[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.