO General (launcher.cpp : 246) Deduplicating paths [spades] 0:00:21.782 219M / 5G INFO General (launcher.cpp : 250) Paths deduplicated [spades] 0:00:21.782 219M / 5G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps [spades] 0:00:21.783 219M / 5G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths [spades] 0:00:21.784 219M / 5G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps [spades] 0:00:21.785 219M / 5G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps [spades] 0:00:21.786 219M / 5G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps [spades] 0:00:21.787 219M / 5G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths [spades] 0:00:21.788 219M / 5G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths [spades] 0:00:21.789 219M / 5G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed [spades] 0:00:21.791 219M / 5G INFO General (launcher.cpp : 267) Paths finalized [spades] 0:00:21.791 219M / 5G INFO General (launcher.cpp : 439) Closing gaps in paths [spades] 0:00:21.794 219M / 5G INFO General (launcher.cpp : 467) Gap closing completed [spades] 0:00:21.796 219M / 5G INFO General (launcher.cpp : 296) Traversing tandem repeats [spades] 0:00:21.799 219M / 5G INFO General (launcher.cpp : 306) Traversed 0 loops [spades] 0:00:21.800 219M / 5G INFO General (launcher.cpp : 244) Finalizing paths [spades] 0:00:21.800 219M / 5G INFO General (launcher.cpp : 246) Deduplicating paths [spades] 0:00:21.801 219M / 5G INFO General (launcher.cpp : 250) Paths deduplicated [spades] 0:00:21.802 219M / 5G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps [spades] 0:00:21.803 219M / 5G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths [spades] 0:00:21.804 219M / 5G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps [spades] 0:00:21.804 219M / 5G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps [spades] 0:00:21.805 219M / 5G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps [spades] 0:00:21.806 219M / 5G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths [spades] 0:00:21.807 219M / 5G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths [spades] 0:00:21.808 219M / 5G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed [spades] 0:00:21.810 219M / 5G INFO General (launcher.cpp : 267) Paths finalized [spades] 0:00:21.810 219M / 5G INFO General (launcher.cpp : 596) ExSPAnder repeat resolving tool finished [spades] 0:00:21.812 219M / 5G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:21.813 219M / 5G INFO General (contig_output.hpp : 21) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/before_rr.fasta [spades] 0:00:21.865 219M / 5G INFO General (contig_output_stage.cpp : 146) Writing GFA graph to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/assembly_graph_with_scaffolds.gfa [spades] 0:00:21.906 219M / 5G INFO General (contig_output_stage.cpp : 160) Outputting FastG graph to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/assembly_graph.fastg [spades] 0:00:22.078 219M / 5G INFO General (contig_output_stage.cpp : 190) Breaking scaffolds [spades] 0:00:22.115 219M / 5G INFO General (contig_output_stage.cpp : 95) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/final_contigs.fasta [spades] 0:00:22.161 219M / 5G INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/final_contigs.paths [spades] 0:00:22.195 219M / 5G INFO General (contig_output_stage.cpp : 95) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/scaffolds.fasta [spades] 0:00:22.240 219M / 5G INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/scaffolds.paths [spades] 0:00:22.242 219M / 5G INFO General (contig_output_stage.cpp : 108) Populating GFA with scaffold paths [spades] 0:00:22.244 219M / 5G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:22.306 137M / 5G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 22 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/Enterococcus/spades/K121/before_rr.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/before_rr.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/assembly_graph_after_simplification.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/assembly_graph_after_simplification.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/final_contigs.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/contigs.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/first_pe_contigs.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/first_pe_contigs.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/strain_graph.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/strain_graph.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/scaffolds.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/scaffolds.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/scaffolds.paths /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/scaffolds.paths /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/assembly_graph_with_scaffolds.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/assembly_graph_with_scaffolds.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/assembly_graph.fastg /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/assembly_graph.fastg /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/K121/final_contigs.paths /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/spades/scaffolds.fasta --misc_dir /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/spades/contigs.fasta [spades] * Assembled scaffolds are in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/scaffolds.fasta [spades] * Paths in the assembly graph corresponding to the contigs are in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/contigs.paths [spades] * Paths in the assembly graph corresponding to the scaffolds are in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/scaffolds.paths [spades] * Assembly graph is in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/spades/assembly_graph.fastg [spades] * Assembly graph in GFA format is in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/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/Enterococcus/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... 0.04 sec [bwa-index] [bwa_index] Construct BWT for the packed sequence... [bwa-index] [bwa_index] 0.77 seconds elapse. [bwa-index] [bwa_index] Update BWT... 0.04 sec [bwa-index] [bwa_index] Pack forward-only FASTA... 0.03 sec [bwa-index] [bwa_index] Construct SA from BWT and Occ... 0.36 sec [bwa-index] [main] Version: 0.7.17-r1188 [bwa-index] [main] CMD: bwa index spades.fasta [bwa-index] [main] Real time: 1.582 sec; CPU: 1.249 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/K1KwOhehG5 -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 321 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): (3, 989382, 4, 8) [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: (247, 280, 315) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (111, 451) [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (281.64, 51.68) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (43, 519) [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 233.540 CPU sec, 13.868 real sec [bwa+samtools-sort] [samclip] Processed 100000 records... [bwa+samtools-sort] [M::process] read 983284 sequences (147492600 bp)... [bwa+samtools-sort] [samclip] Processed 200000 records... [bwa+samtools-sort] [samclip] Processed 300000 records... [bwa+samtools-sort] [samclip] Processed 400000 records... [bwa+samtools-sort] [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 485549, 1, 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: (254, 288, 324) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (114, 464) [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (289.51, 53.71) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (44, 534) [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 983284 reads in 111.041 CPU sec, 5.698 real sec [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] [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] [samclip] Processed 1500000 records... [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] [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: 32.720 sec; CPU: 354.687 sec [bwa+samtools-sort] [samclip] Total SAM records 2984933, removed 70026, allowed 64678, passed 2914907 [bwa+samtools-sort] [samclip] Header contained 322 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: 3329954 [pilon] Processing NODE_296_length_413_cov_1.171233:1-413 [pilon] Processing NODE_136_length_1934_cov_1.483177:1-1934 [pilon] Processing NODE_212_length_688_cov_0.857143:1-688 [pilon] Processing NODE_205_length_734_cov_1.396411:1-734 [pilon] Processing NODE_155_length_1485_cov_26.517595:1-1485 [pilon] Processing NODE_27_length_33277_cov_41.556129:1-33277 [pilon] Processing NODE_37_length_23923_cov_36.924460:1-23923 [pilon] Processing NODE_126_length_2517_cov_9.371452:1-2517 [pilon] Processing NODE_320_length_131_cov_150.500000:1-131 [pilon] Processing NODE_278_length_435_cov_1.515924:1-435 [pilon] Processing NODE_203_length_735_cov_24.827362:1-735 [pilon] Processing NODE_283_length_430_cov_2.116505:1-430 [pilon] Processing NODE_114_length_3679_cov_1.526419:1-3679 [pilon] Processing NODE_32_length_29053_cov_40.728916:1-29053 [pilon] Processing NODE_115_length_3492_cov_1.908039:1-3492 [pilon] Processing NODE_291_length_424_cov_1.293729:1-424 [pilon] Processing NODE_106_length_5037_cov_2.420464:1-5037 [pilon] Processing NODE_50_length_18596_cov_41.225548:1-18596 [pilon] Processing NODE_10_length_74867_cov_39.030878:1-74867 [pilon] Processing NODE_228_length_572_cov_0.647450:1-572 [pilon] Processing NODE_20_length_41428_cov_45.772024:1-41428 [pilon] Processing NODE_294_length_421_cov_6.890000:1-421 [pilon] Processing NODE_273_length_445_cov_1.691358:1-445 [pilon] Processing NODE_64_length_15088_cov_36.671210:1-15088 [pilon] Processing NODE_152_length_1507_cov_1.676046:1-1507 [pilon] Processing NODE_265_length_454_cov_1.372372:1-454 [pilon] Processing NODE_48_length_19096_cov_39.760843:1-19096 [pilon] Processing NODE_321_length_122_cov_2116.000000:1-122 [pilon] Processing NODE_156_length_1479_cov_1.826215:1-1479 [pilon] Processing NODE_44_length_21667_cov_38.379421:1-21667 [pilon] NODE_320_length_131_cov_150.500000:1-131 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 0, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 131 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_320_length_131_cov_150.500000:1-131 [pilon] Processing NODE_24_length_36041_cov_44.520184:1-36041 [pilon] NODE_291_length_424_cov_1.293729:1-424 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 13, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 424 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_291_length_424_cov_1.293729:1-424 [pilon] Processing NODE_165_length_1325_cov_38.567276:1-1325 [pilon] NODE_265_length_454_cov_1.372372:1-454 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 14, Coverage: 2, minDepth: 5 [pilon] Confirmed 28 of 454 bases (6.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_265_length_454_cov_1.372372:1-454 [pilon] Processing NODE_194_length_790_cov_1.804185:1-790 [pilon] NODE_294_length_421_cov_6.890000:1-421 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 49, Coverage: 15, minDepth: 5 [pilon] Confirmed 344 of 421 bases (81.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_294_length_421_cov_6.890000:1-421 [pilon] Processing NODE_42_length_22534_cov_41.322893:1-22534 [pilon] NODE_321_length_122_cov_2116.000000:1-122 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 154, 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_321_length_122_cov_2116.000000:1-122 [pilon] Processing NODE_275_length_444_cov_2.814241:1-444 [pilon] NODE_278_length_435_cov_1.515924:1-435 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 177 of 435 bases (40.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_278_length_435_cov_1.515924:1-435 [pilon] Processing NODE_285_length_429_cov_2.103896:1-429 [pilon] NODE_273_length_445_cov_1.691358:1-445 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 19, Coverage: 4, minDepth: 5 [pilon] Confirmed 150 of 445 bases (33.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_296_length_413_cov_1.171233:1-413 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 9, Coverage: 3, minDepth: 5 [pilon] Confirmed 56 of 413 bases (13.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_296_length_413_cov_1.171233:1-413 [pilon] Processing NODE_196_length_787_cov_22.267267:1-787 [pilon] NODE_283_length_430_cov_2.116505:1-430 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 130 of 430 bases (30.23%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_283_length_430_cov_2.116505:1-430 [pilon] Processing NODE_223_length_611_cov_2.104082:1-611 [pilon] NODE_212_length_688_cov_0.857143:1-688 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 15, Coverage: 2, minDepth: 5 [pilon] Confirmed 14 of 688 bases (2.03%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_212_length_688_cov_0.857143:1-688 [pilon] Processing NODE_185_length_926_cov_27.334161:1-926 [pilon] Finished processing NODE_273_length_445_cov_1.691358:1-445 [pilon] Processing NODE_150_length_1543_cov_1.447257:1-1543 [pilon] NODE_205_length_734_cov_1.396411:1-734 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 35, Coverage: 4, minDepth: 5 [pilon] Confirmed 278 of 734 bases (37.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_205_length_734_cov_1.396411:1-734 [pilon] Processing NODE_45_length_21051_cov_36.297993:1-21051 [pilon] NODE_228_length_572_cov_0.647450:1-572 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 24, Coverage: 5, minDepth: 5 [pilon] Confirmed 283 of 572 bases (49.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_228_length_572_cov_0.647450:1-572 [pilon] Processing NODE_305_length_404_cov_1.374558:1-404 [pilon] NODE_156_length_1479_cov_1.826215:1-1479 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 61, Coverage: 5, minDepth: 5 [pilon] Confirmed 764 of 1479 bases (51.66%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_156_length_1479_cov_1.826215:1-1479 [pilon] Processing NODE_128_length_2271_cov_4.622791:1-2271 [pilon] NODE_203_length_735_cov_24.827362:1-735 log: [pilon] frags shovill.bam: coverage 61 [pilon] Total Reads: 351, Coverage: 61, minDepth: 15 [pilon] Confirmed 550 of 735 bases (74.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_203_length_735_cov_24.827362:1-735 [pilon] Processing NODE_87_length_9100_cov_36.575120:1-9100 [pilon] NODE_152_length_1507_cov_1.676046:1-1507 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 57, Coverage: 5, minDepth: 5 [pilon] Confirmed 799 of 1507 bases (53.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_152_length_1507_cov_1.676046:1-1507 [pilon] Processing NODE_295_length_415_cov_0.965986:1-415 [pilon] NODE_275_length_444_cov_2.814241:1-444 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 28, Coverage: 7, minDepth: 5 [pilon] Confirmed 308 of 444 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_275_length_444_cov_2.814241:1-444 [pilon] Processing NODE_195_length_788_cov_19.280360:1-788 [pilon] NODE_223_length_611_cov_2.104082:1-611 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 27, Coverage: 5, minDepth: 5 [pilon] Confirmed 328 of 611 bases (53.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_223_length_611_cov_2.104082:1-611 [pilon] NODE_305_length_404_cov_1.374558:1-404 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 9, Coverage: 3, 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] Processing NODE_63_length_15678_cov_35.801247:1-15678 [pilon] NODE_194_length_790_cov_1.804185:1-790 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 31, Coverage: 5, minDepth: 5 [pilon] Confirmed 417 of 790 bases (52.78%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_194_length_790_cov_1.804185:1-790 [pilon] Processing NODE_199_length_758_cov_1.469388:1-758 [pilon] NODE_136_length_1934_cov_1.483177:1-1934 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 79, Coverage: 5, minDepth: 5 [pilon] Confirmed 1193 of 1934 bases (61.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_136_length_1934_cov_1.483177:1-1934 [pilon] Processing NODE_133_length_2086_cov_6.873282:1-2086 [pilon] Finished processing NODE_305_length_404_cov_1.374558:1-404 [pilon] Processing NODE_168_length_1284_cov_1.371453:1-1284 [pilon] NODE_285_length_429_cov_2.103896:1-429 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 232 of 429 bases (54.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_285_length_429_cov_2.103896:1-429 [pilon] Processing NODE_219_length_641_cov_1.178846:1-641 [pilon] NODE_295_length_415_cov_0.965986:1-415 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 5, Coverage: 1, 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_295_length_415_cov_0.965986:1-415 [pilon] Processing NODE_261_length_459_cov_15.896450:1-459 [pilon] NODE_150_length_1543_cov_1.447257:1-1543 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 60, Coverage: 5, minDepth: 5 [pilon] Confirmed 982 of 1543 bases (63.64%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_150_length_1543_cov_1.447257:1-1543 [pilon] Processing NODE_35_length_26304_cov_39.876714:1-26304 [pilon] NODE_155_length_1485_cov_26.517595:1-1485 log: [pilon] frags shovill.bam: coverage 74 [pilon] Total Reads: 851, Coverage: 74, minDepth: 19 [pilon] Confirmed 1122 of 1485 bases (75.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_155_length_1485_cov_26.517595:1-1485 [pilon] Processing NODE_139_length_1840_cov_34.005817:1-1840 [pilon] NODE_219_length_641_cov_1.178846:1-641 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 16, Coverage: 3, minDepth: 5 [pilon] Confirmed 141 of 641 bases (22.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_219_length_641_cov_1.178846:1-641 [pilon] Processing NODE_221_length_623_cov_0.635458:1-623 [pilon] NODE_196_length_787_cov_22.267267:1-787 log: [pilon] frags shovill.bam: coverage 53 [pilon] Total Reads: 321, Coverage: 53, minDepth: 13 [pilon] Confirmed 631 of 787 bases (80.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_196_length_787_cov_22.267267:1-787 [pilon] Processing NODE_164_length_1384_cov_30.623911:1-1384 [pilon] NODE_199_length_758_cov_1.469388:1-758 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 24, Coverage: 4, minDepth: 5 [pilon] Confirmed 206 of 758 bases (27.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_261_length_459_cov_15.896450:1-459 log: [pilon] frags shovill.bam: coverage 33 [pilon] Total Reads: 117, Coverage: 33, minDepth: 8 [pilon] Confirmed 352 of 459 bases (76.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_261_length_459_cov_15.896450:1-459 [pilon] Finished processing NODE_199_length_758_cov_1.469388:1-758 [pilon] Processing NODE_304_length_405_cov_0.947183:1-405 [pilon] Processing NODE_230_length_563_cov_15.149321:1-563 [pilon] NODE_185_length_926_cov_27.334161:1-926 log: [pilon] frags shovill.bam: coverage 66 [pilon] Total Reads: 470, Coverage: 66, minDepth: 17 [pilon] Confirmed 760 of 926 bases (82.07%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_185_length_926_cov_27.334161:1-926 [pilon] Processing NODE_166_length_1309_cov_16.159933:1-1309 [pilon] NODE_195_length_788_cov_19.280360:1-788 log: [pilon] frags shovill.bam: coverage 47 [pilon] Total Reads: 286, Coverage: 47, minDepth: 12 [pilon] Confirmed 529 of 788 bases (67.13%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_195_length_788_cov_19.280360:1-788 [pilon] NODE_126_length_2517_cov_9.371452:1-2517 log: [pilon] frags shovill.bam: coverage 27 [pilon] Total Reads: 525, Coverage: 27, minDepth: 7 [pilon] Confirmed 2076 of 2517 bases (82.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_126_length_2517_cov_9.371452:1-2517 [pilon] Processing NODE_96_length_7198_cov_34.948848:1-7198 [pilon] Processing NODE_68_length_13793_cov_24.897674:1-13793 [pilon] NODE_304_length_405_cov_0.947183:1-405 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 53 of 405 bases (13.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_304_length_405_cov_0.947183:1-405 [pilon] NODE_221_length_623_cov_0.635458:1-623 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 623 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_221_length_623_cov_0.635458:1-623 [pilon] Processing NODE_98_length_6490_cov_35.739677:1-6490 [pilon] NODE_230_length_563_cov_15.149321:1-563 log: [pilon] frags shovill.bam: coverage 34 [pilon] Total Reads: 151, Coverage: 34, minDepth: 9 [pilon] Confirmed 402 of 563 bases (71.40%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_230_length_563_cov_15.149321:1-563 [pilon] Processing NODE_59_length_16928_cov_38.076992:1-16928 [pilon] NODE_168_length_1284_cov_1.371453:1-1284 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 44, Coverage: 4, minDepth: 5 [pilon] Confirmed 493 of 1284 bases (38.40%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_168_length_1284_cov_1.371453:1-1284 [pilon] Processing NODE_77_length_12325_cov_36.597345:1-12325 [pilon] NODE_115_length_3492_cov_1.908039:1-3492 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 163, Coverage: 6, minDepth: 5 [pilon] Confirmed 2264 of 3492 bases (64.83%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_115_length_3492_cov_1.908039:1-3492 [pilon] Processing NODE_92_length_8239_cov_1.768662:1-8239 [pilon] NODE_128_length_2271_cov_4.622791:1-2271 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 235, Coverage: 13, minDepth: 5 [pilon] Confirmed 1512 of 2271 bases (66.58%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_128_length_2271_cov_4.622791:1-2271 [pilon] Processing NODE_162_length_1398_cov_1.983555:1-1398 [pilon] NODE_165_length_1325_cov_38.567276:1-1325 log: [pilon] frags shovill.bam: coverage 106 [pilon] Total Reads: 1085, Coverage: 106, minDepth: 27 [pilon] Confirmed 1024 of 1325 bases (77.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_165_length_1325_cov_38.567276:1-1325 [pilon] Processing NODE_184_length_930_cov_7.402967:1-930 [pilon] Processing NODE_173_length_1120_cov_29.476476:1-1120 [pilon] NODE_114_length_3679_cov_1.526419:1-3679 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 129, Coverage: 5, minDepth: 5 [pilon] Confirmed 1755 of 3679 bases (47.70%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_114_length_3679_cov_1.526419:1-3679 [pilon] Processing NODE_270_length_447_cov_1.107362:1-447 [pilon] NODE_133_length_2086_cov_6.873282:1-2086 log: [pilon] frags shovill.bam: coverage 19 [pilon] Total Reads: 319, Coverage: 19, minDepth: 5 [pilon] Confirmed 1869 of 2086 bases (89.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_133_length_2086_cov_6.873282:1-2086 [pilon] Processing NODE_100_length_6000_cov_33.545161:1-6000 [pilon] NODE_166_length_1309_cov_16.159933:1-1309 log: [pilon] frags shovill.bam: coverage 46 [pilon] Total Reads: 459, Coverage: 46, minDepth: 12 [pilon] Confirmed 961 of 1309 bases (73.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_166_length_1309_cov_16.159933:1-1309 [pilon] Processing NODE_183_length_957_cov_1.834928:1-957 [pilon] NODE_164_length_1384_cov_30.623911:1-1384 log: [pilon] frags shovill.bam: coverage 85 [pilon] Total Reads: 911, Coverage: 85, minDepth: 21 [pilon] Confirmed 1011 of 1384 bases (73.05%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_164_length_1384_cov_30.623911:1-1384 [pilon] Processing NODE_73_length_13039_cov_36.896346:1-13039 [pilon] NODE_270_length_447_cov_1.107362:1-447 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 16, Coverage: 3, minDepth: 5 [pilon] Confirmed 78 of 447 bases (17.45%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_270_length_447_cov_1.107362:1-447 [pilon] Processing NODE_134_length_2066_cov_23.597429:1-2066 [pilon] NODE_106_length_5037_cov_2.420464:1-5037 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 287, Coverage: 7, minDepth: 5 [pilon] Confirmed 3965 of 5037 bases (78.72%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_106_length_5037_cov_2.420464:1-5037 [pilon] Processing NODE_307_length_403_cov_17.588652:1-403 [pilon] NODE_139_length_1840_cov_34.005817:1-1840 log: [pilon] frags shovill.bam: coverage 94 [pilon] Total Reads: 1348, Coverage: 94, minDepth: 24 [pilon] Confirmed 1509 of 1840 bases (82.01%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_139_length_1840_cov_34.005817:1-1840 [pilon] Processing NODE_306_length_404_cov_0.749117:1-404 [pilon] NODE_184_length_930_cov_7.402967:1-930 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 131, Coverage: 18, minDepth: 5 [pilon] Confirmed 692 of 930 bases (74.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_184_length_930_cov_7.402967:1-930 [pilon] Processing NODE_108_length_4343_cov_30.180483:1-4343 [pilon] NODE_173_length_1120_cov_29.476476:1-1120 log: [pilon] frags shovill.bam: coverage 74 [pilon] Total Reads: 654, Coverage: 74, minDepth: 19 [pilon] Confirmed 822 of 1120 bases (73.39%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_173_length_1120_cov_29.476476:1-1120 [pilon] Processing NODE_94_length_7522_cov_33.198757:1-7522 [pilon] NODE_183_length_957_cov_1.834928:1-957 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 38, Coverage: 5, minDepth: 5 [pilon] Confirmed 492 of 957 bases (51.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_183_length_957_cov_1.834928:1-957 [pilon] Processing NODE_269_length_447_cov_1.340491:1-447 [pilon] NODE_162_length_1398_cov_1.983555:1-1398 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 56, Coverage: 5, minDepth: 5 [pilon] Confirmed 1043 of 1398 bases (74.61%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_162_length_1398_cov_1.983555:1-1398 [pilon] Processing NODE_277_length_436_cov_1.923810:1-436 [pilon] NODE_307_length_403_cov_17.588652:1-403 log: [pilon] frags shovill.bam: coverage 28 [pilon] Total Reads: 116, Coverage: 28, minDepth: 7 [pilon] Confirmed 333 of 403 bases (82.63%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_307_length_403_cov_17.588652:1-403 [pilon] Processing NODE_34_length_26453_cov_47.303395:1-26453 [pilon] NODE_306_length_404_cov_0.749117:1-404 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, 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] Finished processing NODE_306_length_404_cov_0.749117:1-404 [pilon] Processing NODE_302_length_406_cov_1.091228:1-406 [pilon] NODE_269_length_447_cov_1.340491:1-447 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 119 of 447 bases (26.62%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_269_length_447_cov_1.340491:1-447 [pilon] Processing NODE_66_length_14434_cov_28.647942:1-14434 [pilon] NODE_277_length_436_cov_1.923810:1-436 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 175 of 436 bases (40.14%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_277_length_436_cov_1.923810:1-436 [pilon] Processing NODE_78_length_12257_cov_37.023401:1-12257 [pilon] NODE_134_length_2066_cov_23.597429:1-2066 log: [pilon] frags shovill.bam: coverage 66 [pilon] Total Reads: 1090, Coverage: 66, minDepth: 17 [pilon] Confirmed 1609 of 2066 bases (77.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_134_length_2066_cov_23.597429:1-2066 [pilon] Processing NODE_89_length_8407_cov_42.825609:1-8407 [pilon] NODE_302_length_406_cov_1.091228:1-406 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 8, Coverage: 3, minDepth: 5 [pilon] Confirmed 13 of 406 bases (3.20%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_302_length_406_cov_1.091228:1-406 [pilon] Processing NODE_319_length_233_cov_54.169643:1-233 [pilon] NODE_319_length_233_cov_54.169643:1-233 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 64, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 233 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_319_length_233_cov_54.169643:1-233 [pilon] Processing NODE_54_length_17669_cov_37.209369:1-17669 [pilon] NODE_92_length_8239_cov_1.768662:1-8239 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 356, Coverage: 6, minDepth: 5 [pilon] Confirmed 5052 of 8239 bases (61.32%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_92_length_8239_cov_1.768662:1-8239 [pilon] Processing NODE_206_length_725_cov_1.622517:1-725 [pilon] NODE_206_length_725_cov_1.622517:1-725 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 28, Coverage: 4, minDepth: 5 [pilon] Confirmed 359 of 725 bases (49.52%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_206_length_725_cov_1.622517:1-725 [pilon] Processing NODE_142_length_1702_cov_36.578748:1-1702 [pilon] NODE_142_length_1702_cov_36.578748:1-1702 log: [pilon] frags shovill.bam: coverage 100 [pilon] Total Reads: 1329, Coverage: 100, minDepth: 25 [pilon] Confirmed 1481 of 1702 bases (87.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_142_length_1702_cov_36.578748:1-1702 [pilon] Processing NODE_111_length_4214_cov_1.432690:1-4214 [pilon] NODE_87_length_9100_cov_36.575120:1-9100 log: [pilon] frags shovill.bam: coverage 106 [pilon] Total Reads: 7430, Coverage: 106, minDepth: 27 [pilon] Confirmed 8812 of 9100 bases (96.84%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_87_length_9100_cov_36.575120:1-9100 [pilon] Processing NODE_229_length_567_cov_9.645740:1-567 [pilon] NODE_108_length_4343_cov_30.180483:1-4343 log: [pilon] frags shovill.bam: coverage 83 [pilon] Total Reads: 2802, Coverage: 83, minDepth: 21 [pilon] Confirmed 3629 of 4343 bases (83.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_108_length_4343_cov_30.180483:1-4343 [pilon] Processing NODE_268_length_449_cov_2.899390:1-449 [pilon] NODE_229_length_567_cov_9.645740:1-567 log: [pilon] frags shovill.bam: coverage 20 [pilon] Total Reads: 88, Coverage: 20, minDepth: 5 [pilon] Confirmed 383 of 567 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_229_length_567_cov_9.645740:1-567 [pilon] Processing NODE_248_length_500_cov_2.189974:1-500 [pilon] NODE_268_length_449_cov_2.899390:1-449 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 21, Coverage: 6, minDepth: 5 [pilon] Confirmed 282 of 449 bases (62.81%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_268_length_449_cov_2.899390:1-449 [pilon] Processing NODE_141_length_1740_cov_14.904880:1-1740 [pilon] NODE_248_length_500_cov_2.189974:1-500 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 22, Coverage: 6, minDepth: 5 [pilon] Confirmed 326 of 500 bases (65.20%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_248_length_500_cov_2.189974:1-500 [pilon] NODE_100_length_6000_cov_33.545161:1-6000 log: [pilon] frags shovill.bam: coverage 98 [pilon] Total Reads: 4549, Coverage: 98, minDepth: 25 [pilon] Confirmed 5140 of 6000 bases (85.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_100_length_6000_cov_33.545161:1-6000 [pilon] Processing NODE_19_length_41453_cov_36.788856:1-41453 [pilon] NODE_98_length_6490_cov_35.739677:1-6490 log: [pilon] frags shovill.bam: coverage 103 [pilon] Total Reads: 5177, Coverage: 103, minDepth: 26 [pilon] Confirmed 5694 of 6490 bases (87.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_98_length_6490_cov_35.739677:1-6490 [pilon] Processing NODE_15_length_49167_cov_45.054500:1-49167 [pilon] NODE_141_length_1740_cov_14.904880:1-1740 log: [pilon] frags shovill.bam: coverage 41 [pilon] Total Reads: 549, Coverage: 41, minDepth: 10 [pilon] Confirmed 1482 of 1740 bases (85.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_141_length_1740_cov_14.904880:1-1740 [pilon] NODE_111_length_4214_cov_1.432690:1-4214 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 155, Coverage: 5, minDepth: 5 [pilon] Confirmed 2077 of 4214 bases (49.29%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_111_length_4214_cov_1.432690:1-4214 [pilon] Processing NODE_46_length_20176_cov_42.376215:1-20176 [pilon] NODE_96_length_7198_cov_34.948848:1-7198 log: [pilon] frags shovill.bam: coverage 100 [pilon] Total Reads: 5583, Coverage: 100, minDepth: 25 [pilon] Confirmed 6832 of 7198 bases (94.92%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_96_length_7198_cov_34.948848:1-7198 [pilon] Processing NODE_74_length_12953_cov_39.385910:1-12953 [pilon] NODE_94_length_7522_cov_33.198757:1-7522 log: [pilon] frags shovill.bam: coverage 93 [pilon] Total Reads: 5582, Coverage: 93, minDepth: 23 [pilon] Confirmed 6639 of 7522 bases (88.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_94_length_7522_cov_33.198757:1-7522 [pilon] Processing NODE_187_length_895_cov_2.182171:1-895 [pilon] NODE_89_length_8407_cov_42.825609:1-8407 log: [pilon] frags shovill.bam: coverage 124 [pilon] Total Reads: 8125, Coverage: 124, minDepth: 31 [pilon] Confirmed 8024 of 8407 bases (95.44%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_89_length_8407_cov_42.825609:1-8407 [pilon] Processing NODE_188_length_895_cov_1.788114:1-895 [pilon] NODE_187_length_895_cov_2.182171:1-895 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 39, Coverage: 6, minDepth: 5 [pilon] Confirmed 578 of 895 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_187_length_895_cov_2.182171:1-895 [pilon] Processing NODE_5_length_99564_cov_41.069748:1-99564 [pilon] NODE_188_length_895_cov_1.788114:1-895 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 30, Coverage: 4, minDepth: 5 [pilon] Confirmed 501 of 895 bases (55.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_188_length_895_cov_1.788114:1-895 [pilon] Processing NODE_238_length_525_cov_1.534653:1-525 [pilon] NODE_78_length_12257_cov_37.023401:1-12257 log: [pilon] frags shovill.bam: coverage 108 [pilon] Total Reads: 10188, Coverage: 108, minDepth: 27 [pilon] Confirmed 11338 of 12257 bases (92.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_78_length_12257_cov_37.023401:1-12257 [pilon] Processing NODE_284_length_429_cov_3.376623:1-429 [pilon] NODE_238_length_525_cov_1.534653:1-525 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 18, Coverage: 4, minDepth: 5 [pilon] Confirmed 191 of 525 bases (36.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_77_length_12325_cov_36.597345:1-12325 log: [pilon] frags shovill.bam: coverage 105 [pilon] Total Reads: 10060, Coverage: 105, minDepth: 26 [pilon] Confirmed 11325 of 12325 bases (91.89%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_238_length_525_cov_1.534653:1-525 [pilon] Finished processing NODE_77_length_12325_cov_36.597345:1-12325 [pilon] Processing NODE_208_length_710_cov_1.478778:1-710 [pilon] Processing NODE_252_length_483_cov_2.870166:1-483 [pilon] NODE_68_length_13793_cov_24.897674:1-13793 log: [pilon] frags shovill.bam: coverage 72 [pilon] Total Reads: 7702, Coverage: 72, minDepth: 18 [pilon] Confirmed 12169 of 13793 bases (88.23%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_68_length_13793_cov_24.897674:1-13793 [pilon] Processing NODE_175_length_1110_cov_1.882710:1-1110 [pilon] NODE_73_length_13039_cov_36.896346:1-13039 log: [pilon] frags shovill.bam: coverage 106 [pilon] Total Reads: 10838, Coverage: 106, minDepth: 27 [pilon] Confirmed 12477 of 13039 bases (95.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_73_length_13039_cov_36.896346:1-13039 [pilon] Processing NODE_13_length_57913_cov_40.487905:1-57913 [pilon] NODE_64_length_15088_cov_36.671210:1-15088 log: [pilon] frags shovill.bam: coverage 107 [pilon] Total Reads: 12430, Coverage: 107, minDepth: 27 [pilon] Confirmed 14230 of 15088 bases (94.31%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_64_length_15088_cov_36.671210:1-15088 [pilon] Processing NODE_301_length_408_cov_1.414634:1-408 [pilon] NODE_66_length_14434_cov_28.647942:1-14434 log: [pilon] frags shovill.bam: coverage 83 [pilon] Total Reads: 9303, Coverage: 83, minDepth: 21 [pilon] Confirmed 13051 of 14434 bases (90.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_66_length_14434_cov_28.647942:1-14434 [pilon] Processing NODE_217_length_652_cov_1.653484:1-652 [pilon] Processing NODE_161_length_1406_cov_3.118288:1-1406 [pilon] NODE_284_length_429_cov_3.376623:1-429 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 28, Coverage: 6, minDepth: 5 [pilon] Confirmed 293 of 429 bases (68.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_284_length_429_cov_3.376623:1-429 [pilon] Processing NODE_313_length_325_cov_1.862745:1-325 [pilon] NODE_252_length_483_cov_2.870166:1-483 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 27, Coverage: 6, minDepth: 5 [pilon] Confirmed 224 of 483 bases (46.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_252_length_483_cov_2.870166:1-483 [pilon] Processing NODE_38_length_23860_cov_36.975441:1-23860 [pilon] NODE_63_length_15678_cov_35.801247:1-15678 log: [pilon] frags shovill.bam: coverage 103 [pilon] Total Reads: 12507, Coverage: 103, minDepth: 26 [pilon] Confirmed 15135 of 15678 bases (96.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_63_length_15678_cov_35.801247:1-15678 [pilon] Processing NODE_236_length_534_cov_4.273608:1-534 [pilon] NODE_208_length_710_cov_1.478778:1-710 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 23, Coverage: 3, minDepth: 5 [pilon] Confirmed 277 of 710 bases (39.01%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_208_length_710_cov_1.478778:1-710 [pilon] Processing NODE_95_length_7246_cov_34.194947:1-7246 [pilon] NODE_59_length_16928_cov_38.076992:1-16928 log: [pilon] frags shovill.bam: coverage 111 [pilon] Total Reads: 14483, Coverage: 111, minDepth: 28 [pilon] Confirmed 16509 of 16928 bases (97.52%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_59_length_16928_cov_38.076992:1-16928 [pilon] NODE_175_length_1110_cov_1.882710:1-1110 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 53, Coverage: 6, minDepth: 5 [pilon] Confirmed 747 of 1110 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_175_length_1110_cov_1.882710:1-1110 [pilon] Processing NODE_287_length_428_cov_1.342020:1-428 [pilon] NODE_50_length_18596_cov_41.225548:1-18596 log: [pilon] frags shovill.bam: coverage 120 [pilon] Total Reads: 17221, Coverage: 120, minDepth: 30 [pilon] Confirmed 18196 of 18596 bases (97.85%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_50_length_18596_cov_41.225548:1-18596 [pilon] Processing NODE_83_length_10794_cov_38.301883:1-10794 [pilon] NODE_301_length_408_cov_1.414634:1-408 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 70 of 408 bases (17.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_301_length_408_cov_1.414634:1-408 [pilon] Processing NODE_144_length_1663_cov_18.050584:1-1663 [pilon] NODE_48_length_19096_cov_39.760843:1-19096 log: [pilon] frags shovill.bam: coverage 114 [pilon] Total Reads: 16838, Coverage: 114, minDepth: 29 [pilon] Confirmed 18729 of 19096 bases (98.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_48_length_19096_cov_39.760843:1-19096 [pilon] NODE_217_length_652_cov_1.653484:1-652 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 34, Coverage: 6, minDepth: 5 [pilon] Confirmed 384 of 652 bases (58.90%) [pilon] Corrected 4 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_217_length_652_cov_1.653484:1-652 [pilon] Processing NODE_117_length_3364_cov_32.188714:1-3364 [pilon] Processing NODE_257_length_468_cov_2.553314:1-468 [pilon] NODE_236_length_534_cov_4.273608:1-534 log: [pilon] frags shovill.bam: coverage 12 [pilon] Total Reads: 50, Coverage: 12, minDepth: 5 [pilon] Confirmed 393 of 534 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_236_length_534_cov_4.273608:1-534 [pilon] Processing NODE_36_length_25575_cov_40.748723:1-25575 [pilon] NODE_161_length_1406_cov_3.118288:1-1406 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 84, Coverage: 7, minDepth: 5 [pilon] Confirmed 1175 of 1406 bases (83.57%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_161_length_1406_cov_3.118288:1-1406 [pilon] Processing NODE_167_length_1288_cov_1.916881:1-1288 [pilon] NODE_54_length_17669_cov_37.209369:1-17669 log: [pilon] frags shovill.bam: coverage 108 [pilon] Total Reads: 14845, Coverage: 108, minDepth: 27 [pilon] Confirmed 16612 of 17669 bases (94.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_54_length_17669_cov_37.209369:1-17669 [pilon] Processing NODE_226_length_577_cov_2.717105:1-577 [pilon] NODE_313_length_325_cov_1.862745:1-325 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 17, Coverage: 3, minDepth: 5 [pilon] Confirmed 102 of 325 bases (31.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_313_length_325_cov_1.862745:1-325 [pilon] Processing NODE_314_length_320_cov_7.663317:1-320 [pilon] NODE_287_length_428_cov_1.342020:1-428 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 11, 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_287_length_428_cov_1.342020:1-428 [pilon] Processing NODE_200_length_741_cov_1.825806:1-741 [pilon] NODE_257_length_468_cov_2.553314:1-468 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 19, Coverage: 4, minDepth: 5 [pilon] Confirmed 257 of 468 bases (54.91%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_257_length_468_cov_2.553314:1-468 [pilon] Processing NODE_122_length_2913_cov_44.440544:1-2913 [pilon] NODE_314_length_320_cov_7.663317:1-320 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 42, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 320 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_314_length_320_cov_7.663317:1-320 [pilon] Processing NODE_297_length_413_cov_0.671233:1-413 [pilon] NODE_226_length_577_cov_2.717105:1-577 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 39, Coverage: 8, minDepth: 5 [pilon] Confirmed 337 of 577 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_226_length_577_cov_2.717105:1-577 [pilon] Processing NODE_253_length_480_cov_1.350975:1-480 [pilon] NODE_297_length_413_cov_0.671233:1-413 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 7, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 413 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_297_length_413_cov_0.671233:1-413 [pilon] Processing NODE_6_length_90772_cov_44.578416:1-90772 [pilon] NODE_167_length_1288_cov_1.916881:1-1288 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 57, Coverage: 6, minDepth: 5 [pilon] Confirmed 787 of 1288 bases (61.10%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_167_length_1288_cov_1.916881:1-1288 [pilon] Processing NODE_43_length_22353_cov_33.611956:1-22353 [pilon] NODE_200_length_741_cov_1.825806:1-741 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 28, Coverage: 4, minDepth: 5 [pilon] Confirmed 397 of 741 bases (53.58%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_200_length_741_cov_1.825806:1-741 [pilon] Processing NODE_51_length_18377_cov_32.977651:1-18377 [pilon] NODE_144_length_1663_cov_18.050584:1-1663 log: [pilon] frags shovill.bam: coverage 50 [pilon] Total Reads: 650, Coverage: 50, minDepth: 13 [pilon] Confirmed 1209 of 1663 bases (72.70%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_144_length_1663_cov_18.050584:1-1663 [pilon] Processing NODE_11_length_70956_cov_44.750575:1-70956 [pilon] NODE_253_length_480_cov_1.350975:1-480 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 209 of 480 bases (43.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_253_length_480_cov_1.350975:1-480 [pilon] Processing NODE_282_length_432_cov_1.221865:1-432 [pilon] NODE_45_length_21051_cov_36.297993:1-21051 log: [pilon] frags shovill.bam: coverage 105 [pilon] Total Reads: 17164, Coverage: 105, minDepth: 26 [pilon] Confirmed 20557 of 21051 bases (97.65%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_45_length_21051_cov_36.297993:1-21051 [pilon] Processing NODE_146_length_1620_cov_13.585724:1-1620 [pilon] NODE_37_length_23923_cov_36.924460:1-23923 log: [pilon] frags shovill.bam: coverage 107 [pilon] Total Reads: 19829, Coverage: 107, minDepth: 27 [pilon] Confirmed 23430 of 23923 bases (97.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_37_length_23923_cov_36.924460:1-23923 [pilon] Processing NODE_225_length_584_cov_2.481641:1-584 [pilon] NODE_44_length_21667_cov_38.379421:1-21667 log: [pilon] frags shovill.bam: coverage 112 [pilon] Total Reads: 18831, Coverage: 112, minDepth: 28 [pilon] Confirmed 21002 of 21667 bases (96.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_44_length_21667_cov_38.379421:1-21667 [pilon] Processing NODE_72_length_13073_cov_38.653490:1-13073 [pilon] NODE_42_length_22534_cov_41.322893:1-22534 log: [pilon] frags shovill.bam: coverage 120 [pilon] Total Reads: 20951, Coverage: 120, minDepth: 30 [pilon] Confirmed 21238 of 22534 bases (94.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_42_length_22534_cov_41.322893:1-22534 [pilon] Processing NODE_267_length_453_cov_0.322289:1-453 [pilon] NODE_282_length_432_cov_1.221865:1-432 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 12, Coverage: 4, minDepth: 5 [pilon] Confirmed 159 of 432 bases (36.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_282_length_432_cov_1.221865:1-432 [pilon] Processing NODE_207_length_710_cov_17.456706:1-710 [pilon] NODE_117_length_3364_cov_32.188714:1-3364 log: [pilon] frags shovill.bam: coverage 89 [pilon] Total Reads: 2327, Coverage: 89, minDepth: 22 [pilon] Confirmed 3000 of 3364 bases (89.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_117_length_3364_cov_32.188714:1-3364 [pilon] NODE_225_length_584_cov_2.481641:1-584 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 31, Coverage: 6, minDepth: 5 [pilon] Confirmed 265 of 584 bases (45.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_225_length_584_cov_2.481641:1-584 [pilon] NODE_267_length_453_cov_0.322289:1-453 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 453 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_138_length_1845_cov_8.606729:1-1845 [pilon] Finished processing NODE_267_length_453_cov_0.322289:1-453 [pilon] Processing NODE_57_length_17095_cov_38.169495:1-17095 [pilon] NODE_32_length_29053_cov_40.728916:1-29053 log: [pilon] frags shovill.bam: coverage 119 [pilon] Total Reads: 26813, Coverage: 119, minDepth: 30 [pilon] Confirmed 28785 of 29053 bases (99.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_32_length_29053_cov_40.728916:1-29053 [pilon] Processing NODE_153_length_1489_cov_1.625000:1-1489 [pilon] NODE_35_length_26304_cov_39.876714:1-26304 log: [pilon] frags shovill.bam: coverage 116 [pilon] Total Reads: 23613, Coverage: 116, minDepth: 29 [pilon] Confirmed 21280 of 26304 bases (80.90%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_35_length_26304_cov_39.876714:1-26304 [pilon] Processing NODE_110_length_4234_cov_27.448578:1-4234 [pilon] NODE_146_length_1620_cov_13.585724:1-1620 log: [pilon] frags shovill.bam: coverage 37 [pilon] Total Reads: 459, Coverage: 37, minDepth: 9 [pilon] Confirmed 1199 of 1620 bases (74.01%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_146_length_1620_cov_13.585724:1-1620 [pilon] Processing NODE_197_length_778_cov_56.852359:1-778 [pilon] NODE_207_length_710_cov_17.456706:1-710 log: [pilon] frags shovill.bam: coverage 39 [pilon] Total Reads: 213, Coverage: 39, minDepth: 10 [pilon] Confirmed 452 of 710 bases (63.66%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_207_length_710_cov_17.456706:1-710 [pilon] Processing NODE_69_length_13513_cov_41.553689:1-13513 [pilon] NODE_34_length_26453_cov_47.303395:1-26453 log: [pilon] frags shovill.bam: coverage 138 [pilon] Total Reads: 28355, Coverage: 138, minDepth: 35 [pilon] Confirmed 25954 of 26453 bases (98.11%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_34_length_26453_cov_47.303395:1-26453 [pilon] Processing NODE_149_length_1554_cov_34.883461:1-1554 [pilon] NODE_122_length_2913_cov_44.440544:1-2913 log: [pilon] frags shovill.bam: coverage 122 [pilon] Total Reads: 2773, Coverage: 122, minDepth: 31 [pilon] Confirmed 2429 of 2913 bases (83.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_122_length_2913_cov_44.440544:1-2913 [pilon] Processing NODE_147_length_1600_cov_5.146045:1-1600 [pilon] NODE_153_length_1489_cov_1.625000:1-1489 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 57, Coverage: 5, minDepth: 5 [pilon] Confirmed 917 of 1489 bases (61.58%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_153_length_1489_cov_1.625000:1-1489 [pilon] Processing NODE_231_length_549_cov_0.665888:1-549 [pilon] NODE_138_length_1845_cov_8.606729:1-1845 log: [pilon] frags shovill.bam: coverage 23 [pilon] Total Reads: 331, Coverage: 23, minDepth: 6 [pilon] Confirmed 1282 of 1845 bases (69.49%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_138_length_1845_cov_8.606729:1-1845 [pilon] Processing NODE_251_length_484_cov_1.528926:1-484 [pilon] NODE_74_length_12953_cov_39.385910:1-12953 log: [pilon] frags shovill.bam: coverage 114 [pilon] Total Reads: 11453, Coverage: 114, minDepth: 29 [pilon] Confirmed 12687 of 12953 bases (97.95%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_74_length_12953_cov_39.385910:1-12953 [pilon] Processing NODE_81_length_11385_cov_43.908825:1-11385 [pilon] NODE_147_length_1600_cov_5.146045:1-1600 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 181, Coverage: 14, minDepth: 5 [pilon] Confirmed 1262 of 1600 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_147_length_1600_cov_5.146045:1-1600 [pilon] Processing NODE_65_length_15071_cov_38.313712:1-15071 [pilon] NODE_197_length_778_cov_56.852359:1-778 log: [pilon] frags shovill.bam: coverage 90 [pilon] Total Reads: 949, Coverage: 90, minDepth: 23 [pilon] Confirmed 369 of 778 bases (47.43%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_197_length_778_cov_56.852359:1-778 [pilon] Processing NODE_227_length_576_cov_3.404396:1-576 [pilon] NODE_251_length_484_cov_1.528926:1-484 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 29, Coverage: 5, minDepth: 5 [pilon] Confirmed 376 of 484 bases (77.69%) [pilon] Corrected 3 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_251_length_484_cov_1.528926:1-484 [pilon] Processing NODE_235_length_536_cov_1.260241:1-536 [pilon] NODE_231_length_549_cov_0.665888:1-549 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 14, Coverage: 3, minDepth: 5 [pilon] Confirmed 110 of 549 bases (20.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_231_length_549_cov_0.665888:1-549 [pilon] Processing NODE_193_length_805_cov_1.698830:1-805 [pilon] NODE_95_length_7246_cov_34.194947:1-7246 log: [pilon] frags shovill.bam: coverage 99 [pilon] Total Reads: 5515, Coverage: 99, minDepth: 25 [pilon] Confirmed 6814 of 7246 bases (94.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_95_length_7246_cov_34.194947:1-7246 [pilon] Processing NODE_158_length_1474_cov_1.725055:1-1474 [pilon] NODE_27_length_33277_cov_41.556129:1-33277 log: [pilon] frags shovill.bam: coverage 121 [pilon] Total Reads: 31167, Coverage: 121, minDepth: 30 [pilon] Confirmed 31116 of 33277 bases (93.51%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_27_length_33277_cov_41.556129:1-33277 [pilon] Processing NODE_143_length_1673_cov_2.508376:1-1673 [pilon] NODE_24_length_36041_cov_44.520184:1-36041 log: [pilon] frags shovill.bam: coverage 131 [pilon] Total Reads: 36566, Coverage: 131, minDepth: 33 [pilon] Confirmed 34782 of 36041 bases (96.51%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_24_length_36041_cov_44.520184:1-36041 [pilon] Processing NODE_119_length_3200_cov_31.319909:1-3200 [pilon] NODE_235_length_536_cov_1.260241:1-536 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 15, Coverage: 3, minDepth: 5 [pilon] Confirmed 73 of 536 bases (13.62%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_235_length_536_cov_1.260241:1-536 [pilon] Processing NODE_198_length_770_cov_1.665639:1-770 [pilon] NODE_227_length_576_cov_3.404396:1-576 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 36, Coverage: 8, minDepth: 5 [pilon] Confirmed 326 of 576 bases (56.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_227_length_576_cov_3.404396:1-576 [pilon] NODE_149_length_1554_cov_34.883461:1-1554 log: [pilon] frags shovill.bam: coverage 94 [pilon] Total Reads: 1129, Coverage: 94, minDepth: 24 [pilon] Confirmed 1011 of 1554 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_149_length_1554_cov_34.883461:1-1554 [pilon] Processing NODE_23_length_36801_cov_40.309024:1-36801 [pilon] NODE_193_length_805_cov_1.698830:1-805 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 28, Coverage: 4, minDepth: 5 [pilon] Confirmed 273 of 805 bases (33.91%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_193_length_805_cov_1.698830:1-805 [pilon] Processing NODE_181_length_980_cov_1.408615:1-980 [pilon] NODE_158_length_1474_cov_1.725055:1-1474 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 65, Coverage: 5, minDepth: 5 [pilon] Confirmed 822 of 1474 bases (55.77%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_158_length_1474_cov_1.725055:1-1474 [pilon] Processing NODE_232_length_547_cov_3.507042:1-547 [pilon] NODE_143_length_1673_cov_2.508376:1-1673 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 93, Coverage: 7, minDepth: 5 [pilon] Confirmed 1206 of 1673 bases (72.09%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_143_length_1673_cov_2.508376:1-1673 [pilon] Processing NODE_211_length_700_cov_4.773748:1-700 [pilon] Processing NODE_258_length_467_cov_1.783237:1-467 [pilon] Processing NODE_239_length_523_cov_2.708955:1-523 [pilon] NODE_198_length_770_cov_1.665639:1-770 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 20, Coverage: 3, minDepth: 5 [pilon] Confirmed 265 of 770 bases (34.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_198_length_770_cov_1.665639:1-770 [pilon] Processing NODE_109_length_4271_cov_1.896867:1-4271 [pilon] NODE_181_length_980_cov_1.408615:1-980 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 32, Coverage: 4, minDepth: 5 [pilon] Confirmed 421 of 980 bases (42.96%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_181_length_980_cov_1.408615:1-980 [pilon] Processing NODE_16_length_48541_cov_37.671004:1-48541 [pilon] NODE_232_length_547_cov_3.507042:1-547 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 37, Coverage: 7, minDepth: 5 [pilon] Confirmed 397 of 547 bases (72.58%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_232_length_547_cov_3.507042:1-547 [pilon] Processing NODE_160_length_1413_cov_1.832817:1-1413 [pilon] NODE_211_length_700_cov_4.773748:1-700 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 61, Coverage: 11, minDepth: 5 [pilon] Confirmed 446 of 700 bases (63.71%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_211_length_700_cov_4.773748:1-700 [pilon] Processing NODE_56_length_17394_cov_36.424130:1-17394 [pilon] NODE_258_length_467_cov_1.783237:1-467 log: [pilon] NODE_239_length_523_cov_2.708955:1-523 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 215 of 467 bases (46.04%) [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: 29, Coverage: 6, minDepth: 5 [pilon] Confirmed 319 of 523 bases (60.99%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_258_length_467_cov_1.783237:1-467 [pilon] Finished processing NODE_239_length_523_cov_2.708955:1-523 [pilon] Processing NODE_210_length_701_cov_1.636207:1-701 [pilon] Processing NODE_67_length_14047_cov_40.839006:1-14047 [pilon] NODE_110_length_4234_cov_27.448578:1-4234 log: [pilon] frags shovill.bam: coverage 80 [pilon] Total Reads: 2608, Coverage: 80, minDepth: 20 [pilon] Confirmed 3678 of 4234 bases (86.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_110_length_4234_cov_27.448578:1-4234 [pilon] Processing NODE_132_length_2120_cov_1.625813:1-2120 [pilon] NODE_210_length_701_cov_1.636207:1-701 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 24, Coverage: 4, minDepth: 5 [pilon] Confirmed 318 of 701 bases (45.36%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_210_length_701_cov_1.636207:1-701 [pilon] Processing NODE_279_length_434_cov_1.840256:1-434 [pilon] NODE_160_length_1413_cov_1.832817:1-1413 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 68, Coverage: 6, minDepth: 5 [pilon] Confirmed 997 of 1413 bases (70.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_160_length_1413_cov_1.832817:1-1413 [pilon] Processing NODE_80_length_11679_cov_34.443416:1-11679 [pilon] NODE_279_length_434_cov_1.840256:1-434 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 9, Coverage: 3, minDepth: 5 [pilon] Confirmed 10 of 434 bases (2.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_279_length_434_cov_1.840256:1-434 [pilon] Processing NODE_97_length_6544_cov_25.393430:1-6544 [pilon] NODE_132_length_2120_cov_1.625813:1-2120 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 83, Coverage: 5, minDepth: 5 [pilon] Confirmed 1298 of 2120 bases (61.23%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_132_length_2120_cov_1.625813:1-2120 [pilon] Processing NODE_49_length_19027_cov_38.216175:1-19027 [pilon] NODE_109_length_4271_cov_1.896867:1-4271 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 206, Coverage: 6, minDepth: 5 [pilon] Confirmed 3207 of 4271 bases (75.09%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_109_length_4271_cov_1.896867:1-4271 [pilon] Processing NODE_130_length_2221_cov_2.081905:1-2221 [pilon] NODE_83_length_10794_cov_38.301883:1-10794 log: [pilon] frags shovill.bam: coverage 112 [pilon] Total Reads: 9328, Coverage: 112, minDepth: 28 [pilon] Confirmed 10226 of 10794 bases (94.74%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_83_length_10794_cov_38.301883:1-10794 [pilon] Processing NODE_259_length_460_cov_6.507375:1-460 [pilon] NODE_119_length_3200_cov_31.319909:1-3200 log: [pilon] frags shovill.bam: coverage 89 [pilon] Total Reads: 2194, Coverage: 89, minDepth: 22 [pilon] Confirmed 2484 of 3200 bases (77.63%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_119_length_3200_cov_31.319909:1-3200 [pilon] Processing NODE_124_length_2683_cov_2.113193:1-2683 [pilon] NODE_259_length_460_cov_6.507375:1-460 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 56, Coverage: 16, minDepth: 5 [pilon] Confirmed 352 of 460 bases (76.52%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_259_length_460_cov_6.507375:1-460 [pilon] Processing NODE_88_length_8685_cov_34.595983:1-8685 [pilon] NODE_20_length_41428_cov_45.772024:1-41428 log: [pilon] frags shovill.bam: coverage 135 [pilon] Total Reads: 43333, Coverage: 135, minDepth: 34 [pilon] Confirmed 40108 of 41428 bases (96.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_20_length_41428_cov_45.772024:1-41428 [pilon] NODE_46_length_20176_cov_42.376215:1-20176 log: [pilon] frags shovill.bam: coverage 123 [pilon] Total Reads: 19172, Coverage: 123, minDepth: 31 [pilon] Confirmed 19607 of 20176 bases (97.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_46_length_20176_cov_42.376215:1-20176 [pilon] Processing NODE_256_length_471_cov_3.342857:1-471 [pilon] NODE_130_length_2221_cov_2.081905:1-2221 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 114, Coverage: 7, minDepth: 5 [pilon] Confirmed 1774 of 2221 bases (79.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_130_length_2221_cov_2.081905:1-2221 [pilon] Processing NODE_311_length_347_cov_96.057522:1-347 [pilon] NODE_256_length_471_cov_3.342857:1-471 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 30, Coverage: 7, minDepth: 5 [pilon] Confirmed 288 of 471 bases (61.15%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_256_length_471_cov_3.342857:1-471 [pilon] Processing NODE_41_length_23264_cov_36.084864:1-23264 [pilon] NODE_124_length_2683_cov_2.113193:1-2683 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 126, Coverage: 6, minDepth: 5 [pilon] Confirmed 1721 of 2683 bases (64.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_124_length_2683_cov_2.113193:1-2683 [pilon] Processing NODE_140_length_1791_cov_26.069461:1-1791 [pilon] Processing NODE_254_length_476_cov_1.118310:1-476 [pilon] NODE_311_length_347_cov_96.057522:1-347 log: [pilon] frags shovill.bam: coverage 84 [pilon] Total Reads: 479, Coverage: 84, minDepth: 21 [pilon] Confirmed 298 of 347 bases (85.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_311_length_347_cov_96.057522:1-347 [pilon] Processing NODE_266_length_453_cov_1.512048:1-453 [pilon] NODE_254_length_476_cov_1.118310:1-476 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 11, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 476 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_254_length_476_cov_1.118310:1-476 [pilon] Processing NODE_192_length_816_cov_0.981295:1-816 [pilon] NODE_266_length_453_cov_1.512048:1-453 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 84 of 453 bases (18.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_266_length_453_cov_1.512048:1-453 [pilon] Processing NODE_222_length_615_cov_1.943320:1-615 [pilon] NODE_192_length_816_cov_0.981295:1-816 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 18, Coverage: 3, minDepth: 5 [pilon] Confirmed 237 of 816 bases (29.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_192_length_816_cov_0.981295:1-816 [pilon] Processing NODE_241_length_513_cov_2.926020:1-513 [pilon] NODE_140_length_1791_cov_26.069461:1-1791 log: [pilon] frags shovill.bam: coverage 74 [pilon] Total Reads: 1021, Coverage: 74, minDepth: 19 [pilon] Confirmed 1512 of 1791 bases (84.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_140_length_1791_cov_26.069461:1-1791 [pilon] Processing NODE_177_length_1098_cov_0.805527:1-1098 [pilon] NODE_222_length_615_cov_1.943320:1-615 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 20, Coverage: 4, minDepth: 5 [pilon] Confirmed 257 of 615 bases (41.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_222_length_615_cov_1.943320:1-615 [pilon] Processing NODE_214_length_665_cov_1.400735:1-665 [pilon] NODE_241_length_513_cov_2.926020:1-513 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 32, Coverage: 8, minDepth: 5 [pilon] Confirmed 290 of 513 bases (56.53%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_241_length_513_cov_2.926020:1-513 [pilon] Processing NODE_182_length_959_cov_32.090692:1-959 [pilon] NODE_214_length_665_cov_1.400735:1-665 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 23, Coverage: 3, minDepth: 5 [pilon] Confirmed 152 of 665 bases (22.86%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_177_length_1098_cov_0.805527:1-1098 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 23, Coverage: 3, minDepth: 5 [pilon] Confirmed 105 of 1098 bases (9.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_214_length_665_cov_1.400735:1-665 [pilon] Finished processing NODE_177_length_1098_cov_0.805527:1-1098 [pilon] Processing NODE_249_length_496_cov_8.280000:1-496 [pilon] Processing NODE_101_length_5869_cov_30.946590:1-5869 [pilon] NODE_97_length_6544_cov_25.393430:1-6544 log: [pilon] frags shovill.bam: coverage 73 [pilon] Total Reads: 3704, Coverage: 73, minDepth: 18 [pilon] Confirmed 5160 of 6544 bases (78.85%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_97_length_6544_cov_25.393430:1-6544 [pilon] Processing NODE_9_length_82413_cov_37.298717:1-82413 [pilon] NODE_249_length_496_cov_8.280000:1-496 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 59, Coverage: 14, minDepth: 5 [pilon] Confirmed 263 of 496 bases (53.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_249_length_496_cov_8.280000:1-496 [pilon] Processing NODE_159_length_1447_cov_1.398190:1-1447 [pilon] NODE_182_length_959_cov_32.090692:1-959 log: [pilon] frags shovill.bam: coverage 85 [pilon] Total Reads: 638, Coverage: 85, minDepth: 21 [pilon] Confirmed 683 of 959 bases (71.22%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_182_length_959_cov_32.090692:1-959 [pilon] Processing NODE_303_length_405_cov_2.049296:1-405 [pilon] NODE_303_length_405_cov_2.049296:1-405 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 15, Coverage: 4, minDepth: 5 [pilon] Confirmed 137 of 405 bases (33.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_303_length_405_cov_2.049296:1-405 [pilon] Processing NODE_145_length_1623_cov_19.392144:1-1623 [pilon] NODE_72_length_13073_cov_38.653490:1-13073 log: [pilon] frags shovill.bam: coverage 111 [pilon] Total Reads: 11330, Coverage: 111, minDepth: 28 [pilon] Confirmed 12292 of 13073 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_72_length_13073_cov_38.653490:1-13073 [pilon] Processing NODE_4_length_133398_cov_40.014841:1-133398 [pilon] NODE_159_length_1447_cov_1.398190:1-1447 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 44, Coverage: 4, minDepth: 5 [pilon] Confirmed 436 of 1447 bases (30.13%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_159_length_1447_cov_1.398190:1-1447 [pilon] Processing NODE_262_length_459_cov_1.721893:1-459 [pilon] NODE_262_length_459_cov_1.721893:1-459 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 16, Coverage: 3, minDepth: 5 [pilon] Confirmed 128 of 459 bases (27.89%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_262_length_459_cov_1.721893:1-459 [pilon] Processing NODE_40_length_23270_cov_32.884012:1-23270 [pilon] NODE_81_length_11385_cov_43.908825:1-11385 log: [pilon] frags shovill.bam: coverage 128 [pilon] Total Reads: 11323, Coverage: 128, minDepth: 32 [pilon] Confirmed 10571 of 11385 bases (92.85%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_81_length_11385_cov_43.908825:1-11385 [pilon] Processing NODE_47_length_19186_cov_38.512457:1-19186 [pilon] NODE_145_length_1623_cov_19.392144:1-1623 log: [pilon] frags shovill.bam: coverage 51 [pilon] Total Reads: 633, Coverage: 51, minDepth: 13 [pilon] Confirmed 1085 of 1623 bases (66.85%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_145_length_1623_cov_19.392144:1-1623 [pilon] Processing NODE_102_length_5740_cov_1.908525:1-5740 [pilon] NODE_88_length_8685_cov_34.595983:1-8685 log: [pilon] frags shovill.bam: coverage 99 [pilon] Total Reads: 6673, Coverage: 99, minDepth: 25 [pilon] Confirmed 7892 of 8685 bases (90.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_19_length_41453_cov_36.788856:1-41453 log: [pilon] frags shovill.bam: coverage 108 [pilon] Total Reads: 34658, Coverage: 108, minDepth: 27 [pilon] Confirmed 40429 of 41453 bases (97.53%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_19_length_41453_cov_36.788856:1-41453 [pilon] Processing NODE_116_length_3490_cov_41.778569:1-3490 [pilon] Finished processing NODE_88_length_8685_cov_34.595983:1-8685 [pilon] Processing NODE_176_length_1105_cov_1.231707:1-1105 [pilon] NODE_69_length_13513_cov_41.553689:1-13513 log: [pilon] frags shovill.bam: coverage 121 [pilon] Total Reads: 12642, Coverage: 121, minDepth: 30 [pilon] Confirmed 13250 of 13513 bases (98.05%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_69_length_13513_cov_41.553689:1-13513 [pilon] Processing NODE_299_length_410_cov_1.228374:1-410 [pilon] NODE_176_length_1105_cov_1.231707:1-1105 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 28, Coverage: 3, minDepth: 5 [pilon] Confirmed 318 of 1105 bases (28.78%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_176_length_1105_cov_1.231707:1-1105 [pilon] Processing NODE_62_length_15999_cov_43.115695:1-15999 [pilon] NODE_299_length_410_cov_1.228374:1-410 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 9, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 410 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_410_cov_1.228374:1-410 [pilon] Processing NODE_292_length_424_cov_1.227723:1-424 [pilon] NODE_51_length_18377_cov_32.977651:1-18377 log: [pilon] frags shovill.bam: coverage 95 [pilon] Total Reads: 13560, Coverage: 95, minDepth: 24 [pilon] Confirmed 17099 of 18377 bases (93.05%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_51_length_18377_cov_32.977651:1-18377 [pilon] NODE_101_length_5869_cov_30.946590:1-5869 log: [pilon] frags shovill.bam: coverage 89 [pilon] Total Reads: 4023, Coverage: 89, minDepth: 22 [pilon] Confirmed 5397 of 5869 bases (91.96%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_101_length_5869_cov_30.946590:1-5869 [pilon] Processing NODE_286_length_428_cov_2.368078:1-428 [pilon] Processing NODE_2_length_150434_cov_42.254070:1-150434 [pilon] NODE_80_length_11679_cov_34.443416:1-11679 log: [pilon] frags shovill.bam: coverage 100 [pilon] Total Reads: 9160, Coverage: 100, minDepth: 25 [pilon] Confirmed 9607 of 11679 bases (82.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_80_length_11679_cov_34.443416:1-11679 [pilon] Processing NODE_281_length_434_cov_1.376997:1-434 [pilon] NODE_102_length_5740_cov_1.908525:1-5740 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 267, Coverage: 6, minDepth: 5 [pilon] Confirmed 4045 of 5740 bases (70.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_102_length_5740_cov_1.908525:1-5740 [pilon] Processing NODE_75_length_12675_cov_39.741278:1-12675 [pilon] NODE_292_length_424_cov_1.227723:1-424 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 5 of 424 bases (1.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_292_length_424_cov_1.227723:1-424 [pilon] Processing NODE_190_length_837_cov_1.180168:1-837 [pilon] NODE_65_length_15071_cov_38.313712:1-15071 log: [pilon] frags shovill.bam: coverage 111 [pilon] Total Reads: 12981, Coverage: 111, minDepth: 28 [pilon] Confirmed 14374 of 15071 bases (95.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_65_length_15071_cov_38.313712:1-15071 [pilon] Processing NODE_178_length_1082_cov_1.150884:1-1082 [pilon] NODE_286_length_428_cov_2.368078:1-428 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 16, Coverage: 5, minDepth: 5 [pilon] Confirmed 222 of 428 bases (51.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_286_length_428_cov_2.368078:1-428 [pilon] Processing NODE_202_length_740_cov_2.513732:1-740 [pilon] NODE_281_length_434_cov_1.376997:1-434 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 14, Coverage: 4, minDepth: 5 [pilon] Confirmed 166 of 434 bases (38.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_281_length_434_cov_1.376997:1-434 [pilon] Processing NODE_112_length_4192_cov_38.119135:1-4192 [pilon] NODE_190_length_837_cov_1.180168:1-837 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 18, Coverage: 3, minDepth: 5 [pilon] Confirmed 102 of 837 bases (12.19%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_190_length_837_cov_1.180168:1-837 [pilon] Processing NODE_317_length_243_cov_148.475410:1-243 [pilon] NODE_202_length_740_cov_2.513732:1-740 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 37, Coverage: 6, minDepth: 5 [pilon] Confirmed 423 of 740 bases (57.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_202_length_740_cov_2.513732:1-740 [pilon] Processing NODE_7_length_90439_cov_39.840619:1-90439 [pilon] NODE_178_length_1082_cov_1.150884:1-1082 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 26, Coverage: 3, minDepth: 5 [pilon] Confirmed 240 of 1082 bases (22.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_178_length_1082_cov_1.150884:1-1082 [pilon] Processing NODE_148_length_1585_cov_21.817623:1-1585 [pilon] NODE_317_length_243_cov_148.475410:1-243 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 334, 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_317_length_243_cov_148.475410:1-243 [pilon] Processing NODE_84_length_10443_cov_34.274075:1-10443 [pilon] NODE_57_length_17095_cov_38.169495:1-17095 log: [pilon] frags shovill.bam: coverage 110 [pilon] Total Reads: 14594, Coverage: 110, minDepth: 28 [pilon] Confirmed 16708 of 17095 bases (97.74%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_57_length_17095_cov_38.169495:1-17095 [pilon] Processing NODE_121_length_2947_cov_1.952229:1-2947 [pilon] NODE_38_length_23860_cov_36.975441:1-23860 log: [pilon] frags shovill.bam: coverage 107 [pilon] Total Reads: 19832, Coverage: 107, minDepth: 27 [pilon] Confirmed 23113 of 23860 bases (96.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_38_length_23860_cov_36.975441:1-23860 [pilon] Processing NODE_31_length_29574_cov_40.616813:1-29574 [pilon] NODE_116_length_3490_cov_41.778569:1-3490 log: [pilon] frags shovill.bam: coverage 115 [pilon] Total Reads: 3120, Coverage: 115, minDepth: 29 [pilon] Confirmed 3309 of 3490 bases (94.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_116_length_3490_cov_41.778569:1-3490 [pilon] NODE_43_length_22353_cov_33.611956:1-22353 log: [pilon] frags shovill.bam: coverage 98 [pilon] Total Reads: 16992, Coverage: 98, minDepth: 25 [pilon] Confirmed 18359 of 22353 bases (82.13%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_43_length_22353_cov_33.611956:1-22353 [pilon] Processing NODE_104_length_5293_cov_35.713264:1-5293 [pilon] NODE_67_length_14047_cov_40.839006:1-14047 log: [pilon] frags shovill.bam: coverage 117 [pilon] Total Reads: 12894, Coverage: 117, minDepth: 29 [pilon] Confirmed 13942 of 14047 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_67_length_14047_cov_40.839006:1-14047 [pilon] Processing NODE_8_length_84837_cov_43.408660:1-84837 [pilon] Processing NODE_318_length_240_cov_47.428571:1-240 [pilon] NODE_148_length_1585_cov_21.817623:1-1585 log: [pilon] frags shovill.bam: coverage 62 [pilon] Total Reads: 764, Coverage: 62, minDepth: 16 [pilon] Confirmed 1394 of 1585 bases (87.95%) [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_1585_cov_21.817623:1-1585 [pilon] Processing NODE_55_length_17586_cov_39.556542:1-17586 [pilon] NODE_121_length_2947_cov_1.952229:1-2947 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 128, Coverage: 6, minDepth: 5 [pilon] Confirmed 1809 of 2947 bases (61.38%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_121_length_2947_cov_1.952229:1-2947 [pilon] NODE_318_length_240_cov_47.428571:1-240 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 112, Coverage: 8, minDepth: 5 [pilon] Confirmed 181 of 240 bases (75.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_318_length_240_cov_47.428571:1-240 [pilon] Processing NODE_154_length_1487_cov_71.467057:1-1487 [pilon] NODE_112_length_4192_cov_38.119135:1-4192 log: [pilon] frags shovill.bam: coverage 109 [pilon] Total Reads: 3544, Coverage: 109, minDepth: 27 [pilon] Confirmed 3738 of 4192 bases (89.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_112_length_4192_cov_38.119135:1-4192 [pilon] Processing NODE_250_length_496_cov_2.618667:1-496 [pilon] NODE_56_length_17394_cov_36.424130:1-17394 log: [pilon] frags shovill.bam: coverage 106 [pilon] Total Reads: 14245, Coverage: 106, minDepth: 27 [pilon] Confirmed 16597 of 17394 bases (95.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_56_length_17394_cov_36.424130:1-17394 [pilon] Processing NODE_99_length_6136_cov_11.217456:1-6136 [pilon] NODE_250_length_496_cov_2.618667:1-496 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 23, Coverage: 6, minDepth: 5 [pilon] Confirmed 335 of 496 bases (67.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_250_length_496_cov_2.618667:1-496 [pilon] NODE_154_length_1487_cov_71.467057:1-1487 log: [pilon] frags shovill.bam: coverage 168 [pilon] Total Reads: 2201, Coverage: 168, minDepth: 42 [pilon] Confirmed 1367 of 1487 bases (91.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_154_length_1487_cov_71.467057:1-1487 [pilon] Processing NODE_233_length_542_cov_1.501188:1-542 [pilon] NODE_36_length_25575_cov_40.748723:1-25575 log: [pilon] frags shovill.bam: coverage 120 [pilon] Total Reads: 23706, Coverage: 120, minDepth: 30 [pilon] Confirmed 24852 of 25575 bases (97.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_36_length_25575_cov_40.748723:1-25575 [pilon] Processing NODE_53_length_18092_cov_43.690891:1-18092 [pilon] Processing NODE_52_length_18170_cov_48.514211:1-18170 [pilon] NODE_233_length_542_cov_1.501188:1-542 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 16, Coverage: 4, minDepth: 5 [pilon] Confirmed 254 of 542 bases (46.86%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_233_length_542_cov_1.501188:1-542 [pilon] Processing NODE_170_length_1225_cov_22.330616:1-1225 [pilon] NODE_104_length_5293_cov_35.713264:1-5293 log: [pilon] frags shovill.bam: coverage 101 [pilon] Total Reads: 4152, Coverage: 101, minDepth: 25 [pilon] Confirmed 4995 of 5293 bases (94.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_104_length_5293_cov_35.713264:1-5293 [pilon] Processing NODE_151_length_1514_cov_64.797559:1-1514 [pilon] NODE_99_length_6136_cov_11.217456:1-6136 log: [pilon] frags shovill.bam: coverage 32 [pilon] Total Reads: 1517, Coverage: 32, minDepth: 8 [pilon] Confirmed 2394 of 6136 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_99_length_6136_cov_11.217456:1-6136 [pilon] Processing NODE_113_length_3975_cov_2.471718:1-3975 [pilon] NODE_49_length_19027_cov_38.216175:1-19027 log: [pilon] frags shovill.bam: coverage 112 [pilon] Total Reads: 16541, Coverage: 112, minDepth: 28 [pilon] Confirmed 18091 of 19027 bases (95.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_49_length_19027_cov_38.216175:1-19027 [pilon] Processing NODE_70_length_13439_cov_36.711443:1-13439 [pilon] NODE_170_length_1225_cov_22.330616:1-1225 log: [pilon] frags shovill.bam: coverage 63 [pilon] Total Reads: 635, Coverage: 63, minDepth: 16 [pilon] Confirmed 1008 of 1225 bases (82.29%) [pilon] Corrected 5 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_170_length_1225_cov_22.330616:1-1225 [pilon] Processing NODE_300_length_409_cov_1.361111:1-409 [pilon] NODE_300_length_409_cov_1.361111:1-409 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 9, Coverage: 3, 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_300_length_409_cov_1.361111:1-409 [pilon] Processing NODE_247_length_502_cov_0.427822:1-502 [pilon] NODE_113_length_3975_cov_2.471718:1-3975 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 239, Coverage: 8, minDepth: 5 [pilon] Confirmed 3278 of 3975 bases (82.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_113_length_3975_cov_2.471718:1-3975 [pilon] Processing NODE_172_length_1142_cov_6.557297:1-1142 [pilon] NODE_247_length_502_cov_0.427822:1-502 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 31, Coverage: 4, minDepth: 5 [pilon] Confirmed 176 of 502 bases (35.06%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_247_length_502_cov_0.427822:1-502 [pilon] Processing NODE_157_length_1477_cov_1.721239:1-1477 [pilon] NODE_151_length_1514_cov_64.797559:1-1514 log: [pilon] frags shovill.bam: coverage 160 [pilon] Total Reads: 1984, Coverage: 160, minDepth: 40 [pilon] Confirmed 1219 of 1514 bases (80.52%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_151_length_1514_cov_64.797559:1-1514 [pilon] Processing NODE_125_length_2568_cov_1.874132:1-2568 [pilon] NODE_172_length_1142_cov_6.557297:1-1142 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 149, Coverage: 17, minDepth: 5 [pilon] Confirmed 557 of 1142 bases (48.77%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_172_length_1142_cov_6.557297:1-1142 [pilon] Processing NODE_76_length_12462_cov_36.309699:1-12462 [pilon] NODE_157_length_1477_cov_1.721239:1-1477 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 60, Coverage: 5, minDepth: 5 [pilon] Confirmed 839 of 1477 bases (56.80%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_157_length_1477_cov_1.721239:1-1477 [pilon] Processing NODE_33_length_27543_cov_38.672963:1-27543 [pilon] NODE_75_length_12675_cov_39.741278:1-12675 log: [pilon] frags shovill.bam: coverage 115 [pilon] Total Reads: 11283, Coverage: 115, minDepth: 29 [pilon] Confirmed 12110 of 12675 bases (95.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_75_length_12675_cov_39.741278:1-12675 [pilon] Processing NODE_17_length_47986_cov_46.945346:1-47986 [pilon] NODE_84_length_10443_cov_34.274075:1-10443 log: [pilon] frags shovill.bam: coverage 98 [pilon] Total Reads: 8031, Coverage: 98, minDepth: 25 [pilon] Confirmed 10043 of 10443 bases (96.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_84_length_10443_cov_34.274075:1-10443 [pilon] Processing NODE_30_length_31388_cov_36.131672:1-31388 [pilon] NODE_125_length_2568_cov_1.874132:1-2568 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 114, Coverage: 6, minDepth: 5 [pilon] Confirmed 1499 of 2568 bases (58.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_125_length_2568_cov_1.874132:1-2568 [pilon] Processing NODE_180_length_1004_cov_3.565119:1-1004 [pilon] NODE_41_length_23264_cov_36.084864:1-23264 log: [pilon] frags shovill.bam: coverage 105 [pilon] Total Reads: 18903, Coverage: 105, minDepth: 26 [pilon] Confirmed 22686 of 23264 bases (97.52%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_41_length_23264_cov_36.084864:1-23264 [pilon] Processing NODE_39_length_23287_cov_45.632824:1-23287 [pilon] NODE_180_length_1004_cov_3.565119:1-1004 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 89, Coverage: 11, minDepth: 5 [pilon] Confirmed 623 of 1004 bases (62.05%) [pilon] Corrected 2 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_180_length_1004_cov_3.565119:1-1004 [pilon] Processing NODE_12_length_62444_cov_38.225775:1-62444 [pilon] NODE_15_length_49167_cov_45.054500:1-49167 log: [pilon] frags shovill.bam: coverage 132 [pilon] Total Reads: 50340, Coverage: 132, minDepth: 33 [pilon] Confirmed 48697 of 49167 bases (99.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_15_length_49167_cov_45.054500:1-49167 [pilon] Processing NODE_1_length_167507_cov_43.826073:1-167507 [pilon] NODE_47_length_19186_cov_38.512457:1-19186 log: [pilon] frags shovill.bam: coverage 112 [pilon] Total Reads: 16729, Coverage: 112, minDepth: 28 [pilon] Confirmed 17231 of 19186 bases (89.81%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_47_length_19186_cov_38.512457:1-19186 [pilon] Processing NODE_186_length_911_cov_12.203797:1-911 [pilon] NODE_40_length_23270_cov_32.884012:1-23270 log: [pilon] frags shovill.bam: coverage 96 [pilon] Total Reads: 17322, Coverage: 96, minDepth: 24 [pilon] Confirmed 21954 of 23270 bases (94.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_40_length_23270_cov_32.884012:1-23270 [pilon] Processing NODE_82_length_10832_cov_36.249837:1-10832 [pilon] NODE_62_length_15999_cov_43.115695:1-15999 log: [pilon] frags shovill.bam: coverage 126 [pilon] Total Reads: 15558, Coverage: 126, minDepth: 32 [pilon] Confirmed 15632 of 15999 bases (97.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_62_length_15999_cov_43.115695:1-15999 [pilon] Processing NODE_22_length_37870_cov_37.932157:1-37870 [pilon] NODE_10_length_74867_cov_39.030878:1-74867 log: [pilon] frags shovill.bam: coverage 115 [pilon] Total Reads: 66713, Coverage: 115, minDepth: 29 [pilon] Confirmed 73683 of 74867 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_10_length_74867_cov_39.030878:1-74867 [pilon] Processing NODE_240_length_514_cov_1.743003:1-514 [pilon] NODE_186_length_911_cov_12.203797:1-911 log: [pilon] frags shovill.bam: coverage 30 [pilon] Total Reads: 213, Coverage: 30, minDepth: 8 [pilon] Confirmed 646 of 911 bases (70.91%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_186_length_911_cov_12.203797:1-911 [pilon] Processing NODE_61_length_16345_cov_34.207409:1-16345 [pilon] NODE_240_length_514_cov_1.743003:1-514 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 25, Coverage: 5, minDepth: 5 [pilon] Confirmed 257 of 514 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_240_length_514_cov_1.743003:1-514 [pilon] Processing NODE_204_length_734_cov_12.647635:1-734 [pilon] NODE_204_length_734_cov_12.647635:1-734 log: [pilon] frags shovill.bam: coverage 32 [pilon] Total Reads: 181, Coverage: 32, minDepth: 8 [pilon] Confirmed 526 of 734 bases (71.66%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_204_length_734_cov_12.647635:1-734 [pilon] Processing NODE_234_length_537_cov_1.024038:1-537 [pilon] NODE_234_length_537_cov_1.024038:1-537 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 17, Coverage: 4, minDepth: 5 [pilon] Confirmed 243 of 537 bases (45.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_234_length_537_cov_1.024038:1-537 [pilon] Processing NODE_216_length_655_cov_1.485019:1-655 [pilon] NODE_216_length_655_cov_1.485019:1-655 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 17, Coverage: 3, minDepth: 5 [pilon] Confirmed 151 of 655 bases (23.05%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_216_length_655_cov_1.485019:1-655 [pilon] Processing NODE_14_length_49730_cov_42.987361:1-49730 [pilon] NODE_76_length_12462_cov_36.309699:1-12462 log: [pilon] frags shovill.bam: coverage 107 [pilon] Total Reads: 10374, Coverage: 107, minDepth: 27 [pilon] Confirmed 12208 of 12462 bases (97.96%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_76_length_12462_cov_36.309699:1-12462 [pilon] NODE_55_length_17586_cov_39.556542:1-17586 log: [pilon] frags shovill.bam: coverage 115 [pilon] Total Reads: 15649, Coverage: 115, minDepth: 29 [pilon] Confirmed 16524 of 17586 bases (93.96%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_55_length_17586_cov_39.556542:1-17586 [pilon] Processing NODE_289_length_426_cov_1.800000:1-426 [pilon] NODE_289_length_426_cov_1.800000:1-426 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 12, Coverage: 4, minDepth: 5 [pilon] Confirmed 140 of 426 bases (32.86%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_289_length_426_cov_1.800000:1-426 [pilon] Processing NODE_316_length_271_cov_1.226667:1-271 [pilon] NODE_316_length_271_cov_1.226667:1-271 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 23, Coverage: 3, minDepth: 5 [pilon] Confirmed 83 of 271 bases (30.63%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_316_length_271_cov_1.226667:1-271 [pilon] Processing NODE_274_length_445_cov_0.756173:1-445 [pilon] NODE_274_length_445_cov_0.756173:1-445 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, 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_274_length_445_cov_0.756173:1-445 [pilon] Processing NODE_255_length_475_cov_1.700565:1-475 [pilon] NODE_255_length_475_cov_1.700565:1-475 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 19, Coverage: 4, minDepth: 5 [pilon] Confirmed 274 of 475 bases (57.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_255_length_475_cov_1.700565:1-475 [pilon] Processing NODE_163_length_1386_cov_20.388142:1-1386 [pilon] NODE_163_length_1386_cov_20.388142:1-1386 log: [pilon] frags shovill.bam: coverage 53 [pilon] Total Reads: 570, Coverage: 53, minDepth: 13 [pilon] Confirmed 1139 of 1386 bases (82.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_163_length_1386_cov_20.388142:1-1386 [pilon] Processing NODE_189_length_842_cov_14.296810:1-842 [pilon] NODE_189_length_842_cov_14.296810:1-842 log: [pilon] frags shovill.bam: coverage 37 [pilon] Total Reads: 242, Coverage: 37, minDepth: 9 [pilon] Confirmed 537 of 842 bases (63.78%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_189_length_842_cov_14.296810:1-842 [pilon] Processing NODE_120_length_3098_cov_198.760161:1-3098 [pilon] NODE_82_length_10832_cov_36.249837:1-10832 log: [pilon] frags shovill.bam: coverage 105 [pilon] Total Reads: 8839, Coverage: 105, minDepth: 26 [pilon] Confirmed 10134 of 10832 bases (93.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_82_length_10832_cov_36.249837:1-10832 [pilon] Processing NODE_264_length_454_cov_2.369369:1-454 [pilon] NODE_70_length_13439_cov_36.711443:1-13439 log: [pilon] frags shovill.bam: coverage 106 [pilon] Total Reads: 11056, Coverage: 106, minDepth: 27 [pilon] Confirmed 13131 of 13439 bases (97.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_70_length_13439_cov_36.711443:1-13439 [pilon] Processing NODE_213_length_687_cov_5.402827:1-687 [pilon] NODE_23_length_36801_cov_40.309024:1-36801 log: [pilon] frags shovill.bam: coverage 118 [pilon] Total Reads: 33482, Coverage: 118, minDepth: 30 [pilon] Confirmed 35420 of 36801 bases (96.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_23_length_36801_cov_40.309024:1-36801 [pilon] NODE_264_length_454_cov_2.369369:1-454 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 23, Coverage: 6, minDepth: 5 [pilon] Confirmed 266 of 454 bases (58.59%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_263_length_456_cov_1.468657:1-456 [pilon] Finished processing NODE_264_length_454_cov_2.369369:1-454 [pilon] Processing NODE_243_length_511_cov_1.394872:1-511 [pilon] NODE_53_length_18092_cov_43.690891:1-18092 log: [pilon] frags shovill.bam: coverage 128 [pilon] Total Reads: 17962, Coverage: 128, minDepth: 32 [pilon] Confirmed 17799 of 18092 bases (98.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_53_length_18092_cov_43.690891:1-18092 [pilon] Processing NODE_242_length_513_cov_0.290816:1-513 [pilon] NODE_213_length_687_cov_5.402827:1-687 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 69, Coverage: 13, minDepth: 5 [pilon] Confirmed 490 of 687 bases (71.32%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_213_length_687_cov_5.402827:1-687 [pilon] Processing NODE_220_length_629_cov_2.027559:1-629 [pilon] NODE_243_length_511_cov_1.394872:1-511 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 12, Coverage: 3, minDepth: 5 [pilon] Confirmed 110 of 511 bases (21.53%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_243_length_511_cov_1.394872:1-511 [pilon] Processing NODE_260_length_460_cov_1.129794:1-460 [pilon] NODE_263_length_456_cov_1.468657:1-456 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 19, Coverage: 4, minDepth: 5 [pilon] Confirmed 163 of 456 bases (35.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_263_length_456_cov_1.468657:1-456 [pilon] NODE_242_length_513_cov_0.290816:1-513 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 7, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 513 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_242_length_513_cov_0.290816:1-513 [pilon] NODE_260_length_460_cov_1.129794:1-460 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 20, Coverage: 3, minDepth: 5 [pilon] Confirmed 131 of 460 bases (28.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_260_length_460_cov_1.129794:1-460 [pilon] Processing NODE_86_length_9358_cov_43.687561:1-9358 [pilon] NODE_220_length_629_cov_2.027559:1-629 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 25, Coverage: 5, minDepth: 5 [pilon] Confirmed 382 of 629 bases (60.73%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_220_length_629_cov_2.027559:1-629 [pilon] Processing NODE_71_length_13201_cov_48.459862:1-13201 [pilon] NODE_61_length_16345_cov_34.207409:1-16345 log: [pilon] frags shovill.bam: coverage 99 [pilon] Total Reads: 12593, Coverage: 99, minDepth: 25 [pilon] Confirmed 14725 of 16345 bases (90.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_61_length_16345_cov_34.207409:1-16345 [pilon] Processing NODE_280_length_434_cov_1.527157:1-434 [pilon] NODE_52_length_18170_cov_48.514211:1-18170 log: [pilon] frags shovill.bam: coverage 140 [pilon] Total Reads: 19725, Coverage: 140, minDepth: 35 [pilon] Confirmed 17722 of 18170 bases (97.53%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_52_length_18170_cov_48.514211:1-18170 [pilon] Processing NODE_174_length_1117_cov_1.532129:1-1117 [pilon] NODE_280_length_434_cov_1.527157:1-434 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 10, Coverage: 2, minDepth: 5 [pilon] Confirmed 59 of 434 bases (13.59%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_280_length_434_cov_1.527157:1-434 [pilon] Processing NODE_271_length_446_cov_6.775385:1-446 [pilon] NODE_174_length_1117_cov_1.532129:1-1117 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 42, Coverage: 5, minDepth: 5 [pilon] Confirmed 621 of 1117 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_174_length_1117_cov_1.532129:1-1117 [pilon] NODE_271_length_446_cov_6.775385:1-446 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 51, Coverage: 15, minDepth: 5 [pilon] Confirmed 336 of 446 bases (75.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_271_length_446_cov_6.775385:1-446 [pilon] Processing NODE_290_length_424_cov_1.881188:1-424 [pilon] NODE_290_length_424_cov_1.881188:1-424 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 13, Coverage: 2, minDepth: 5 [pilon] Confirmed 80 of 424 bases (18.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_290_length_424_cov_1.881188:1-424 [pilon] Processing NODE_129_length_2268_cov_43.610154:1-2268 [pilon] NODE_33_length_27543_cov_38.672963:1-27543 log: [pilon] frags shovill.bam: coverage 113 [pilon] Total Reads: 23996, Coverage: 113, minDepth: 28 [pilon] Confirmed 27086 of 27543 bases (98.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_33_length_27543_cov_38.672963:1-27543 [pilon] Processing NODE_29_length_31490_cov_38.062769:1-31490 [pilon] Processing NODE_60_length_16898_cov_37.101150:1-16898 [pilon] NODE_31_length_29574_cov_40.616813:1-29574 log: [pilon] frags shovill.bam: coverage 119 [pilon] Total Reads: 27258, Coverage: 119, minDepth: 30 [pilon] Confirmed 27923 of 29574 bases (94.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_31_length_29574_cov_40.616813:1-29574 [pilon] Processing NODE_201_length_740_cov_20.476575:1-740 [pilon] NODE_201_length_740_cov_20.476575:1-740 log: [pilon] frags shovill.bam: coverage 48 [pilon] Total Reads: 275, Coverage: 48, minDepth: 12 [pilon] Confirmed 525 of 740 bases (70.95%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_201_length_740_cov_20.476575:1-740 [pilon] Processing NODE_90_length_8360_cov_38.618764:1-8360 [pilon] NODE_129_length_2268_cov_43.610154:1-2268 log: [pilon] frags shovill.bam: coverage 121 [pilon] Total Reads: 2128, Coverage: 121, minDepth: 30 [pilon] Confirmed 1843 of 2268 bases (81.26%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_129_length_2268_cov_43.610154:1-2268 [pilon] Processing NODE_191_length_834_cov_2.826087:1-834 [pilon] NODE_39_length_23287_cov_45.632824:1-23287 log: [pilon] frags shovill.bam: coverage 133 [pilon] Total Reads: 24031, Coverage: 133, minDepth: 33 [pilon] Confirmed 22472 of 23287 bases (96.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_39_length_23287_cov_45.632824:1-23287 [pilon] Processing NODE_312_length_325_cov_4.544118:1-325 [pilon] NODE_191_length_834_cov_2.826087:1-834 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 46, Coverage: 7, minDepth: 5 [pilon] Confirmed 477 of 834 bases (57.19%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_191_length_834_cov_2.826087:1-834 [pilon] Processing NODE_105_length_5195_cov_41.893575:1-5195 [pilon] NODE_16_length_48541_cov_37.671004:1-48541 log: [pilon] frags shovill.bam: coverage 110 [pilon] Total Reads: 41325, Coverage: 110, minDepth: 28 [pilon] Confirmed 47835 of 48541 bases (98.55%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_16_length_48541_cov_37.671004:1-48541 [pilon] Processing NODE_118_length_3238_cov_2.180622:1-3238 [pilon] NODE_312_length_325_cov_4.544118:1-325 log: [pilon] frags shovill.bam: coverage 35 [pilon] Total Reads: 190, Coverage: 35, minDepth: 9 [pilon] Confirmed 215 of 325 bases (66.15%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_312_length_325_cov_4.544118:1-325 [pilon] NODE_118_length_3238_cov_2.180622:1-3238 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 163, Coverage: 7, minDepth: 5 [pilon] Confirmed 2419 of 3238 bases (74.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_118_length_3238_cov_2.180622:1-3238 [pilon] Processing NODE_103_length_5689_cov_42.655352:1-5689 [pilon] NODE_30_length_31388_cov_36.131672:1-31388 log: [pilon] frags shovill.bam: coverage 106 [pilon] Total Reads: 25650, Coverage: 106, minDepth: 27 [pilon] Confirmed 30801 of 31388 bases (98.13%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_30_length_31388_cov_36.131672:1-31388 [pilon] Processing NODE_169_length_1250_cov_1.516386:1-1250 [pilon] NODE_120_length_3098_cov_198.760161:1-3098 log: [pilon] frags shovill.bam: coverage 543 [pilon] Total Reads: 13712, Coverage: 543, minDepth: 136 [pilon] Confirmed 2989 of 3098 bases (96.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_120_length_3098_cov_198.760161:1-3098 [pilon] NODE_169_length_1250_cov_1.516386:1-1250 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 42, Coverage: 4, minDepth: 5 [pilon] Confirmed 461 of 1250 bases (36.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_169_length_1250_cov_1.516386:1-1250 [pilon] Processing NODE_244_length_507_cov_1.727979:1-507 [pilon] NODE_244_length_507_cov_1.727979:1-507 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 17, Coverage: 4, minDepth: 5 [pilon] Confirmed 168 of 507 bases (33.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_244_length_507_cov_1.727979:1-507 [pilon] Processing NODE_298_length_410_cov_1.574394:1-410 [pilon] NODE_298_length_410_cov_1.574394:1-410 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 130 of 410 bases (31.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_298_length_410_cov_1.574394:1-410 [pilon] Processing NODE_137_length_1864_cov_43.737235:1-1864 [pilon] NODE_13_length_57913_cov_40.487905:1-57913 log: [pilon] frags shovill.bam: coverage 118 [pilon] Total Reads: 52837, Coverage: 118, minDepth: 30 [pilon] Confirmed 57140 of 57913 bases (98.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_13_length_57913_cov_40.487905:1-57913 [pilon] Processing NODE_91_length_8289_cov_37.619246:1-8289 [pilon] Processing NODE_209_length_708_cov_20.228279:1-708 [pilon] NODE_209_length_708_cov_20.228279:1-708 log: [pilon] frags shovill.bam: coverage 52 [pilon] Total Reads: 286, Coverage: 52, minDepth: 13 [pilon] Confirmed 566 of 708 bases (79.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_209_length_708_cov_20.228279:1-708 [pilon] Processing NODE_171_length_1219_cov_2.189435:1-1219 [pilon] NODE_86_length_9358_cov_43.687561:1-9358 log: [pilon] frags shovill.bam: coverage 126 [pilon] Total Reads: 9175, Coverage: 126, minDepth: 32 [pilon] Confirmed 9185 of 9358 bases (98.15%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_86_length_9358_cov_43.687561:1-9358 [pilon] Processing NODE_218_length_646_cov_2.081905:1-646 [pilon] Processing NODE_288_length_428_cov_0.426710:1-428 [pilon] Processing NODE_28_length_32969_cov_47.506941:1-32969 [pilon] NODE_90_length_8360_cov_38.618764:1-8360 log: [pilon] frags shovill.bam: coverage 112 [pilon] Total Reads: 7255, Coverage: 112, minDepth: 28 [pilon] Confirmed 7772 of 8360 bases (92.97%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_90_length_8360_cov_38.618764:1-8360 [pilon] Processing NODE_293_length_422_cov_3.455150:1-422 [pilon] NODE_171_length_1219_cov_2.189435:1-1219 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 55, Coverage: 5, minDepth: 5 [pilon] Confirmed 755 of 1219 bases (61.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_171_length_1219_cov_2.189435:1-1219 [pilon] Processing NODE_135_length_2043_cov_20.566597:1-2043 [pilon] NODE_288_length_428_cov_0.426710:1-428 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 7, Coverage: 1, 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_288_length_428_cov_0.426710:1-428 [pilon] NODE_218_length_646_cov_2.081905:1-646 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 20, Coverage: 4, minDepth: 5 [pilon] Confirmed 308 of 646 bases (47.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_137_length_1864_cov_43.737235:1-1864 log: [pilon] frags shovill.bam: coverage 121 [pilon] Total Reads: 1746, Coverage: 121, minDepth: 30 [pilon] Confirmed 1568 of 1864 bases (84.12%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_137_length_1864_cov_43.737235:1-1864 [pilon] NODE_293_length_422_cov_3.455150:1-422 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 25, Coverage: 7, minDepth: 5 [pilon] Confirmed 267 of 422 bases (63.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_293_length_422_cov_3.455150:1-422 [pilon] Finished processing NODE_218_length_646_cov_2.081905:1-646 [pilon] Processing NODE_3_length_144312_cov_47.836668:1-144312 [pilon] NODE_105_length_5195_cov_41.893575:1-5195 log: [pilon] frags shovill.bam: coverage 118 [pilon] Total Reads: 4820, Coverage: 118, minDepth: 30 [pilon] Confirmed 4860 of 5195 bases (93.55%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_105_length_5195_cov_41.893575:1-5195 [pilon] NODE_135_length_2043_cov_20.566597:1-2043 log: [pilon] frags shovill.bam: coverage 58 [pilon] Total Reads: 922, Coverage: 58, minDepth: 15 [pilon] Confirmed 1580 of 2043 bases (77.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_135_length_2043_cov_20.566597:1-2043 [pilon] NODE_103_length_5689_cov_42.655352:1-5689 log: [pilon] frags shovill.bam: coverage 122 [pilon] Total Reads: 5382, Coverage: 122, minDepth: 31 [pilon] Confirmed 5313 of 5689 bases (93.39%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_103_length_5689_cov_42.655352:1-5689 [pilon] Processing NODE_310_length_402_cov_1.224199:1-402 [pilon] NODE_310_length_402_cov_1.224199:1-402 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 6, Coverage: 1, 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_310_length_402_cov_1.224199:1-402 [pilon] Processing NODE_276_length_444_cov_1.390093:1-444 [pilon] NODE_276_length_444_cov_1.390093:1-444 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 45 of 444 bases (10.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_276_length_444_cov_1.390093:1-444 [pilon] NODE_60_length_16898_cov_37.101150:1-16898 log: [pilon] frags shovill.bam: coverage 108 [pilon] Total Reads: 14075, Coverage: 108, minDepth: 27 [pilon] Confirmed 15525 of 16898 bases (91.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_60_length_16898_cov_37.101150:1-16898 [pilon] Processing NODE_127_length_2461_cov_31.148291:1-2461 [pilon] NODE_71_length_13201_cov_48.459862:1-13201 log: [pilon] frags shovill.bam: coverage 140 [pilon] Total Reads: 14340, Coverage: 140, minDepth: 35 [pilon] Confirmed 12770 of 13201 bases (96.74%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_71_length_13201_cov_48.459862:1-13201 [pilon] NODE_91_length_8289_cov_37.619246:1-8289 log: [pilon] frags shovill.bam: coverage 109 [pilon] Total Reads: 6957, Coverage: 109, minDepth: 27 [pilon] Confirmed 7693 of 8289 bases (92.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_91_length_8289_cov_37.619246:1-8289 [pilon] NODE_127_length_2461_cov_31.148291:1-2461 log: [pilon] frags shovill.bam: coverage 87 [pilon] Total Reads: 1649, Coverage: 87, minDepth: 22 [pilon] Confirmed 2021 of 2461 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_127_length_2461_cov_31.148291:1-2461 [pilon] NODE_22_length_37870_cov_37.932157:1-37870 log: [pilon] frags shovill.bam: coverage 111 [pilon] Total Reads: 32497, Coverage: 111, minDepth: 28 [pilon] Confirmed 37292 of 37870 bases (98.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_22_length_37870_cov_37.932157:1-37870 [pilon] Processing NODE_224_length_603_cov_0.655602:1-603 [pilon] NODE_224_length_603_cov_0.655602:1-603 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 10, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 603 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_224_length_603_cov_0.655602:1-603 [pilon] Processing NODE_309_length_403_cov_1.450355:1-403 [pilon] NODE_309_length_403_cov_1.450355:1-403 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 17, Coverage: 3, minDepth: 5 [pilon] Confirmed 115 of 403 bases (28.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_309_length_403_cov_1.450355:1-403 [pilon] Processing NODE_85_length_9502_cov_35.530860:1-9502 [pilon] NODE_11_length_70956_cov_44.750575:1-70956 log: [pilon] frags shovill.bam: coverage 131 [pilon] Total Reads: 72243, Coverage: 131, minDepth: 33 [pilon] Confirmed 66945 of 70956 bases (94.35%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_11_length_70956_cov_44.750575:1-70956 [pilon] Processing NODE_245_length_505_cov_2.583333:1-505 [pilon] NODE_245_length_505_cov_2.583333:1-505 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 22, Coverage: 6, minDepth: 5 [pilon] Confirmed 296 of 505 bases (58.61%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_245_length_505_cov_2.583333:1-505 [pilon] NODE_14_length_49730_cov_42.987361:1-49730 log: [pilon] frags shovill.bam: coverage 125 [pilon] Total Reads: 48167, Coverage: 125, minDepth: 31 [pilon] Confirmed 48591 of 49730 bases (97.71%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_14_length_49730_cov_42.987361:1-49730 [pilon] Processing NODE_26_length_33295_cov_43.961958:1-33295 [pilon] NODE_85_length_9502_cov_35.530860:1-9502 log: [pilon] frags shovill.bam: coverage 102 [pilon] Total Reads: 7551, Coverage: 102, minDepth: 26 [pilon] Confirmed 8195 of 9502 bases (86.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_85_length_9502_cov_35.530860:1-9502 [pilon] NODE_29_length_31490_cov_38.062769:1-31490 log: [pilon] frags shovill.bam: coverage 111 [pilon] Total Reads: 26935, Coverage: 111, minDepth: 28 [pilon] Confirmed 31128 of 31490 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_29_length_31490_cov_38.062769:1-31490 [pilon] NODE_17_length_47986_cov_46.945346:1-47986 log: [pilon] frags shovill.bam: coverage 138 [pilon] Total Reads: 51298, Coverage: 138, minDepth: 35 [pilon] Confirmed 46615 of 47986 bases (97.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_17_length_47986_cov_46.945346:1-47986 [pilon] Processing NODE_93_length_7768_cov_44.602328:1-7768 [pilon] NODE_9_length_82413_cov_37.298717:1-82413 log: [pilon] frags shovill.bam: coverage 109 [pilon] Total Reads: 69377, Coverage: 109, minDepth: 27 [pilon] Confirmed 81328 of 82413 bases (98.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_9_length_82413_cov_37.298717:1-82413 [pilon] NODE_12_length_62444_cov_38.225775:1-62444 log: [pilon] frags shovill.bam: coverage 112 [pilon] Total Reads: 53972, Coverage: 112, minDepth: 28 [pilon] Confirmed 61046 of 62444 bases (97.76%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_12_length_62444_cov_38.225775:1-62444 [pilon] Processing NODE_58_length_16987_cov_37.402348:1-16987 [pilon] NODE_93_length_7768_cov_44.602328:1-7768 log: [pilon] frags shovill.bam: coverage 128 [pilon] Total Reads: 7720, Coverage: 128, minDepth: 32 [pilon] Confirmed 7269 of 7768 bases (93.58%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_93_length_7768_cov_44.602328:1-7768 [pilon] Processing NODE_123_length_2805_cov_1.891207:1-2805 [pilon] NODE_123_length_2805_cov_1.891207:1-2805 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 144, Coverage: 7, minDepth: 5 [pilon] Confirmed 2048 of 2805 bases (73.01%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_123_length_2805_cov_1.891207:1-2805 [pilon] Processing NODE_215_length_657_cov_2.347015:1-657 [pilon] NODE_5_length_99564_cov_41.069748:1-99564 log: [pilon] frags shovill.bam: coverage 120 [pilon] Total Reads: 92461, Coverage: 120, minDepth: 30 [pilon] Confirmed 97941 of 99564 bases (98.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_5_length_99564_cov_41.069748:1-99564 [pilon] Processing NODE_131_length_2170_cov_41.783309:1-2170 [pilon] NODE_6_length_90772_cov_44.578416:1-90772 log: [pilon] frags shovill.bam: coverage 130 [pilon] Total Reads: 91511, Coverage: 130, minDepth: 33 [pilon] Confirmed 88581 of 90772 bases (97.59%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_6_length_90772_cov_44.578416:1-90772 [pilon] NODE_28_length_32969_cov_47.506941:1-32969 log: [pilon] frags shovill.bam: coverage 138 [pilon] Total Reads: 35547, Coverage: 138, minDepth: 35 [pilon] Confirmed 32087 of 32969 bases (97.32%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_215_length_657_cov_2.347015:1-657 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 31, Coverage: 6, minDepth: 5 [pilon] Confirmed 282 of 657 bases (42.92%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_28_length_32969_cov_47.506941:1-32969 [pilon] Processing NODE_315_length_291_cov_46.382353:1-291 [pilon] Finished processing NODE_215_length_657_cov_2.347015:1-657 [pilon] Processing NODE_308_length_403_cov_1.485816:1-403 [pilon] NODE_315_length_291_cov_46.382353:1-291 log: [pilon] frags shovill.bam: coverage 24 [pilon] Total Reads: 189, Coverage: 24, minDepth: 6 [pilon] Confirmed 276 of 291 bases (94.85%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_315_length_291_cov_46.382353:1-291 [pilon] NODE_308_length_403_cov_1.485816:1-403 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 10, Coverage: 3, minDepth: 5 [pilon] Confirmed 18 of 403 bases (4.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_308_length_403_cov_1.485816:1-403 [pilon] Processing NODE_21_length_41366_cov_48.120839:1-41366 [pilon] NODE_131_length_2170_cov_41.783309:1-2170 log: [pilon] frags shovill.bam: coverage 108 [pilon] Total Reads: 1909, Coverage: 108, minDepth: 27 [pilon] Confirmed 2003 of 2170 bases (92.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_131_length_2170_cov_41.783309:1-2170 [pilon] NODE_7_length_90439_cov_39.840619:1-90439 log: [pilon] frags shovill.bam: coverage 117 [pilon] Total Reads: 81854, Coverage: 117, minDepth: 29 [pilon] Confirmed 80812 of 90439 bases (89.36%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_7_length_90439_cov_39.840619:1-90439 [pilon] Processing NODE_272_length_446_cov_1.526154:1-446 [pilon] NODE_272_length_446_cov_1.526154:1-446 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 13, Coverage: 3, minDepth: 5 [pilon] Confirmed 162 of 446 bases (36.32%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_272_length_446_cov_1.526154:1-446 [pilon] Processing NODE_18_length_46879_cov_37.861778:1-46879 [pilon] NODE_58_length_16987_cov_37.402348:1-16987 log: [pilon] frags shovill.bam: coverage 109 [pilon] Total Reads: 14316, Coverage: 109, minDepth: 27 [pilon] Confirmed 16029 of 16987 bases (94.36%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_58_length_16987_cov_37.402348:1-16987 [pilon] Processing NODE_237_length_533_cov_0.849515:1-533 [pilon] NODE_237_length_533_cov_0.849515:1-533 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 8, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 533 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_237_length_533_cov_0.849515:1-533 [pilon] NODE_8_length_84837_cov_43.408660:1-84837 log: [pilon] frags shovill.bam: coverage 127 [pilon] Total Reads: 83681, Coverage: 127, minDepth: 32 [pilon] Confirmed 83720 of 84837 bases (98.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_8_length_84837_cov_43.408660:1-84837 [pilon] Processing NODE_246_length_505_cov_0.747396:1-505 [pilon] NODE_246_length_505_cov_0.747396:1-505 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 11, Coverage: 2, minDepth: 5 [pilon] Confirmed 101 of 505 bases (20.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_246_length_505_cov_0.747396:1-505 [pilon] NODE_26_length_33295_cov_43.961958:1-33295 log: [pilon] frags shovill.bam: coverage 128 [pilon] Total Reads: 33056, Coverage: 128, minDepth: 32 [pilon] Confirmed 32116 of 33295 bases (96.46%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_26_length_33295_cov_43.961958:1-33295 [pilon] NODE_4_length_133398_cov_40.014841:1-133398 log: [pilon] frags shovill.bam: coverage 117 [pilon] Total Reads: 120800, Coverage: 117, minDepth: 29 [pilon] Confirmed 125755 of 133398 bases (94.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_4_length_133398_cov_40.014841:1-133398 [pilon] Processing NODE_107_length_4855_cov_2.085340:1-4855 [pilon] NODE_107_length_4855_cov_2.085340:1-4855 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 244, Coverage: 6, minDepth: 5 [pilon] Confirmed 3490 of 4855 bases (71.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_107_length_4855_cov_2.085340:1-4855 [pilon] Processing NODE_25_length_34642_cov_39.393268:1-34642 [pilon] NODE_21_length_41366_cov_48.120839:1-41366 log: [pilon] frags shovill.bam: coverage 140 [pilon] Total Reads: 44714, Coverage: 140, minDepth: 35 [pilon] Confirmed 40565 of 41366 bases (98.06%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_21_length_41366_cov_48.120839:1-41366 [pilon] NODE_18_length_46879_cov_37.861778:1-46879 log: [pilon] frags shovill.bam: coverage 111 [pilon] Total Reads: 40381, Coverage: 111, minDepth: 28 [pilon] Confirmed 44578 of 46879 bases (95.09%) [pilon] Corrected 3 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_18_length_46879_cov_37.861778:1-46879 [pilon] NODE_25_length_34642_cov_39.393268:1-34642 log: [pilon] frags shovill.bam: coverage 115 [pilon] Total Reads: 30772, Coverage: 115, minDepth: 29 [pilon] Confirmed 33885 of 34642 bases (97.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_25_length_34642_cov_39.393268:1-34642 [pilon] NODE_2_length_150434_cov_42.254070:1-150434 log: [pilon] frags shovill.bam: coverage 124 [pilon] Total Reads: 144529, Coverage: 124, minDepth: 31 [pilon] Confirmed 145717 of 150434 bases (96.86%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_2_length_150434_cov_42.254070:1-150434 [pilon] Processing NODE_179_length_1042_cov_1.646037:1-1042 [pilon] NODE_179_length_1042_cov_1.646037:1-1042 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 42, Coverage: 5, minDepth: 5 [pilon] Confirmed 543 of 1042 bases (52.11%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_179_length_1042_cov_1.646037:1-1042 [pilon] NODE_1_length_167507_cov_43.826073:1-167507 log: [pilon] frags shovill.bam: coverage 128 [pilon] Total Reads: 166556, Coverage: 128, minDepth: 32 [pilon] Confirmed 165078 of 167507 bases (98.55%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_1_length_167507_cov_43.826073:1-167507 [pilon] Processing NODE_79_length_12029_cov_40.301562:1-12029 [pilon] NODE_79_length_12029_cov_40.301562:1-12029 log: [pilon] frags shovill.bam: coverage 117 [pilon] Total Reads: 10879, Coverage: 117, minDepth: 29 [pilon] Confirmed 11630 of 12029 bases (96.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_79_length_12029_cov_40.301562:1-12029 [pilon] NODE_3_length_144312_cov_47.836668:1-144312 log: [pilon] frags shovill.bam: coverage 141 [pilon] Total Reads: 157077, Coverage: 141, minDepth: 35 [pilon] Confirmed 140630 of 144312 bases (97.45%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_3_length_144312_cov_47.836668:1-144312 [pilon] Writing NODE_1_length_167507_cov_43.826073:1-167507 changes to pilon.changes [pilon] Writing updated NODE_1_length_167507_cov_43.826073_pilon to pilon.fasta [pilon] Writing NODE_2_length_150434_cov_42.254070:1-150434 changes to pilon.changes [pilon] Writing updated NODE_2_length_150434_cov_42.254070_pilon to pilon.fasta [pilon] Writing NODE_3_length_144312_cov_47.836668:1-144312 changes to pilon.changes [pilon] Writing updated NODE_3_length_144312_cov_47.836668_pilon to pilon.fasta [pilon] Writing NODE_4_length_133398_cov_40.014841:1-133398 changes to pilon.changes [pilon] Writing updated NODE_4_length_133398_cov_40.014841_pilon to pilon.fasta [pilon] Writing NODE_5_length_99564_cov_41.069748:1-99564 changes to pilon.changes [pilon] Writing updated NODE_5_length_99564_cov_41.069748_pilon to pilon.fasta [pilon] Writing NODE_6_length_90772_cov_44.578416:1-90772 changes to pilon.changes [pilon] Writing updated NODE_6_length_90772_cov_44.578416_pilon to pilon.fasta [pilon] Writing NODE_7_length_90439_cov_39.840619:1-90439 changes to pilon.changes [pilon] Writing updated NODE_7_length_90439_cov_39.840619_pilon to pilon.fasta [pilon] Writing NODE_8_length_84837_cov_43.408660:1-84837 changes to pilon.changes [pilon] Writing updated NODE_8_length_84837_cov_43.408660_pilon to pilon.fasta [pilon] Writing NODE_9_length_82413_cov_37.298717:1-82413 changes to pilon.changes [pilon] Writing updated NODE_9_length_82413_cov_37.298717_pilon to pilon.fasta [pilon] Writing NODE_10_length_74867_cov_39.030878:1-74867 changes to pilon.changes [pilon] Writing updated NODE_10_length_74867_cov_39.030878_pilon to pilon.fasta [pilon] Writing NODE_11_length_70956_cov_44.750575:1-70956 changes to pilon.changes [pilon] Writing updated NODE_11_length_70956_cov_44.750575_pilon to pilon.fasta [pilon] Writing NODE_12_length_62444_cov_38.225775:1-62444 changes to pilon.changes [pilon] Writing updated NODE_12_length_62444_cov_38.225775_pilon to pilon.fasta [pilon] Writing NODE_13_length_57913_cov_40.487905:1-57913 changes to pilon.changes [pilon] Writing updated NODE_13_length_57913_cov_40.487905_pilon to pilon.fasta [pilon] Writing NODE_14_length_49730_cov_42.987361:1-49730 changes to pilon.changes [pilon] Writing updated NODE_14_length_49730_cov_42.987361_pilon to pilon.fasta [pilon] Writing NODE_15_length_49167_cov_45.054500:1-49167 changes to pilon.changes [pilon] Writing updated NODE_15_length_49167_cov_45.054500_pilon to pilon.fasta [pilon] Writing NODE_16_length_48541_cov_37.671004:1-48541 changes to pilon.changes [pilon] Writing updated NODE_16_length_48541_cov_37.671004_pilon to pilon.fasta [pilon] Writing NODE_17_length_47986_cov_46.945346:1-47986 changes to pilon.changes [pilon] Writing updated NODE_17_length_47986_cov_46.945346_pilon to pilon.fasta [pilon] Writing NODE_18_length_46879_cov_37.861778:1-46879 changes to pilon.changes [pilon] Writing updated NODE_18_length_46879_cov_37.861778_pilon to pilon.fasta [pilon] Writing NODE_19_length_41453_cov_36.788856:1-41453 changes to pilon.changes [pilon] Writing updated NODE_19_length_41453_cov_36.788856_pilon to pilon.fasta [pilon] Writing NODE_20_length_41428_cov_45.772024:1-41428 changes to pilon.changes [pilon] Writing updated NODE_20_length_41428_cov_45.772024_pilon to pilon.fasta [pilon] Writing NODE_21_length_41366_cov_48.120839:1-41366 changes to pilon.changes [pilon] Writing updated NODE_21_length_41366_cov_48.120839_pilon to pilon.fasta [pilon] Writing NODE_22_length_37870_cov_37.932157:1-37870 changes to pilon.changes [pilon] Writing updated NODE_22_length_37870_cov_37.932157_pilon to pilon.fasta [pilon] Writing NODE_23_length_36801_cov_40.309024:1-36801 changes to pilon.changes [pilon] Writing updated NODE_23_length_36801_cov_40.309024_pilon to pilon.fasta [pilon] Writing NODE_24_length_36041_cov_44.520184:1-36041 changes to pilon.changes [pilon] Writing updated NODE_24_length_36041_cov_44.520184_pilon to pilon.fasta [pilon] Writing NODE_25_length_34642_cov_39.393268:1-34642 changes to pilon.changes [pilon] Writing updated NODE_25_length_34642_cov_39.393268_pilon to pilon.fasta [pilon] Writing NODE_26_length_33295_cov_43.961958:1-33295 changes to pilon.changes [pilon] Writing updated NODE_26_length_33295_cov_43.961958_pilon to pilon.fasta [pilon] Writing NODE_27_length_33277_cov_41.556129:1-33277 changes to pilon.changes [pilon] Writing updated NODE_27_length_33277_cov_41.556129_pilon to pilon.fasta [pilon] Writing NODE_28_length_32969_cov_47.506941:1-32969 changes to pilon.changes [pilon] Writing updated NODE_28_length_32969_cov_47.506941_pilon to pilon.fasta [pilon] Writing NODE_29_length_31490_cov_38.062769:1-31490 changes to pilon.changes [pilon] Writing updated NODE_29_length_31490_cov_38.062769_pilon to pilon.fasta [pilon] Writing NODE_30_length_31388_cov_36.131672:1-31388 changes to pilon.changes [pilon] Writing updated NODE_30_length_31388_cov_36.131672_pilon to pilon.fasta [pilon] Writing NODE_31_length_29574_cov_40.616813:1-29574 changes to pilon.changes [pilon] Writing updated NODE_31_length_29574_cov_40.616813_pilon to pilon.fasta [pilon] Writing NODE_32_length_29053_cov_40.728916:1-29053 changes to pilon.changes [pilon] Writing updated NODE_32_length_29053_cov_40.728916_pilon to pilon.fasta [pilon] Writing NODE_33_length_27543_cov_38.672963:1-27543 changes to pilon.changes [pilon] Writing updated NODE_33_length_27543_cov_38.672963_pilon to pilon.fasta [pilon] Writing NODE_34_length_26453_cov_47.303395:1-26453 changes to pilon.changes [pilon] Writing updated NODE_34_length_26453_cov_47.303395_pilon to pilon.fasta [pilon] Writing NODE_35_length_26304_cov_39.876714:1-26304 changes to pilon.changes [pilon] Writing updated NODE_35_length_26304_cov_39.876714_pilon to pilon.fasta [pilon] Writing NODE_36_length_25575_cov_40.748723:1-25575 changes to pilon.changes [pilon] Writing updated NODE_36_length_25575_cov_40.748723_pilon to pilon.fasta [pilon] Writing NODE_37_length_23923_cov_36.924460:1-23923 changes to pilon.changes [pilon] Writing updated NODE_37_length_23923_cov_36.924460_pilon to pilon.fasta [pilon] Writing NODE_38_length_23860_cov_36.975441:1-23860 changes to pilon.changes [pilon] Writing updated NODE_38_length_23860_cov_36.975441_pilon to pilon.fasta [pilon] Writing NODE_39_length_23287_cov_45.632824:1-23287 changes to pilon.changes [pilon] Writing updated NODE_39_length_23287_cov_45.632824_pilon to pilon.fasta [pilon] Writing NODE_40_length_23270_cov_32.884012:1-23270 changes to pilon.changes [pilon] Writing updated NODE_40_length_23270_cov_32.884012_pilon to pilon.fasta [pilon] Writing NODE_41_length_23264_cov_36.084864:1-23264 changes to pilon.changes [pilon] Writing updated NODE_41_length_23264_cov_36.084864_pilon to pilon.fasta [pilon] Writing NODE_42_length_22534_cov_41.322893:1-22534 changes to pilon.changes [pilon] Writing updated NODE_42_length_22534_cov_41.322893_pilon to pilon.fasta [pilon] Writing NODE_43_length_22353_cov_33.611956:1-22353 changes to pilon.changes [pilon] Writing updated NODE_43_length_22353_cov_33.611956_pilon to pilon.fasta [pilon] Writing NODE_44_length_21667_cov_38.379421:1-21667 changes to pilon.changes [pilon] Writing updated NODE_44_length_21667_cov_38.379421_pilon to pilon.fasta [pilon] Writing NODE_45_length_21051_cov_36.297993:1-21051 changes to pilon.changes [pilon] Writing updated NODE_45_length_21051_cov_36.297993_pilon to pilon.fasta [pilon] Writing NODE_46_length_20176_cov_42.376215:1-20176 changes to pilon.changes [pilon] Writing updated NODE_46_length_20176_cov_42.376215_pilon to pilon.fasta [pilon] Writing NODE_47_length_19186_cov_38.512457:1-19186 changes to pilon.changes [pilon] Writing updated NODE_47_length_19186_cov_38.512457_pilon to pilon.fasta [pilon] Writing NODE_48_length_19096_cov_39.760843:1-19096 changes to pilon.changes [pilon] Writing updated NODE_48_length_19096_cov_39.760843_pilon to pilon.fasta [pilon] Writing NODE_49_length_19027_cov_38.216175:1-19027 changes to pilon.changes [pilon] Writing updated NODE_49_length_19027_cov_38.216175_pilon to pilon.fasta [pilon] Writing NODE_50_length_18596_cov_41.225548:1-18596 changes to pilon.changes [pilon] Writing updated NODE_50_length_18596_cov_41.225548_pilon to pilon.fasta [pilon] Writing NODE_51_length_18377_cov_32.977651:1-18377 changes to pilon.changes [pilon] Writing updated NODE_51_length_18377_cov_32.977651_pilon to pilon.fasta [pilon] Writing NODE_52_length_18170_cov_48.514211:1-18170 changes to pilon.changes [pilon] Writing updated NODE_52_length_18170_cov_48.514211_pilon to pilon.fasta [pilon] Writing NODE_53_length_18092_cov_43.690891:1-18092 changes to pilon.changes [pilon] Writing updated NODE_53_length_18092_cov_43.690891_pilon to pilon.fasta [pilon] Writing NODE_54_length_17669_cov_37.209369:1-17669 changes to pilon.changes [pilon] Writing updated NODE_54_length_17669_cov_37.209369_pilon to pilon.fasta [pilon] Writing NODE_55_length_17586_cov_39.556542:1-17586 changes to pilon.changes [pilon] Writing updated NODE_55_length_17586_cov_39.556542_pilon to pilon.fasta [pilon] Writing NODE_56_length_17394_cov_36.424130:1-17394 changes to pilon.changes [pilon] Writing updated NODE_56_length_17394_cov_36.424130_pilon to pilon.fasta [pilon] Writing NODE_57_length_17095_cov_38.169495:1-17095 changes to pilon.changes [pilon] Writing updated NODE_57_length_17095_cov_38.169495_pilon to pilon.fasta [pilon] Writing NODE_58_length_16987_cov_37.402348:1-16987 changes to pilon.changes [pilon] Writing updated NODE_58_length_16987_cov_37.402348_pilon to pilon.fasta [pilon] Writing NODE_59_length_16928_cov_38.076992:1-16928 changes to pilon.changes [pilon] Writing updated NODE_59_length_16928_cov_38.076992_pilon to pilon.fasta [pilon] Writing NODE_60_length_16898_cov_37.101150:1-16898 changes to pilon.changes [pilon] Writing updated NODE_60_length_16898_cov_37.101150_pilon to pilon.fasta [pilon] Writing NODE_61_length_16345_cov_34.207409:1-16345 changes to pilon.changes [pilon] Writing updated NODE_61_length_16345_cov_34.207409_pilon to pilon.fasta [pilon] Writing NODE_62_length_15999_cov_43.115695:1-15999 changes to pilon.changes [pilon] Writing updated NODE_62_length_15999_cov_43.115695_pilon to pilon.fasta [pilon] Writing NODE_63_length_15678_cov_35.801247:1-15678 changes to pilon.changes [pilon] Writing updated NODE_63_length_15678_cov_35.801247_pilon to pilon.fasta [pilon] Writing NODE_64_length_15088_cov_36.671210:1-15088 changes to pilon.changes [pilon] Writing updated NODE_64_length_15088_cov_36.671210_pilon to pilon.fasta [pilon] Writing NODE_65_length_15071_cov_38.313712:1-15071 changes to pilon.changes [pilon] Writing updated NODE_65_length_15071_cov_38.313712_pilon to pilon.fasta [pilon] Writing NODE_66_length_14434_cov_28.647942:1-14434 changes to pilon.changes [pilon] Writing updated NODE_66_length_14434_cov_28.647942_pilon to pilon.fasta [pilon] Writing NODE_67_length_14047_cov_40.839006:1-14047 changes to pilon.changes [pilon] Writing updated NODE_67_length_14047_cov_40.839006_pilon to pilon.fasta [pilon] Writing NODE_68_length_13793_cov_24.897674:1-13793 changes to pilon.changes [pilon] Writing updated NODE_68_length_13793_cov_24.897674_pilon to pilon.fasta [pilon] Writing NODE_69_length_13513_cov_41.553689:1-13513 changes to pilon.changes [pilon] Writing updated NODE_69_length_13513_cov_41.553689_pilon to pilon.fasta [pilon] Writing NODE_70_length_13439_cov_36.711443:1-13439 changes to pilon.changes [pilon] Writing updated NODE_70_length_13439_cov_36.711443_pilon to pilon.fasta [pilon] Writing NODE_71_length_13201_cov_48.459862:1-13201 changes to pilon.changes [pilon] Writing updated NODE_71_length_13201_cov_48.459862_pilon to pilon.fasta [pilon] Writing NODE_72_length_13073_cov_38.653490:1-13073 changes to pilon.changes [pilon] Writing updated NODE_72_length_13073_cov_38.653490_pilon to pilon.fasta [pilon] Writing NODE_73_length_13039_cov_36.896346:1-13039 changes to pilon.changes [pilon] Writing updated NODE_73_length_13039_cov_36.896346_pilon to pilon.fasta [pilon] Writing NODE_74_length_12953_cov_39.385910:1-12953 changes to pilon.changes [pilon] Writing updated NODE_74_length_12953_cov_39.385910_pilon to pilon.fasta [pilon] Writing NODE_75_length_12675_cov_39.741278:1-12675 changes to pilon.changes [pilon] Writing updated NODE_75_length_12675_cov_39.741278_pilon to pilon.fasta [pilon] Writing NODE_76_length_12462_cov_36.309699:1-12462 changes to pilon.changes [pilon] Writing updated NODE_76_length_12462_cov_36.309699_pilon to pilon.fasta [pilon] Writing NODE_77_length_12325_cov_36.597345:1-12325 changes to pilon.changes [pilon] Writing updated NODE_77_length_12325_cov_36.597345_pilon to pilon.fasta [pilon] Writing NODE_78_length_12257_cov_37.023401:1-12257 changes to pilon.changes [pilon] Writing updated NODE_78_length_12257_cov_37.023401_pilon to pilon.fasta [pilon] Writing NODE_79_length_12029_cov_40.301562:1-12029 changes to pilon.changes [pilon] Writing updated NODE_79_length_12029_cov_40.301562_pilon to pilon.fasta [pilon] Writing NODE_80_length_11679_cov_34.443416:1-11679 changes to pilon.changes [pilon] Writing updated NODE_80_length_11679_cov_34.443416_pilon to pilon.fasta [pilon] Writing NODE_81_length_11385_cov_43.908825:1-11385 changes to pilon.changes [pilon] Writing updated NODE_81_length_11385_cov_43.908825_pilon to pilon.fasta [pilon] Writing NODE_82_length_10832_cov_36.249837:1-10832 changes to pilon.changes [pilon] Writing updated NODE_82_length_10832_cov_36.249837_pilon to pilon.fasta [pilon] Writing NODE_83_length_10794_cov_38.301883:1-10794 changes to pilon.changes [pilon] Writing updated NODE_83_length_10794_cov_38.301883_pilon to pilon.fasta [pilon] Writing NODE_84_length_10443_cov_34.274075:1-10443 changes to pilon.changes [pilon] Writing updated NODE_84_length_10443_cov_34.274075_pilon to pilon.fasta [pilon] Writing NODE_85_length_9502_cov_35.530860:1-9502 changes to pilon.changes [pilon] Writing updated NODE_85_length_9502_cov_35.530860_pilon to pilon.fasta [pilon] Writing NODE_86_length_9358_cov_43.687561:1-9358 changes to pilon.changes [pilon] Writing updated NODE_86_length_9358_cov_43.687561_pilon to pilon.fasta [pilon] Writing NODE_87_length_9100_cov_36.575120:1-9100 changes to pilon.changes [pilon] Writing updated NODE_87_length_9100_cov_36.575120_pilon to pilon.fasta [pilon] Writing NODE_88_length_8685_cov_34.595983:1-8685 changes to pilon.changes [pilon] Writing updated NODE_88_length_8685_cov_34.595983_pilon to pilon.fasta [pilon] Writing NODE_89_length_8407_cov_42.825609:1-8407 changes to pilon.changes [pilon] Writing updated NODE_89_length_8407_cov_42.825609_pilon to pilon.fasta [pilon] Writing NODE_90_length_8360_cov_38.618764:1-8360 changes to pilon.changes [pilon] Writing updated NODE_90_length_8360_cov_38.618764_pilon to pilon.fasta [pilon] Writing NODE_91_length_8289_cov_37.619246:1-8289 changes to pilon.changes [pilon] Writing updated NODE_91_length_8289_cov_37.619246_pilon to pilon.fasta [pilon] Writing NODE_92_length_8239_cov_1.768662:1-8239 changes to pilon.changes [pilon] Writing updated NODE_92_length_8239_cov_1.768662_pilon to pilon.fasta [pilon] Writing NODE_93_length_7768_cov_44.602328:1-7768 changes to pilon.changes [pilon] Writing updated NODE_93_length_7768_cov_44.602328_pilon to pilon.fasta [pilon] Writing NODE_94_length_7522_cov_33.198757:1-7522 changes to pilon.changes [pilon] Writing updated NODE_94_length_7522_cov_33.198757_pilon to pilon.fasta [pilon] Writing NODE_95_length_7246_cov_34.194947:1-7246 changes to pilon.changes [pilon] Writing updated NODE_95_length_7246_cov_34.194947_pilon to pilon.fasta [pilon] Writing NODE_96_length_7198_cov_34.948848:1-7198 changes to pilon.changes [pilon] Writing updated NODE_96_length_7198_cov_34.948848_pilon to pilon.fasta [pilon] Writing NODE_97_length_6544_cov_25.393430:1-6544 changes to pilon.changes [pilon] Writing updated NODE_97_length_6544_cov_25.393430_pilon to pilon.fasta [pilon] Writing NODE_98_length_6490_cov_35.739677:1-6490 changes to pilon.changes [pilon] Writing updated NODE_98_length_6490_cov_35.739677_pilon to pilon.fasta [pilon] Writing NODE_99_length_6136_cov_11.217456:1-6136 changes to pilon.changes [pilon] Writing updated NODE_99_length_6136_cov_11.217456_pilon to pilon.fasta [pilon] Writing NODE_100_length_6000_cov_33.545161:1-6000 changes to pilon.changes [pilon] Writing updated NODE_100_length_6000_cov_33.545161_pilon to pilon.fasta [pilon] Writing NODE_101_length_5869_cov_30.946590:1-5869 changes to pilon.changes [pilon] Writing updated NODE_101_length_5869_cov_30.946590_pilon to pilon.fasta [pilon] Writing NODE_102_length_5740_cov_1.908525:1-5740 changes to pilon.changes [pilon] Writing updated NODE_102_length_5740_cov_1.908525_pilon to pilon.fasta [pilon] Writing NODE_103_length_5689_cov_42.655352:1-5689 changes to pilon.changes [pilon] Writing updated NODE_103_length_5689_cov_42.655352_pilon to pilon.fasta [pilon] Writing NODE_104_length_5293_cov_35.713264:1-5293 changes to pilon.changes [pilon] Writing updated NODE_104_length_5293_cov_35.713264_pilon to pilon.fasta [pilon] Writing NODE_105_length_5195_cov_41.893575:1-5195 changes to pilon.changes [pilon] Writing updated NODE_105_length_5195_cov_41.893575_pilon to pilon.fasta [pilon] Writing NODE_106_length_5037_cov_2.420464:1-5037 changes to pilon.changes [pilon] Writing updated NODE_106_length_5037_cov_2.420464_pilon to pilon.fasta [pilon] Writing NODE_107_length_4855_cov_2.085340:1-4855 changes to pilon.changes [pilon] Writing updated NODE_107_length_4855_cov_2.085340_pilon to pilon.fasta [pilon] Writing NODE_108_length_4343_cov_30.180483:1-4343 changes to pilon.changes [pilon] Writing updated NODE_108_length_4343_cov_30.180483_pilon to pilon.fasta [pilon] Writing NODE_109_length_4271_cov_1.896867:1-4271 changes to pilon.changes [pilon] Writing updated NODE_109_length_4271_cov_1.896867_pilon to pilon.fasta [pilon] Writing NODE_110_length_4234_cov_27.448578:1-4234 changes to pilon.changes [pilon] Writing updated NODE_110_length_4234_cov_27.448578_pilon to pilon.fasta [pilon] Writing NODE_111_length_4214_cov_1.432690:1-4214 changes to pilon.changes [pilon] Writing updated NODE_111_length_4214_cov_1.432690_pilon to pilon.fasta [pilon] Writing NODE_112_length_4192_cov_38.119135:1-4192 changes to pilon.changes [pilon] Writing updated NODE_112_length_4192_cov_38.119135_pilon to pilon.fasta [pilon] Writing NODE_113_length_3975_cov_2.471718:1-3975 changes to pilon.changes [pilon] Writing updated NODE_113_length_3975_cov_2.471718_pilon to pilon.fasta [pilon] Writing NODE_114_length_3679_cov_1.526419:1-3679 changes to pilon.changes [pilon] Writing updated NODE_114_length_3679_cov_1.526419_pilon to pilon.fasta [pilon] Writing NODE_115_length_3492_cov_1.908039:1-3492 changes to pilon.changes [pilon] Writing updated NODE_115_length_3492_cov_1.908039_pilon to pilon.fasta [pilon] Writing NODE_116_length_3490_cov_41.778569:1-3490 changes to pilon.changes [pilon] Writing updated NODE_116_length_3490_cov_41.778569_pilon to pilon.fasta [pilon] Writing NODE_117_length_3364_cov_32.188714:1-3364 changes to pilon.changes [pilon] Writing updated NODE_117_length_3364_cov_32.188714_pilon to pilon.fasta [pilon] Writing NODE_118_length_3238_cov_2.180622:1-3238 changes to pilon.changes [pilon] Writing updated NODE_118_length_3238_cov_2.180622_pilon to pilon.fasta [pilon] Writing NODE_119_length_3200_cov_31.319909:1-3200 changes to pilon.changes [pilon] Writing updated NODE_119_length_3200_cov_31.319909_pilon to pilon.fasta [pilon] Writing NODE_120_length_3098_cov_198.760161:1-3098 changes to pilon.changes [pilon] Writing updated NODE_120_length_3098_cov_198.760161_pilon to pilon.fasta [pilon] Writing NODE_121_length_2947_cov_1.952229:1-2947 changes to pilon.changes [pilon] Writing updated NODE_121_length_2947_cov_1.952229_pilon to pilon.fasta [pilon] Writing NODE_122_length_2913_cov_44.440544:1-2913 changes to pilon.changes [pilon] Writing updated NODE_122_length_2913_cov_44.440544_pilon to pilon.fasta [pilon] Writing NODE_123_length_2805_cov_1.891207:1-2805 changes to pilon.changes [pilon] Writing updated NODE_123_length_2805_cov_1.891207_pilon to pilon.fasta [pilon] Writing NODE_124_length_2683_cov_2.113193:1-2683 changes to pilon.changes [pilon] Writing updated NODE_124_length_2683_cov_2.113193_pilon to pilon.fasta [pilon] Writing NODE_125_length_2568_cov_1.874132:1-2568 changes to pilon.changes [pilon] Writing updated NODE_125_length_2568_cov_1.874132_pilon to pilon.fasta [pilon] Writing NODE_126_length_2517_cov_9.371452:1-2517 changes to pilon.changes [pilon] Writing updated NODE_126_length_2517_cov_9.371452_pilon to pilon.fasta [pilon] Writing NODE_127_length_2461_cov_31.148291:1-2461 changes to pilon.changes [pilon] Writing updated NODE_127_length_2461_cov_31.148291_pilon to pilon.fasta [pilon] Writing NODE_128_length_2271_cov_4.622791:1-2271 changes to pilon.changes [pilon] Writing updated NODE_128_length_2271_cov_4.622791_pilon to pilon.fasta [pilon] Writing NODE_129_length_2268_cov_43.610154:1-2268 changes to pilon.changes [pilon] Writing updated NODE_129_length_2268_cov_43.610154_pilon to pilon.fasta [pilon] Writing NODE_130_length_2221_cov_2.081905:1-2221 changes to pilon.changes [pilon] Writing updated NODE_130_length_2221_cov_2.081905_pilon to pilon.fasta [pilon] Writing NODE_131_length_2170_cov_41.783309:1-2170 changes to pilon.changes [pilon] Writing updated NODE_131_length_2170_cov_41.783309_pilon to pilon.fasta [pilon] Writing NODE_132_length_2120_cov_1.625813:1-2120 changes to pilon.changes [pilon] Writing updated NODE_132_length_2120_cov_1.625813_pilon to pilon.fasta [pilon] Writing NODE_133_length_2086_cov_6.873282:1-2086 changes to pilon.changes [pilon] Writing updated NODE_133_length_2086_cov_6.873282_pilon to pilon.fasta [pilon] Writing NODE_134_length_2066_cov_23.597429:1-2066 changes to pilon.changes [pilon] Writing updated NODE_134_length_2066_cov_23.597429_pilon to pilon.fasta [pilon] Writing NODE_135_length_2043_cov_20.566597:1-2043 changes to pilon.changes [pilon] Writing updated NODE_135_length_2043_cov_20.566597_pilon to pilon.fasta [pilon] Writing NODE_136_length_1934_cov_1.483177:1-1934 changes to pilon.changes [pilon] Writing updated NODE_136_length_1934_cov_1.483177_pilon to pilon.fasta [pilon] Writing NODE_137_length_1864_cov_43.737235:1-1864 changes to pilon.changes [pilon] Writing updated NODE_137_length_1864_cov_43.737235_pilon to pilon.fasta [pilon] Writing NODE_138_length_1845_cov_8.606729:1-1845 changes to pilon.changes [pilon] Writing updated NODE_138_length_1845_cov_8.606729_pilon to pilon.fasta [pilon] Writing NODE_139_length_1840_cov_34.005817:1-1840 changes to pilon.changes [pilon] Writing updated NODE_139_length_1840_cov_34.005817_pilon to pilon.fasta [pilon] Writing NODE_140_length_1791_cov_26.069461:1-1791 changes to pilon.changes [pilon] Writing updated NODE_140_length_1791_cov_26.069461_pilon to pilon.fasta [pilon] Writing NODE_141_length_1740_cov_14.904880:1-1740 changes to pilon.changes [pilon] Writing updated NODE_141_length_1740_cov_14.904880_pilon to pilon.fasta [pilon] Writing NODE_142_length_1702_cov_36.578748:1-1702 changes to pilon.changes [pilon] Writing updated NODE_142_length_1702_cov_36.578748_pilon to pilon.fasta [pilon] Writing NODE_143_length_1673_cov_2.508376:1-1673 changes to pilon.changes [pilon] Writing updated NODE_143_length_1673_cov_2.508376_pilon to pilon.fasta [pilon] Writing NODE_144_length_1663_cov_18.050584:1-1663 changes to pilon.changes [pilon] Writing updated NODE_144_length_1663_cov_18.050584_pilon to pilon.fasta [pilon] Writing NODE_145_length_1623_cov_19.392144:1-1623 changes to pilon.changes [pilon] Writing updated NODE_145_length_1623_cov_19.392144_pilon to pilon.fasta [pilon] Writing NODE_146_length_1620_cov_13.585724:1-1620 changes to pilon.changes [pilon] Writing updated NODE_146_length_1620_cov_13.585724_pilon to pilon.fasta [pilon] Writing NODE_147_length_1600_cov_5.146045:1-1600 changes to pilon.changes [pilon] Writing updated NODE_147_length_1600_cov_5.146045_pilon to pilon.fasta [pilon] Writing NODE_148_length_1585_cov_21.817623:1-1585 changes to pilon.changes [pilon] Writing updated NODE_148_length_1585_cov_21.817623_pilon to pilon.fasta [pilon] Writing NODE_149_length_1554_cov_34.883461:1-1554 changes to pilon.changes [pilon] Writing updated NODE_149_length_1554_cov_34.883461_pilon to pilon.fasta [pilon] Writing NODE_150_length_1543_cov_1.447257:1-1543 changes to pilon.changes [pilon] Writing updated NODE_150_length_1543_cov_1.447257_pilon to pilon.fasta [pilon] Writing NODE_151_length_1514_cov_64.797559:1-1514 changes to pilon.changes [pilon] Writing updated NODE_151_length_1514_cov_64.797559_pilon to pilon.fasta [pilon] Writing NODE_152_length_1507_cov_1.676046:1-1507 changes to pilon.changes [pilon] Writing updated NODE_152_length_1507_cov_1.676046_pilon to pilon.fasta [pilon] Writing NODE_153_length_1489_cov_1.625000:1-1489 changes to pilon.changes [pilon] Writing updated NODE_153_length_1489_cov_1.625000_pilon to pilon.fasta [pilon] Writing NODE_154_length_1487_cov_71.467057:1-1487 changes to pilon.changes [pilon] Writing updated NODE_154_length_1487_cov_71.467057_pilon to pilon.fasta [pilon] Writing NODE_155_length_1485_cov_26.517595:1-1485 changes to pilon.changes [pilon] Writing updated NODE_155_length_1485_cov_26.517595_pilon to pilon.fasta [pilon] Writing NODE_156_length_1479_cov_1.826215:1-1479 changes to pilon.changes [pilon] Writing updated NODE_156_length_1479_cov_1.826215_pilon to pilon.fasta [pilon] Writing NODE_157_length_1477_cov_1.721239:1-1477 changes to pilon.changes [pilon] Writing updated NODE_157_length_1477_cov_1.721239_pilon to pilon.fasta [pilon] Writing NODE_158_length_1474_cov_1.725055:1-1474 changes to pilon.changes [pilon] Writing updated NODE_158_length_1474_cov_1.725055_pilon to pilon.fasta [pilon] Writing NODE_159_length_1447_cov_1.398190:1-1447 changes to pilon.changes [pilon] Writing updated NODE_159_length_1447_cov_1.398190_pilon to pilon.fasta [pilon] Writing NODE_160_length_1413_cov_1.832817:1-1413 changes to pilon.changes [pilon] Writing updated NODE_160_length_1413_cov_1.832817_pilon to pilon.fasta [pilon] Writing NODE_161_length_1406_cov_3.118288:1-1406 changes to pilon.changes [pilon] Writing updated NODE_161_length_1406_cov_3.118288_pilon to pilon.fasta [pilon] Writing NODE_162_length_1398_cov_1.983555:1-1398 changes to pilon.changes [pilon] Writing updated NODE_162_length_1398_cov_1.983555_pilon to pilon.fasta [pilon] Writing NODE_163_length_1386_cov_20.388142:1-1386 changes to pilon.changes [pilon] Writing updated NODE_163_length_1386_cov_20.388142_pilon to pilon.fasta [pilon] Writing NODE_164_length_1384_cov_30.623911:1-1384 changes to pilon.changes [pilon] Writing updated NODE_164_length_1384_cov_30.623911_pilon to pilon.fasta [pilon] Writing NODE_165_length_1325_cov_38.567276:1-1325 changes to pilon.changes [pilon] Writing updated NODE_165_length_1325_cov_38.567276_pilon to pilon.fasta [pilon] Writing NODE_166_length_1309_cov_16.159933:1-1309 changes to pilon.changes [pilon] Writing updated NODE_166_length_1309_cov_16.159933_pilon to pilon.fasta [pilon] Writing NODE_167_length_1288_cov_1.916881:1-1288 changes to pilon.changes [pilon] Writing updated NODE_167_length_1288_cov_1.916881_pilon to pilon.fasta [pilon] Writing NODE_168_length_1284_cov_1.371453:1-1284 changes to pilon.changes [pilon] Writing updated NODE_168_length_1284_cov_1.371453_pilon to pilon.fasta [pilon] Writing NODE_169_length_1250_cov_1.516386:1-1250 changes to pilon.changes [pilon] Writing updated NODE_169_length_1250_cov_1.516386_pilon to pilon.fasta [pilon] Writing NODE_170_length_1225_cov_22.330616:1-1225 changes to pilon.changes [pilon] Writing updated NODE_170_length_1225_cov_22.330616_pilon to pilon.fasta [pilon] Writing NODE_171_length_1219_cov_2.189435:1-1219 changes to pilon.changes [pilon] Writing updated NODE_171_length_1219_cov_2.189435_pilon to pilon.fasta [pilon] Writing NODE_172_length_1142_cov_6.557297:1-1142 changes to pilon.changes [pilon] Writing updated NODE_172_length_1142_cov_6.557297_pilon to pilon.fasta [pilon] Writing NODE_173_length_1120_cov_29.476476:1-1120 changes to pilon.changes [pilon] Writing updated NODE_173_length_1120_cov_29.476476_pilon to pilon.fasta [pilon] Writing NODE_174_length_1117_cov_1.532129:1-1117 changes to pilon.changes [pilon] Writing updated NODE_174_length_1117_cov_1.532129_pilon to pilon.fasta [pilon] Writing NODE_175_length_1110_cov_1.882710:1-1110 changes to pilon.changes [pilon] Writing updated NODE_175_length_1110_cov_1.882710_pilon to pilon.fasta [pilon] Writing NODE_176_length_1105_cov_1.231707:1-1105 changes to pilon.changes [pilon] Writing updated NODE_176_length_1105_cov_1.231707_pilon to pilon.fasta [pilon] Writing NODE_177_length_1098_cov_0.805527:1-1098 changes to pilon.changes [pilon] Writing updated NODE_177_length_1098_cov_0.805527_pilon to pilon.fasta [pilon] Writing NODE_178_length_1082_cov_1.150884:1-1082 changes to pilon.changes [pilon] Writing updated NODE_178_length_1082_cov_1.150884_pilon to pilon.fasta [pilon] Writing NODE_179_length_1042_cov_1.646037:1-1042 changes to pilon.changes [pilon] Writing updated NODE_179_length_1042_cov_1.646037_pilon to pilon.fasta [pilon] Writing NODE_180_length_1004_cov_3.565119:1-1004 changes to pilon.changes [pilon] Writing updated NODE_180_length_1004_cov_3.565119_pilon to pilon.fasta [pilon] Writing NODE_181_length_980_cov_1.408615:1-980 changes to pilon.changes [pilon] Writing updated NODE_181_length_980_cov_1.408615_pilon to pilon.fasta [pilon] Writing NODE_182_length_959_cov_32.090692:1-959 changes to pilon.changes [pilon] Writing updated NODE_182_length_959_cov_32.090692_pilon to pilon.fasta [pilon] Writing NODE_183_length_957_cov_1.834928:1-957 changes to pilon.changes [pilon] Writing updated NODE_183_length_957_cov_1.834928_pilon to pilon.fasta [pilon] Writing NODE_184_length_930_cov_7.402967:1-930 changes to pilon.changes [pilon] Writing updated NODE_184_length_930_cov_7.402967_pilon to pilon.fasta [pilon] Writing NODE_185_length_926_cov_27.334161:1-926 changes to pilon.changes [pilon] Writing updated NODE_185_length_926_cov_27.334161_pilon to pilon.fasta [pilon] Writing NODE_186_length_911_cov_12.203797:1-911 changes to pilon.changes [pilon] Writing updated NODE_186_length_911_cov_12.203797_pilon to pilon.fasta [pilon] Writing NODE_187_length_895_cov_2.182171:1-895 changes to pilon.changes [pilon] Writing updated NODE_187_length_895_cov_2.182171_pilon to pilon.fasta [pilon] Writing NODE_188_length_895_cov_1.788114:1-895 changes to pilon.changes [pilon] Writing updated NODE_188_length_895_cov_1.788114_pilon to pilon.fasta [pilon] Writing NODE_189_length_842_cov_14.296810:1-842 changes to pilon.changes [pilon] Writing updated NODE_189_length_842_cov_14.296810_pilon to pilon.fasta [pilon] Writing NODE_190_length_837_cov_1.180168:1-837 changes to pilon.changes [pilon] Writing updated NODE_190_length_837_cov_1.180168_pilon to pilon.fasta [pilon] Writing NODE_191_length_834_cov_2.826087:1-834 changes to pilon.changes [pilon] Writing updated NODE_191_length_834_cov_2.826087_pilon to pilon.fasta [pilon] Writing NODE_192_length_816_cov_0.981295:1-816 changes to pilon.changes [pilon] Writing updated NODE_192_length_816_cov_0.981295_pilon to pilon.fasta [pilon] Writing NODE_193_length_805_cov_1.698830:1-805 changes to pilon.changes [pilon] Writing updated NODE_193_length_805_cov_1.698830_pilon to pilon.fasta [pilon] Writing NODE_194_length_790_cov_1.804185:1-790 changes to pilon.changes [pilon] Writing updated NODE_194_length_790_cov_1.804185_pilon to pilon.fasta [pilon] Writing NODE_195_length_788_cov_19.280360:1-788 changes to pilon.changes [pilon] Writing updated NODE_195_length_788_cov_19.280360_pilon to pilon.fasta [pilon] Writing NODE_196_length_787_cov_22.267267:1-787 changes to pilon.changes [pilon] Writing updated NODE_196_length_787_cov_22.267267_pilon to pilon.fasta [pilon] Writing NODE_197_length_778_cov_56.852359:1-778 changes to pilon.changes [pilon] Writing updated NODE_197_length_778_cov_56.852359_pilon to pilon.fasta [pilon] Writing NODE_198_length_770_cov_1.665639:1-770 changes to pilon.changes [pilon] Writing updated NODE_198_length_770_cov_1.665639_pilon to pilon.fasta [pilon] Writing NODE_199_length_758_cov_1.469388:1-758 changes to pilon.changes [pilon] Writing updated NODE_199_length_758_cov_1.469388_pilon to pilon.fasta [pilon] Writing NODE_200_length_741_cov_1.825806:1-741 changes to pilon.changes [pilon] Writing updated NODE_200_length_741_cov_1.825806_pilon to pilon.fasta [pilon] Writing NODE_201_length_740_cov_20.476575:1-740 changes to pilon.changes [pilon] Writing updated NODE_201_length_740_cov_20.476575_pilon to pilon.fasta [pilon] Writing NODE_202_length_740_cov_2.513732:1-740 changes to pilon.changes [pilon] Writing updated NODE_202_length_740_cov_2.513732_pilon to pilon.fasta [pilon] Writing NODE_203_length_735_cov_24.827362:1-735 changes to pilon.changes [pilon] Writing updated NODE_203_length_735_cov_24.827362_pilon to pilon.fasta [pilon] Writing NODE_204_length_734_cov_12.647635:1-734 changes to pilon.changes [pilon] Writing updated NODE_204_length_734_cov_12.647635_pilon to pilon.fasta [pilon] Writing NODE_205_length_734_cov_1.396411:1-734 changes to pilon.changes [pilon] Writing updated NODE_205_length_734_cov_1.396411_pilon to pilon.fasta [pilon] Writing NODE_206_length_725_cov_1.622517:1-725 changes to pilon.changes [pilon] Writing updated NODE_206_length_725_cov_1.622517_pilon to pilon.fasta [pilon] Writing NODE_207_length_710_cov_17.456706:1-710 changes to pilon.changes [pilon] Writing updated NODE_207_length_710_cov_17.456706_pilon to pilon.fasta [pilon] Writing NODE_208_length_710_cov_1.478778:1-710 changes to pilon.changes [pilon] Writing updated NODE_208_length_710_cov_1.478778_pilon to pilon.fasta [pilon] Writing NODE_209_length_708_cov_20.228279:1-708 changes to pilon.changes [pilon] Writing updated NODE_209_length_708_cov_20.228279_pilon to pilon.fasta [pilon] Writing NODE_210_length_701_cov_1.636207:1-701 changes to pilon.changes [pilon] Writing updated NODE_210_length_701_cov_1.636207_pilon to pilon.fasta [pilon] Writing NODE_211_length_700_cov_4.773748:1-700 changes to pilon.changes [pilon] Writing updated NODE_211_length_700_cov_4.773748_pilon to pilon.fasta [pilon] Writing NODE_212_length_688_cov_0.857143:1-688 changes to pilon.changes [pilon] Writing updated NODE_212_length_688_cov_0.857143_pilon to pilon.fasta [pilon] Writing NODE_213_length_687_cov_5.402827:1-687 changes to pilon.changes [pilon] Writing updated NODE_213_length_687_cov_5.402827_pilon to pilon.fasta [pilon] Writing NODE_214_length_665_cov_1.400735:1-665 changes to pilon.changes [pilon] Writing updated NODE_214_length_665_cov_1.400735_pilon to pilon.fasta [pilon] Writing NODE_215_length_657_cov_2.347015:1-657 changes to pilon.changes [pilon] Writing updated NODE_215_length_657_cov_2.347015_pilon to pilon.fasta [pilon] Writing NODE_216_length_655_cov_1.485019:1-655 changes to pilon.changes [pilon] Writing updated NODE_216_length_655_cov_1.485019_pilon to pilon.fasta [pilon] Writing NODE_217_length_652_cov_1.653484:1-652 changes to pilon.changes [pilon] Writing updated NODE_217_length_652_cov_1.653484_pilon to pilon.fasta [pilon] Writing NODE_218_length_646_cov_2.081905:1-646 changes to pilon.changes [pilon] Writing updated NODE_218_length_646_cov_2.081905_pilon to pilon.fasta [pilon] Writing NODE_219_length_641_cov_1.178846:1-641 changes to pilon.changes [pilon] Writing updated NODE_219_length_641_cov_1.178846_pilon to pilon.fasta [pilon] Writing NODE_220_length_629_cov_2.027559:1-629 changes to pilon.changes [pilon] Writing updated NODE_220_length_629_cov_2.027559_pilon to pilon.fasta [pilon] Writing NODE_221_length_623_cov_0.635458:1-623 changes to pilon.changes [pilon] Writing updated NODE_221_length_623_cov_0.635458_pilon to pilon.fasta [pilon] Writing NODE_222_length_615_cov_1.943320:1-615 changes to pilon.changes [pilon] Writing updated NODE_222_length_615_cov_1.943320_pilon to pilon.fasta [pilon] Writing NODE_223_length_611_cov_2.104082:1-611 changes to pilon.changes [pilon] Writing updated NODE_223_length_611_cov_2.104082_pilon to pilon.fasta [pilon] Writing NODE_224_length_603_cov_0.655602:1-603 changes to pilon.changes [pilon] Writing updated NODE_224_length_603_cov_0.655602_pilon to pilon.fasta [pilon] Writing NODE_225_length_584_cov_2.481641:1-584 changes to pilon.changes [pilon] Writing updated NODE_225_length_584_cov_2.481641_pilon to pilon.fasta [pilon] Writing NODE_226_length_577_cov_2.717105:1-577 changes to pilon.changes [pilon] Writing updated NODE_226_length_577_cov_2.717105_pilon to pilon.fasta [pilon] Writing NODE_227_length_576_cov_3.404396:1-576 changes to pilon.changes [pilon] Writing updated NODE_227_length_576_cov_3.404396_pilon to pilon.fasta [pilon] Writing NODE_228_length_572_cov_0.647450:1-572 changes to pilon.changes [pilon] Writing updated NODE_228_length_572_cov_0.647450_pilon to pilon.fasta [pilon] Writing NODE_229_length_567_cov_9.645740:1-567 changes to pilon.changes [pilon] Writing updated NODE_229_length_567_cov_9.645740_pilon to pilon.fasta [pilon] Writing NODE_230_length_563_cov_15.149321:1-563 changes to pilon.changes [pilon] Writing updated NODE_230_length_563_cov_15.149321_pilon to pilon.fasta [pilon] Writing NODE_231_length_549_cov_0.665888:1-549 changes to pilon.changes [pilon] Writing updated NODE_231_length_549_cov_0.665888_pilon to pilon.fasta [pilon] Writing NODE_232_length_547_cov_3.507042:1-547 changes to pilon.changes [pilon] Writing updated NODE_232_length_547_cov_3.507042_pilon to pilon.fasta [pilon] Writing NODE_233_length_542_cov_1.501188:1-542 changes to pilon.changes [pilon] Writing updated NODE_233_length_542_cov_1.501188_pilon to pilon.fasta [pilon] Writing NODE_234_length_537_cov_1.024038:1-537 changes to pilon.changes [pilon] Writing updated NODE_234_length_537_cov_1.024038_pilon to pilon.fasta [pilon] Writing NODE_235_length_536_cov_1.260241:1-536 changes to pilon.changes [pilon] Writing updated NODE_235_length_536_cov_1.260241_pilon to pilon.fasta [pilon] Writing NODE_236_length_534_cov_4.273608:1-534 changes to pilon.changes [pilon] Writing updated NODE_236_length_534_cov_4.273608_pilon to pilon.fasta [pilon] Writing NODE_237_length_533_cov_0.849515:1-533 changes to pilon.changes [pilon] Writing updated NODE_237_length_533_cov_0.849515_pilon to pilon.fasta [pilon] Writing NODE_238_length_525_cov_1.534653:1-525 changes to pilon.changes [pilon] Writing updated NODE_238_length_525_cov_1.534653_pilon to pilon.fasta [pilon] Writing NODE_239_length_523_cov_2.708955:1-523 changes to pilon.changes [pilon] Writing updated NODE_239_length_523_cov_2.708955_pilon to pilon.fasta [pilon] Writing NODE_240_length_514_cov_1.743003:1-514 changes to pilon.changes [pilon] Writing updated NODE_240_length_514_cov_1.743003_pilon to pilon.fasta [pilon] Writing NODE_241_length_513_cov_2.926020:1-513 changes to pilon.changes [pilon] Writing updated NODE_241_length_513_cov_2.926020_pilon to pilon.fasta [pilon] Writing NODE_242_length_513_cov_0.290816:1-513 changes to pilon.changes [pilon] Writing updated NODE_242_length_513_cov_0.290816_pilon to pilon.fasta [pilon] Writing NODE_243_length_511_cov_1.394872:1-511 changes to pilon.changes [pilon] Writing updated NODE_243_length_511_cov_1.394872_pilon to pilon.fasta [pilon] Writing NODE_244_length_507_cov_1.727979:1-507 changes to pilon.changes [pilon] Writing updated NODE_244_length_507_cov_1.727979_pilon to pilon.fasta [pilon] Writing NODE_245_length_505_cov_2.583333:1-505 changes to pilon.changes [pilon] Writing updated NODE_245_length_505_cov_2.583333_pilon to pilon.fasta [pilon] Writing NODE_246_length_505_cov_0.747396:1-505 changes to pilon.changes [pilon] Writing updated NODE_246_length_505_cov_0.747396_pilon to pilon.fasta [pilon] Writing NODE_247_length_502_cov_0.427822:1-502 changes to pilon.changes [pilon] Writing updated NODE_247_length_502_cov_0.427822_pilon to pilon.fasta [pilon] Writing NODE_248_length_500_cov_2.189974:1-500 changes to pilon.changes [pilon] Writing updated NODE_248_length_500_cov_2.189974_pilon to pilon.fasta [pilon] Writing NODE_249_length_496_cov_8.280000:1-496 changes to pilon.changes [pilon] Writing updated NODE_249_length_496_cov_8.280000_pilon to pilon.fasta [pilon] Writing NODE_250_length_496_cov_2.618667:1-496 changes to pilon.changes [pilon] Writing updated NODE_250_length_496_cov_2.618667_pilon to pilon.fasta [pilon] Writing NODE_251_length_484_cov_1.528926:1-484 changes to pilon.changes [pilon] Writing updated NODE_251_length_484_cov_1.528926_pilon to pilon.fasta [pilon] Writing NODE_252_length_483_cov_2.870166:1-483 changes to pilon.changes [pilon] Writing updated NODE_252_length_483_cov_2.870166_pilon to pilon.fasta [pilon] Writing NODE_253_length_480_cov_1.350975:1-480 changes to pilon.changes [pilon] Writing updated NODE_253_length_480_cov_1.350975_pilon to pilon.fasta [pilon] Writing NODE_254_length_476_cov_1.118310:1-476 changes to pilon.changes [pilon] Writing updated NODE_254_length_476_cov_1.118310_pilon to pilon.fasta [pilon] Writing NODE_255_length_475_cov_1.700565:1-475 changes to pilon.changes [pilon] Writing updated NODE_255_length_475_cov_1.700565_pilon to pilon.fasta [pilon] Writing NODE_256_length_471_cov_3.342857:1-471 changes to pilon.changes [pilon] Writing updated NODE_256_length_471_cov_3.342857_pilon to pilon.fasta [pilon] Writing NODE_257_length_468_cov_2.553314:1-468 changes to pilon.changes [pilon] Writing updated NODE_257_length_468_cov_2.553314_pilon to pilon.fasta [pilon] Writing NODE_258_length_467_cov_1.783237:1-467 changes to pilon.changes [pilon] Writing updated NODE_258_length_467_cov_1.783237_pilon to pilon.fasta [pilon] Writing NODE_259_length_460_cov_6.507375:1-460 changes to pilon.changes [pilon] Writing updated NODE_259_length_460_cov_6.507375_pilon to pilon.fasta [pilon] Writing NODE_260_length_460_cov_1.129794:1-460 changes to pilon.changes [pilon] Writing updated NODE_260_length_460_cov_1.129794_pilon to pilon.fasta [pilon] Writing NODE_261_length_459_cov_15.896450:1-459 changes to pilon.changes [pilon] Writing updated NODE_261_length_459_cov_15.896450_pilon to pilon.fasta [pilon] Writing NODE_262_length_459_cov_1.721893:1-459 changes to pilon.changes [pilon] Writing updated NODE_262_length_459_cov_1.721893_pilon to pilon.fasta [pilon] Writing NODE_263_length_456_cov_1.468657:1-456 changes to pilon.changes [pilon] Writing updated NODE_263_length_456_cov_1.468657_pilon to pilon.fasta [pilon] Writing NODE_264_length_454_cov_2.369369:1-454 changes to pilon.changes [pilon] Writing updated NODE_264_length_454_cov_2.369369_pilon to pilon.fasta [pilon] Writing NODE_265_length_454_cov_1.372372:1-454 changes to pilon.changes [pilon] Writing updated NODE_265_length_454_cov_1.372372_pilon to pilon.fasta [pilon] Writing NODE_266_length_453_cov_1.512048:1-453 changes to pilon.changes [pilon] Writing updated NODE_266_length_453_cov_1.512048_pilon to pilon.fasta [pilon] Writing NODE_267_length_453_cov_0.322289:1-453 changes to pilon.changes [pilon] Writing updated NODE_267_length_453_cov_0.322289_pilon to pilon.fasta [pilon] Writing NODE_268_length_449_cov_2.899390:1-449 changes to pilon.changes [pilon] Writing updated NODE_268_length_449_cov_2.899390_pilon to pilon.fasta [pilon] Writing NODE_269_length_447_cov_1.340491:1-447 changes to pilon.changes [pilon] Writing updated NODE_269_length_447_cov_1.340491_pilon to pilon.fasta [pilon] Writing NODE_270_length_447_cov_1.107362:1-447 changes to pilon.changes [pilon] Writing updated NODE_270_length_447_cov_1.107362_pilon to pilon.fasta [pilon] Writing NODE_271_length_446_cov_6.775385:1-446 changes to pilon.changes [pilon] Writing updated NODE_271_length_446_cov_6.775385_pilon to pilon.fasta [pilon] Writing NODE_272_length_446_cov_1.526154:1-446 changes to pilon.changes [pilon] Writing updated NODE_272_length_446_cov_1.526154_pilon to pilon.fasta [pilon] Writing NODE_273_length_445_cov_1.691358:1-445 changes to pilon.changes [pilon] Writing updated NODE_273_length_445_cov_1.691358_pilon to pilon.fasta [pilon] Writing NODE_274_length_445_cov_0.756173:1-445 changes to pilon.changes [pilon] Writing updated NODE_274_length_445_cov_0.756173_pilon to pilon.fasta [pilon] Writing NODE_275_length_444_cov_2.814241:1-444 changes to pilon.changes [pilon] Writing updated NODE_275_length_444_cov_2.814241_pilon to pilon.fasta [pilon] Writing NODE_276_length_444_cov_1.390093:1-444 changes to pilon.changes [pilon] Writing updated NODE_276_length_444_cov_1.390093_pilon to pilon.fasta [pilon] Writing NODE_277_length_436_cov_1.923810:1-436 changes to pilon.changes [pilon] Writing updated NODE_277_length_436_cov_1.923810_pilon to pilon.fasta [pilon] Writing NODE_278_length_435_cov_1.515924:1-435 changes to pilon.changes [pilon] Writing updated NODE_278_length_435_cov_1.515924_pilon to pilon.fasta [pilon] Writing NODE_279_length_434_cov_1.840256:1-434 changes to pilon.changes [pilon] Writing updated NODE_279_length_434_cov_1.840256_pilon to pilon.fasta [pilon] Writing NODE_280_length_434_cov_1.527157:1-434 changes to pilon.changes [pilon] Writing updated NODE_280_length_434_cov_1.527157_pilon to pilon.fasta [pilon] Writing NODE_281_length_434_cov_1.376997:1-434 changes to pilon.changes [pilon] Writing updated NODE_281_length_434_cov_1.376997_pilon to pilon.fasta [pilon] Writing NODE_282_length_432_cov_1.221865:1-432 changes to pilon.changes [pilon] Writing updated NODE_282_length_432_cov_1.221865_pilon to pilon.fasta [pilon] Writing NODE_283_length_430_cov_2.116505:1-430 changes to pilon.changes [pilon] Writing updated NODE_283_length_430_cov_2.116505_pilon to pilon.fasta [pilon] Writing NODE_284_length_429_cov_3.376623:1-429 changes to pilon.changes [pilon] Writing updated NODE_284_length_429_cov_3.376623_pilon to pilon.fasta [pilon] Writing NODE_285_length_429_cov_2.103896:1-429 changes to pilon.changes [pilon] Writing updated NODE_285_length_429_cov_2.103896_pilon to pilon.fasta [pilon] Writing NODE_286_length_428_cov_2.368078:1-428 changes to pilon.changes [pilon] Writing updated NODE_286_length_428_cov_2.368078_pilon to pilon.fasta [pilon] Writing NODE_287_length_428_cov_1.342020:1-428 changes to pilon.changes [pilon] Writing updated NODE_287_length_428_cov_1.342020_pilon to pilon.fasta [pilon] Writing NODE_288_length_428_cov_0.426710:1-428 changes to pilon.changes [pilon] Writing updated NODE_288_length_428_cov_0.426710_pilon to pilon.fasta [pilon] Writing NODE_289_length_426_cov_1.800000:1-426 changes to pilon.changes [pilon] Writing updated NODE_289_length_426_cov_1.800000_pilon to pilon.fasta [pilon] Writing NODE_290_length_424_cov_1.881188:1-424 changes to pilon.changes [pilon] Writing updated NODE_290_length_424_cov_1.881188_pilon to pilon.fasta [pilon] Writing NODE_291_length_424_cov_1.293729:1-424 changes to pilon.changes [pilon] Writing updated NODE_291_length_424_cov_1.293729_pilon to pilon.fasta [pilon] Writing NODE_292_length_424_cov_1.227723:1-424 changes to pilon.changes [pilon] Writing updated NODE_292_length_424_cov_1.227723_pilon to pilon.fasta [pilon] Writing NODE_293_length_422_cov_3.455150:1-422 changes to pilon.changes [pilon] Writing updated NODE_293_length_422_cov_3.455150_pilon to pilon.fasta [pilon] Writing NODE_294_length_421_cov_6.890000:1-421 changes to pilon.changes [pilon] Writing updated NODE_294_length_421_cov_6.890000_pilon to pilon.fasta [pilon] Writing NODE_295_length_415_cov_0.965986:1-415 changes to pilon.changes [pilon] Writing updated NODE_295_length_415_cov_0.965986_pilon to pilon.fasta [pilon] Writing NODE_296_length_413_cov_1.171233:1-413 changes to pilon.changes [pilon] Writing updated NODE_296_length_413_cov_1.171233_pilon to pilon.fasta [pilon] Writing NODE_297_length_413_cov_0.671233:1-413 changes to pilon.changes [pilon] Writing updated NODE_297_length_413_cov_0.671233_pilon to pilon.fasta [pilon] Writing NODE_298_length_410_cov_1.574394:1-410 changes to pilon.changes [pilon] Writing updated NODE_298_length_410_cov_1.574394_pilon to pilon.fasta [pilon] Writing NODE_299_length_410_cov_1.228374:1-410 changes to pilon.changes [pilon] Writing updated NODE_299_length_410_cov_1.228374_pilon to pilon.fasta [pilon] Writing NODE_300_length_409_cov_1.361111:1-409 changes to pilon.changes [pilon] Writing updated NODE_300_length_409_cov_1.361111_pilon to pilon.fasta [pilon] Writing NODE_301_length_408_cov_1.414634:1-408 changes to pilon.changes [pilon] Writing updated NODE_301_length_408_cov_1.414634_pilon to pilon.fasta [pilon] Writing NODE_302_length_406_cov_1.091228:1-406 changes to pilon.changes [pilon] Writing updated NODE_302_length_406_cov_1.091228_pilon to pilon.fasta [pilon] Writing NODE_303_length_405_cov_2.049296:1-405 changes to pilon.changes [pilon] Writing updated NODE_303_length_405_cov_2.049296_pilon to pilon.fasta [pilon] Writing NODE_304_length_405_cov_0.947183:1-405 changes to pilon.changes [pilon] Writing updated NODE_304_length_405_cov_0.947183_pilon to pilon.fasta [pilon] Writing NODE_305_length_404_cov_1.374558:1-404 changes to pilon.changes [pilon] Writing updated NODE_305_length_404_cov_1.374558_pilon to pilon.fasta [pilon] Writing NODE_306_length_404_cov_0.749117:1-404 changes to pilon.changes [pilon] Writing updated NODE_306_length_404_cov_0.749117_pilon to pilon.fasta [pilon] Writing NODE_307_length_403_cov_17.588652:1-403 changes to pilon.changes [pilon] Writing updated NODE_307_length_403_cov_17.588652_pilon to pilon.fasta [pilon] Writing NODE_308_length_403_cov_1.485816:1-403 changes to pilon.changes [pilon] Writing updated NODE_308_length_403_cov_1.485816_pilon to pilon.fasta [pilon] Writing NODE_309_length_403_cov_1.450355:1-403 changes to pilon.changes [pilon] Writing updated NODE_309_length_403_cov_1.450355_pilon to pilon.fasta [pilon] Writing NODE_310_length_402_cov_1.224199:1-402 changes to pilon.changes [pilon] Writing updated NODE_310_length_402_cov_1.224199_pilon to pilon.fasta [pilon] Writing NODE_311_length_347_cov_96.057522:1-347 changes to pilon.changes [pilon] Writing updated NODE_311_length_347_cov_96.057522_pilon to pilon.fasta [pilon] Writing NODE_312_length_325_cov_4.544118:1-325 changes to pilon.changes [pilon] Writing updated NODE_312_length_325_cov_4.544118_pilon to pilon.fasta [pilon] Writing NODE_313_length_325_cov_1.862745:1-325 changes to pilon.changes [pilon] Writing updated NODE_313_length_325_cov_1.862745_pilon to pilon.fasta [pilon] Writing NODE_314_length_320_cov_7.663317:1-320 changes to pilon.changes [pilon] Writing updated NODE_314_length_320_cov_7.663317_pilon to pilon.fasta [pilon] Writing NODE_315_length_291_cov_46.382353:1-291 changes to pilon.changes [pilon] Writing updated NODE_315_length_291_cov_46.382353_pilon to pilon.fasta [pilon] Writing NODE_316_length_271_cov_1.226667:1-271 changes to pilon.changes [pilon] Writing updated NODE_316_length_271_cov_1.226667_pilon to pilon.fasta [pilon] Writing NODE_317_length_243_cov_148.475410:1-243 changes to pilon.changes [pilon] Writing updated NODE_317_length_243_cov_148.475410_pilon to pilon.fasta [pilon] Writing NODE_318_length_240_cov_47.428571:1-240 changes to pilon.changes [pilon] Writing updated NODE_318_length_240_cov_47.428571_pilon to pilon.fasta [pilon] Writing NODE_319_length_233_cov_54.169643:1-233 changes to pilon.changes [pilon] Writing updated NODE_319_length_233_cov_54.169643_pilon to pilon.fasta [pilon] Writing NODE_320_length_131_cov_150.500000:1-131 changes to pilon.changes [pilon] Writing updated NODE_320_length_131_cov_150.500000_pilon to pilon.fasta [pilon] Writing NODE_321_length_122_cov_2116.000000:1-122 changes to pilon.changes [pilon] Writing updated NODE_321_length_122_cov_2116.000000_pilon to pilon.fasta [pilon] Mean frags coverage: 113 [pilon] Mean total coverage: 113 [shovill] Repaired 28 contigs from spades.fasta at 44 positions. [shovill] Removing low coverage contig (< 2 x): NODE_92_length_8239_cov_1.768662_pilon [shovill] Removing low coverage contig (< 2 x): NODE_102_length_5740_cov_1.908525_pilon [shovill] Removing low coverage contig (< 2 x): NODE_109_length_4271_cov_1.896867_pilon [shovill] Removing low coverage contig (< 2 x): NODE_111_length_4214_cov_1.432690_pilon [shovill] Removing low coverage contig (< 2 x): NODE_114_length_3679_cov_1.526419_pilon [shovill] Removing low coverage contig (< 2 x): NODE_115_length_3492_cov_1.908039_pilon [shovill] Removing low coverage contig (< 2 x): NODE_121_length_2947_cov_1.952229_pilon [shovill] Removing low coverage contig (< 2 x): NODE_123_length_2805_cov_1.891207_pilon [shovill] Removing low coverage contig (< 2 x): NODE_125_length_2568_cov_1.874132_pilon [shovill] Removing low coverage contig (< 2 x): NODE_132_length_2120_cov_1.625813_pilon [shovill] Removing low coverage contig (< 2 x): NODE_136_length_1934_cov_1.483177_pilon [shovill] Removing low coverage contig (< 2 x): NODE_150_length_1543_cov_1.447257_pilon [shovill] Removing low coverage contig (< 2 x): NODE_152_length_1507_cov_1.676046_pilon [shovill] Removing low coverage contig (< 2 x): NODE_153_length_1489_cov_1.625000_pilon [shovill] Removing low coverage contig (< 2 x): NODE_156_length_1479_cov_1.826215_pilon [shovill] Removing low coverage contig (< 2 x): NODE_157_length_1477_cov_1.721239_pilon [shovill] Removing low coverage contig (< 2 x): NODE_158_length_1474_cov_1.725055_pilon [shovill] Removing low coverage contig (< 2 x): NODE_159_length_1447_cov_1.398190_pilon [shovill] Removing low coverage contig (< 2 x): NODE_160_length_1413_cov_1.832817_pilon [shovill] Removing low coverage contig (< 2 x): NODE_162_length_1398_cov_1.983555_pilon [shovill] Removing low coverage contig (< 2 x): NODE_167_length_1288_cov_1.916881_pilon [shovill] Removing low coverage contig (< 2 x): NODE_168_length_1284_cov_1.371453_pilon [shovill] Removing low coverage contig (< 2 x): NODE_169_length_1250_cov_1.516386_pilon [shovill] Removing low coverage contig (< 2 x): NODE_174_length_1117_cov_1.532129_pilon [shovill] Removing low coverage contig (< 2 x): NODE_175_length_1110_cov_1.882710_pilon [shovill] Removing low coverage contig (< 2 x): NODE_176_length_1105_cov_1.231707_pilon [shovill] Removing low coverage contig (< 2 x): NODE_177_length_1098_cov_0.805527_pilon [shovill] Removing low coverage contig (< 2 x): NODE_178_length_1082_cov_1.150884_pilon [shovill] Removing low coverage contig (< 2 x): NODE_179_length_1042_cov_1.646037_pilon [shovill] Removing low coverage contig (< 2 x): NODE_181_length_980_cov_1.408615_pilon [shovill] Removing low coverage contig (< 2 x): NODE_183_length_957_cov_1.834928_pilon [shovill] Removing low coverage contig (< 2 x): NODE_188_length_895_cov_1.788114_pilon [shovill] Removing low coverage contig (< 2 x): NODE_190_length_837_cov_1.180168_pilon [shovill] Removing low coverage contig (< 2 x): NODE_192_length_816_cov_0.981295_pilon [shovill] Removing low coverage contig (< 2 x): NODE_193_length_805_cov_1.698830_pilon [shovill] Removing low coverage contig (< 2 x): NODE_194_length_790_cov_1.804185_pilon [shovill] Removing low coverage contig (< 2 x): NODE_198_length_770_cov_1.665639_pilon [shovill] Removing low coverage contig (< 2 x): NODE_199_length_758_cov_1.469388_pilon [shovill] Removing low coverage contig (< 2 x): NODE_200_length_741_cov_1.825806_pilon [shovill] Removing low coverage contig (< 2 x): NODE_205_length_734_cov_1.396411_pilon [shovill] Removing low coverage contig (< 2 x): NODE_206_length_725_cov_1.622517_pilon [shovill] Removing low coverage contig (< 2 x): NODE_208_length_710_cov_1.478778_pilon [shovill] Removing low coverage contig (< 2 x): NODE_210_length_701_cov_1.636207_pilon [shovill] Removing low coverage contig (< 2 x): NODE_212_length_688_cov_0.857143_pilon [shovill] Removing low coverage contig (< 2 x): NODE_214_length_665_cov_1.400735_pilon [shovill] Removing low coverage contig (< 2 x): NODE_216_length_655_cov_1.485019_pilon [shovill] Removing low coverage contig (< 2 x): NODE_217_length_652_cov_1.653484_pilon [shovill] Removing low coverage contig (< 2 x): NODE_219_length_641_cov_1.178846_pilon [shovill] Removing low coverage contig (< 2 x): NODE_221_length_623_cov_0.635458_pilon [shovill] Removing low coverage contig (< 2 x): NODE_222_length_615_cov_1.943320_pilon [shovill] Removing low coverage contig (< 2 x): NODE_224_length_603_cov_0.655602_pilon [shovill] Removing low coverage contig (< 2 x): NODE_228_length_572_cov_0.647450_pilon [shovill] Removing low coverage contig (< 2 x): NODE_231_length_549_cov_0.665888_pilon [shovill] Removing low coverage contig (< 2 x): NODE_233_length_542_cov_1.501188_pilon [shovill] Removing low coverage contig (< 2 x): NODE_234_length_537_cov_1.024038_pilon [shovill] Removing low coverage contig (< 2 x): NODE_235_length_536_cov_1.260241_pilon [shovill] Removing low coverage contig (< 2 x): NODE_237_length_533_cov_0.849515_pilon [shovill] Removing low coverage contig (< 2 x): NODE_238_length_525_cov_1.534653_pilon [shovill] Removing low coverage contig (< 2 x): NODE_240_length_514_cov_1.743003_pilon [shovill] Removing low coverage contig (< 2 x): NODE_242_length_513_cov_0.290816_pilon [shovill] Removing low coverage contig (< 2 x): NODE_243_length_511_cov_1.394872_pilon [shovill] Removing low coverage contig (< 2 x): NODE_244_length_507_cov_1.727979_pilon [shovill] Removing low coverage contig (< 2 x): NODE_246_length_505_cov_0.747396_pilon [shovill] Removing low coverage contig (< 2 x): NODE_247_length_502_cov_0.427822_pilon [shovill] Removing low coverage contig (< 2 x): NODE_251_length_484_cov_1.528926_pilon [shovill] Removing low coverage contig (< 2 x): NODE_253_length_480_cov_1.350975_pilon [shovill] Removing low coverage contig (< 2 x): NODE_254_length_476_cov_1.118310_pilon [shovill] Removing low coverage contig (< 2 x): NODE_255_length_475_cov_1.700565_pilon [shovill] Removing low coverage contig (< 2 x): NODE_258_length_467_cov_1.783237_pilon [shovill] Removing low coverage contig (< 2 x): NODE_260_length_460_cov_1.129794_pilon [shovill] Removing low coverage contig (< 2 x): NODE_262_length_459_cov_1.721893_pilon [shovill] Removing low coverage contig (< 2 x): NODE_263_length_456_cov_1.468657_pilon [shovill] Removing low coverage contig (< 2 x): NODE_265_length_454_cov_1.372372_pilon [shovill] Removing low coverage contig (< 2 x): NODE_266_length_453_cov_1.512048_pilon [shovill] Removing low coverage contig (< 2 x): NODE_267_length_453_cov_0.322289_pilon [shovill] Removing low coverage contig (< 2 x): NODE_269_length_447_cov_1.340491_pilon [shovill] Removing low coverage contig (< 2 x): NODE_270_length_447_cov_1.107362_pilon [shovill] Removing low coverage contig (< 2 x): NODE_272_length_446_cov_1.526154_pilon [shovill] Removing low coverage contig (< 2 x): NODE_273_length_445_cov_1.691358_pilon [shovill] Removing low coverage contig (< 2 x): NODE_274_length_445_cov_0.756173_pilon [shovill] Removing low coverage contig (< 2 x): NODE_276_length_444_cov_1.390093_pilon [shovill] Removing low coverage contig (< 2 x): NODE_277_length_436_cov_1.923810_pilon [shovill] Removing low coverage contig (< 2 x): NODE_278_length_435_cov_1.515924_pilon [shovill] Removing low coverage contig (< 2 x): NODE_281_length_434_cov_1.376997_pilon [shovill] Removing low coverage contig (< 2 x): NODE_280_length_434_cov_1.527157_pilon [shovill] Removing low coverage contig (< 2 x): NODE_279_length_434_cov_1.840256_pilon [shovill] Removing low coverage contig (< 2 x): NODE_282_length_432_cov_1.221865_pilon [shovill] Removing low coverage contig (< 2 x): NODE_287_length_428_cov_1.342020_pilon [shovill] Removing low coverage contig (< 2 x): NODE_288_length_428_cov_0.426710_pilon [shovill] Removing low coverage contig (< 2 x): NODE_289_length_426_cov_1.800000_pilon [shovill] Removing low coverage contig (< 2 x): NODE_291_length_424_cov_1.293729_pilon [shovill] Removing low coverage contig (< 2 x): NODE_290_length_424_cov_1.881188_pilon [shovill] Removing low coverage contig (< 2 x): NODE_292_length_424_cov_1.227723_pilon [shovill] Removing low coverage contig (< 2 x): NODE_295_length_415_cov_0.965986_pilon [shovill] Removing low coverage contig (< 2 x): NODE_297_length_413_cov_0.671233_pilon [shovill] Removing low coverage contig (< 2 x): NODE_296_length_413_cov_1.171233_pilon [shovill] Removing low coverage contig (< 2 x): NODE_298_length_410_cov_1.574394_pilon [shovill] Removing low coverage contig (< 2 x): NODE_299_length_410_cov_1.228374_pilon [shovill] Removing low coverage contig (< 2 x): NODE_300_length_409_cov_1.361111_pilon [shovill] Removing low coverage contig (< 2 x): NODE_301_length_408_cov_1.414634_pilon [shovill] Removing low coverage contig (< 2 x): NODE_302_length_406_cov_1.091228_pilon [shovill] Removing low coverage contig (< 2 x): NODE_304_length_405_cov_0.947183_pilon [shovill] Removing low coverage contig (< 2 x): NODE_306_length_404_cov_0.749117_pilon [shovill] Removing low coverage contig (< 2 x): NODE_305_length_404_cov_1.374558_pilon [shovill] Removing low coverage contig (< 2 x): NODE_309_length_403_cov_1.450355_pilon [shovill] Removing low coverage contig (< 2 x): NODE_308_length_403_cov_1.485816_pilon [shovill] Removing low coverage contig (< 2 x): NODE_310_length_402_cov_1.224199_pilon [shovill] Removing low coverage contig (< 2 x): NODE_313_length_325_cov_1.862745_pilon [shovill] Removing low coverage contig (< 2 x): NODE_316_length_271_cov_1.226667_pilon [shovill] Removing short contig (< 200 bp): NODE_320_length_131_cov_150.500000_pilon [shovill] Removing short contig (< 200 bp): NODE_321_length_122_cov_2116.000000_pilon [shovill] Assembly is 3221631, estimated genome size was 3000000 (+7.39%) [shovill] Using genome graph file 'spades/assembly_graph_with_scaffolds.gfa' => 'contigs.gfa' [shovill] Walltime used: 6 min 34 sec [shovill] Results in: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus [shovill] Final assembly graph: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/contigs.gfa [shovill] Final assembly contigs: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Enterococcus/contigs.fa [shovill] It contains 210 (min=200) contigs totalling 3221631 bp. [shovill] Remember, an assembly is just a _hypothesis_ of the original sequence! [shovill] Done.
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Created: 12th Nov 2021 at 23:20
Last updated: 12th Nov 2021 at 23:20
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Version 1 (earliest) Created 12th Nov 2021 at 23:20 by Marko Petek
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https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
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National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
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This project’s main objective was to identify novel Colorado potato beetle gene targets for the development of specific RNAi insecticides and further validate prospective targets using transcriptomics. The work included gene selection, establishment of double-stranded RNA (dsRNA) production methodology and the evaluation of dsRNAs’ insecticidal potential in CPB feeding laboratory and field trials.
Programme: NIBSys
Public web page: http://projects.nib.si/rnainval/
Start date: 1st Nov 2014
End date: 31st Oct 2017
Advanced Investigations list for this Document with search and filtering
Short Name: 03_Omics Title: Omics analysis of RNAi response in CPB Description: Transcriptomics and metagenome changes upon feeding CPB larvae with dsRNA Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_01_ns-dsRNA_trans, _S_02_metagenome_resp
Assays: _A_01-DNAisol, _A_01_RNA-Seq_dsEGFP-NGS, _A_02-DNASeq, _A_02_CLC-RNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _I_03_Omics-files, _S_01_ns-dsRNA_trans-files, _S_02_metagenome_resp-files
Advanced Studies list for this Document with search and filtering
Short Name: 02_metagenome_resp Title: CPB gut microbiome response to dsRNA feeding Description: Response of CPB gut microbiome to dsRNA feeding on the level of microbe abundance Raw Data: pISA Study creation date: 2021-01-15 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_03_Omics
Assays: _A_01-DNAisol, _A_02-DNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _S_02_metagenome_resp-files
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Short Name: 06_extr_bact-assembly Assay Class: DRY Assay Type: assembly Title: De novo genome assembly of bacteria Description: De novo genome assembly of bacteria from rcf-extracted shotgun metagenomics reads pISA Assay creation date: 2021-01-16 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_03_Omics
Study: _S_02_metagenome_resp
