[shovill] Hello administrator [shovill] You ran: /home/administrator/conda2/envs/shovill/bin/shovill --force --outdir ./shovill/Lactococcus/ --R1 ./fq/incl1358_R1.fastq --R2 ./fq/incl1358_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/Lactococcus/ [shovill] Using tempdir: /tmp/5n2VNtoOQH [shovill] Changing into folder: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus [shovill] Collecting raw read statistics with 'seqtk' [shovill] Running: seqtk fqchk -q3 \/DATB\/markop\/CPB\/CPB_rcf_DNAseq\/fq\/incl1358_R1\.fastq >/tmp/7F1xfhoPlr 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log [shovill] Read stats: avg_len = 150 [shovill] Read stats: min_len = 150 [shovill] Read stats: total_bp = 27306960300 [shovill] Read stats: max_len = 150 [shovill] Using genome size 3000000 bp [shovill] Estimated sequencing depth: 9102 x [shovill] Subsampling reads by factor 0.016 to get from 9102x to 150x [shovill] Running: seqtk sample \/DATB\/markop\/CPB\/CPB_rcf_DNAseq\/fq\/incl1358_R1\.fastq 0.016 | 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\/incl1358_R2\.fastq 0.016 | 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] [2021-01-21 12:48:16] =============Start==================== [lighter] [2021-01-21 12:48:16] Scanning the input files to infer alpha(sampling rate) [lighter] [2021-01-21 12:48:21] Average coverage is 145.698 and alpha is 0.048 [lighter] [2021-01-21 12:48:23] Bad quality threshold is ";" [lighter] [2021-01-21 12:48:44] Finish sampling kmers [lighter] [2021-01-21 12:48:44] Bloom filter A's false positive rate: 0.002643 [lighter] [2021-01-21 12:48:55] Finish storing trusted kmers [lighter] [2021-01-21 12:49:17] Finish error correction [lighter] Processed 2913952 reads: [lighter] 2508503 are error-free [lighter] Corrected 644464 bases(1.589507 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 1456976 read pairs [FLASH] [FLASH] Read combination statistics: [FLASH] Total pairs: 1456976 [FLASH] Combined pairs: 574944 [FLASH] Uncombined pairs: 882032 [FLASH] Percent combined: 39.46% [FLASH] [FLASH] Writing histogram files. [FLASH] [FLASH] FLASH v1.2.11 complete! [FLASH] 48.367 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/5n2VNtoOQH -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/Lactococcus/flash.notCombined_1.fastq.gz -2 /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/flash.notCombined_2.fastq.gz --isolate --threads 30 --memory 240 -o /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades --tmp-dir /tmp/5n2VNtoOQH -k 31,41,51,61,71,81,91,101,111,121 --merged /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/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/Lactococcus/flash.notCombined_1.fastq.gz'] [spades] right reads: ['/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/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/5n2VNtoOQH [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/Lactococcus/spades/spades.log [spades] [spades] /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/flash.notCombined_1.fastq.gz: max reads length: 150 [spades] /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/spades/K31/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/spades/K31/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/Lactococcus/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/Lactococcus/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] 0:00:00.001 7M / 9M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion [spades] 0:00:00.003 7M / 9M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) [spades] 0:00:00.003 7M / 9M INFO General (read_converter.cpp : 73) Converting paired reads [spades] 0:00:00.906 203M / 203M INFO General (binary_converter.cpp : 96) 16384 reads processed [spades] 0:00:00.980 222M / 222M INFO General (binary_converter.cpp : 96) 32768 reads processed [spades] 0:00:01.146 262M / 262M INFO General (binary_converter.cpp : 96) 65536 reads processed [spades] 0:00:01.440 308M / 308M INFO General (binary_converter.cpp : 96) 131072 reads processed [spades] 0:00:02.193 399M / 399M INFO General (binary_converter.cpp : 96) 262144 reads processed [spades] 0:00:03.585 523M / 523M INFO General (binary_converter.cpp : 96) 524288 reads processed [spades] 0:00:05.821 598M / 632M INFO General (binary_converter.cpp : 111) 882032 reads written [spades] 0:00:05.823 574M / 632M INFO General (read_converter.cpp : 81) Converting single reads [spades] 0:00:05.824 584M / 632M INFO General (binary_converter.cpp : 111) 0 reads written [spades] 0:00:05.824 574M / 632M INFO General (read_converter.cpp : 87) Converting merged reads [spades] 0:00:06.442 625M / 632M INFO General (binary_converter.cpp : 96) 16384 reads processed [spades] 0:00:06.483 630M / 632M INFO General (binary_converter.cpp : 96) 32768 reads processed [spades] 0:00:06.567 641M / 641M INFO General (binary_converter.cpp : 96) 65536 reads processed [spades] 0:00:07.076 692M / 692M INFO General (binary_converter.cpp : 96) 131072 reads processed [spades] 0:00:07.818 764M / 764M INFO General (binary_converter.cpp : 96) 262144 reads processed [spades] 0:00:09.620 860M / 860M INFO General (binary_converter.cpp : 96) 524288 reads processed [spades] 0:00:09.950 858M / 858M INFO General (binary_converter.cpp : 111) 574944 reads written [spades] 0:00:09.987 111M / 858M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:09.991 111M / 858M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:09.992 111M / 858M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:09.992 111M / 858M INFO General (construction.cpp : 156) Average read length 172.524 [spades] 0:00:09.993 111M / 858M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:09.994 111M / 858M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:09.996 111M / 858M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:09.997 111M / 858M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66664 Gb [spades] 0:00:09.998 111M / 858M INFO General (kmer_splitters.hpp : 97) Using cell size of 74565 [spades] 0:00:13.597 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4678016 reads [spades] 0:00:13.827 285M / 3G INFO General (kmer_splitters.hpp : 293) Used 4678016 reads [spades] 0:00:13.827 285M / 3G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:14.026 285M / 3G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5402542 kmers in total. [spades] 0:00:14.029 285M / 3G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:14.111 272M / 3G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:14.112 272M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:14.113 272M / 3G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:14.115 272M / 3G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:14.117 272M / 3G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:14.118 272M / 3G INFO General (kmer_splitters.hpp : 97) Using cell size of 139810 [spades] 0:00:14.381 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 5402542 kmers [spades] 0:00:14.382 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 5402542 kmers. [spades] 0:00:14.441 297M / 3G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:14.602 248M / 3G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5401536 kmers in total. [spades] 0:00:14.603 248M / 3G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:14.669 248M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:14.824 256M / 3G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:14.898 256M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2513104 bytes occupied (3.72206 bits per kmer). [spades] 0:00:14.910 256M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:15.081 256M / 3G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:15.086 256M / 3G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping [spades] 0:00:15.088 256M / 3G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) [spades] 0:00:15.090 256M / 3G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping [spades] 0:00:15.258 265M / 3G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 33408 [spades] 0:00:15.260 265M / 3G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 33552 [spades] 0:00:15.268 265M / 3G INFO Early tip clipping (early_simplification.hpp : 30) 1276354 32-mers were removed by early tip clipper [spades] 0:00:15.269 265M / 3G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:15.271 265M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:15.427 262M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 41151 sequences extracted [spades] 0:00:15.537 262M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:15.589 262M / 3G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 5 loops collected [spades] 0:00:15.779 250M / 3G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:15.780 250M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:15.781 250M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:15.887 256M / 3G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2520832 bytes occupied (3.73281 bits per kmer). [spades] 0:00:15.902 280M / 3G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:20.223 277M / 3G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:20.352 277M / 3G INFO General (construction.cpp : 505) Processed 82262 edges [spades] 0:00:20.389 177M / 3G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:20.391 177M / 3G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 13 [spades] 0:00:20.392 177M / 3G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 119 [spades] 0:00:20.393 177M / 3G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 122. Coverage mad: 32.6172 [spades] 0:00:20.394 177M / 3G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:20.554 177M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:20.983 177M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:22.420 177M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:25.307 177M / 3G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:25.979 177M / 3G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 123.438. Fitted coverage std. dev: 28.1571 [spades] 0:00:25.985 177M / 3G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.986767 [spades] 0:00:25.985 177M / 3G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 64 [spades] 0:00:25.986 177M / 3G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 64 [spades] 0:00:25.986 177M / 3G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2375286 [spades] 0:00:25.987 177M / 3G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 123.438 [spades] 0:00:25.988 177M / 3G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 64 [spades] 0:00:25.988 177M / 3G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:25.989 177M / 3G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:25.989 177M / 3G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:25.990 177M / 3G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:25.991 177M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:25.994 177M / 3G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:25.995 177M / 3G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:25.996 177M / 3G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:25.997 177M / 3G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:25.998 177M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:25.999 177M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.008 174M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 216 times [spades] 0:00:26.009 174M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.225 104M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6609 times [spades] 0:00:26.226 104M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.323 104M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3425 times [spades] 0:00:26.324 104M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:26.324 104M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.329 104M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 67 times [spades] 0:00:26.330 104M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.332 104M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 15 times [spades] 0:00:26.332 104M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.335 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 47 times [spades] 0:00:26.336 105M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:26.337 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.337 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.338 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.339 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.339 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.340 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 13 times [spades] 0:00:26.341 105M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:26.341 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.342 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.343 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.344 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times [spades] 0:00:26.344 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.345 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times [spades] 0:00:26.346 105M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:26.346 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.347 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.347 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.348 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:26.349 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.350 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 13 times [spades] 0:00:26.350 105M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:26.351 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.351 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.352 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.353 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.353 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.354 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:26.355 105M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:26.355 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.356 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.356 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.357 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.358 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.358 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:26.359 105M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:26.360 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.360 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.361 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.362 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.362 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.363 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 9 times [spades] 0:00:26.364 105M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:26.365 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.365 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.366 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.367 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.367 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.368 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times [spades] 0:00:26.368 105M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:26.369 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.370 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.370 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.371 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.372 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.372 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times [spades] 0:00:26.373 105M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:26.374 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.377 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8 times [spades] 0:00:26.378 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.385 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 6 times [spades] 0:00:26.386 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.388 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:26.389 105M / 3G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 [spades] 0:00:26.390 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.391 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.392 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.393 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.394 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:26.395 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:26.397 105M / 3G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:26.398 105M / 3G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:26.399 105M / 3G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:26.400 105M / 3G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:26.401 105M / 3G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:26.402 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.405 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.406 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.411 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:26.412 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:26.414 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:26.415 105M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:26.421 105M / 3G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:26.422 105M / 3G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:26.430 104M / 3G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:26.458 104M / 3G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 9558 times [spades] 0:00:26.459 104M / 3G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:26.460 104M / 3G INFO General (simplification.cpp : 502) Average coverage = 130.237 [spades] 0:00:26.461 104M / 3G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:26.461 104M / 3G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K31/simplified_contigs [spades] 0:00:26.465 108M / 3G INFO General (binary_converter.cpp : 111) 1819 reads written [spades] 0:00:26.467 109M / 3G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:26.471 109M / 3G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 26 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/Lactococcus/spades/K41/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/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/Lactococcus/spades/K41/configs/config.info [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 75) Loaded config from /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K41/configs/isolate_mode.info [spades] 0:00:00.001 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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] 0:00:00.005 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/Lactococcus/spades/K31/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] 0:00:00.009 8M / 9M INFO General (construction.cpp : 156) Average read length 172.524 [spades] 0:00:00.009 8M / 9M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.009 8M / 9M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.010 8M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.010 8M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.010 8M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 37282 [spades] 0:00:03.955 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4681654 reads [spades] 0:00:04.351 402M / 5G INFO General (kmer_splitters.hpp : 293) Used 4681654 reads [spades] 0:00:04.352 402M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.663 404M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5383425 kmers in total. [spades] 0:00:04.665 404M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.784 399M / 5G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:04.785 399M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:04.785 399M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:04.786 399M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:04.786 399M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:04.787 399M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:05.114 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 5383425 kmers [spades] 0:00:05.115 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 5383425 kmers. [spades] 0:00:05.181 412M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:05.358 412M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5387355 kmers in total. [spades] 0:00:05.359 412M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:05.460 412M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:05.598 416M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:05.750 416M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2506560 bytes occupied (3.72214 bits per kmer). [spades] 0:00:05.763 416M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:05.958 416M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:05.962 416M / 5G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping [spades] 0:00:05.964 416M / 5G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) [spades] 0:00:05.966 416M / 5G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping [spades] 0:00:06.146 425M / 5G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 33496 [spades] 0:00:06.148 425M / 5G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 33635 [spades] 0:00:06.157 425M / 5G INFO Early tip clipping (early_simplification.hpp : 30) 1226108 42-mers were removed by early tip clipper [spades] 0:00:06.158 425M / 5G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:06.161 425M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:06.324 364M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 33761 sequences extracted [spades] 0:00:06.438 364M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:06.491 364M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 4 loops collected [spades] 0:00:06.654 265M / 5G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:06.655 265M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:06.656 265M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:06.763 276M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2511808 bytes occupied (3.73265 bits per kmer). [spades] 0:00:06.779 300M / 5G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:10.845 300M / 5G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:10.970 300M / 5G INFO General (construction.cpp : 505) Processed 67511 edges [spades] 0:00:11.007 152M / 5G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:11.009 152M / 5G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 13 [spades] 0:00:11.010 152M / 5G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 113 [spades] 0:00:11.010 152M / 5G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 113. Coverage mad: 29.652 [spades] 0:00:11.011 152M / 5G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:11.162 152M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:11.557 152M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:12.863 152M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:15.514 152M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:16.741 152M / 5G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 114.637. Fitted coverage std. dev: 26.3869 [spades] 0:00:16.746 152M / 5G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.981462 [spades] 0:00:16.747 152M / 5G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 59 [spades] 0:00:16.747 152M / 5G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 59 [spades] 0:00:16.748 152M / 5G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2380082 [spades] 0:00:16.749 152M / 5G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 114.637 [spades] 0:00:16.749 152M / 5G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 59 [spades] 0:00:16.750 152M / 5G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:16.750 152M / 5G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:16.751 152M / 5G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:16.752 152M / 5G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:16.752 152M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:16.755 152M / 5G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:16.756 152M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:16.757 152M / 5G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:16.758 152M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:16.759 152M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:16.760 152M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.767 152M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 189 times [spades] 0:00:16.768 152M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.954 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 5212 times [spades] 0:00:16.955 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.044 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1809 times [spades] 0:00:17.044 86M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:17.045 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.048 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 36 times [spades] 0:00:17.049 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.050 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 7 times [spades] 0:00:17.051 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.053 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 32 times [spades] 0:00:17.054 86M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:17.054 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.055 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.055 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.056 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.057 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.058 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times [spades] 0:00:17.059 86M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:17.059 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.060 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.061 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.061 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.062 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.063 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 9 times [spades] 0:00:17.063 86M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:17.064 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.065 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.065 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.066 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.067 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.068 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10 times [spades] 0:00:17.068 86M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:17.069 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.070 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.070 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.071 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.072 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.072 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6 times [spades] 0:00:17.073 86M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:17.073 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.074 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.075 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.075 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:17.076 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.077 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:17.077 86M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:17.078 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.078 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.079 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.080 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.080 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.081 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:17.082 86M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:17.082 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.083 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.084 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.084 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.085 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.086 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:17.086 86M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:17.087 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.088 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.088 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.089 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.090 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.090 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:17.091 86M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:17.091 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.109 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:17.110 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.143 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:17.144 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.172 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:17.173 86M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 [spades] 0:00:17.174 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.175 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.175 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.176 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.177 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.178 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:17.204 86M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:17.205 86M / 5G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:17.206 86M / 5G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:17.206 86M / 5G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:17.207 86M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:17.208 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.240 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.241 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.274 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times [spades] 0:00:17.275 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.308 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.309 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.314 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.315 86M / 5G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:17.324 86M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:17.354 86M / 5G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 11276 times [spades] 0:00:17.355 86M / 5G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:17.356 86M / 5G INFO General (simplification.cpp : 502) Average coverage = 121.014 [spades] 0:00:17.357 86M / 5G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:17.357 86M / 5G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K41/simplified_contigs [spades] 0:00:17.361 90M / 5G INFO General (binary_converter.cpp : 111) 1321 reads written [spades] 0:00:17.363 90M / 5G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:17.366 90M / 5G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 17 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/Lactococcus/spades/K51/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/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/Lactococcus/spades/K51/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/Lactococcus/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/Lactococcus/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] 0:00:00.005 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/Lactococcus/spades/K41/simplified_contigs [spades] 0:00:00.010 9M / 9M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.011 9M / 9M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.011 9M / 9M INFO General (construction.cpp : 156) Average read length 172.524 [spades] 0:00:00.011 9M / 9M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.011 9M / 9M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.013 9M / 9M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.013 9M / 9M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.013 9M / 9M INFO General (kmer_splitters.hpp : 97) Using cell size of 37282 [spades] 0:00:03.676 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4680658 reads [spades] 0:00:04.046 532M / 5G INFO General (kmer_splitters.hpp : 293) Used 4680658 reads [spades] 0:00:04.047 532M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.349 534M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5323761 kmers in total. [spades] 0:00:04.351 534M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.464 529M / 5G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:04.465 529M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:04.465 529M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:04.466 529M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:04.466 529M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:04.467 529M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:04.770 19G / 19G INFO General (kmer_splitters.hpp : 364) Processed 5323761 kmers [spades] 0:00:04.771 19G / 19G INFO General (kmer_splitters.hpp : 369) Used 5323761 kmers. [spades] 0:00:04.836 558M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:05.012 558M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5330910 kmers in total. [spades] 0:00:05.013 558M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:05.113 558M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:05.241 562M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:05.383 562M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2480232 bytes occupied (3.72204 bits per kmer). [spades] 0:00:05.392 562M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:05.593 562M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:05.596 552M / 5G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping [spades] 0:00:05.597 552M / 5G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K) [spades] 0:00:05.598 552M / 5G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping [spades] 0:00:05.772 561M / 5G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 33498 [spades] 0:00:05.774 561M / 5G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 33628 [spades] 0:00:05.784 561M / 5G INFO Early tip clipping (early_simplification.hpp : 30) 1199363 52-mers were removed by early tip clipper [spades] 0:00:05.785 561M / 5G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:05.787 561M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:05.949 534M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 29610 sequences extracted [spades] 0:00:06.062 534M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:06.113 534M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 3 loops collected [spades] 0:00:06.272 413M / 5G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:06.273 413M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:06.274 413M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:06.378 423M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2484568 bytes occupied (3.73355 bits per kmer). [spades] 0:00:06.397 447M / 5G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:10.195 423M / 5G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:10.316 423M / 5G INFO General (construction.cpp : 505) Processed 59213 edges [spades] 0:00:10.357 399M / 5G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:10.359 399M / 5G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 13 [spades] 0:00:10.360 399M / 5G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 101 [spades] 0:00:10.361 399M / 5G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 104. Coverage mad: 28.1694 [spades] 0:00:10.361 399M / 5G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:10.501 399M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:10.883 399M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:12.212 399M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:14.799 399M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:15.633 399M / 5G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 105.86. Fitted coverage std. dev: 24.5924 [spades] 0:00:15.638 399M / 5G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.97372 [spades] 0:00:15.638 399M / 5G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 54 [spades] 0:00:15.639 399M / 5G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 54 [spades] 0:00:15.639 399M / 5G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2383795 [spades] 0:00:15.640 399M / 5G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 105.86 [spades] 0:00:15.641 399M / 5G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 54 [spades] 0:00:15.641 399M / 5G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:15.642 399M / 5G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:15.642 399M / 5G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:15.643 399M / 5G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:15.644 399M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:15.648 399M / 5G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:15.649 399M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:15.649 399M / 5G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:15.650 399M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:15.651 399M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:15.652 399M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.659 399M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 210 times [spades] 0:00:15.660 399M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.814 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 4061 times [spades] 0:00:15.815 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.876 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1131 times [spades] 0:00:15.877 85M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:15.878 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.881 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 38 times [spades] 0:00:15.881 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.882 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times [spades] 0:00:15.883 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.886 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 33 times [spades] 0:00:15.886 85M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:15.887 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.888 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.888 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.889 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.890 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.891 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 14 times [spades] 0:00:15.892 85M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:15.892 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.893 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.893 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.894 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:15.895 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.896 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 9 times [spades] 0:00:15.897 85M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:15.897 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.898 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.898 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.899 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.900 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.900 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8 times [spades] 0:00:15.901 85M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:15.901 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.902 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.903 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.903 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.904 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.905 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:15.905 85M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:15.906 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.907 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.907 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.908 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.908 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.909 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6 times [spades] 0:00:15.910 85M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:15.910 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.911 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.911 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.912 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.913 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.913 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:15.914 85M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:15.915 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.915 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.916 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.916 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.917 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.918 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:15.918 85M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:15.919 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.919 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.920 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.921 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.921 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.922 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:15.923 85M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:15.923 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.925 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.926 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.930 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.931 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.933 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:15.935 85M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:15.936 85M / 5G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:15.937 85M / 5G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:15.938 85M / 5G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:15.938 85M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:15.939 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.942 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.942 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.946 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.947 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.949 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.950 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.953 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.954 85M / 5G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:15.961 85M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:15.991 85M / 5G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 12567 times [spades] 0:00:15.992 85M / 5G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:15.993 85M / 5G INFO General (simplification.cpp : 502) Average coverage = 111.828 [spades] 0:00:15.994 85M / 5G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:16.002 85M / 5G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K51/simplified_contigs [spades] 0:00:16.008 89M / 5G INFO General (binary_converter.cpp : 111) 1028 reads written [spades] 0:00:16.011 89M / 5G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:16.014 89M / 5G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 16 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/Lactococcus/spades/K61/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/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/Lactococcus/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/Lactococcus/spades/K61/configs/isolate_mode.info [spades] 0:00:00.000 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/dataset.info) with K=61 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 30 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 194) SPAdes started [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 218) Will need read mapping, kmer mapper will be attached [spades] 0:00:00.001 7M / 9M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion [spades] 0:00:00.003 7M / 9M INFO General (read_converter.cpp : 53) Binary reads detected [spades] 0:00:00.004 8M / 9M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:00.005 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K51/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 172.524 [spades] 0:00:00.009 9M / 10M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.012 9M / 10M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.013 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] 0:00:03.462 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4680072 reads [spades] 0:00:03.811 368M / 5G INFO General (kmer_splitters.hpp : 293) Used 4680072 reads [spades] 0:00:03.812 368M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.100 370M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5239317 kmers in total. [spades] 0:00:04.102 370M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.220 366M / 5G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:04.220 366M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:04.221 366M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:04.221 366M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:04.222 366M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:04.222 366M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:04.508 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 5239317 kmers [spades] 0:00:04.509 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 5239317 kmers. [spades] 0:00:04.572 398M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.741 398M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5248688 kmers in total. [spades] 0:00:04.742 398M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.840 398M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:04.971 403M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:05.134 403M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2441856 bytes occupied (3.72185 bits per kmer). [spades] 0:00:05.145 403M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:05.345 403M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:05.349 392M / 5G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:05.354 392M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:05.548 377M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 93626 sequences extracted [spades] 0:00:05.686 377M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:05.738 377M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:06.158 295M / 5G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:06.164 295M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:06.165 295M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:06.264 308M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2445280 bytes occupied (3.73374 bits per kmer). [spades] 0:00:06.279 328M / 5G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:09.770 319M / 5G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:09.932 319M / 5G INFO General (construction.cpp : 505) Processed 187247 edges [spades] 0:00:09.968 202M / 5G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:09.970 202M / 5G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 11 [spades] 0:00:09.971 202M / 5G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 92 [spades] 0:00:09.972 202M / 5G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 96. Coverage mad: 26.6868 [spades] 0:00:09.972 202M / 5G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:10.088 202M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:10.434 202M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:11.583 202M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:13.673 202M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:13.916 202M / 5G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 97.0884. Fitted coverage std. dev: 22.7917 [spades] 0:00:13.920 202M / 5G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.977179 [spades] 0:00:13.921 202M / 5G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 49 [spades] 0:00:13.921 202M / 5G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 49 [spades] 0:00:13.922 202M / 5G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2386961 [spades] 0:00:13.923 202M / 5G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 97.0884 [spades] 0:00:13.923 202M / 5G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 49 [spades] 0:00:13.924 202M / 5G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:13.924 202M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:13.925 202M / 5G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:13.926 202M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:13.926 202M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:13.927 202M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:13.929 202M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66626 Gb [spades] 0:00:13.929 202M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:14.123 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 187247 edges [spades] 0:00:14.125 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 187247 sequences. [spades] 0:00:14.179 220M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:14.364 219M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5239317 kmers in total. [spades] 0:00:14.367 219M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:14.462 219M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:14.593 205M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:14.747 205M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2437496 bytes occupied (3.72185 bits per kmer). [spades] 0:00:14.808 285M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:14.912 285M / 5G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:14.915 285M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:15.020 288M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:15.595 255M / 5G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:15.596 255M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:15.624 255M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:15.705 255M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 4 gaps after checking 144 candidates [spades] 0:00:15.722 255M / 5G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:15.729 175M / 5G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:15.730 175M / 5G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:15.731 175M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:15.739 175M / 5G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:15.739 175M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:15.740 175M / 5G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:15.741 175M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:15.742 175M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:15.743 175M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.069 169M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 33579 times [spades] 0:00:16.070 169M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.599 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3319 times [spades] 0:00:16.600 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.658 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 809 times [spades] 0:00:16.659 182M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:16.660 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.663 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 29 times [spades] 0:00:16.663 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.665 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2 times [spades] 0:00:16.666 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.667 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 31 times [spades] 0:00:16.668 182M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:16.669 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.669 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.670 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.671 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.671 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.674 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 18 times [spades] 0:00:16.675 182M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:16.676 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.676 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.677 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.677 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.678 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.680 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times [spades] 0:00:16.681 182M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:16.681 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.682 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.682 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.684 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:16.684 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.685 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:16.686 182M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:16.686 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.687 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.687 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.688 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.689 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.690 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:16.690 182M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:16.691 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.692 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:16.692 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.693 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.693 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.694 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6 times [spades] 0:00:16.695 182M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:16.695 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.696 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.697 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.697 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.698 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.699 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:16.699 182M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:16.700 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.701 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.701 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.702 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.702 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.703 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:16.704 182M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:16.704 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.705 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.706 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.706 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.707 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.708 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:16.708 182M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:16.709 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.712 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 2 times [spades] 0:00:16.713 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.718 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.719 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.722 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.723 182M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 [spades] 0:00:16.724 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.725 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.726 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.726 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.727 182M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.728 182M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.732 182M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:16.732 182M / 5G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:16.733 182M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:16.734 182M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:16.735 182M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:16.737 182M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66594 Gb [spades] 0:00:16.738 182M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 69905 [spades] 0:00:16.871 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 29072 edges [spades] 0:00:16.872 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 29072 sequences. [spades] 0:00:16.923 176M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:17.080 176M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3750442 kmers in total. [spades] 0:00:17.083 176M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:17.168 176M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:17.281 177M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:17.380 177M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1747408 bytes occupied (3.72736 bits per kmer). [spades] 0:00:17.437 241M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:17.538 241M / 5G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:17.541 241M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:17.579 243M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:18.128 242M / 5G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:18.130 242M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:18.150 242M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:18.167 242M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 1 gaps after checking 78 candidates [spades] 0:00:18.179 242M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:18.180 242M / 5G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:18.181 242M / 5G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:18.182 242M / 5G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:18.183 242M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:18.183 242M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:18.187 242M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:18.188 242M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:18.193 242M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:18.193 242M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:18.197 242M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:18.198 242M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:18.202 242M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:18.203 242M / 5G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:18.216 242M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:18.914 230M / 5G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 13672 times [spades] 0:00:18.916 230M / 5G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:18.918 230M / 5G INFO General (simplification.cpp : 502) Average coverage = 102.582 [spades] 0:00:18.918 230M / 5G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:18.919 230M / 5G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K61/simplified_contigs [spades] 0:00:18.925 231M / 5G INFO General (binary_converter.cpp : 111) 863 reads written [spades] 0:00:18.928 230M / 5G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:19.000 159M / 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/Lactococcus/spades/K71/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/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/Lactococcus/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/Lactococcus/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/Lactococcus/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] 0:00:00.005 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/Lactococcus/spades/K61/simplified_contigs [spades] 0:00:00.009 8M / 10M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.009 8M / 10M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.009 8M / 10M INFO General (construction.cpp : 156) Average read length 172.524 [spades] 0:00:00.010 8M / 10M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.010 8M / 10M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.011 8M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.011 8M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.011 8M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 24855 [spades] 0:00:03.561 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4679742 reads [spades] 0:00:04.013 490M / 6G INFO General (kmer_splitters.hpp : 293) Used 4679742 reads [spades] 0:00:04.014 490M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.307 492M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5134506 kmers in total. [spades] 0:00:04.309 492M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.456 492M / 6G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:04.457 492M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:04.457 492M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:04.458 492M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:04.458 492M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:04.459 492M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:04.806 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 5134506 kmers [spades] 0:00:04.807 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 5134506 kmers. [spades] 0:00:04.880 513M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:05.073 513M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5145942 kmers in total. [spades] 0:00:05.074 513M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:05.205 513M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:05.356 523M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:05.552 523M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2394264 bytes occupied (3.72218 bits per kmer). [spades] 0:00:05.561 523M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:05.771 523M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:05.773 523M / 6G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:05.776 523M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:05.976 455M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 91322 sequences extracted [spades] 0:00:06.118 455M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:06.170 455M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:06.590 333M / 6G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:06.591 333M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:06.592 333M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:06.700 347M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2396792 bytes occupied (3.73441 bits per kmer). [spades] 0:00:06.723 367M / 6G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:10.019 360M / 6G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:10.186 360M / 6G INFO General (construction.cpp : 505) Processed 182641 edges [spades] 0:00:10.236 330M / 6G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:10.238 330M / 6G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 11 [spades] 0:00:10.239 330M / 6G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 82 [spades] 0:00:10.239 330M / 6G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 87. Coverage mad: 23.7216 [spades] 0:00:10.240 330M / 6G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:10.349 330M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:10.664 330M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:11.680 330M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:13.194 330M / 6G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 88.3169. Fitted coverage std. dev: 20.9744 [spades] 0:00:13.198 330M / 6G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.965067 [spades] 0:00:13.199 330M / 6G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 44 [spades] 0:00:13.200 330M / 6G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 44 [spades] 0:00:13.200 330M / 6G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2389761 [spades] 0:00:13.201 330M / 6G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 88.3169 [spades] 0:00:13.201 330M / 6G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 44 [spades] 0:00:13.202 330M / 6G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:13.203 330M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:13.203 330M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:13.204 330M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:13.205 330M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:13.209 181M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:13.210 181M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66626 Gb [spades] 0:00:13.210 181M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:13.441 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 182641 edges [spades] 0:00:13.442 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 182641 sequences. [spades] 0:00:13.498 199M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:13.697 193M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5134506 kmers in total. [spades] 0:00:13.701 193M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:13.832 193M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:13.979 177M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:14.182 177M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2389008 bytes occupied (3.72228 bits per kmer). [spades] 0:00:14.239 257M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:14.346 257M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:14.349 257M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:14.461 263M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:15.008 195M / 6G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:15.009 195M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:15.040 195M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:15.119 198M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 3 gaps after checking 137 candidates [spades] 0:00:15.136 195M / 6G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:15.143 115M / 6G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:15.144 115M / 6G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:15.145 115M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:15.153 115M / 6G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:15.154 115M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:15.154 115M / 6G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:15.155 115M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:15.156 115M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:15.157 115M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.487 113M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 32933 times [spades] 0:00:15.488 113M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.014 138M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2717 times [spades] 0:00:16.015 138M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.067 138M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 659 times [spades] 0:00:16.068 138M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:16.068 138M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.071 138M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 20 times [spades] 0:00:16.071 138M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.073 138M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 3 times [spades] 0:00:16.074 138M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.076 138M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 31 times [spades] 0:00:16.076 138M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:16.077 138M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.077 138M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.078 138M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.079 138M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.079 138M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.083 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 16 times [spades] 0:00:16.084 139M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:16.085 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.085 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.086 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.086 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.087 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.089 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 8 times [spades] 0:00:16.089 139M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:16.090 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.090 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.091 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.092 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.092 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.094 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 7 times [spades] 0:00:16.094 139M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:16.095 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.096 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.096 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.097 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.097 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.099 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:16.099 139M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:16.100 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.100 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.101 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.102 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.102 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.103 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:16.104 139M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:16.104 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.105 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.106 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.106 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.107 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.108 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:16.108 139M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:16.109 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.109 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.110 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.111 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.111 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.112 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:16.113 139M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:16.113 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.114 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.114 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.115 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.116 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.116 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:16.117 139M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:16.118 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.121 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.122 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.127 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.128 139M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:16.131 139M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:16.136 139M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:16.137 139M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:16.138 139M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:16.139 139M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:16.140 139M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:16.141 139M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66586 Gb [spades] 0:00:16.142 139M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:16.303 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 31441 edges [spades] 0:00:16.304 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 31441 sequences. [spades] 0:00:16.358 174M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:16.500 174M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3719986 kmers in total. [spades] 0:00:16.504 174M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:16.607 174M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:16.716 170M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:16.870 170M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1733224 bytes occupied (3.72738 bits per kmer). [spades] 0:00:16.932 234M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:17.049 234M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:17.053 234M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:17.092 235M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:17.636 234M / 6G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:17.639 234M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:17.669 234M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:17.687 234M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 1 gaps after checking 62 candidates [spades] 0:00:17.695 230M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:17.696 230M / 6G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:17.697 230M / 6G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:17.698 230M / 6G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:17.698 230M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:17.699 230M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.703 230M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.704 230M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.709 230M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.709 230M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.713 230M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.714 230M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.718 230M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.719 230M / 6G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:17.733 230M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:18.516 227M / 6G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 14951 times [spades] 0:00:18.517 227M / 6G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:18.518 227M / 6G INFO General (simplification.cpp : 502) Average coverage = 93.2314 [spades] 0:00:18.519 227M / 6G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:18.520 227M / 6G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K71/simplified_contigs [spades] 0:00:18.528 228M / 6G INFO General (binary_converter.cpp : 111) 769 reads written [spades] 0:00:18.532 228M / 6G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:18.615 155M / 6G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 18 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/Lactococcus/spades/K81/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/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/Lactococcus/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/Lactococcus/spades/K81/configs/isolate_mode.info [spades] 0:00:00.001 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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] 0:00:00.004 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/Lactococcus/spades/K71/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 172.524 [spades] 0:00:00.008 8M / 10M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.009 8M / 10M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.009 8M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.010 8M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.010 8M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 24855 [spades] 0:00:03.154 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4679554 reads [spades] 0:00:03.569 403M / 6G INFO General (kmer_splitters.hpp : 293) Used 4679554 reads [spades] 0:00:03.570 403M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:03.893 403M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5008839 kmers in total. [spades] 0:00:03.895 403M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.045 403M / 6G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:04.046 403M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:04.046 403M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:04.047 403M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:04.048 403M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:04.048 403M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:04.381 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 5008839 kmers [spades] 0:00:04.382 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 5008839 kmers. [spades] 0:00:04.454 418M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.654 418M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5022294 kmers in total. [spades] 0:00:04.656 418M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.786 418M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:04.920 428M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:05.119 428M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2337032 bytes occupied (3.72265 bits per kmer). [spades] 0:00:05.129 428M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:05.329 428M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:05.332 428M / 6G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:05.339 428M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:05.529 387M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 89151 sequences extracted [spades] 0:00:05.671 387M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:05.721 387M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:06.155 271M / 6G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:06.160 271M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:06.161 271M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:06.267 272M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2338376 bytes occupied (3.7348 bits per kmer). [spades] 0:00:06.282 292M / 6G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:09.338 292M / 6G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:09.491 292M / 6G INFO General (construction.cpp : 505) Processed 178301 edges [spades] 0:00:09.531 272M / 6G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:09.532 272M / 6G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 11 [spades] 0:00:09.533 272M / 6G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 72 [spades] 0:00:09.534 272M / 6G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 78. Coverage mad: 22.239 [spades] 0:00:09.534 272M / 6G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:09.628 272M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:09.910 272M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:10.890 272M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:13.383 272M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:14.366 117M / 6G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 79.556. Fitted coverage std. dev: 19.1382 [spades] 0:00:14.369 117M / 6G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.943785 [spades] 0:00:14.370 117M / 6G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 40 [spades] 0:00:14.371 117M / 6G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 40 [spades] 0:00:14.371 117M / 6G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2389878 [spades] 0:00:14.372 117M / 6G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 79.556 [spades] 0:00:14.373 117M / 6G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 40 [spades] 0:00:14.373 117M / 6G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:14.374 117M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:14.375 117M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:14.375 117M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:14.376 117M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:14.377 117M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:14.378 117M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.6663 Gb [spades] 0:00:14.379 117M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:14.606 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 178301 edges [spades] 0:00:14.607 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 178301 sequences. [spades] 0:00:14.663 154M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:14.849 154M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 5008839 kmers in total. [spades] 0:00:14.852 154M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:14.980 154M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:15.121 153M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:15.311 153M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2330864 bytes occupied (3.7228 bits per kmer). [spades] 0:00:15.373 233M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:15.475 233M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:15.478 233M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:15.592 235M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:16.096 223M / 6G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:16.098 223M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:16.129 222M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:16.206 222M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 3 gaps after checking 117 candidates [spades] 0:00:16.220 216M / 6G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:16.226 136M / 6G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:16.227 136M / 6G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:16.228 136M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:16.235 136M / 6G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:16.236 136M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:16.237 136M / 6G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:16.238 136M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:16.239 136M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:16.239 136M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.562 134M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 32025 times [spades] 0:00:16.564 134M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.051 152M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 2243 times [spades] 0:00:17.052 152M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.112 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 553 times [spades] 0:00:17.113 153M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:17.113 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.115 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 16 times [spades] 0:00:17.116 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.117 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:17.118 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.120 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 36 times [spades] 0:00:17.120 153M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:17.121 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.122 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.122 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.123 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.124 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.125 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 9 times [spades] 0:00:17.126 153M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:17.127 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.127 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.128 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.129 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.129 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.132 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 14 times [spades] 0:00:17.133 153M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:17.134 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.134 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.135 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.135 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.136 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.137 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:17.138 153M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:17.139 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.139 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.140 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.140 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.141 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.142 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:17.142 153M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:17.143 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.144 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.144 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.145 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.145 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.146 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:17.147 153M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:17.147 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.148 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.148 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.149 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.150 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.151 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:17.151 153M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:17.152 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.152 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.153 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.154 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.154 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.155 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:17.156 153M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:17.156 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.157 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.157 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.158 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.159 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.159 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:17.160 153M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:17.161 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.178 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.179 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.183 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.184 153M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:17.188 153M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:17.192 153M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:17.193 153M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:17.194 153M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:17.195 153M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:17.196 153M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:17.198 153M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.6659 Gb [spades] 0:00:17.198 153M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:17.367 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 34001 edges [spades] 0:00:17.369 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 34001 sequences. [spades] 0:00:17.422 156M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:17.577 156M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3668852 kmers in total. [spades] 0:00:17.580 156M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:17.681 156M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:17.791 157M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:17.933 157M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1709512 bytes occupied (3.72762 bits per kmer). [spades] 0:00:17.995 213M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:18.103 213M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:18.105 213M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:18.148 215M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:18.644 215M / 6G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:18.646 215M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:18.669 215M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:18.689 215M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 0 gaps after checking 79 candidates [spades] 0:00:18.696 215M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:18.698 215M / 6G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:18.698 215M / 6G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:18.699 215M / 6G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:18.700 215M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:18.701 215M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:18.705 215M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:18.706 215M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:18.711 215M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:18.711 215M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:18.715 215M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:18.716 215M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:18.720 215M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:18.721 215M / 6G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:18.735 215M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:19.467 212M / 6G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 16347 times [spades] 0:00:19.468 212M / 6G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:19.470 212M / 6G INFO General (simplification.cpp : 502) Average coverage = 84.0077 [spades] 0:00:19.470 212M / 6G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:19.471 212M / 6G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K81/simplified_contigs [spades] 0:00:19.477 212M / 6G INFO General (binary_converter.cpp : 111) 654 reads written [spades] 0:00:19.479 212M / 6G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:19.551 150M / 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/Lactococcus/spades/K91/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/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/Lactococcus/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/Lactococcus/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/Lactococcus/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] 0:00:00.005 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/Lactococcus/spades/K81/simplified_contigs [spades] 0:00:00.008 9M / 9M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.009 9M / 9M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.009 9M / 9M INFO General (construction.cpp : 156) Average read length 172.524 [spades] 0:00:00.009 9M / 9M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.012 9M / 9M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.014 9M / 9M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.014 9M / 9M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.014 9M / 9M INFO General (kmer_splitters.hpp : 97) Using cell size of 24855 [spades] 0:00:02.891 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4679324 reads [spades] 0:00:03.258 509M / 5G INFO General (kmer_splitters.hpp : 293) Used 4679324 reads [spades] 0:00:03.258 509M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:03.573 506M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4861650 kmers in total. [spades] 0:00:03.574 506M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:03.723 506M / 5G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:03.723 506M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:03.724 506M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:03.724 506M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:03.725 506M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:03.726 506M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:04.065 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 4861650 kmers [spades] 0:00:04.066 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 4861650 kmers. [spades] 0:00:04.138 526M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.338 526M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4877393 kmers in total. [spades] 0:00:04.340 526M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.462 526M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:04.592 534M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:04.795 534M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2269832 bytes occupied (3.72302 bits per kmer). [spades] 0:00:04.807 534M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:05.003 534M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:05.006 532M / 5G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:05.011 532M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:05.204 483M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 86826 sequences extracted [spades] 0:00:05.344 483M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:05.393 483M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:05.819 360M / 5G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:05.825 360M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:05.825 360M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:05.929 371M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2270176 bytes occupied (3.73565 bits per kmer). [spades] 0:00:05.944 391M / 5G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:08.636 391M / 5G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:08.786 391M / 5G INFO General (construction.cpp : 505) Processed 173653 edges [spades] 0:00:08.825 361M / 5G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:08.827 361M / 5G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 12 [spades] 0:00:08.828 361M / 5G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 63 [spades] 0:00:08.828 361M / 5G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 70. Coverage mad: 19.2738 [spades] 0:00:08.829 361M / 5G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:08.917 361M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:09.177 361M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:10.142 361M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:11.907 221M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:12.870 221M / 5G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 70.8195. Fitted coverage std. dev: 17.1367 [spades] 0:00:12.873 221M / 5G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.909228 [spades] 0:00:12.874 221M / 5G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 36 [spades] 0:00:12.875 221M / 5G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 36 [spades] 0:00:12.875 221M / 5G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2388473 [spades] 0:00:12.876 221M / 5G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 70.8195 [spades] 0:00:12.877 221M / 5G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 36 [spades] 0:00:12.877 221M / 5G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:12.878 221M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:12.879 221M / 5G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:12.879 221M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:12.880 221M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:12.881 221M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:12.882 221M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66628 Gb [spades] 0:00:12.883 221M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:13.099 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 173653 edges [spades] 0:00:13.100 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 173653 sequences. [spades] 0:00:13.156 246M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:13.341 240M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4861650 kmers in total. [spades] 0:00:13.343 240M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:13.471 240M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:13.612 227M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:13.805 227M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2262616 bytes occupied (3.72321 bits per kmer). [spades] 0:00:13.866 307M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:13.984 307M / 5G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:13.986 307M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:14.104 311M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:14.572 208M / 5G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:14.573 208M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:14.610 207M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:14.685 207M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 3 gaps after checking 113 candidates [spades] 0:00:14.702 207M / 5G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:14.708 127M / 5G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:14.709 127M / 5G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:14.710 127M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:14.717 127M / 5G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:14.718 127M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:14.719 127M / 5G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:14.720 127M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:14.721 127M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:14.721 127M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.040 118M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 30743 times [spades] 0:00:15.041 118M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.468 134M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1813 times [spades] 0:00:15.469 134M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.517 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 472 times [spades] 0:00:15.518 135M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:15.519 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.520 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 12 times [spades] 0:00:15.521 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.522 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:15.523 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.525 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 36 times [spades] 0:00:15.525 135M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:15.526 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.526 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:15.527 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.528 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.528 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.530 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 11 times [spades] 0:00:15.531 135M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:15.531 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.532 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.533 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.533 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.534 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.538 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 14 times [spades] 0:00:15.538 135M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:15.539 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.539 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.540 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.541 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.541 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.542 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:15.543 135M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:15.544 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.544 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.545 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.545 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.546 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.547 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:15.547 135M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:15.548 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.549 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.549 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.550 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.550 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.551 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:15.552 135M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:15.552 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.553 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.554 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.554 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.555 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.556 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:15.556 135M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:15.557 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.558 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.558 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.559 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.559 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.560 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:15.561 135M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:15.562 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.562 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.563 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.563 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.564 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.565 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:15.565 135M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:15.566 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.570 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.571 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.576 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.576 135M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.580 135M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:15.584 135M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:15.585 135M / 5G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:15.586 135M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:15.587 135M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:15.588 135M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:15.590 135M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66595 Gb [spades] 0:00:15.590 135M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 46603 [spades] 0:00:15.748 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 37330 edges [spades] 0:00:15.750 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 37330 sequences. [spades] 0:00:15.803 166M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:15.952 166M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3613320 kmers in total. [spades] 0:00:15.956 166M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:16.059 166M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:16.177 163M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:16.324 163M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1683968 bytes occupied (3.72836 bits per kmer). [spades] 0:00:16.386 219M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:16.484 219M / 5G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:16.486 219M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:16.529 220M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:17.045 220M / 5G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:17.047 220M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:17.079 219M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:17.102 219M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 0 gaps after checking 79 candidates [spades] 0:00:17.111 219M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:17.112 219M / 5G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:17.114 219M / 5G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:17.114 219M / 5G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:17.115 219M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:17.116 219M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.121 219M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.122 219M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.126 219M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.127 219M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:17.131 219M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:17.133 219M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:17.137 219M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:17.138 219M / 5G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:17.154 212M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:17.887 209M / 5G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 18097 times [spades] 0:00:17.888 209M / 5G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:17.890 209M / 5G INFO General (simplification.cpp : 502) Average coverage = 74.7833 [spades] 0:00:17.891 209M / 5G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:17.902 209M / 5G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K91/simplified_contigs [spades] 0:00:17.916 209M / 5G INFO General (binary_converter.cpp : 111) 568 reads written [spades] 0:00:17.920 209M / 5G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:17.991 146M / 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/Lactococcus/spades/K101/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/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/Lactococcus/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/Lactococcus/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/Lactococcus/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/Lactococcus/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] 0:00:00.010 9M / 10M INFO General (construction.cpp : 156) Average read length 172.524 [spades] 0:00:00.010 9M / 10M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.010 9M / 10M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.011 9M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.011 9M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.011 9M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 18641 [spades] 0:00:02.819 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4679152 reads [spades] 0:00:03.253 559M / 6G INFO General (kmer_splitters.hpp : 293) Used 4679152 reads [spades] 0:00:03.253 559M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:03.552 561M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4688239 kmers in total. [spades] 0:00:03.554 561M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:03.727 554M / 6G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:03.727 554M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:03.728 554M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:03.728 554M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:03.729 554M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:03.729 554M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:04.096 19G / 19G INFO General (kmer_splitters.hpp : 364) Processed 4688239 kmers [spades] 0:00:04.097 19G / 19G INFO General (kmer_splitters.hpp : 369) Used 4688239 kmers. [spades] 0:00:04.171 594M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.377 591M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4706838 kmers in total. [spades] 0:00:04.379 591M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.537 591M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:04.683 598M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:04.941 598M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2190840 bytes occupied (3.72367 bits per kmer). [spades] 0:00:04.949 598M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:05.153 598M / 6G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:05.155 594M / 6G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:05.158 594M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:05.344 564M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 83893 sequences extracted [spades] 0:00:05.485 564M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:05.532 564M / 6G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:05.944 410M / 6G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:05.945 410M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:05.946 410M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:06.047 412M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2189952 bytes occupied (3.73693 bits per kmer). [spades] 0:00:06.070 432M / 6G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:08.500 426M / 6G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:08.663 426M / 6G INFO General (construction.cpp : 505) Processed 167788 edges [spades] 0:00:08.707 393M / 6G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:08.709 393M / 6G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 12 [spades] 0:00:08.709 393M / 6G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 57 [spades] 0:00:08.710 393M / 6G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 61. Coverage mad: 17.7912 [spades] 0:00:08.711 393M / 6G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:08.791 393M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:09.017 393M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:09.873 393M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:11.499 393M / 6G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:12.383 393M / 6G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 62.099. Fitted coverage std. dev: 15.2869 [spades] 0:00:12.386 393M / 6G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.842537 [spades] 0:00:12.386 393M / 6G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 31 [spades] 0:00:12.387 393M / 6G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 31 [spades] 0:00:12.387 393M / 6G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2390131 [spades] 0:00:12.388 393M / 6G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 62.099 [spades] 0:00:12.389 393M / 6G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 31 [spades] 0:00:12.389 393M / 6G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:12.390 393M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:12.391 393M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:12.391 393M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:12.392 393M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:12.395 253M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:12.396 253M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66631 Gb [spades] 0:00:12.397 253M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:12.653 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 167788 edges [spades] 0:00:12.654 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 167788 sequences. [spades] 0:00:12.713 302M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:12.916 302M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4688239 kmers in total. [spades] 0:00:12.918 302M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:13.073 302M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:13.206 292M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:13.445 292M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2182176 bytes occupied (3.72366 bits per kmer). [spades] 0:00:13.501 372M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:13.603 372M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:13.605 372M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:13.715 377M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:14.153 240M / 6G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:14.154 240M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:14.186 239M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:14.258 232M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 3 gaps after checking 101 candidates [spades] 0:00:14.271 231M / 6G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:14.277 151M / 6G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:14.278 151M / 6G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:14.279 151M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:14.287 151M / 6G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:14.287 151M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:14.288 151M / 6G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:14.289 151M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:14.290 151M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:14.291 151M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:14.596 148M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 28971 times [spades] 0:00:14.597 148M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:14.958 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1340 times [spades] 0:00:14.959 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.003 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 398 times [spades] 0:00:15.004 162M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:15.004 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.005 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 11 times [spades] 0:00:15.006 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.007 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.007 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.009 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 38 times [spades] 0:00:15.010 162M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:15.011 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.011 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:15.012 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.013 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.013 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.015 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 17 times [spades] 0:00:15.016 162M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:15.017 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.017 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.018 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.019 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.019 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.022 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:15.023 162M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:15.023 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.024 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.024 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.025 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.026 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.027 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:15.028 162M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:15.028 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.029 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.030 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.030 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.031 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.032 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:15.032 162M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:15.033 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.033 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.034 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.035 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.035 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.036 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:15.037 162M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:15.037 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.038 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.038 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.039 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.040 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.041 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:15.041 162M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:15.042 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.042 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.043 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.044 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.044 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.045 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:15.046 162M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:15.046 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.047 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.047 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.048 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.049 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.049 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:15.050 162M / 6G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:15.051 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.055 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.056 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.061 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.062 162M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:15.066 162M / 6G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:15.070 162M / 6G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:15.071 162M / 6G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:15.072 162M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:15.073 162M / 6G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:15.074 162M / 6G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:15.076 162M / 6G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66598 Gb [spades] 0:00:15.077 162M / 6G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:15.282 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 41782 edges [spades] 0:00:15.284 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 41782 sequences. [spades] 0:00:15.341 154M / 6G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:15.511 154M / 6G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3554495 kmers in total. [spades] 0:00:15.514 154M / 6G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:15.634 154M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:15.741 155M / 6G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:15.940 155M / 6G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1656520 bytes occupied (3.72828 bits per kmer). [spades] 0:00:16.010 211M / 6G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:16.110 211M / 6G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:16.113 211M / 6G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:16.159 205M / 6G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:16.600 203M / 6G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:16.601 203M / 6G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:16.640 203M / 6G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:16.666 203M / 6G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 0 gaps after checking 107 candidates [spades] 0:00:16.674 203M / 6G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:16.675 203M / 6G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:16.676 203M / 6G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:16.677 203M / 6G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:16.678 203M / 6G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:16.679 203M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.684 203M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.684 203M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.689 203M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.690 203M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:16.694 203M / 6G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:16.694 203M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:16.699 203M / 6G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:16.700 203M / 6G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:16.714 203M / 6G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:17.454 199M / 6G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 20383 times [spades] 0:00:17.455 199M / 6G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:17.457 199M / 6G INFO General (simplification.cpp : 502) Average coverage = 65.5332 [spades] 0:00:17.457 199M / 6G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:17.458 199M / 6G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K101/simplified_contigs [spades] 0:00:17.463 200M / 6G INFO General (binary_converter.cpp : 111) 508 reads written [spades] 0:00:17.466 200M / 6G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:17.513 133M / 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/Lactococcus/spades/K111/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/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/Lactococcus/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/Lactococcus/spades/K111/configs/isolate_mode.info [spades] 0:00:00.000 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.000 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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] 0:00:00.002 7M / 9M INFO General (read_converter.cpp : 53) Binary reads detected [spades] 0:00:00.004 8M / 9M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:00.004 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K101/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 172.524 [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 18641 [spades] 0:00:02.606 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4679032 reads [spades] 0:00:02.969 500M / 5G INFO General (kmer_splitters.hpp : 293) Used 4679032 reads [spades] 0:00:02.970 500M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:03.249 502M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4483398 kmers in total. [spades] 0:00:03.251 502M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:03.417 497M / 5G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:03.417 497M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:03.418 497M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:03.418 497M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:03.419 497M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:03.419 497M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:03.763 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 4483398 kmers [spades] 0:00:03.764 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 4483398 kmers. [spades] 0:00:03.835 504M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:04.040 504M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4505508 kmers in total. [spades] 0:00:04.042 504M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:04.194 504M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:04.317 513M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:04.546 513M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2097520 bytes occupied (3.72437 bits per kmer). [spades] 0:00:04.556 513M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:04.713 513M / 5G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:04.715 513M / 5G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:04.718 513M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:04.893 485M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 80445 sequences extracted [spades] 0:00:05.031 485M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:05.078 485M / 5G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:05.476 368M / 5G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:05.477 368M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:05.478 368M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:05.587 373M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2094752 bytes occupied (3.73779 bits per kmer). [spades] 0:00:05.601 393M / 5G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:07.736 383M / 5G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:07.883 383M / 5G INFO General (construction.cpp : 505) Processed 160892 edges [spades] 0:00:07.923 363M / 5G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:07.925 363M / 5G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 17 [spades] 0:00:07.925 363M / 5G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 48 [spades] 0:00:07.926 363M / 5G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 52. Coverage mad: 14.826 [spades] 0:00:07.927 363M / 5G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:07.997 363M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:08.194 363M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:08.911 363M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:10.323 363M / 5G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 [spades] 0:00:10.952 363M / 5G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 53.381. Fitted coverage std. dev: 13.4288 [spades] 0:00:10.955 363M / 5G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.308186 [spades] 0:00:10.955 363M / 5G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 27 [spades] 0:00:10.956 363M / 5G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 27 [spades] 0:00:10.956 363M / 5G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2386303 [spades] 0:00:10.957 363M / 5G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 53.381 [spades] 0:00:10.958 363M / 5G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 27 [spades] 0:00:10.958 363M / 5G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:10.959 363M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:10.960 363M / 5G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:10.960 363M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:10.961 363M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:10.972 222M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:10.975 222M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66632 Gb [spades] 0:00:10.977 222M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:11.244 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 160892 edges [spades] 0:00:11.245 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 160892 sequences. [spades] 0:00:11.305 266M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:11.490 249M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4483398 kmers in total. [spades] 0:00:11.493 249M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:11.643 249M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:11.779 234M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:12.018 234M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 2087168 bytes occupied (3.72426 bits per kmer). [spades] 0:00:12.069 314M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:12.181 314M / 5G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:12.183 314M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:12.295 317M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:12.698 235M / 5G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:12.699 235M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:12.731 234M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:12.803 231M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 6 gaps after checking 106 candidates [spades] 0:00:12.820 231M / 5G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:12.825 151M / 5G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:12.826 151M / 5G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled [spades] 0:00:12.827 151M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:12.834 151M / 5G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:12.835 151M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:12.835 151M / 5G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:12.836 151M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:12.837 151M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:12.838 151M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.127 149M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 26572 times [spades] 0:00:13.128 149M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.389 155M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 856 times [spades] 0:00:13.391 155M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.435 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 328 times [spades] 0:00:13.436 154M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:13.437 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.438 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 10 times [spades] 0:00:13.438 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.439 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.440 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.442 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 44 times [spades] 0:00:13.443 154M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:13.443 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.444 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.445 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.445 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.446 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.448 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 16 times [spades] 0:00:13.448 154M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:13.449 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.450 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.450 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.451 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.452 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.455 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 6 times [spades] 0:00:13.455 154M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:13.456 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.457 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.457 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.458 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.459 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.460 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:13.461 154M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:13.461 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.462 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.463 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.463 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.464 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.465 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:13.465 154M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:13.466 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.466 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.467 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.468 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.468 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.469 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:13.469 154M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:13.470 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.471 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.471 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.472 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.473 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.473 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:13.474 154M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:13.475 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.475 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.476 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.477 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.477 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.478 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 2 times [spades] 0:00:13.478 154M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:13.479 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.480 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.480 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.481 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.482 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.482 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:13.483 154M / 5G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:13.483 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:13.488 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:13.489 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:13.494 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:13.495 154M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:13.499 154M / 5G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:13.503 154M / 5G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:13.504 154M / 5G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:13.505 154M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:13.506 154M / 5G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:13.507 154M / 5G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:13.508 154M / 5G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66608 Gb [spades] 0:00:13.509 154M / 5G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:13.689 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 47586 edges [spades] 0:00:13.691 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 47586 sequences. [spades] 0:00:13.746 144M / 5G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:13.907 144M / 5G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3480219 kmers in total. [spades] 0:00:13.910 144M / 5G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:14.031 144M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:14.144 145M / 5G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:14.313 145M / 5G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1622128 bytes occupied (3.7288 bits per kmer). [spades] 0:00:14.379 201M / 5G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:14.476 201M / 5G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:14.478 201M / 5G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:14.529 203M / 5G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:14.934 197M / 5G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:14.935 197M / 5G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:14.966 197M / 5G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:14.995 197M / 5G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 0 gaps after checking 107 candidates [spades] 0:00:15.004 197M / 5G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:15.005 197M / 5G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:15.006 197M / 5G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:15.007 197M / 5G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:15.008 197M / 5G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:15.009 197M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.014 197M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.014 197M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.019 197M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.020 197M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:15.025 197M / 5G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:15.026 197M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:15.030 197M / 5G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:15.031 197M / 5G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:15.050 197M / 5G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:15.781 195M / 5G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 23326 times [spades] 0:00:15.782 195M / 5G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:15.784 195M / 5G INFO General (simplification.cpp : 502) Average coverage = 56.3355 [spades] 0:00:15.785 195M / 5G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:15.786 195M / 5G INFO General (read_converter.cpp : 102) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K111/simplified_contigs [spades] 0:00:15.790 195M / 5G INFO General (binary_converter.cpp : 111) 467 reads written [spades] 0:00:15.793 196M / 5G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:15.845 139M / 5G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 15 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/Lactococcus/spades/K121/configs/config.info /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/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/Lactococcus/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/Lactococcus/spades/K121/configs/isolate_mode.info [spades] 0:00:00.001 7M / 9M INFO General (memory_limit.cpp : 49) Memory limit set to 240 Gb [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 86) Maximum k-mer length: 128 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 87) Assembling dataset (/DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/dataset.info) with K=121 [spades] 0:00:00.001 7M / 9M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 30 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 194) SPAdes started [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0 [spades] 0:00:00.001 7M / 9M INFO General (pipeline.cpp : 218) Will need read mapping, kmer mapper will be attached [spades] 0:00:00.001 7M / 9M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion [spades] 0:00:00.003 7M / 9M INFO General (read_converter.cpp : 53) Binary reads detected [spades] 0:00:00.005 8M / 9M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction [spades] 0:00:00.005 8M / 9M INFO General (construction.cpp : 115) Contigs from previous K will be used: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K111/simplified_contigs [spades] 0:00:00.008 8M / 9M INFO General (construction.cpp : 150) Max read length 280 [spades] 0:00:00.008 8M / 9M INFO General (construction.cpp : 153) Max read length without merged 150 [spades] 0:00:00.008 8M / 9M INFO General (construction.cpp : 156) Average read length 172.524 [spades] 0:00:00.009 8M / 9M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting [spades] 0:00:00.009 8M / 9M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 900 files using 30 threads. This might take a while. [spades] 0:00:00.010 8M / 10M INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:00.010 8M / 10M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66665 Gb [spades] 0:00:00.010 8M / 10M INFO General (kmer_splitters.hpp : 97) Using cell size of 18641 [spades] 0:00:02.203 21G / 21G INFO General (kmer_splitters.hpp : 287) Processed 4678950 reads [spades] 0:00:02.511 371M / 4G INFO General (kmer_splitters.hpp : 293) Used 4678950 reads [spades] 0:00:02.512 371M / 4G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:02.796 375M / 4G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4240779 kmers in total. [spades] 0:00:02.798 375M / 4G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:02.955 370M / 4G INFO General (stage.cpp : 113) PROCEDURE == Extension index construction [spades] 0:00:02.956 370M / 4G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:02.956 370M / 4G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:02.957 370M / 4G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:02.958 370M / 4G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66662 Gb [spades] 0:00:02.958 370M / 4G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:03.309 18G / 18G INFO General (kmer_splitters.hpp : 364) Processed 4240779 kmers [spades] 0:00:03.310 18G / 18G INFO General (kmer_splitters.hpp : 369) Used 4240779 kmers. [spades] 0:00:03.383 387M / 4G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:03.563 387M / 4G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4267045 kmers in total. [spades] 0:00:03.565 387M / 4G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:03.712 387M / 4G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:03.829 392M / 4G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:04.047 392M / 4G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1986704 bytes occupied (3.72474 bits per kmer). [spades] 0:00:04.055 392M / 4G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers [spades] 0:00:04.243 392M / 4G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. [spades] 0:00:04.247 392M / 4G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph [spades] 0:00:04.253 392M / 4G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths [spades] 0:00:04.429 381M / 4G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 76329 sequences extracted [spades] 0:00:04.558 381M / 4G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops [spades] 0:00:04.602 381M / 4G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 1 loops collected [spades] 0:00:04.991 268M / 4G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM) [spades] 0:00:04.992 268M / 4G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:04.993 268M / 4G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:05.102 281M / 4G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1982120 bytes occupied (3.73916 bits per kmer). [spades] 0:00:05.115 301M / 4G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while. [spades] 0:00:06.961 301M / 4G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM [spades] 0:00:07.098 301M / 4G INFO General (construction.cpp : 505) Processed 152660 edges [spades] 0:00:07.139 281M / 4G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding [spades] 0:00:07.141 281M / 4G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 14 [spades] 0:00:07.142 281M / 4G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 42 [spades] 0:00:07.142 281M / 4G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 44. Coverage mad: 13.3434 [spades] 0:00:07.143 281M / 4G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model [spades] 0:00:07.208 281M / 4G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 [spades] 0:00:07.376 281M / 4G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 [spades] 0:00:07.891 281M / 4G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 [spades] 0:00:08.450 281M / 4G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 44.6822. Fitted coverage std. dev: 11.5546 [spades] 0:00:08.453 281M / 4G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.288561 [spades] 0:00:08.454 281M / 4G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 22 [spades] 0:00:08.454 281M / 4G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 22 [spades] 0:00:08.455 281M / 4G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 2387326 [spades] 0:00:08.456 281M / 4G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 44.6822 [spades] 0:00:08.456 281M / 4G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 22 [spades] 0:00:08.457 281M / 4G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0 [spades] 0:00:08.458 281M / 4G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:08.458 281M / 4G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:08.459 281M / 4G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:08.460 281M / 4G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:08.462 174M / 4G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:08.463 174M / 4G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.66629 Gb [spades] 0:00:08.464 174M / 4G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:08.711 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 152660 edges [spades] 0:00:08.713 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 152660 sequences. [spades] 0:00:08.775 189M / 4G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:08.959 189M / 4G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 4240779 kmers in total. [spades] 0:00:08.962 189M / 4G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:09.105 189M / 4G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:09.225 174M / 4G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:09.441 174M / 4G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1974600 bytes occupied (3.72498 bits per kmer). [spades] 0:00:09.494 254M / 4G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:09.586 239M / 4G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:09.588 239M / 4G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:09.700 243M / 4G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:10.066 238M / 4G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:10.067 238M / 4G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:10.100 238M / 4G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:10.168 231M / 4G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 16 gaps after checking 114 candidates [spades] 0:00:10.188 231M / 4G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification [spades] 0:00:10.193 151M / 4G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning [spades] 0:00:10.194 151M / 4G INFO General (simplification.cpp : 63) Most init cleaning disabled on main iteration [spades] 0:00:10.195 151M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover [spades] 0:00:10.202 151M / 4G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times [spades] 0:00:10.203 151M / 4G INFO StageManager (stage.cpp : 166) STAGE == Simplification [spades] 0:00:10.204 151M / 4G INFO General (simplification.cpp : 383) Graph simplification started [spades] 0:00:10.204 151M / 4G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:10.205 151M / 4G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1 [spades] 0:00:10.206 151M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:10.479 142M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 23486 times [spades] 0:00:10.480 142M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:10.638 144M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 430 times [spades] 0:00:10.639 144M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:10.678 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 230 times [spades] 0:00:10.679 145M / 4G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2 [spades] 0:00:10.680 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:10.681 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 8 times [spades] 0:00:10.681 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:10.682 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:10.683 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:10.685 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 43 times [spades] 0:00:10.686 145M / 4G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3 [spades] 0:00:10.686 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:10.687 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:10.688 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:10.688 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:10.689 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:10.691 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 13 times [spades] 0:00:10.691 145M / 4G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4 [spades] 0:00:10.692 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:10.692 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:10.693 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:10.694 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:10.695 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:10.697 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 10 times [spades] 0:00:10.697 145M / 4G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5 [spades] 0:00:10.698 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:10.698 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:10.699 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:10.700 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:10.700 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:10.702 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 4 times [spades] 0:00:10.703 145M / 4G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6 [spades] 0:00:10.704 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:10.704 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:10.705 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:10.705 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:10.706 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:10.708 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 5 times [spades] 0:00:10.708 145M / 4G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7 [spades] 0:00:10.709 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:10.710 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:10.710 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:10.711 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:10.711 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:10.712 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 1 times [spades] 0:00:10.713 145M / 4G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8 [spades] 0:00:10.713 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:10.714 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:10.715 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:10.715 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:10.716 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:10.717 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times [spades] 0:00:10.717 145M / 4G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9 [spades] 0:00:10.718 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:10.719 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:10.719 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:10.721 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 1 times [spades] 0:00:10.721 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:10.722 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:10.722 145M / 4G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10 [spades] 0:00:10.723 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:10.724 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:10.724 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:10.725 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:10.725 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:10.726 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:10.727 145M / 4G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11 [spades] 0:00:10.727 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:10.732 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times [spades] 0:00:10.733 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:10.739 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:10.740 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:10.744 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:10.745 145M / 4G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 12 [spades] 0:00:10.746 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:10.747 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:10.748 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:10.748 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:10.749 145M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover [spades] 0:00:10.750 145M / 4G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times [spades] 0:00:10.755 145M / 4G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer [spades] 0:00:10.756 145M / 4G INFO General (graph_pack.hpp : 105) Index refill [spades] 0:00:10.756 145M / 4G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index [spades] 0:00:10.757 145M / 4G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 480 files using 30 threads. This might take a while. [spades] 0:00:10.758 145M / 4G INFO General (file_limit.hpp : 32) Open file limit set to 10000 [spades] 0:00:10.760 145M / 4G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 2.6662 Gb [spades] 0:00:10.761 145M / 4G INFO General (kmer_splitters.hpp : 97) Using cell size of 34952 [spades] 0:00:10.933 18G / 18G INFO General (edge_index_builders.hpp : 77) Processed 54722 edges [spades] 0:00:10.934 18G / 18G INFO General (edge_index_builders.hpp : 82) Used 54722 sequences. [spades] 0:00:10.989 171M / 4G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. [spades] 0:00:11.157 171M / 4G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3369653 kmers in total. [spades] 0:00:11.160 171M / 4G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. [spades] 0:00:11.279 171M / 4G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices [spades] 0:00:11.382 171M / 4G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. [spades] 0:00:11.564 171M / 4G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 1570832 bytes occupied (3.72936 bits per kmer). [spades] 0:00:11.638 227M / 4G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. [spades] 0:00:11.730 227M / 4G INFO General (edge_index.hpp : 92) Index refilled [spades] 0:00:11.732 227M / 4G INFO General (gap_closer.cpp : 147) Preparing shift maps [spades] 0:00:11.787 229M / 4G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while) [spades] 0:00:12.162 213M / 4G INFO General (gap_closer.cpp : 126) Used 882032 paired reads [spades] 0:00:12.163 213M / 4G INFO General (gap_closer.cpp : 128) Merging paired indices [spades] 0:00:12.198 212M / 4G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps [spades] 0:00:12.231 212M / 4G INFO GapCloser (gap_closer.cpp : 366) Closing short gaps complete: filled 0 gaps after checking 97 candidates [spades] 0:00:12.241 212M / 4G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup [spades] 0:00:12.242 212M / 4G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification [spades] 0:00:12.243 212M / 4G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled [spades] 0:00:12.243 212M / 4G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled [spades] 0:00:12.244 212M / 4G INFO General (graph_simplification.hpp : 643) Creating parallel br instance [spades] 0:00:12.245 212M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.250 212M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:12.251 212M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.256 212M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:12.257 212M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper [spades] 0:00:12.261 212M / 4G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times [spades] 0:00:12.262 212M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover [spades] 0:00:12.267 212M / 4G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times [spades] 0:00:12.268 212M / 4G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges [spades] 0:00:12.285 212M / 4G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges [spades] 0:00:12.983 198M / 4G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 26940 times [spades] 0:00:12.984 198M / 4G INFO General (simplification.cpp : 496) Counting average coverage [spades] 0:00:12.985 198M / 4G INFO General (simplification.cpp : 502) Average coverage = 47.1616 [spades] 0:00:12.986 198M / 4G INFO StageManager (stage.cpp : 166) STAGE == Mismatch Correction [spades] 0:00:12.986 198M / 4G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 106568 kmers to process [spades] 0:00:13.007 198M / 4G INFO General (graph_pack.hpp : 115) Normalizing done [spades] 0:00:15.397 212M / 4G INFO General (mismatch_shall_not_pass.hp: 195) Finished collecting potential mismatches positions [spades] 0:00:15.437 194M / 4G INFO General (mismatch_shall_not_pass.hp: 310) All edges processed [spades] 0:00:15.438 194M / 4G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides [spades] 0:00:15.439 194M / 4G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:15.440 194M / 4G INFO General (contig_output.hpp : 21) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/before_rr.fasta [spades] 0:00:15.470 194M / 4G INFO General (contig_output_stage.cpp : 146) Writing GFA graph to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/assembly_graph_after_simplification.gfa [spades] 0:00:15.493 194M / 4G INFO StageManager (stage.cpp : 166) STAGE == Paired Information Counting [spades] 0:00:15.496 182M / 4G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 106568 kmers to process [spades] 0:00:15.497 182M / 4G INFO General (graph_pack.hpp : 115) Normalizing done [spades] 0:00:15.498 182M / 4G INFO General (pair_info_count.cpp : 322) Min edge length for estimation: 56944 [spades] 0:00:15.498 182M / 4G INFO General (pair_info_count.cpp : 333) Estimating insert size for library #0 [spades] 0:00:15.499 182M / 4G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) [spades] 0:00:15.767 678M / 4G INFO General (pair_info_count.cpp : 39) Selecting usual mapper [spades] 0:00:17.022 660M / 4G INFO General (sequence_mapper_notifier.h: 94) Total 1456976 reads processed [spades] 0:00:17.108 660M / 4G INFO General (pair_info_count.cpp : 208) Edge pairs: 3390 [spades] 0:00:17.109 660M / 4G INFO General (pair_info_count.cpp : 212) 690994 paired reads (47.4266% of all) aligned to long edges [spades] 0:00:17.128 164M / 4G INFO General (pair_info_count.cpp : 356) Insert size = 297.719, deviation = 61.6775, left quantile = 222, right quantile = 377, read length = 150 [spades] 0:00:17.129 164M / 4G INFO General (pair_info_count.cpp : 373) Filtering data for library #0 [spades] 0:00:17.130 164M / 4G INFO General (pair_info_count.cpp : 39) Selecting usual mapper [spades] 0:00:17.762 163M / 4G INFO General (sequence_mapper_notifier.h: 94) Total 1456976 reads processed [spades] 0:00:17.764 163M / 4G INFO General (pair_info_count.cpp : 385) Mapping library #0 [spades] 0:00:17.765 163M / 4G INFO General (pair_info_count.cpp : 387) Mapping paired reads (takes a while) [spades] 0:00:17.766 163M / 4G INFO General (pair_info_count.cpp : 288) Left insert size quantile 222, right insert size quantile 377, filtering threshold 2, rounding threshold 0 [spades] 0:00:17.777 168M / 4G INFO General (pair_info_count.cpp : 39) Selecting usual mapper [spades] 0:00:18.512 167M / 4G INFO General (sequence_mapper_notifier.h: 94) Total 1456976 reads processed [spades] 0:00:18.519 167M / 4G INFO StageManager (stage.cpp : 166) STAGE == Distance Estimation [spades] 0:00:18.520 167M / 4G INFO General (distance_estimation.cpp : 174) Processing library #0 [spades] 0:00:18.521 167M / 4G INFO General (distance_estimation.cpp : 150) Weight Filter Done [spades] 0:00:18.522 167M / 4G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator [spades] 0:00:18.527 162M / 4G INFO General (distance_estimation.cpp : 35) Filtering info [spades] 0:00:18.528 162M / 4G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2448 [spades] 0:00:18.530 162M / 4G INFO General (pair_info_filters.hpp : 263) Done filtering [spades] 0:00:18.531 162M / 4G INFO General (distance_estimation.cpp : 157) Refining clustered pair information [spades] 0:00:18.532 162M / 4G INFO General (distance_estimation.cpp : 159) The refining of clustered pair information has been finished [spades] 0:00:18.533 162M / 4G INFO General (distance_estimation.cpp : 161) Improving paired information [spades] 0:00:18.540 162M / 4G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 54; contradictional = 10 [spades] 0:00:18.547 162M / 4G INFO PairInfoImprover (pair_info_improver.hpp : 103) Paired info stats: missing = 0; contradictional = 0 [spades] 0:00:18.548 162M / 4G INFO General (distance_estimation.cpp : 104) Filling scaffolding index [spades] 0:00:18.554 162M / 4G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator [spades] 0:00:18.558 163M / 4G INFO General (distance_estimation.cpp : 35) Filtering info [spades] 0:00:18.559 163M / 4G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 885 [spades] 0:00:18.561 163M / 4G INFO General (pair_info_filters.hpp : 263) Done filtering [spades] 0:00:18.561 163M / 4G INFO General (distance_estimation.cpp : 183) Clearing raw paired index [spades] 0:00:18.563 163M / 4G INFO StageManager (stage.cpp : 166) STAGE == Repeat Resolving [spades] 0:00:18.564 163M / 4G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving [spades] 0:00:18.565 163M / 4G INFO General (launcher.cpp : 538) ExSPAnder repeat resolving tool started [spades] 0:00:18.569 164M / 4G INFO General (launcher.cpp : 404) Creating main extenders, unique edge length = 2000 [spades] 0:00:18.571 164M / 4G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #0 is 47.1616 [spades] 0:00:18.573 164M / 4G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #0 is 47.1616 [spades] 0:00:18.575 164M / 4G INFO General (extenders_logic.cpp : 519) Using 1 paired-end library [spades] 0:00:18.576 164M / 4G INFO General (extenders_logic.cpp : 520) Using 1 paired-end scaffolding library [spades] 0:00:18.577 164M / 4G INFO General (extenders_logic.cpp : 521) Using 0 single read libraries [spades] 0:00:18.578 164M / 4G INFO General (launcher.cpp : 432) Total number of extenders is 3 [spades] 0:00:18.579 164M / 4G INFO General (path_extender.hpp : 894) Processed 0 paths from 408 (0%) [spades] 0:00:18.603 165M / 4G INFO General (path_extender.hpp : 894) Processed 41 paths from 408 (10%) [spades] 0:00:18.621 165M / 4G INFO General (path_extender.hpp : 894) Processed 82 paths from 408 (20%) [spades] 0:00:18.629 166M / 4G INFO General (path_extender.hpp : 894) Processed 123 paths from 408 (30%) [spades] 0:00:18.631 166M / 4G INFO General (path_extender.hpp : 892) Processed 128 paths from 408 (31%) [spades] 0:00:18.637 166M / 4G INFO General (path_extender.hpp : 894) Processed 164 paths from 408 (40%) [spades] 0:00:18.644 166M / 4G INFO General (path_extender.hpp : 894) Processed 205 paths from 408 (50%) [spades] 0:00:18.650 167M / 4G INFO General (path_extender.hpp : 894) Processed 246 paths from 408 (60%) [spades] 0:00:18.651 167M / 4G INFO General (path_extender.hpp : 892) Processed 256 paths from 408 (62%) [spades] 0:00:18.652 167M / 4G INFO General (path_extender.hpp : 894) Processed 287 paths from 408 (70%) [spades] 0:00:18.660 167M / 4G INFO General (path_extender.hpp : 894) Processed 328 paths from 408 (80%) [spades] 0:00:18.662 167M / 4G INFO General (path_extender.hpp : 894) Processed 369 paths from 408 (90%) [spades] 0:00:18.662 167M / 4G INFO General (launcher.cpp : 244) Finalizing paths [spades] 0:00:18.663 167M / 4G INFO General (launcher.cpp : 246) Deduplicating paths [spades] 0:00:18.665 167M / 4G INFO General (launcher.cpp : 250) Paths deduplicated [spades] 0:00:18.666 167M / 4G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps [spades] 0:00:18.667 167M / 4G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths [spades] 0:00:18.668 167M / 4G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps [spades] 0:00:18.668 167M / 4G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps [spades] 0:00:18.670 167M / 4G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps [spades] 0:00:18.673 167M / 4G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths [spades] 0:00:18.674 167M / 4G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths [spades] 0:00:18.676 167M / 4G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed [spades] 0:00:18.677 167M / 4G INFO General (launcher.cpp : 267) Paths finalized [spades] 0:00:18.678 167M / 4G INFO General (launcher.cpp : 439) Closing gaps in paths [spades] 0:00:18.680 167M / 4G INFO General (launcher.cpp : 467) Gap closing completed [spades] 0:00:18.681 167M / 4G INFO General (launcher.cpp : 296) Traversing tandem repeats [spades] 0:00:18.684 167M / 4G INFO General (launcher.cpp : 306) Traversed 0 loops [spades] 0:00:18.685 167M / 4G INFO General (launcher.cpp : 244) Finalizing paths [spades] 0:00:18.686 167M / 4G INFO General (launcher.cpp : 246) Deduplicating paths [spades] 0:00:18.687 167M / 4G INFO General (launcher.cpp : 250) Paths deduplicated [spades] 0:00:18.687 167M / 4G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps [spades] 0:00:18.688 167M / 4G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths [spades] 0:00:18.689 167M / 4G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps [spades] 0:00:18.690 167M / 4G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps [spades] 0:00:18.691 167M / 4G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps [spades] 0:00:18.692 167M / 4G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths [spades] 0:00:18.693 167M / 4G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths [spades] 0:00:18.693 167M / 4G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed [spades] 0:00:18.695 167M / 4G INFO General (launcher.cpp : 267) Paths finalized [spades] 0:00:18.696 167M / 4G INFO General (launcher.cpp : 596) ExSPAnder repeat resolving tool finished [spades] 0:00:18.698 167M / 4G INFO StageManager (stage.cpp : 166) STAGE == Contig Output [spades] 0:00:18.699 167M / 4G INFO General (contig_output.hpp : 21) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/before_rr.fasta [spades] 0:00:18.739 167M / 4G INFO General (contig_output_stage.cpp : 146) Writing GFA graph to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/assembly_graph_with_scaffolds.gfa [spades] 0:00:18.771 167M / 4G INFO General (contig_output_stage.cpp : 160) Outputting FastG graph to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/assembly_graph.fastg [spades] 0:00:18.902 167M / 4G INFO General (contig_output_stage.cpp : 190) Breaking scaffolds [spades] 0:00:18.946 168M / 4G INFO General (contig_output_stage.cpp : 95) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/final_contigs.fasta [spades] 0:00:18.981 168M / 4G INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/final_contigs.paths [spades] 0:00:19.008 168M / 4G INFO General (contig_output_stage.cpp : 95) Outputting contigs to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/scaffolds.fasta [spades] 0:00:19.040 168M / 4G INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/scaffolds.paths [spades] 0:00:19.041 168M / 4G INFO General (contig_output_stage.cpp : 108) Populating GFA with scaffold paths [spades] 0:00:19.043 168M / 4G INFO General (pipeline.cpp : 259) SPAdes finished [spades] 0:00:19.082 106M / 4G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 19 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/Lactococcus/spades/K121/before_rr.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/before_rr.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/assembly_graph_after_simplification.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/assembly_graph_after_simplification.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/final_contigs.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/contigs.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/first_pe_contigs.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/first_pe_contigs.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/strain_graph.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/strain_graph.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/scaffolds.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/scaffolds.fasta /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/scaffolds.paths /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/scaffolds.paths /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/assembly_graph_with_scaffolds.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/assembly_graph_with_scaffolds.gfa /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/assembly_graph.fastg /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/assembly_graph.fastg /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/K121/final_contigs.paths /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/spades/scaffolds.fasta --misc_dir /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/spades/contigs.fasta [spades] * Assembled scaffolds are in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/scaffolds.fasta [spades] * Paths in the assembly graph corresponding to the contigs are in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/contigs.paths [spades] * Paths in the assembly graph corresponding to the scaffolds are in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/scaffolds.paths [spades] * Assembly graph is in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/spades/assembly_graph.fastg [spades] * Assembly graph in GFA format is in /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/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/Lactococcus/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] 0.55 seconds elapse. [bwa-index] [bwa_index] Update BWT... 0.03 sec [bwa-index] [bwa_index] Pack forward-only FASTA... 0.03 sec [bwa-index] [bwa_index] Construct SA from BWT and Occ... 0.28 sec [bwa-index] [main] Version: 0.7.17-r1188 [bwa-index] [main] CMD: bwa index spades.fasta [bwa-index] [main] Real time: 1.244 sec; CPU: 0.924 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/5n2VNtoOQH -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 245 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): (11, 959975, 36, 5) [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation FF... [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (145, 248, 305) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 625) [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (216.60, 83.94) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (1, 785) [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation FR... [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (263, 302, 343) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (103, 503) [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (303.41, 61.44) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (23, 583) [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation RF... [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (506, 536, 553) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (412, 647) [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (527.50, 39.51) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (365, 694) [bwa+samtools-sort] [M::mem_pestat] skip orientation RR as there are not enough pairs [bwa+samtools-sort] [M::mem_pestat] skip orientation FF [bwa+samtools-sort] [M::mem_pestat] skip orientation RF [bwa+samtools-sort] [M::mem_process_seqs] Processed 2000000 reads in 233.447 CPU sec, 13.543 real sec [bwa+samtools-sort] [M::process] read 913952 sequences (137092800 bp)... [bwa+samtools-sort] [samclip] Processed 100000 records... [bwa+samtools-sort] [samclip] Processed 200000 records... [bwa+samtools-sort] [samclip] Processed 300000 records... [bwa+samtools-sort] [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 440187, 10, 5) [bwa+samtools-sort] [M::mem_pestat] skip orientation FF as there are not enough pairs [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation FR... [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (243, 276, 314) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (101, 456) [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (279.39, 54.21) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (30, 527) [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation RF... [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (496, 521, 564) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (360, 700) [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (521.60, 47.53) [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (292, 768) [bwa+samtools-sort] [M::mem_pestat] skip orientation RR as there are not enough pairs [bwa+samtools-sort] [M::mem_pestat] skip orientation RF [bwa+samtools-sort] [M::mem_process_seqs] Processed 913952 reads in 103.879 CPU sec, 5.691 real sec [bwa+samtools-sort] [samclip] Processed 400000 records... [bwa+samtools-sort] [samclip] Processed 500000 records... [bwa+samtools-sort] [samclip] Processed 600000 records... [bwa+samtools-sort] [samclip] Processed 700000 records... [bwa+samtools-sort] [samclip] Processed 800000 records... [bwa+samtools-sort] [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[samclip] Total SAM records 2915101, removed 54663, allowed 61710, passed 2860438 [bwa+samtools-sort] [samclip] Header contained 246 lines [bwa+samtools-sort] [samclip] Done. [bwa+samtools-sort] [bwa+samtools-sort] [main] Real time: 31.957 sec; CPU: 346.900 sec [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: 2541749 [pilon] Processing NODE_65_length_3859_cov_46.880150:1-3859 [pilon] Processing NODE_237_length_240_cov_52.882353:1-240 [pilon] Processing NODE_94_length_2082_cov_25.812851:1-2082 [pilon] Processing NODE_178_length_695_cov_3.146341:1-695 [pilon] Processing NODE_201_length_432_cov_1.257235:1-432 [pilon] Processing NODE_102_length_1806_cov_36.555490:1-1806 [pilon] Processing NODE_220_length_355_cov_31.337607:1-355 [pilon] Processing NODE_229_length_261_cov_73.464286:1-261 [pilon] Processing NODE_43_length_8142_cov_39.854632:1-8142 [pilon] Processing NODE_106_length_1728_cov_76.780336:1-1728 [pilon] Processing NODE_91_length_2143_cov_108.869931:1-2143 [pilon] Processing NODE_48_length_7076_cov_77.874191:1-7076 [pilon] Processing NODE_9_length_73464_cov_33.170173:1-73464 [pilon] Processing NODE_241_length_232_cov_65.252252:1-232 [pilon] Processing NODE_25_length_27770_cov_54.426345:1-27770 [pilon] Processing NODE_133_length_1052_cov_121.211600:1-1052 [pilon] Processing NODE_103_length_1802_cov_38.196312:1-1802 [pilon] Processing NODE_206_length_409_cov_48.888889:1-409 [pilon] Processing NODE_204_length_413_cov_52.547945:1-413 [pilon] Processing NODE_20_length_35358_cov_60.026733:1-35358 [pilon] Processing NODE_242_length_222_cov_59.168317:1-222 [pilon] Processing NODE_34_length_14248_cov_60.176329:1-14248 [pilon] Processing NODE_55_length_5916_cov_40.733563:1-5916 [pilon] Processing NODE_128_length_1169_cov_43.748092:1-1169 [pilon] Processing NODE_244_length_124_cov_87.000000:1-124 [pilon] Processing NODE_24_length_27859_cov_33.842022:1-27859 [pilon] Processing NODE_2_length_206873_cov_35.744501:1-206873 [pilon] Processing NODE_236_length_240_cov_167.823529:1-240 [pilon] Processing NODE_73_length_2986_cov_46.962653:1-2986 [pilon] Processing NODE_209_length_408_cov_0.881533:1-408 [pilon] NODE_244_length_124_cov_87.000000:1-124 log: [pilon] NODE_201_length_432_cov_1.257235:1-432 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 8, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 124 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 7, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 432 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_201_length_432_cov_1.257235:1-432 [pilon] Processing NODE_82_length_2490_cov_154.097087:1-2490 [pilon] Finished processing NODE_244_length_124_cov_87.000000:1-124 [pilon] Processing NODE_95_length_2039_cov_45.280501:1-2039 [pilon] NODE_220_length_355_cov_31.337607:1-355 log: [pilon] frags shovill.bam: coverage 19 [pilon] Total Reads: 153, Coverage: 19, minDepth: 5 [pilon] Confirmed 241 of 355 bases (67.89%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_220_length_355_cov_31.337607:1-355 [pilon] Processing NODE_28_length_24965_cov_56.849863:1-24965 [pilon] NODE_237_length_240_cov_52.882353:1-240 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 203, Coverage: 7, minDepth: 5 [pilon] Confirmed 168 of 240 bases (70.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_209_length_408_cov_0.881533:1-408 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 408 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_209_length_408_cov_0.881533:1-408 [pilon] Processing NODE_218_length_377_cov_119.761719:1-377 [pilon] Finished processing NODE_237_length_240_cov_52.882353:1-240 [pilon] Processing NODE_151_length_867_cov_4.878016:1-867 [pilon] NODE_241_length_232_cov_65.252252:1-232 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 150, Coverage: 7, minDepth: 5 [pilon] Confirmed 135 of 232 bases (58.19%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_241_length_232_cov_65.252252:1-232 [pilon] Processing NODE_46_length_7733_cov_93.546506:1-7733 [pilon] NODE_242_length_222_cov_59.168317:1-222 log: [pilon] NODE_229_length_261_cov_73.464286:1-261 log: [pilon] frags shovill.bam: coverage 13 [pilon] Total Reads: 211, Coverage: 13, minDepth: 5 [pilon] Confirmed 211 of 261 bases (80.84%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_229_length_261_cov_73.464286:1-261 [pilon] Processing NODE_131_length_1124_cov_29.725823:1-1124 [pilon] NODE_178_length_695_cov_3.146341:1-695 log: [pilon] frags shovill.bam: coverage 9 [pilon] Total Reads: 48, Coverage: 9, minDepth: 5 [pilon] Confirmed 452 of 695 bases (65.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_178_length_695_cov_3.146341:1-695 [pilon] Processing NODE_125_length_1220_cov_36.185623:1-1220 [pilon] NODE_204_length_413_cov_52.547945:1-413 log: [pilon] frags shovill.bam: coverage 40 [pilon] Total Reads: 400, Coverage: 40, minDepth: 10 [pilon] Confirmed 288 of 413 bases (69.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_204_length_413_cov_52.547945:1-413 [pilon] Processing NODE_13_length_57066_cov_38.945544:1-57066 [pilon] NODE_206_length_409_cov_48.888889:1-409 log: [pilon] frags shovill.bam: coverage 38 [pilon] Total Reads: 343, Coverage: 38, minDepth: 10 [pilon] Confirmed 288 of 409 bases (70.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_206_length_409_cov_48.888889:1-409 [pilon] Processing NODE_92_length_2104_cov_28.162885:1-2104 [pilon] NODE_236_length_240_cov_167.823529:1-240 log: [pilon] frags shovill.bam: coverage 31 [pilon] Total Reads: 501, Coverage: 31, minDepth: 8 [pilon] Confirmed 221 of 240 bases (92.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_236_length_240_cov_167.823529:1-240 [pilon] Processing NODE_33_length_15095_cov_57.026579:1-15095 [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 118, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 222 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_222_cov_59.168317:1-222 [pilon] Processing NODE_45_length_7758_cov_75.902580:1-7758 [pilon] NODE_218_length_377_cov_119.761719:1-377 log: [pilon] frags shovill.bam: coverage 63 [pilon] Total Reads: 739, Coverage: 63, minDepth: 16 [pilon] Confirmed 248 of 377 bases (65.78%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_218_length_377_cov_119.761719:1-377 [pilon] Processing NODE_15_length_46866_cov_57.877548:1-46866 [pilon] NODE_131_length_1124_cov_29.725823:1-1124 log: [pilon] frags shovill.bam: coverage 84 [pilon] Total Reads: 733, Coverage: 84, minDepth: 21 [pilon] Confirmed 791 of 1124 bases (70.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_131_length_1124_cov_29.725823:1-1124 [pilon] Processing NODE_177_length_701_cov_7.705172:1-701 [pilon] NODE_133_length_1052_cov_121.211600:1-1052 log: [pilon] frags shovill.bam: coverage 284 [pilon] Total Reads: 2694, Coverage: 284, minDepth: 71 [pilon] Confirmed 931 of 1052 bases (88.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_133_length_1052_cov_121.211600:1-1052 [pilon] Processing NODE_166_length_766_cov_21.088372:1-766 [pilon] NODE_151_length_867_cov_4.878016:1-867 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 93, Coverage: 14, minDepth: 5 [pilon] Confirmed 590 of 867 bases (68.05%) [pilon] Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_151_length_867_cov_4.878016:1-867 [pilon] Processing NODE_180_length_675_cov_8.315884:1-675 [pilon] NODE_94_length_2082_cov_25.812851:1-2082 log: [pilon] frags shovill.bam: coverage 78 [pilon] Total Reads: 1261, Coverage: 78, minDepth: 20 [pilon] Confirmed 1673 of 2082 bases (80.36%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_94_length_2082_cov_25.812851:1-2082 [pilon] Processing NODE_26_length_26480_cov_58.159604:1-26480 [pilon] NODE_128_length_1169_cov_43.748092:1-1169 log: [pilon] frags shovill.bam: coverage 124 [pilon] Total Reads: 1121, Coverage: 124, minDepth: 31 [pilon] Confirmed 954 of 1169 bases (81.61%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_128_length_1169_cov_43.748092:1-1169 [pilon] Processing NODE_127_length_1177_cov_57.232008:1-1177 [pilon] NODE_102_length_1806_cov_36.555490:1-1806 log: [pilon] frags shovill.bam: coverage 111 [pilon] Total Reads: 1549, Coverage: 111, minDepth: 28 [pilon] Confirmed 1225 of 1806 bases (67.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_102_length_1806_cov_36.555490:1-1806 [pilon] Processing NODE_199_length_468_cov_1.409222:1-468 [pilon] NODE_103_length_1802_cov_38.196312:1-1802 log: [pilon] frags shovill.bam: coverage 112 [pilon] Total Reads: 1565, Coverage: 112, minDepth: 28 [pilon] Confirmed 1473 of 1802 bases (81.74%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_103_length_1802_cov_38.196312:1-1802 [pilon] Processing NODE_181_length_662_cov_5.432532:1-662 [pilon] NODE_125_length_1220_cov_36.185623:1-1220 log: [pilon] frags shovill.bam: coverage 101 [pilon] Total Reads: 967, Coverage: 101, minDepth: 25 [pilon] Confirmed 910 of 1220 bases (74.59%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_125_length_1220_cov_36.185623:1-1220 [pilon] Processing NODE_148_length_891_cov_14.910390:1-891 [pilon] NODE_180_length_675_cov_8.315884:1-675 log: [pilon] frags shovill.bam: coverage 22 [pilon] Total Reads: 118, Coverage: 22, minDepth: 6 [pilon] Confirmed 557 of 675 bases (82.52%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_180_length_675_cov_8.315884:1-675 [pilon] Processing NODE_107_length_1726_cov_25.937695:1-1726 [pilon] NODE_177_length_701_cov_7.705172:1-701 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 136, Coverage: 18, minDepth: 5 [pilon] Confirmed 589 of 701 bases (84.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_177_length_701_cov_7.705172:1-701 [pilon] Processing NODE_129_length_1166_cov_30.761722:1-1166 [pilon] NODE_106_length_1728_cov_76.780336:1-1728 log: [pilon] frags shovill.bam: coverage 185 [pilon] Total Reads: 2960, Coverage: 185, minDepth: 46 [pilon] Confirmed 1437 of 1728 bases (83.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_106_length_1728_cov_76.780336:1-1728 [pilon] Processing NODE_153_length_849_cov_50.174451:1-849 [pilon] NODE_199_length_468_cov_1.409222:1-468 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 13, Coverage: 3, minDepth: 5 [pilon] Confirmed 148 of 468 bases (31.62%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_199_length_468_cov_1.409222:1-468 [pilon] Processing NODE_190_length_587_cov_135.416309:1-587 [pilon] NODE_166_length_766_cov_21.088372:1-766 log: [pilon] frags shovill.bam: coverage 57 [pilon] Total Reads: 335, Coverage: 57, minDepth: 14 [pilon] Confirmed 550 of 766 bases (71.80%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_166_length_766_cov_21.088372:1-766 [pilon] Processing NODE_145_length_924_cov_9.550436:1-924 [pilon] NODE_181_length_662_cov_5.432532:1-662 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 75, Coverage: 15, minDepth: 5 [pilon] Confirmed 523 of 662 bases (79.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_181_length_662_cov_5.432532:1-662 [pilon] Processing NODE_21_length_31170_cov_46.522207:1-31170 [pilon] NODE_92_length_2104_cov_28.162885:1-2104 log: [pilon] frags shovill.bam: coverage 83 [pilon] Total Reads: 1353, Coverage: 83, minDepth: 21 [pilon] Confirmed 1741 of 2104 bases (82.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_92_length_2104_cov_28.162885:1-2104 [pilon] Processing NODE_185_length_624_cov_6.166998:1-624 [pilon] NODE_95_length_2039_cov_45.280501:1-2039 log: [pilon] frags shovill.bam: coverage 122 [pilon] Total Reads: 2133, Coverage: 122, minDepth: 31 [pilon] Confirmed 1750 of 2039 bases (85.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_95_length_2039_cov_45.280501:1-2039 [pilon] Processing NODE_1_length_256070_cov_43.389882:1-256070 [pilon] NODE_148_length_891_cov_14.910390:1-891 log: [pilon] frags shovill.bam: coverage 62 [pilon] Total Reads: 429, Coverage: 62, minDepth: 16 [pilon] Confirmed 555 of 891 bases (62.29%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_148_length_891_cov_14.910390:1-891 [pilon] Processing NODE_38_length_10396_cov_58.472895:1-10396 [pilon] NODE_91_length_2143_cov_108.869931:1-2143 log: [pilon] frags shovill.bam: coverage 226 [pilon] Total Reads: 4948, Coverage: 226, minDepth: 57 [pilon] Confirmed 1738 of 2143 bases (81.10%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_91_length_2143_cov_108.869931:1-2143 [pilon] Processing NODE_215_length_403_cov_0.411348:1-403 [pilon] NODE_127_length_1177_cov_57.232008:1-1177 log: [pilon] frags shovill.bam: coverage 135 [pilon] Total Reads: 1479, Coverage: 135, minDepth: 34 [pilon] Confirmed 1089 of 1177 bases (92.52%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_127_length_1177_cov_57.232008:1-1177 [pilon] Processing NODE_27_length_26025_cov_36.316553:1-26025 [pilon] NODE_73_length_2986_cov_46.962653:1-2986 log: [pilon] frags shovill.bam: coverage 134 [pilon] Total Reads: 3197, Coverage: 134, minDepth: 34 [pilon] Confirmed 2720 of 2986 bases (91.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_73_length_2986_cov_46.962653:1-2986 [pilon] Processing NODE_64_length_3915_cov_22.312335:1-3915 [pilon] NODE_145_length_924_cov_9.550436:1-924 log: [pilon] frags shovill.bam: coverage 28 [pilon] Total Reads: 201, Coverage: 28, minDepth: 7 [pilon] Confirmed 667 of 924 bases (72.19%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_145_length_924_cov_9.550436:1-924 [pilon] Processing NODE_164_length_789_cov_8.868263:1-789 [pilon] NODE_185_length_624_cov_6.166998:1-624 log: [pilon] frags shovill.bam: coverage 15 [pilon] Total Reads: 71, Coverage: 15, minDepth: 5 [pilon] Confirmed 517 of 624 bases (82.85%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_185_length_624_cov_6.166998:1-624 [pilon] NODE_153_length_849_cov_50.174451:1-849 log: [pilon] frags shovill.bam: coverage 100 [pilon] Total Reads: 896, Coverage: 100, minDepth: 25 [pilon] Confirmed 600 of 849 bases (70.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_118_length_1421_cov_76.483077:1-1421 [pilon] Finished processing NODE_153_length_849_cov_50.174451:1-849 [pilon] Processing NODE_239_length_239_cov_29.288136:1-239 [pilon] NODE_215_length_403_cov_0.411348:1-403 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 4, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 403 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_215_length_403_cov_0.411348:1-403 [pilon] NODE_129_length_1166_cov_30.761722:1-1166 log: [pilon] frags shovill.bam: coverage 86 [pilon] Total Reads: 771, Coverage: 86, minDepth: 22 [pilon] Confirmed 936 of 1166 bases (80.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_129_length_1166_cov_30.761722:1-1166 [pilon] Processing NODE_187_length_603_cov_1.628631:1-603 [pilon] Processing NODE_59_length_5253_cov_47.182970:1-5253 [pilon] NODE_190_length_587_cov_135.416309:1-587 log: [pilon] frags shovill.bam: coverage 229 [pilon] Total Reads: 1551, Coverage: 229, minDepth: 57 [pilon] Confirmed 513 of 587 bases (87.39%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_190_length_587_cov_135.416309:1-587 [pilon] Processing NODE_160_length_807_cov_16.803207:1-807 [pilon] NODE_239_length_239_cov_29.288136:1-239 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 132, Coverage: 4, minDepth: 5 [pilon] Confirmed 114 of 239 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_239_length_239_cov_29.288136:1-239 [pilon] Processing NODE_210_length_408_cov_0.634146:1-408 [pilon] NODE_107_length_1726_cov_25.937695:1-1726 log: [pilon] frags shovill.bam: coverage 64 [pilon] Total Reads: 1021, Coverage: 64, minDepth: 16 [pilon] Confirmed 1264 of 1726 bases (73.23%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_107_length_1726_cov_25.937695:1-1726 [pilon] Processing NODE_63_length_4055_cov_60.968480:1-4055 [pilon] NODE_164_length_789_cov_8.868263:1-789 log: [pilon] frags shovill.bam: coverage 23 [pilon] Total Reads: 143, Coverage: 23, minDepth: 6 [pilon] Confirmed 568 of 789 bases (71.99%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_164_length_789_cov_8.868263:1-789 [pilon] NODE_65_length_3859_cov_46.880150:1-3859 log: [pilon] frags shovill.bam: coverage 139 [pilon] Total Reads: 4253, Coverage: 139, minDepth: 35 [pilon] Confirmed 3595 of 3859 bases (93.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_65_length_3859_cov_46.880150:1-3859 [pilon] Processing NODE_157_length_836_cov_10.777622:1-836 [pilon] NODE_187_length_603_cov_1.628631:1-603 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 20, Coverage: 4, minDepth: 5 [pilon] Confirmed 223 of 603 bases (36.98%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_187_length_603_cov_1.628631:1-603 [pilon] Processing NODE_88_length_2287_cov_22.660203:1-2287 [pilon] NODE_160_length_807_cov_16.803207:1-807 log: [pilon] frags shovill.bam: coverage 46 [pilon] Total Reads: 286, Coverage: 46, minDepth: 12 [pilon] Confirmed 578 of 807 bases (71.62%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_160_length_807_cov_16.803207:1-807 [pilon] Processing NODE_219_length_357_cov_65.419492:1-357 [pilon] NODE_55_length_5916_cov_40.733563:1-5916 log: [pilon] frags shovill.bam: coverage 99 [pilon] Total Reads: 5236, Coverage: 99, minDepth: 25 [pilon] Confirmed 5477 of 5916 bases (92.58%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_55_length_5916_cov_40.733563:1-5916 [pilon] Processing NODE_79_length_2601_cov_68.245161:1-2601 [pilon] NODE_157_length_836_cov_10.777622:1-836 log: [pilon] frags shovill.bam: coverage 29 [pilon] Total Reads: 187, Coverage: 29, minDepth: 7 [pilon] Confirmed 619 of 836 bases (74.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_157_length_836_cov_10.777622:1-836 [pilon] Processing NODE_42_length_8186_cov_24.711345:1-8186 [pilon] NODE_219_length_357_cov_65.419492:1-357 log: [pilon] frags shovill.bam: coverage 63 [pilon] Total Reads: 408, Coverage: 63, minDepth: 16 [pilon] Confirmed 308 of 357 bases (86.27%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_219_length_357_cov_65.419492:1-357 [pilon] Processing NODE_196_length_538_cov_1.561151:1-538 [pilon] NODE_210_length_408_cov_0.634146:1-408 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 5, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 408 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_210_length_408_cov_0.634146:1-408 [pilon] Processing NODE_154_length_842_cov_28.624133:1-842 [pilon] NODE_82_length_2490_cov_154.097087:1-2490 log: [pilon] frags shovill.bam: coverage 417 [pilon] Total Reads: 8921, Coverage: 417, minDepth: 104 [pilon] Confirmed 2427 of 2490 bases (97.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_82_length_2490_cov_154.097087:1-2490 [pilon] Processing NODE_110_length_1656_cov_16.851466:1-1656 [pilon] NODE_118_length_1421_cov_76.483077:1-1421 log: [pilon] frags shovill.bam: coverage 221 [pilon] Total Reads: 2429, Coverage: 221, minDepth: 55 [pilon] Confirmed 850 of 1421 bases (59.82%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_118_length_1421_cov_76.483077:1-1421 [pilon] Processing NODE_57_length_5712_cov_85.235736:1-5712 [pilon] NODE_196_length_538_cov_1.561151:1-538 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 20, Coverage: 5, minDepth: 5 [pilon] Confirmed 243 of 538 bases (45.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_196_length_538_cov_1.561151:1-538 [pilon] Processing NODE_5_length_118189_cov_48.804672:1-118189 [pilon] NODE_154_length_842_cov_28.624133:1-842 log: [pilon] frags shovill.bam: coverage 70 [pilon] Total Reads: 454, Coverage: 70, minDepth: 18 [pilon] Confirmed 534 of 842 bases (63.42%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_154_length_842_cov_28.624133:1-842 [pilon] Processing NODE_124_length_1253_cov_836.028269:1-1253 [pilon] NODE_88_length_2287_cov_22.660203:1-2287 log: [pilon] frags shovill.bam: coverage 63 [pilon] Total Reads: 1375, Coverage: 63, minDepth: 16 [pilon] Confirmed 2005 of 2287 bases (87.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_88_length_2287_cov_22.660203:1-2287 [pilon] Processing NODE_18_length_42551_cov_59.168065:1-42551 [pilon] NODE_64_length_3915_cov_22.312335:1-3915 log: [pilon] frags shovill.bam: coverage 68 [pilon] Total Reads: 2066, Coverage: 68, minDepth: 17 [pilon] Confirmed 3116 of 3915 bases (79.59%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_64_length_3915_cov_22.312335:1-3915 [pilon] Processing NODE_230_length_243_cov_92.778689:1-243 [pilon] NODE_230_length_243_cov_92.778689:1-243 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 245, 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_230_length_243_cov_92.778689:1-243 [pilon] Processing NODE_163_length_789_cov_9.603293:1-789 [pilon] NODE_110_length_1656_cov_16.851466:1-1656 log: [pilon] frags shovill.bam: coverage 48 [pilon] Total Reads: 617, Coverage: 48, minDepth: 12 [pilon] Confirmed 1293 of 1656 bases (78.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_110_length_1656_cov_16.851466:1-1656 [pilon] Processing NODE_16_length_46293_cov_41.603699:1-46293 [pilon] NODE_43_length_8142_cov_39.854632:1-8142 log: [pilon] frags shovill.bam: coverage 121 [pilon] Total Reads: 7703, Coverage: 121, minDepth: 30 [pilon] Confirmed 7918 of 8142 bases (97.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_43_length_8142_cov_39.854632:1-8142 [pilon] Processing NODE_62_length_4112_cov_71.900276:1-4112 [pilon] NODE_163_length_789_cov_9.603293:1-789 log: [pilon] frags shovill.bam: coverage 26 [pilon] Total Reads: 158, Coverage: 26, minDepth: 7 [pilon] Confirmed 584 of 789 bases (74.02%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_163_length_789_cov_9.603293:1-789 [pilon] Processing NODE_22_length_30560_cov_31.999310:1-30560 [pilon] NODE_79_length_2601_cov_68.245161:1-2601 log: [pilon] frags shovill.bam: coverage 198 [pilon] Total Reads: 4174, Coverage: 198, minDepth: 50 [pilon] Confirmed 2410 of 2601 bases (92.66%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_79_length_2601_cov_68.245161:1-2601 [pilon] Processing NODE_233_length_243_cov_42.450820:1-243 [pilon] NODE_233_length_243_cov_42.450820:1-243 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 123, 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_233_length_243_cov_42.450820:1-243 [pilon] Processing NODE_194_length_560_cov_0.615034:1-560 [pilon] NODE_194_length_560_cov_0.615034:1-560 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 8, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 560 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_194_length_560_cov_0.615034:1-560 [pilon] Processing NODE_217_length_387_cov_28.992481:1-387 [pilon] NODE_63_length_4055_cov_60.968480:1-4055 log: [pilon] frags shovill.bam: coverage 184 [pilon] Total Reads: 5762, Coverage: 184, minDepth: 46 [pilon] Confirmed 3187 of 4055 bases (78.59%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_63_length_4055_cov_60.968480:1-4055 [pilon] Processing NODE_19_length_39822_cov_45.950329:1-39822 [pilon] NODE_217_length_387_cov_28.992481:1-387 log: [pilon] frags shovill.bam: coverage 46 [pilon] Total Reads: 372, Coverage: 46, minDepth: 12 [pilon] Confirmed 342 of 387 bases (88.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_217_length_387_cov_28.992481:1-387 [pilon] Processing NODE_56_length_5882_cov_44.708210:1-5882 [pilon] NODE_48_length_7076_cov_77.874191:1-7076 log: [pilon] frags shovill.bam: coverage 234 [pilon] Total Reads: 13049, Coverage: 234, minDepth: 59 [pilon] Confirmed 6081 of 7076 bases (85.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_48_length_7076_cov_77.874191:1-7076 [pilon] Processing NODE_198_length_491_cov_1.945946:1-491 [pilon] NODE_198_length_491_cov_1.945946:1-491 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 17, Coverage: 5, minDepth: 5 [pilon] Confirmed 271 of 491 bases (55.19%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_198_length_491_cov_1.945946:1-491 [pilon] Processing NODE_117_length_1440_cov_20.257013:1-1440 [pilon] NODE_59_length_5253_cov_47.182970:1-5253 log: [pilon] frags shovill.bam: coverage 144 [pilon] Total Reads: 5972, Coverage: 144, minDepth: 36 [pilon] Confirmed 4965 of 5253 bases (94.52%) [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_5253_cov_47.182970:1-5253 [pilon] Processing NODE_225_length_306_cov_22.772973:1-306 [pilon] NODE_124_length_1253_cov_836.028269:1-1253 log: [pilon] frags shovill.bam: coverage 2157 [pilon] Total Reads: 23716, Coverage: 2157, minDepth: 539 [pilon] Confirmed 1121 of 1253 bases (89.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_124_length_1253_cov_836.028269:1-1253 [pilon] Processing NODE_159_length_821_cov_11.877143:1-821 [pilon] NODE_225_length_306_cov_22.772973:1-306 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 99, Coverage: 14, minDepth: 5 [pilon] Confirmed 266 of 306 bases (86.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_225_length_306_cov_22.772973:1-306 [pilon] NODE_117_length_1440_cov_20.257013:1-1440 log: [pilon] frags shovill.bam: coverage 58 [pilon] Total Reads: 648, Coverage: 58, minDepth: 15 [pilon] Confirmed 982 of 1440 bases (68.19%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_117_length_1440_cov_20.257013:1-1440 [pilon] Processing NODE_195_length_542_cov_10.425178:1-542 [pilon] NODE_45_length_7758_cov_75.902580:1-7758 log: [pilon] frags shovill.bam: coverage 233 [pilon] Total Reads: 14106, Coverage: 233, minDepth: 58 [pilon] Confirmed 7148 of 7758 bases (92.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_45_length_7758_cov_75.902580:1-7758 [pilon] NODE_159_length_821_cov_11.877143:1-821 log: [pilon] frags shovill.bam: coverage 32 [pilon] Total Reads: 206, Coverage: 32, minDepth: 8 [pilon] Confirmed 570 of 821 bases (69.43%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_159_length_821_cov_11.877143:1-821 [pilon] Processing NODE_158_length_834_cov_27.249649:1-834 [pilon] NODE_62_length_4112_cov_71.900276:1-4112 log: [pilon] frags shovill.bam: coverage 221 [pilon] Total Reads: 7009, Coverage: 221, minDepth: 55 [pilon] Confirmed 3728 of 4112 bases (90.66%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_62_length_4112_cov_71.900276:1-4112 [pilon] Processing NODE_162_length_798_cov_6.648449:1-798 [pilon] NODE_195_length_542_cov_10.425178:1-542 log: [pilon] frags shovill.bam: coverage 25 [pilon] Total Reads: 110, Coverage: 25, minDepth: 6 [pilon] Confirmed 414 of 542 bases (76.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_195_length_542_cov_10.425178:1-542 [pilon] Processing NODE_122_length_1374_cov_22.642458:1-1374 [pilon] NODE_57_length_5712_cov_85.235736:1-5712 log: [pilon] frags shovill.bam: coverage 255 [pilon] Total Reads: 11634, Coverage: 255, minDepth: 64 [pilon] Confirmed 3805 of 5712 bases (66.61%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_57_length_5712_cov_85.235736:1-5712 [pilon] Processing NODE_140_length_975_cov_31.407494:1-975 [pilon] NODE_46_length_7733_cov_93.546506:1-7733 log: [pilon] frags shovill.bam: coverage 285 [pilon] Total Reads: 17394, Coverage: 285, minDepth: 71 [pilon] Confirmed 7002 of 7733 bases (90.55%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_46_length_7733_cov_93.546506:1-7733 [pilon] Processing NODE_67_length_3657_cov_25.732466:1-3657 [pilon] NODE_162_length_798_cov_6.648449:1-798 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 112, Coverage: 18, minDepth: 5 [pilon] Confirmed 544 of 798 bases (68.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_162_length_798_cov_6.648449:1-798 [pilon] Processing NODE_132_length_1066_cov_25.722751:1-1066 [pilon] NODE_42_length_8186_cov_24.711345:1-8186 log: [pilon] frags shovill.bam: coverage 75 [pilon] Total Reads: 4826, Coverage: 75, minDepth: 19 [pilon] Confirmed 6818 of 8186 bases (83.29%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_42_length_8186_cov_24.711345:1-8186 [pilon] Processing NODE_141_length_949_cov_35.725845:1-949 [pilon] NODE_158_length_834_cov_27.249649:1-834 log: [pilon] frags shovill.bam: coverage 74 [pilon] Total Reads: 478, Coverage: 74, minDepth: 19 [pilon] Confirmed 594 of 834 bases (71.22%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_158_length_834_cov_27.249649:1-834 [pilon] Processing NODE_115_length_1571_cov_35.100690:1-1571 [pilon] NODE_122_length_1374_cov_22.642458:1-1374 log: [pilon] frags shovill.bam: coverage 62 [pilon] Total Reads: 712, Coverage: 62, minDepth: 16 [pilon] Confirmed 1197 of 1374 bases (87.12%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_122_length_1374_cov_22.642458:1-1374 [pilon] Processing NODE_136_length_1033_cov_25.697368:1-1033 [pilon] NODE_132_length_1066_cov_25.722751:1-1066 log: [pilon] frags shovill.bam: coverage 73 [pilon] Total Reads: 606, Coverage: 73, minDepth: 18 [pilon] Confirmed 618 of 1066 bases (57.97%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_132_length_1066_cov_25.722751:1-1066 [pilon] NODE_141_length_949_cov_35.725845:1-949 log: [pilon] frags shovill.bam: coverage 99 [pilon] Total Reads: 729, Coverage: 99, minDepth: 25 [pilon] Confirmed 610 of 949 bases (64.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_141_length_949_cov_35.725845:1-949 [pilon] Processing NODE_50_length_6535_cov_104.265513:1-6535 [pilon] NODE_140_length_975_cov_31.407494:1-975 log: [pilon] frags shovill.bam: coverage 88 [pilon] Total Reads: 666, Coverage: 88, minDepth: 22 [pilon] Confirmed 627 of 975 bases (64.31%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_140_length_975_cov_31.407494:1-975 [pilon] Processing NODE_223_length_347_cov_54.097345:1-347 [pilon] NODE_223_length_347_cov_54.097345:1-347 log: [pilon] frags shovill.bam: coverage 42 [pilon] Total Reads: 305, Coverage: 42, minDepth: 11 [pilon] Confirmed 297 of 347 bases (85.59%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_223_length_347_cov_54.097345:1-347 [pilon] NODE_115_length_1571_cov_35.100690:1-1571 log: [pilon] frags shovill.bam: coverage 101 [pilon] Total Reads: 1228, Coverage: 101, minDepth: 25 [pilon] Confirmed 1163 of 1571 bases (74.03%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_4_length_122931_cov_50.676736:1-122931 [pilon] Finished processing NODE_115_length_1571_cov_35.100690:1-1571 [pilon] Processing NODE_232_length_243_cov_56.196721:1-243 [pilon] NODE_136_length_1033_cov_25.697368:1-1033 log: [pilon] frags shovill.bam: coverage 65 [pilon] Total Reads: 581, Coverage: 65, minDepth: 16 [pilon] Confirmed 879 of 1033 bases (85.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_136_length_1033_cov_25.697368:1-1033 [pilon] Processing NODE_240_length_238_cov_50.128205:1-238 [pilon] NODE_56_length_5882_cov_44.708210:1-5882 log: [pilon] frags shovill.bam: coverage 123 [pilon] Total Reads: 6144, Coverage: 123, minDepth: 31 [pilon] Confirmed 5592 of 5882 bases (95.07%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] NODE_232_length_243_cov_56.196721:1-243 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 157, 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_232_length_243_cov_56.196721:1-243 [pilon] Processing NODE_142_length_937_cov_46.539216:1-937 [pilon] Finished processing NODE_56_length_5882_cov_44.708210:1-5882 [pilon] Processing NODE_105_length_1741_cov_30.058025:1-1741 [pilon] NODE_67_length_3657_cov_25.732466:1-3657 log: [pilon] frags shovill.bam: coverage 79 [pilon] Total Reads: 2227, Coverage: 79, minDepth: 20 [pilon] Confirmed 3358 of 3657 bases (91.82%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_67_length_3657_cov_25.732466:1-3657 [pilon] Processing NODE_121_length_1384_cov_89.728424:1-1384 [pilon] NODE_240_length_238_cov_50.128205:1-238 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 143, Coverage: 7, minDepth: 5 [pilon] Confirmed 150 of 238 bases (63.03%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_240_length_238_cov_50.128205:1-238 [pilon] Processing NODE_66_length_3739_cov_17.781371:1-3739 [pilon] NODE_38_length_10396_cov_58.472895:1-10396 log: [pilon] frags shovill.bam: coverage 165 [pilon] Total Reads: 13986, Coverage: 165, minDepth: 41 [pilon] Confirmed 9805 of 10396 bases (94.32%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_38_length_10396_cov_58.472895:1-10396 [pilon] Processing NODE_173_length_719_cov_31.735786:1-719 [pilon] NODE_173_length_719_cov_31.735786:1-719 log: [pilon] frags shovill.bam: coverage 65 [pilon] Total Reads: 452, Coverage: 65, minDepth: 16 [pilon] Confirmed 524 of 719 bases (72.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_173_length_719_cov_31.735786:1-719 [pilon] Processing NODE_113_length_1627_cov_51.319389:1-1627 [pilon] NODE_34_length_14248_cov_60.176329:1-14248 log: [pilon] frags shovill.bam: coverage 184 [pilon] Total Reads: 20559, Coverage: 184, minDepth: 46 [pilon] Confirmed 14121 of 14248 bases (99.11%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_34_length_14248_cov_60.176329:1-14248 [pilon] Processing NODE_74_length_2878_cov_68.913674:1-2878 [pilon] NODE_142_length_937_cov_46.539216:1-937 log: [pilon] frags shovill.bam: coverage 113 [pilon] Total Reads: 954, Coverage: 113, minDepth: 28 [pilon] Confirmed 777 of 937 bases (82.92%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_142_length_937_cov_46.539216:1-937 [pilon] Processing NODE_144_length_927_cov_12.808933:1-927 [pilon] NODE_33_length_15095_cov_57.026579:1-15095 log: [pilon] frags shovill.bam: coverage 148 [pilon] Total Reads: 19496, Coverage: 148, minDepth: 37 [pilon] Confirmed 13841 of 15095 bases (91.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_33_length_15095_cov_57.026579:1-15095 [pilon] Processing NODE_176_length_705_cov_6.952055:1-705 [pilon] NODE_105_length_1741_cov_30.058025:1-1741 log: [pilon] frags shovill.bam: coverage 90 [pilon] Total Reads: 1207, Coverage: 90, minDepth: 23 [pilon] Confirmed 928 of 1741 bases (53.30%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_105_length_1741_cov_30.058025:1-1741 [pilon] Processing NODE_134_length_1048_cov_49.237325:1-1048 [pilon] NODE_144_length_927_cov_12.808933:1-927 log: [pilon] frags shovill.bam: coverage 33 [pilon] Total Reads: 241, Coverage: 33, minDepth: 8 [pilon] Confirmed 618 of 927 bases (66.67%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_144_length_927_cov_12.808933:1-927 [pilon] Processing NODE_69_length_3592_cov_82.280035:1-3592 [pilon] NODE_176_length_705_cov_6.952055:1-705 log: [pilon] frags shovill.bam: coverage 18 [pilon] Total Reads: 100, Coverage: 18, minDepth: 5 [pilon] Confirmed 560 of 705 bases (79.43%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_176_length_705_cov_6.952055:1-705 [pilon] Processing NODE_137_length_1026_cov_61.611050:1-1026 [pilon] NODE_66_length_3739_cov_17.781371:1-3739 log: [pilon] frags shovill.bam: coverage 54 [pilon] Total Reads: 1570, Coverage: 54, minDepth: 14 [pilon] Confirmed 3231 of 3739 bases (86.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_66_length_3739_cov_17.781371:1-3739 [pilon] Processing NODE_11_length_61426_cov_56.116043:1-61426 [pilon] NODE_121_length_1384_cov_89.728424:1-1384 log: [pilon] frags shovill.bam: coverage 220 [pilon] Total Reads: 2723, Coverage: 220, minDepth: 55 [pilon] Confirmed 1272 of 1384 bases (91.91%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_121_length_1384_cov_89.728424:1-1384 [pilon] Processing NODE_171_length_730_cov_29.178982:1-730 [pilon] NODE_134_length_1048_cov_49.237325:1-1048 log: [pilon] frags shovill.bam: coverage 141 [pilon] Total Reads: 1145, Coverage: 141, minDepth: 35 [pilon] Confirmed 695 of 1048 bases (66.32%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_134_length_1048_cov_49.237325:1-1048 [pilon] Processing NODE_70_length_3576_cov_37.180318:1-3576 [pilon] NODE_113_length_1627_cov_51.319389:1-1627 log: [pilon] frags shovill.bam: coverage 137 [pilon] Total Reads: 1883, Coverage: 137, minDepth: 34 [pilon] Confirmed 1410 of 1627 bases (86.66%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_113_length_1627_cov_51.319389:1-1627 [pilon] Processing NODE_165_length_774_cov_8.341501:1-774 [pilon] NODE_28_length_24965_cov_56.849863:1-24965 log: [pilon] frags shovill.bam: coverage 173 [pilon] Total Reads: 33892, Coverage: 173, minDepth: 43 [pilon] Confirmed 24715 of 24965 bases (99.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_28_length_24965_cov_56.849863:1-24965 [pilon] Processing NODE_234_length_242_cov_40.925620:1-242 [pilon] NODE_137_length_1026_cov_61.611050:1-1026 log: [pilon] frags shovill.bam: coverage 136 [pilon] Total Reads: 1402, Coverage: 136, minDepth: 34 [pilon] Confirmed 949 of 1026 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_137_length_1026_cov_61.611050:1-1026 [pilon] Processing NODE_155_length_842_cov_21.274619:1-842 [pilon] NODE_171_length_730_cov_29.178982:1-730 log: [pilon] frags shovill.bam: coverage 62 [pilon] Total Reads: 515, Coverage: 62, minDepth: 16 [pilon] Confirmed 643 of 730 bases (88.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_171_length_730_cov_29.178982:1-730 [pilon] Processing NODE_96_length_1995_cov_24.163821:1-1995 [pilon] NODE_165_length_774_cov_8.341501:1-774 log: [pilon] frags shovill.bam: coverage 34 [pilon] Total Reads: 202, Coverage: 34, minDepth: 9 [pilon] Confirmed 544 of 774 bases (70.28%) [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_774_cov_8.341501:1-774 [pilon] Processing NODE_36_length_12840_cov_38.927353:1-12840 [pilon] NODE_27_length_26025_cov_36.316553:1-26025 log: [pilon] frags shovill.bam: coverage 112 [pilon] Total Reads: 22592, Coverage: 112, minDepth: 28 [pilon] Confirmed 25828 of 26025 bases (99.24%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_27_length_26025_cov_36.316553:1-26025 [pilon] Processing NODE_203_length_414_cov_0.467577:1-414 [pilon] NODE_234_length_242_cov_40.925620:1-242 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 111, Coverage: 8, minDepth: 5 [pilon] Confirmed 200 of 242 bases (82.64%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_234_length_242_cov_40.925620:1-242 [pilon] Processing NODE_226_length_296_cov_28.394286:1-296 [pilon] NODE_155_length_842_cov_21.274619:1-842 log: [pilon] frags shovill.bam: coverage 58 [pilon] Total Reads: 382, Coverage: 58, minDepth: 15 [pilon] Confirmed 572 of 842 bases (67.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_155_length_842_cov_21.274619:1-842 [pilon] Processing NODE_32_length_15314_cov_32.797341:1-15314 [pilon] NODE_203_length_414_cov_0.467577:1-414 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 4, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 414 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_203_length_414_cov_0.467577:1-414 [pilon] Processing NODE_170_length_735_cov_3.469055:1-735 [pilon] NODE_226_length_296_cov_28.394286:1-296 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 119, Coverage: 4, minDepth: 5 [pilon] Confirmed 137 of 296 bases (46.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_226_length_296_cov_28.394286:1-296 [pilon] Processing NODE_224_length_307_cov_59.037634:1-307 [pilon] NODE_26_length_26480_cov_58.159604:1-26480 log: [pilon] frags shovill.bam: coverage 180 [pilon] Total Reads: 36835, Coverage: 180, minDepth: 45 [pilon] Confirmed 25987 of 26480 bases (98.14%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_26_length_26480_cov_58.159604:1-26480 [pilon] NODE_25_length_27770_cov_54.426345:1-27770 log: [pilon] frags shovill.bam: coverage 168 [pilon] Total Reads: 36253, Coverage: 168, minDepth: 42 [pilon] Confirmed 27514 of 27770 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_25_length_27770_cov_54.426345:1-27770 [pilon] Processing NODE_71_length_3531_cov_97.446921:1-3531 [pilon] Processing NODE_6_length_102150_cov_43.147870:1-102150 [pilon] Processing NODE_100_length_1813_cov_10.894208:1-1813 [pilon] NODE_24_length_27859_cov_33.842022:1-27859 log: [pilon] frags shovill.bam: coverage 104 [pilon] Total Reads: 22504, Coverage: 104, minDepth: 26 [pilon] Confirmed 27228 of 27859 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_24_length_27859_cov_33.842022:1-27859 [pilon] Processing NODE_99_length_1833_cov_48.651285:1-1833 [pilon] Processing NODE_120_length_1386_cov_60.144664:1-1386 [pilon] NODE_22_length_30560_cov_31.999310:1-30560 log: [pilon] frags shovill.bam: coverage 99 [pilon] Total Reads: 23316, Coverage: 99, minDepth: 25 [pilon] Confirmed 30283 of 30560 bases (99.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_22_length_30560_cov_31.999310:1-30560 [pilon] Processing NODE_143_length_934_cov_14.063961:1-934 [pilon] NODE_170_length_735_cov_3.469055:1-735 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 60, Coverage: 11, minDepth: 5 [pilon] Confirmed 503 of 735 bases (68.44%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_170_length_735_cov_3.469055:1-735 [pilon] Processing NODE_243_length_132_cov_2.636364:1-132 [pilon] NODE_74_length_2878_cov_68.913674:1-2878 log: [pilon] frags shovill.bam: coverage 209 [pilon] Total Reads: 4641, Coverage: 209, minDepth: 52 [pilon] Confirmed 2433 of 2878 bases (84.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_74_length_2878_cov_68.913674:1-2878 [pilon] Processing NODE_84_length_2374_cov_57.449179:1-2374 [pilon] NODE_96_length_1995_cov_24.163821:1-1995 log: [pilon] frags shovill.bam: coverage 69 [pilon] Total Reads: 1059, Coverage: 69, minDepth: 17 [pilon] Confirmed 1696 of 1995 bases (85.01%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_96_length_1995_cov_24.163821:1-1995 [pilon] Processing NODE_41_length_8710_cov_29.313308:1-8710 [pilon] NODE_224_length_307_cov_59.037634:1-307 log: [pilon] frags shovill.bam: coverage 33 [pilon] Total Reads: 284, Coverage: 33, minDepth: 8 [pilon] Confirmed 288 of 307 bases (93.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_224_length_307_cov_59.037634:1-307 [pilon] Processing NODE_119_length_1411_cov_37.088372:1-1411 [pilon] NODE_243_length_132_cov_2.636364:1-132 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 1, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 132 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_243_length_132_cov_2.636364:1-132 [pilon] Processing NODE_189_length_591_cov_32.878723:1-591 [pilon] NODE_21_length_31170_cov_46.522207:1-31170 log: [pilon] frags shovill.bam: coverage 142 [pilon] Total Reads: 34749, Coverage: 142, minDepth: 36 [pilon] Confirmed 31086 of 31170 bases (99.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_21_length_31170_cov_46.522207:1-31170 [pilon] Processing NODE_211_length_406_cov_0.407018:1-406 [pilon] NODE_143_length_934_cov_14.063961:1-934 log: [pilon] frags shovill.bam: coverage 41 [pilon] Total Reads: 293, Coverage: 41, minDepth: 10 [pilon] Confirmed 724 of 934 bases (77.52%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_143_length_934_cov_14.063961:1-934 [pilon] Processing NODE_51_length_6463_cov_45.929360:1-6463 [pilon] NODE_100_length_1813_cov_10.894208:1-1813 log: [pilon] frags shovill.bam: coverage 31 [pilon] Total Reads: 438, Coverage: 31, minDepth: 8 [pilon] Confirmed 1366 of 1813 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_100_length_1813_cov_10.894208:1-1813 [pilon] Processing NODE_222_length_349_cov_125.583333:1-349 [pilon] NODE_211_length_406_cov_0.407018:1-406 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 4, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 406 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_211_length_406_cov_0.407018:1-406 [pilon] Processing NODE_228_length_270_cov_38.838926:1-270 [pilon] NODE_70_length_3576_cov_37.180318:1-3576 log: [pilon] frags shovill.bam: coverage 107 [pilon] Total Reads: 3086, Coverage: 107, minDepth: 27 [pilon] Confirmed 2499 of 3576 bases (69.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_70_length_3576_cov_37.180318:1-3576 [pilon] Processing NODE_76_length_2733_cov_59.843798:1-2733 [pilon] NODE_120_length_1386_cov_60.144664:1-1386 log: [pilon] frags shovill.bam: coverage 151 [pilon] Total Reads: 1793, Coverage: 151, minDepth: 38 [pilon] Confirmed 1031 of 1386 bases (74.39%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_120_length_1386_cov_60.144664:1-1386 [pilon] Processing NODE_135_length_1040_cov_38.381937:1-1040 [pilon] NODE_99_length_1833_cov_48.651285:1-1833 log: [pilon] frags shovill.bam: coverage 141 [pilon] Total Reads: 2045, Coverage: 141, minDepth: 35 [pilon] Confirmed 1173 of 1833 bases (63.99%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_99_length_1833_cov_48.651285:1-1833 [pilon] Processing NODE_231_length_243_cov_58.229508:1-243 [pilon] NODE_189_length_591_cov_32.878723:1-591 log: [pilon] frags shovill.bam: coverage 55 [pilon] Total Reads: 368, Coverage: 55, minDepth: 14 [pilon] Confirmed 512 of 591 bases (86.63%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_189_length_591_cov_32.878723:1-591 [pilon] Processing NODE_182_length_661_cov_3.612963:1-661 [pilon] NODE_228_length_270_cov_38.838926:1-270 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 163, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 270 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_228_length_270_cov_38.838926:1-270 [pilon] Processing NODE_81_length_2552_cov_73.875771:1-2552 [pilon] NODE_222_length_349_cov_125.583333:1-349 log: [pilon] frags shovill.bam: coverage 101 [pilon] Total Reads: 644, Coverage: 101, minDepth: 25 [pilon] Confirmed 306 of 349 bases (87.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_222_length_349_cov_125.583333:1-349 [pilon] NODE_119_length_1411_cov_37.088372:1-1411 log: [pilon] frags shovill.bam: coverage 107 [pilon] Total Reads: 1172, Coverage: 107, minDepth: 27 [pilon] Confirmed 906 of 1411 bases (64.21%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_119_length_1411_cov_37.088372:1-1411 [pilon] Processing NODE_208_length_408_cov_1.515679:1-408 [pilon] Processing NODE_39_length_9867_cov_55.174123:1-9867 [pilon] NODE_231_length_243_cov_58.229508:1-243 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 151, 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_231_length_243_cov_58.229508:1-243 [pilon] NODE_182_length_661_cov_3.612963:1-661 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 40, Coverage: 8, minDepth: 5 [pilon] Confirmed 372 of 661 bases (56.28%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_182_length_661_cov_3.612963:1-661 [pilon] Processing NODE_192_length_581_cov_15.104348:1-581 [pilon] NODE_208_length_408_cov_1.515679:1-408 log: [pilon] frags shovill.bam: coverage 4 [pilon] Total Reads: 15, Coverage: 4, minDepth: 5 [pilon] Confirmed 206 of 408 bases (50.49%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_208_length_408_cov_1.515679:1-408 [pilon] Processing NODE_216_length_403_cov_0.166667:1-403 [pilon] NODE_69_length_3592_cov_82.280035:1-3592 log: [pilon] frags shovill.bam: coverage 249 [pilon] Total Reads: 7030, Coverage: 249, minDepth: 62 [pilon] Confirmed 2987 of 3592 bases (83.16%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_69_length_3592_cov_82.280035:1-3592 [pilon] Processing NODE_130_length_1139_cov_49.474460:1-1139 [pilon] NODE_20_length_35358_cov_60.026733:1-35358 log: [pilon] frags shovill.bam: coverage 187 [pilon] Total Reads: 51141, Coverage: 187, minDepth: 47 [pilon] Confirmed 34960 of 35358 bases (98.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_20_length_35358_cov_60.026733:1-35358 [pilon] Processing NODE_97_length_1959_cov_80.442329:1-1959 [pilon] NODE_135_length_1040_cov_38.381937:1-1040 log: [pilon] frags shovill.bam: coverage 102 [pilon] Total Reads: 873, Coverage: 102, minDepth: 26 [pilon] Confirmed 641 of 1040 bases (61.63%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_135_length_1040_cov_38.381937:1-1040 [pilon] Processing NODE_23_length_30082_cov_39.311572:1-30082 [pilon] NODE_84_length_2374_cov_57.449179:1-2374 log: [pilon] frags shovill.bam: coverage 167 [pilon] Total Reads: 3224, Coverage: 167, minDepth: 42 [pilon] Confirmed 1902 of 2374 bases (80.12%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_84_length_2374_cov_57.449179:1-2374 [pilon] Processing NODE_87_length_2289_cov_12.089022:1-2289 [pilon] NODE_216_length_403_cov_0.166667:1-403 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 3, Coverage: 0, minDepth: 5 [pilon] Confirmed 0 of 403 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_216_length_403_cov_0.166667:1-403 [pilon] Processing NODE_53_length_6284_cov_72.995457:1-6284 [pilon] NODE_192_length_581_cov_15.104348:1-581 log: [pilon] frags shovill.bam: coverage 22 [pilon] Total Reads: 191, Coverage: 22, minDepth: 6 [pilon] Confirmed 455 of 581 bases (78.31%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_192_length_581_cov_15.104348:1-581 [pilon] Processing NODE_227_length_286_cov_58.272727:1-286 [pilon] NODE_227_length_286_cov_58.272727:1-286 log: [pilon] frags shovill.bam: coverage 23 [pilon] Total Reads: 249, Coverage: 23, minDepth: 6 [pilon] Confirmed 253 of 286 bases (88.46%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_227_length_286_cov_58.272727:1-286 [pilon] Processing NODE_111_length_1650_cov_59.013080:1-1650 [pilon] NODE_130_length_1139_cov_49.474460:1-1139 log: [pilon] frags shovill.bam: coverage 130 [pilon] Total Reads: 1304, Coverage: 130, minDepth: 33 [pilon] Confirmed 918 of 1139 bases (80.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_130_length_1139_cov_49.474460:1-1139 [pilon] Processing NODE_214_length_403_cov_1.078014:1-403 [pilon] NODE_76_length_2733_cov_59.843798:1-2733 log: [pilon] frags shovill.bam: coverage 175 [pilon] Total Reads: 3836, Coverage: 175, minDepth: 44 [pilon] Confirmed 2517 of 2733 bases (92.10%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_76_length_2733_cov_59.843798:1-2733 [pilon] NODE_87_length_2289_cov_12.089022:1-2289 log: [pilon] frags shovill.bam: coverage 36 [pilon] Total Reads: 643, Coverage: 36, minDepth: 9 [pilon] Confirmed 2050 of 2289 bases (89.56%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_87_length_2289_cov_12.089022:1-2289 [pilon] Processing NODE_54_length_6183_cov_101.750742:1-6183 [pilon] NODE_214_length_403_cov_1.078014:1-403 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 6, Coverage: 2, minDepth: 5 [pilon] Confirmed 0 of 403 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_214_length_403_cov_1.078014:1-403 [pilon] Processing NODE_104_length_1747_cov_218.543050:1-1747 [pilon] NODE_81_length_2552_cov_73.875771:1-2552 log: [pilon] frags shovill.bam: coverage 214 [pilon] Total Reads: 4401, Coverage: 214, minDepth: 54 [pilon] Confirmed 2166 of 2552 bases (84.87%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_81_length_2552_cov_73.875771:1-2552 [pilon] Processing NODE_169_length_736_cov_6.398374:1-736 [pilon] Processing NODE_3_length_177459_cov_54.729088:1-177459 [pilon] NODE_16_length_46293_cov_41.603699:1-46293 log: [pilon] frags shovill.bam: coverage 129 [pilon] Total Reads: 46249, Coverage: 129, minDepth: 32 [pilon] Confirmed 46053 of 46293 bases (99.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_16_length_46293_cov_41.603699:1-46293 [pilon] Processing NODE_7_length_95188_cov_38.123429:1-95188 [pilon] NODE_169_length_736_cov_6.398374:1-736 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 90, Coverage: 16, minDepth: 5 [pilon] Confirmed 618 of 736 bases (83.97%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_169_length_736_cov_6.398374:1-736 [pilon] Processing NODE_207_length_409_cov_0.402778:1-409 [pilon] NODE_207_length_409_cov_0.402778:1-409 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 4, Coverage: 0, 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_207_length_409_cov_0.402778:1-409 [pilon] Processing NODE_213_length_403_cov_105.060284:1-403 [pilon] NODE_111_length_1650_cov_59.013080:1-1650 log: [pilon] frags shovill.bam: coverage 155 [pilon] Total Reads: 2168, Coverage: 155, minDepth: 39 [pilon] Confirmed 1438 of 1650 bases (87.15%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_111_length_1650_cov_59.013080:1-1650 [pilon] Processing NODE_172_length_725_cov_2.814570:1-725 [pilon] NODE_213_length_403_cov_105.060284:1-403 log: [pilon] frags shovill.bam: coverage 106 [pilon] Total Reads: 709, Coverage: 106, minDepth: 27 [pilon] Confirmed 351 of 403 bases (87.10%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_213_length_403_cov_105.060284:1-403 [pilon] Processing NODE_238_length_239_cov_52.855932:1-239 [pilon] NODE_13_length_57066_cov_38.945544:1-57066 log: [pilon] frags shovill.bam: coverage 121 [pilon] Total Reads: 53359, Coverage: 121, minDepth: 30 [pilon] Confirmed 56524 of 57066 bases (99.05%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_13_length_57066_cov_38.945544:1-57066 [pilon] Processing NODE_10_length_69806_cov_34.526857:1-69806 [pilon] NODE_238_length_239_cov_52.855932:1-239 log: [pilon] frags shovill.bam: coverage 10 [pilon] Total Reads: 149, Coverage: 10, minDepth: 5 [pilon] Confirmed 201 of 239 bases (84.10%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_238_length_239_cov_52.855932:1-239 [pilon] Processing NODE_14_length_49877_cov_50.484283:1-49877 [pilon] NODE_97_length_1959_cov_80.442329:1-1959 log: [pilon] frags shovill.bam: coverage 169 [pilon] Total Reads: 3375, Coverage: 169, minDepth: 42 [pilon] Confirmed 1692 of 1959 bases (86.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_97_length_1959_cov_80.442329:1-1959 [pilon] Processing NODE_109_length_1679_cov_70.392169:1-1679 [pilon] NODE_172_length_725_cov_2.814570:1-725 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 42, Coverage: 8, minDepth: 5 [pilon] Confirmed 457 of 725 bases (63.03%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_172_length_725_cov_2.814570:1-725 [pilon] Processing NODE_146_length_908_cov_26.869123:1-908 [pilon] NODE_104_length_1747_cov_218.543050:1-1747 log: [pilon] frags shovill.bam: coverage 634 [pilon] Total Reads: 8557, Coverage: 634, minDepth: 159 [pilon] Confirmed 1000 of 1747 bases (57.24%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_104_length_1747_cov_218.543050:1-1747 [pilon] Processing NODE_147_length_906_cov_1448.536306:1-906 [pilon] NODE_146_length_908_cov_26.869123:1-908 log: [pilon] frags shovill.bam: coverage 75 [pilon] Total Reads: 526, Coverage: 75, minDepth: 19 [pilon] Confirmed 688 of 908 bases (75.77%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_146_length_908_cov_26.869123:1-908 [pilon] Processing NODE_72_length_3116_cov_62.176962:1-3116 [pilon] NODE_109_length_1679_cov_70.392169:1-1679 log: [pilon] frags shovill.bam: coverage 193 [pilon] Total Reads: 2673, Coverage: 193, minDepth: 48 [pilon] Confirmed 1495 of 1679 bases (89.04%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_109_length_1679_cov_70.392169:1-1679 [pilon] NODE_71_length_3531_cov_97.446921:1-3531 log: [pilon] frags shovill.bam: coverage 290 [pilon] Total Reads: 8382, Coverage: 290, minDepth: 73 [pilon] Confirmed 3057 of 3531 bases (86.58%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_71_length_3531_cov_97.446921:1-3531 [pilon] Processing NODE_188_length_597_cov_5.487395:1-597 [pilon] NODE_50_length_6535_cov_104.265513:1-6535 log: [pilon] frags shovill.bam: coverage 317 [pilon] Total Reads: 16019, Coverage: 317, minDepth: 79 [pilon] Confirmed 5831 of 6535 bases (89.23%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_50_length_6535_cov_104.265513:1-6535 [pilon] NODE_51_length_6463_cov_45.929360:1-6463 log: [pilon] frags shovill.bam: coverage 140 [pilon] Total Reads: 6972, Coverage: 140, minDepth: 35 [pilon] Confirmed 6102 of 6463 bases (94.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_51_length_6463_cov_45.929360:1-6463 [pilon] Processing NODE_200_length_446_cov_0.784615:1-446 [pilon] NODE_188_length_597_cov_5.487395:1-597 log: [pilon] frags shovill.bam: coverage 14 [pilon] Total Reads: 64, Coverage: 14, minDepth: 5 [pilon] Confirmed 456 of 597 bases (76.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_188_length_597_cov_5.487395:1-597 [pilon] Processing NODE_58_length_5431_cov_55.347646:1-5431 [pilon] NODE_54_length_6183_cov_101.750742:1-6183 log: [pilon] frags shovill.bam: coverage 308 [pilon] Total Reads: 15035, Coverage: 308, minDepth: 77 [pilon] Confirmed 6065 of 6183 bases (98.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_54_length_6183_cov_101.750742:1-6183 [pilon] Processing NODE_12_length_59410_cov_51.720302:1-59410 [pilon] NODE_53_length_6284_cov_72.995457:1-6284 log: [pilon] frags shovill.bam: coverage 222 [pilon] Total Reads: 10932, Coverage: 222, minDepth: 56 [pilon] Confirmed 5883 of 6284 bases (93.62%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_53_length_6284_cov_72.995457:1-6284 [pilon] Processing NODE_37_length_10469_cov_56.914090:1-10469 [pilon] NODE_39_length_9867_cov_55.174123:1-9867 log: [pilon] frags shovill.bam: coverage 168 [pilon] Total Reads: 12986, Coverage: 168, minDepth: 42 [pilon] Confirmed 9772 of 9867 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_39_length_9867_cov_55.174123:1-9867 [pilon] Processing NODE_126_length_1205_cov_19.812731:1-1205 [pilon] NODE_200_length_446_cov_0.784615:1-446 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 6, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 446 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_200_length_446_cov_0.784615:1-446 [pilon] Processing NODE_235_length_241_cov_54.466667:1-241 [pilon] NODE_41_length_8710_cov_29.313308:1-8710 log: [pilon] frags shovill.bam: coverage 89 [pilon] Total Reads: 6016, Coverage: 89, minDepth: 22 [pilon] Confirmed 8511 of 8710 bases (97.72%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_41_length_8710_cov_29.313308:1-8710 [pilon] Processing NODE_8_length_76265_cov_46.522195:1-76265 [pilon] NODE_235_length_241_cov_54.466667:1-241 log: [pilon] frags shovill.bam: coverage 8 [pilon] Total Reads: 151, Coverage: 8, minDepth: 5 [pilon] Confirmed 183 of 241 bases (75.93%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_235_length_241_cov_54.466667:1-241 [pilon] Processing NODE_49_length_6704_cov_20.519064:1-6704 [pilon] NODE_126_length_1205_cov_19.812731:1-1205 log: [pilon] frags shovill.bam: coverage 53 [pilon] Total Reads: 497, Coverage: 53, minDepth: 13 [pilon] Confirmed 930 of 1205 bases (77.18%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_126_length_1205_cov_19.812731:1-1205 [pilon] Processing NODE_35_length_12911_cov_38.730023:1-12911 [pilon] NODE_36_length_12840_cov_38.927353:1-12840 log: [pilon] frags shovill.bam: coverage 118 [pilon] Total Reads: 11726, Coverage: 118, minDepth: 30 [pilon] Confirmed 12531 of 12840 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_36_length_12840_cov_38.927353:1-12840 [pilon] Processing NODE_98_length_1834_cov_40.031524:1-1834 [pilon] NODE_32_length_15314_cov_32.797341:1-15314 log: [pilon] frags shovill.bam: coverage 100 [pilon] Total Reads: 11969, Coverage: 100, minDepth: 25 [pilon] Confirmed 14960 of 15314 bases (97.69%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_32_length_15314_cov_32.797341:1-15314 [pilon] Processing NODE_93_length_2099_cov_55.472700:1-2099 [pilon] NODE_98_length_1834_cov_40.031524:1-1834 log: [pilon] frags shovill.bam: coverage 112 [pilon] Total Reads: 1690, Coverage: 112, minDepth: 28 [pilon] Confirmed 1515 of 1834 bases (82.61%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_98_length_1834_cov_40.031524:1-1834 [pilon] Processing NODE_174_length_718_cov_5.661642:1-718 [pilon] NODE_9_length_73464_cov_33.170173:1-73464 log: [pilon] frags shovill.bam: coverage 103 [pilon] Total Reads: 58410, Coverage: 103, minDepth: 26 [pilon] Confirmed 72880 of 73464 bases (99.21%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_9_length_73464_cov_33.170173:1-73464 [pilon] NODE_72_length_3116_cov_62.176962:1-3116 log: [pilon] frags shovill.bam: coverage 188 [pilon] Total Reads: 4524, Coverage: 188, minDepth: 47 [pilon] Confirmed 2401 of 3116 bases (77.05%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_72_length_3116_cov_62.176962:1-3116 [pilon] Processing NODE_85_length_2357_cov_15.264311:1-2357 [pilon] NODE_174_length_718_cov_5.661642:1-718 log: [pilon] frags shovill.bam: coverage 16 [pilon] Total Reads: 87, Coverage: 16, minDepth: 5 [pilon] Confirmed 583 of 718 bases (81.20%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_174_length_718_cov_5.661642:1-718 [pilon] Processing NODE_40_length_9694_cov_24.666876:1-9694 [pilon] NODE_93_length_2099_cov_55.472700:1-2099 log: [pilon] frags shovill.bam: coverage 167 [pilon] Total Reads: 2715, Coverage: 167, minDepth: 42 [pilon] Confirmed 1689 of 2099 bases (80.47%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_93_length_2099_cov_55.472700:1-2099 [pilon] Processing NODE_150_length_873_cov_4.017287:1-873 [pilon] NODE_49_length_6704_cov_20.519064:1-6704 log: [pilon] frags shovill.bam: coverage 60 [pilon] Total Reads: 3289, Coverage: 60, minDepth: 15 [pilon] Confirmed 6225 of 6704 bases (92.86%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_49_length_6704_cov_20.519064:1-6704 [pilon] Processing NODE_101_length_1806_cov_38.067062:1-1806 [pilon] NODE_85_length_2357_cov_15.264311:1-2357 log: [pilon] frags shovill.bam: coverage 47 [pilon] Total Reads: 866, Coverage: 47, minDepth: 12 [pilon] Confirmed 1830 of 2357 bases (77.64%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_85_length_2357_cov_15.264311:1-2357 [pilon] Processing NODE_112_length_1628_cov_69.434638:1-1628 [pilon] NODE_150_length_873_cov_4.017287:1-873 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 78, Coverage: 11, minDepth: 5 [pilon] Confirmed 562 of 873 bases (64.38%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_150_length_873_cov_4.017287:1-873 [pilon] NODE_15_length_46866_cov_57.877548:1-46866 log: [pilon] frags shovill.bam: coverage 179 [pilon] Total Reads: 65169, Coverage: 179, minDepth: 45 [pilon] Confirmed 46739 of 46866 bases (99.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_15_length_46866_cov_57.877548:1-46866 [pilon] Processing NODE_90_length_2262_cov_28.539468:1-2262 [pilon] NODE_19_length_39822_cov_45.950329:1-39822 log: [pilon] frags shovill.bam: coverage 142 [pilon] Total Reads: 43889, Coverage: 142, minDepth: 36 [pilon] Confirmed 39375 of 39822 bases (98.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_19_length_39822_cov_45.950329:1-39822 [pilon] Processing NODE_149_length_874_cov_133.118194:1-874 [pilon] NODE_58_length_5431_cov_55.347646:1-5431 log: [pilon] frags shovill.bam: coverage 168 [pilon] Total Reads: 7045, Coverage: 168, minDepth: 42 [pilon] Confirmed 5080 of 5431 bases (93.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_58_length_5431_cov_55.347646:1-5431 [pilon] Processing NODE_83_length_2465_cov_20.519625:1-2465 [pilon] NODE_112_length_1628_cov_69.434638:1-1628 log: [pilon] frags shovill.bam: coverage 203 [pilon] Total Reads: 2605, Coverage: 203, minDepth: 51 [pilon] Confirmed 1347 of 1628 bases (82.74%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_112_length_1628_cov_69.434638:1-1628 [pilon] Processing NODE_114_length_1609_cov_188.451613:1-1609 [pilon] NODE_101_length_1806_cov_38.067062:1-1806 log: [pilon] frags shovill.bam: coverage 137 [pilon] Total Reads: 1913, Coverage: 137, minDepth: 34 [pilon] Confirmed 1154 of 1806 bases (63.90%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_101_length_1806_cov_38.067062:1-1806 [pilon] Processing NODE_167_length_759_cov_6.311912:1-759 [pilon] NODE_167_length_759_cov_6.311912:1-759 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 100, Coverage: 17, minDepth: 5 [pilon] Confirmed 520 of 759 bases (68.51%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_167_length_759_cov_6.311912:1-759 [pilon] Processing NODE_80_length_2567_cov_16.834015:1-2567 [pilon] NODE_90_length_2262_cov_28.539468:1-2262 log: [pilon] frags shovill.bam: coverage 83 [pilon] Total Reads: 1677, Coverage: 83, minDepth: 21 [pilon] Confirmed 1767 of 2262 bases (78.12%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_90_length_2262_cov_28.539468:1-2262 [pilon] Processing NODE_60_length_5155_cov_242.537942:1-5155 [pilon] Processing NODE_31_length_20808_cov_55.769710:1-20808 [pilon] NODE_149_length_874_cov_133.118194:1-874 log: [pilon] frags shovill.bam: coverage 288 [pilon] Total Reads: 2447, Coverage: 288, minDepth: 72 [pilon] Confirmed 785 of 874 bases (89.82%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_149_length_874_cov_133.118194:1-874 [pilon] Processing NODE_75_length_2783_cov_52.388805:1-2783 [pilon] NODE_18_length_42551_cov_59.168065:1-42551 log: [pilon] frags shovill.bam: coverage 183 [pilon] Total Reads: 60364, Coverage: 183, minDepth: 46 [pilon] Confirmed 42300 of 42551 bases (99.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_18_length_42551_cov_59.168065:1-42551 [pilon] Processing NODE_44_length_7802_cov_49.704596:1-7802 [pilon] NODE_83_length_2465_cov_20.519625:1-2465 log: [pilon] frags shovill.bam: coverage 61 [pilon] Total Reads: 1170, Coverage: 61, minDepth: 15 [pilon] Confirmed 1960 of 2465 bases (79.51%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_83_length_2465_cov_20.519625:1-2465 [pilon] Processing NODE_86_length_2317_cov_51.236339:1-2317 [pilon] NODE_23_length_30082_cov_39.311572:1-30082 log: [pilon] frags shovill.bam: coverage 121 [pilon] Total Reads: 28336, Coverage: 121, minDepth: 30 [pilon] Confirmed 29946 of 30082 bases (99.55%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_23_length_30082_cov_39.311572:1-30082 [pilon] NODE_35_length_12911_cov_38.730023:1-12911 log: [pilon] frags shovill.bam: coverage 117 [pilon] Total Reads: 11825, Coverage: 117, minDepth: 29 [pilon] Confirmed 12576 of 12911 bases (97.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_35_length_12911_cov_38.730023:1-12911 [pilon] Processing NODE_77_length_2670_cov_38.073754:1-2670 [pilon] NODE_80_length_2567_cov_16.834015:1-2567 log: [pilon] frags shovill.bam: coverage 48 [pilon] Total Reads: 1009, Coverage: 48, minDepth: 12 [pilon] Confirmed 2225 of 2567 bases (86.68%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_80_length_2567_cov_16.834015:1-2567 [pilon] Processing NODE_221_length_354_cov_58.403433:1-354 [pilon] NODE_221_length_354_cov_58.403433:1-354 log: [pilon] frags shovill.bam: coverage 42 [pilon] Total Reads: 338, Coverage: 42, minDepth: 11 [pilon] Confirmed 303 of 354 bases (85.59%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_221_length_354_cov_58.403433:1-354 [pilon] Processing NODE_68_length_3622_cov_34.099400:1-3622 [pilon] NODE_75_length_2783_cov_52.388805:1-2783 log: [pilon] frags shovill.bam: coverage 114 [pilon] Total Reads: 2844, Coverage: 114, minDepth: 29 [pilon] Confirmed 2432 of 2783 bases (87.39%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_75_length_2783_cov_52.388805:1-2783 [pilon] Processing NODE_212_length_405_cov_1.049296:1-405 [pilon] Processing NODE_168_length_736_cov_8.320325:1-736 [pilon] NODE_40_length_9694_cov_24.666876:1-9694 log: [pilon] frags shovill.bam: coverage 75 [pilon] Total Reads: 5779, Coverage: 75, minDepth: 19 [pilon] Confirmed 8325 of 9694 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_40_length_9694_cov_24.666876:1-9694 [pilon] Processing NODE_78_length_2608_cov_79.446723:1-2608 [pilon] NODE_37_length_10469_cov_56.914090:1-10469 log: [pilon] frags shovill.bam: coverage 139 [pilon] Total Reads: 13214, Coverage: 139, minDepth: 35 [pilon] Confirmed 9674 of 10469 bases (92.41%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_37_length_10469_cov_56.914090:1-10469 [pilon] Processing NODE_156_length_836_cov_14.065734:1-836 [pilon] NODE_114_length_1609_cov_188.451613:1-1609 log: [pilon] frags shovill.bam: coverage 569 [pilon] Total Reads: 7087, Coverage: 569, minDepth: 142 [pilon] Confirmed 721 of 1609 bases (44.81%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_114_length_1609_cov_188.451613:1-1609 [pilon] Processing NODE_152_length_852_cov_10.299590:1-852 [pilon] NODE_212_length_405_cov_1.049296:1-405 log: [pilon] frags shovill.bam: coverage 1 [pilon] Total Reads: 4, Coverage: 1, minDepth: 5 [pilon] Confirmed 0 of 405 bases (0.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_212_length_405_cov_1.049296:1-405 [pilon] Processing NODE_61_length_4876_cov_50.439327:1-4876 [pilon] NODE_168_length_736_cov_8.320325:1-736 log: [pilon] frags shovill.bam: coverage 25 [pilon] Total Reads: 142, Coverage: 25, minDepth: 6 [pilon] Confirmed 560 of 736 bases (76.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_168_length_736_cov_8.320325:1-736 [pilon] Processing NODE_245_length_122_cov_6136.000000:1-122 [pilon] NODE_156_length_836_cov_14.065734:1-836 log: [pilon] frags shovill.bam: coverage 37 [pilon] Total Reads: 241, Coverage: 37, minDepth: 9 [pilon] Confirmed 526 of 836 bases (62.92%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_156_length_836_cov_14.065734:1-836 [pilon] Processing NODE_186_length_622_cov_5.117764:1-622 [pilon] NODE_152_length_852_cov_10.299590:1-852 log: [pilon] frags shovill.bam: coverage 26 [pilon] Total Reads: 177, Coverage: 26, minDepth: 7 [pilon] Confirmed 574 of 852 bases (67.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_152_length_852_cov_10.299590:1-852 [pilon] Processing NODE_52_length_6347_cov_31.040315:1-6347 [pilon] NODE_86_length_2317_cov_51.236339:1-2317 log: [pilon] frags shovill.bam: coverage 146 [pilon] Total Reads: 2736, Coverage: 146, minDepth: 37 [pilon] Confirmed 1827 of 2317 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_86_length_2317_cov_51.236339:1-2317 [pilon] Processing NODE_139_length_1002_cov_7.601589:1-1002 [pilon] NODE_245_length_122_cov_6136.000000:1-122 log: [pilon] frags shovill.bam: coverage 0 [pilon] Total Reads: 414, 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_245_length_122_cov_6136.000000:1-122 [pilon] NODE_77_length_2670_cov_38.073754:1-2670 log: [pilon] frags shovill.bam: coverage 117 [pilon] Total Reads: 2412, Coverage: 117, minDepth: 29 [pilon] Confirmed 1730 of 2670 bases (64.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_77_length_2670_cov_38.073754:1-2670 [pilon] NODE_186_length_622_cov_5.117764:1-622 log: [pilon] frags shovill.bam: coverage 11 [pilon] Total Reads: 51, Coverage: 11, minDepth: 5 [pilon] Confirmed 450 of 622 bases (72.35%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_186_length_622_cov_5.117764:1-622 [pilon] NODE_147_length_906_cov_1448.536306:1-906 log: [pilon] frags shovill.bam: coverage 3282 [pilon] Total Reads: 28597, Coverage: 3282, minDepth: 821 [pilon] Confirmed 820 of 906 bases (90.51%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_147_length_906_cov_1448.536306:1-906 [pilon] NODE_139_length_1002_cov_7.601589:1-1002 log: [pilon] frags shovill.bam: coverage 21 [pilon] Total Reads: 170, Coverage: 21, minDepth: 5 [pilon] Confirmed 653 of 1002 bases (65.17%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_139_length_1002_cov_7.601589:1-1002 [pilon] Processing NODE_47_length_7733_cov_84.630321:1-7733 [pilon] NODE_68_length_3622_cov_34.099400:1-3622 log: [pilon] frags shovill.bam: coverage 99 [pilon] Total Reads: 2949, Coverage: 99, minDepth: 25 [pilon] Confirmed 3324 of 3622 bases (91.77%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_68_length_3622_cov_34.099400:1-3622 [pilon] NODE_78_length_2608_cov_79.446723:1-2608 log: [pilon] frags shovill.bam: coverage 229 [pilon] Total Reads: 4785, Coverage: 229, minDepth: 57 [pilon] Confirmed 2376 of 2608 bases (91.10%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_78_length_2608_cov_79.446723:1-2608 [pilon] Processing NODE_138_length_1019_cov_47.689310:1-1019 [pilon] NODE_138_length_1019_cov_47.689310:1-1019 log: [pilon] frags shovill.bam: coverage 107 [pilon] Total Reads: 1032, Coverage: 107, minDepth: 27 [pilon] Confirmed 913 of 1019 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_138_length_1019_cov_47.689310:1-1019 [pilon] Processing NODE_29_length_23079_cov_32.276941:1-23079 [pilon] NODE_52_length_6347_cov_31.040315:1-6347 log: [pilon] frags shovill.bam: coverage 92 [pilon] Total Reads: 4649, Coverage: 92, minDepth: 23 [pilon] Confirmed 6076 of 6347 bases (95.73%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_52_length_6347_cov_31.040315:1-6347 [pilon] Processing NODE_179_length_690_cov_6.340949:1-690 [pilon] NODE_61_length_4876_cov_50.439327:1-4876 log: [pilon] frags shovill.bam: coverage 150 [pilon] Total Reads: 5770, Coverage: 150, minDepth: 38 [pilon] Confirmed 4636 of 4876 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_61_length_4876_cov_50.439327:1-4876 [pilon] NODE_179_length_690_cov_6.340949:1-690 log: [pilon] frags shovill.bam: coverage 17 [pilon] Total Reads: 88, Coverage: 17, minDepth: 5 [pilon] Confirmed 579 of 690 bases (83.91%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_179_length_690_cov_6.340949:1-690 [pilon] NODE_44_length_7802_cov_49.704596:1-7802 log: [pilon] frags shovill.bam: coverage 150 [pilon] Total Reads: 9143, Coverage: 150, minDepth: 38 [pilon] Confirmed 7485 of 7802 bases (95.94%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Processing NODE_30_length_21392_cov_39.908984:1-21392 [pilon] Finished processing NODE_44_length_7802_cov_49.704596:1-7802 [pilon] NODE_60_length_5155_cov_242.537942:1-5155 log: [pilon] frags shovill.bam: coverage 721 [pilon] Total Reads: 30053, Coverage: 721, minDepth: 180 [pilon] Confirmed 4024 of 5155 bases (78.06%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_60_length_5155_cov_242.537942:1-5155 [pilon] Processing NODE_197_length_500_cov_1.817942:1-500 [pilon] NODE_197_length_500_cov_1.817942:1-500 log: [pilon] frags shovill.bam: coverage 6 [pilon] Total Reads: 24, Coverage: 6, minDepth: 5 [pilon] Confirmed 258 of 500 bases (51.60%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_197_length_500_cov_1.817942:1-500 [pilon] NODE_47_length_7733_cov_84.630321:1-7733 log: [pilon] frags shovill.bam: coverage 257 [pilon] Total Reads: 15508, Coverage: 257, minDepth: 64 [pilon] Confirmed 7492 of 7733 bases (96.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_47_length_7733_cov_84.630321:1-7733 [pilon] NODE_31_length_20808_cov_55.769710:1-20808 log: [pilon] frags shovill.bam: coverage 171 [pilon] Total Reads: 27853, Coverage: 171, minDepth: 43 [pilon] Confirmed 20505 of 20808 bases (98.54%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_31_length_20808_cov_55.769710:1-20808 [pilon] Processing NODE_116_length_1516_cov_34.746953:1-1516 [pilon] NODE_116_length_1516_cov_34.746953:1-1516 log: [pilon] frags shovill.bam: coverage 69 [pilon] Total Reads: 1278, Coverage: 69, minDepth: 17 [pilon] Confirmed 703 of 1516 bases (46.37%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_116_length_1516_cov_34.746953:1-1516 [pilon] NODE_29_length_23079_cov_32.276941:1-23079 log: [pilon] frags shovill.bam: coverage 101 [pilon] Total Reads: 18042, Coverage: 101, minDepth: 25 [pilon] Confirmed 22791 of 23079 bases (98.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_29_length_23079_cov_32.276941:1-23079 [pilon] Processing NODE_17_length_44083_cov_45.462877:1-44083 [pilon] NODE_11_length_61426_cov_56.116043:1-61426 log: [pilon] frags shovill.bam: coverage 174 [pilon] Total Reads: 82818, Coverage: 174, minDepth: 44 [pilon] Confirmed 60348 of 61426 bases (98.25%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_11_length_61426_cov_56.116043:1-61426 [pilon] Processing NODE_89_length_2274_cov_72.618672:1-2274 [pilon] NODE_89_length_2274_cov_72.618672:1-2274 log: [pilon] frags shovill.bam: coverage 205 [pilon] Total Reads: 3795, Coverage: 205, minDepth: 51 [pilon] Confirmed 1821 of 2274 bases (80.08%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_89_length_2274_cov_72.618672:1-2274 [pilon] NODE_30_length_21392_cov_39.908984:1-21392 log: [pilon] frags shovill.bam: coverage 123 [pilon] Total Reads: 20413, Coverage: 123, minDepth: 31 [pilon] Confirmed 21292 of 21392 bases (99.53%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_30_length_21392_cov_39.908984:1-21392 [pilon] Processing NODE_193_length_574_cov_28.719647:1-574 [pilon] NODE_193_length_574_cov_28.719647:1-574 log: [pilon] frags shovill.bam: coverage 43 [pilon] Total Reads: 379, Coverage: 43, minDepth: 11 [pilon] Confirmed 398 of 574 bases (69.34%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_193_length_574_cov_28.719647:1-574 [pilon] NODE_14_length_49877_cov_50.484283:1-49877 log: [pilon] frags shovill.bam: coverage 147 [pilon] Total Reads: 60722, Coverage: 147, minDepth: 37 [pilon] Confirmed 49830 of 49877 bases (99.91%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_14_length_49877_cov_50.484283:1-49877 [pilon] Processing NODE_175_length_712_cov_36.543147:1-712 [pilon] NODE_10_length_69806_cov_34.526857:1-69806 log: [pilon] frags shovill.bam: coverage 107 [pilon] Total Reads: 57963, Coverage: 107, minDepth: 27 [pilon] Confirmed 68230 of 69806 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_10_length_69806_cov_34.526857:1-69806 [pilon] Processing NODE_183_length_632_cov_2.011742:1-632 [pilon] NODE_175_length_712_cov_36.543147:1-712 log: [pilon] frags shovill.bam: coverage 74 [pilon] Total Reads: 522, Coverage: 74, minDepth: 19 [pilon] Confirmed 519 of 712 bases (72.89%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_175_length_712_cov_36.543147:1-712 [pilon] NODE_183_length_632_cov_2.011742:1-632 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 26, Coverage: 5, minDepth: 5 [pilon] Confirmed 281 of 632 bases (44.46%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_183_length_632_cov_2.011742:1-632 [pilon] NODE_12_length_59410_cov_51.720302:1-59410 log: [pilon] frags shovill.bam: coverage 160 [pilon] Total Reads: 73875, Coverage: 160, minDepth: 40 [pilon] Confirmed 59104 of 59410 bases (99.48%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_12_length_59410_cov_51.720302:1-59410 [pilon] Processing NODE_108_length_1714_cov_37.838669:1-1714 [pilon] NODE_108_length_1714_cov_37.838669:1-1714 log: [pilon] frags shovill.bam: coverage 106 [pilon] Total Reads: 1412, Coverage: 106, minDepth: 27 [pilon] Confirmed 1371 of 1714 bases (79.99%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_108_length_1714_cov_37.838669:1-1714 [pilon] NODE_5_length_118189_cov_48.804672:1-118189 log: [pilon] frags shovill.bam: coverage 151 [pilon] Total Reads: 138381, Coverage: 151, minDepth: 38 [pilon] Confirmed 117256 of 118189 bases (99.21%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_5_length_118189_cov_48.804672:1-118189 [pilon] NODE_7_length_95188_cov_38.123429:1-95188 log: [pilon] frags shovill.bam: coverage 118 [pilon] Total Reads: 87448, Coverage: 118, minDepth: 30 [pilon] Confirmed 94984 of 95188 bases (99.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_7_length_95188_cov_38.123429:1-95188 [pilon] Processing NODE_184_length_629_cov_1.885827:1-629 [pilon] NODE_6_length_102150_cov_43.147870:1-102150 log: [pilon] NODE_8_length_76265_cov_46.522195:1-76265 log: [pilon] frags shovill.bam: coverage 144 [pilon] Total Reads: 85150, Coverage: 144, minDepth: 36 [pilon] Confirmed 75372 of 76265 bases (98.83%) [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 134 [pilon] Total Reads: 106095, Coverage: 134, minDepth: 34 [pilon] Confirmed 101644 of 102150 bases (99.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_8_length_76265_cov_46.522195:1-76265 [pilon] Finished processing NODE_6_length_102150_cov_43.147870:1-102150 [pilon] Processing NODE_191_length_587_cov_3.429185:1-587 [pilon] Processing NODE_123_length_1353_cov_37.403409:1-1353 [pilon] NODE_184_length_629_cov_1.885827:1-629 log: [pilon] frags shovill.bam: coverage 5 [pilon] Total Reads: 26, Coverage: 5, minDepth: 5 [pilon] Confirmed 244 of 629 bases (38.79%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_184_length_629_cov_1.885827:1-629 [pilon] NODE_191_length_587_cov_3.429185:1-587 log: [pilon] frags shovill.bam: coverage 7 [pilon] Total Reads: 35, Coverage: 7, minDepth: 5 [pilon] Confirmed 317 of 587 bases (54.00%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_191_length_587_cov_3.429185:1-587 [pilon] NODE_123_length_1353_cov_37.403409:1-1353 log: [pilon] frags shovill.bam: coverage 56 [pilon] Total Reads: 834, Coverage: 56, minDepth: 14 [pilon] Confirmed 1136 of 1353 bases (83.96%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_123_length_1353_cov_37.403409:1-1353 [pilon] Processing NODE_202_length_416_cov_0.738983:1-416 [pilon] NODE_202_length_416_cov_0.738983:1-416 log: [pilon] frags shovill.bam: coverage 2 [pilon] Total Reads: 19, Coverage: 2, minDepth: 5 [pilon] Confirmed 52 of 416 bases (12.50%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_202_length_416_cov_0.738983:1-416 [pilon] NODE_17_length_44083_cov_45.462877:1-44083 log: [pilon] frags shovill.bam: coverage 141 [pilon] Total Reads: 48220, Coverage: 141, minDepth: 35 [pilon] Confirmed 43547 of 44083 bases (98.78%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_17_length_44083_cov_45.462877:1-44083 [pilon] NODE_4_length_122931_cov_50.676736:1-122931 log: [pilon] frags shovill.bam: coverage 157 [pilon] Total Reads: 149461, Coverage: 157, minDepth: 39 [pilon] Confirmed 122728 of 122931 bases (99.83%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_4_length_122931_cov_50.676736:1-122931 [pilon] NODE_2_length_206873_cov_35.744501:1-206873 log: [pilon] frags shovill.bam: coverage 111 [pilon] Total Reads: 177637, Coverage: 111, minDepth: 28 [pilon] Confirmed 206347 of 206873 bases (99.75%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_2_length_206873_cov_35.744501:1-206873 [pilon] Processing NODE_205_length_410_cov_1.574394:1-410 [pilon] NODE_205_length_410_cov_1.574394:1-410 log: [pilon] frags shovill.bam: coverage 3 [pilon] Total Reads: 8, Coverage: 3, minDepth: 5 [pilon] Confirmed 10 of 410 bases (2.44%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_205_length_410_cov_1.574394:1-410 [pilon] NODE_3_length_177459_cov_54.729088:1-177459 log: [pilon] frags shovill.bam: coverage 170 [pilon] Total Reads: 233947, Coverage: 170, minDepth: 43 [pilon] Confirmed 176958 of 177459 bases (99.72%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_3_length_177459_cov_54.729088:1-177459 [pilon] Processing NODE_161_length_799_cov_16.939528:1-799 [pilon] NODE_161_length_799_cov_16.939528:1-799 log: [pilon] frags shovill.bam: coverage 47 [pilon] Total Reads: 289, Coverage: 47, minDepth: 12 [pilon] Confirmed 600 of 799 bases (75.09%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_161_length_799_cov_16.939528:1-799 [pilon] NODE_1_length_256070_cov_43.389882:1-256070 log: [pilon] frags shovill.bam: coverage 135 [pilon] Total Reads: 267379, Coverage: 135, minDepth: 34 [pilon] Confirmed 255757 of 256070 bases (99.88%) [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases [pilon] Finished processing NODE_1_length_256070_cov_43.389882:1-256070 [pilon] Writing NODE_1_length_256070_cov_43.389882:1-256070 changes to pilon.changes [pilon] Writing updated NODE_1_length_256070_cov_43.389882_pilon to pilon.fasta [pilon] Writing NODE_2_length_206873_cov_35.744501:1-206873 changes to pilon.changes [pilon] Writing updated NODE_2_length_206873_cov_35.744501_pilon to pilon.fasta [pilon] Writing NODE_3_length_177459_cov_54.729088:1-177459 changes to pilon.changes [pilon] Writing updated NODE_3_length_177459_cov_54.729088_pilon to pilon.fasta [pilon] Writing NODE_4_length_122931_cov_50.676736:1-122931 changes to pilon.changes [pilon] Writing updated NODE_4_length_122931_cov_50.676736_pilon to pilon.fasta [pilon] Writing NODE_5_length_118189_cov_48.804672:1-118189 changes to pilon.changes [pilon] Writing updated NODE_5_length_118189_cov_48.804672_pilon to pilon.fasta [pilon] Writing NODE_6_length_102150_cov_43.147870:1-102150 changes to pilon.changes [pilon] Writing updated NODE_6_length_102150_cov_43.147870_pilon to pilon.fasta [pilon] Writing NODE_7_length_95188_cov_38.123429:1-95188 changes to pilon.changes [pilon] Writing updated NODE_7_length_95188_cov_38.123429_pilon to pilon.fasta [pilon] Writing NODE_8_length_76265_cov_46.522195:1-76265 changes to pilon.changes [pilon] Writing updated NODE_8_length_76265_cov_46.522195_pilon to pilon.fasta [pilon] Writing NODE_9_length_73464_cov_33.170173:1-73464 changes to pilon.changes [pilon] Writing updated NODE_9_length_73464_cov_33.170173_pilon to pilon.fasta [pilon] Writing NODE_10_length_69806_cov_34.526857:1-69806 changes to pilon.changes [pilon] Writing updated NODE_10_length_69806_cov_34.526857_pilon to pilon.fasta [pilon] Writing NODE_11_length_61426_cov_56.116043:1-61426 changes to pilon.changes [pilon] Writing updated NODE_11_length_61426_cov_56.116043_pilon to pilon.fasta [pilon] Writing NODE_12_length_59410_cov_51.720302:1-59410 changes to pilon.changes [pilon] Writing updated NODE_12_length_59410_cov_51.720302_pilon to pilon.fasta [pilon] Writing NODE_13_length_57066_cov_38.945544:1-57066 changes to pilon.changes [pilon] Writing updated NODE_13_length_57066_cov_38.945544_pilon to pilon.fasta [pilon] Writing NODE_14_length_49877_cov_50.484283:1-49877 changes to pilon.changes [pilon] Writing updated NODE_14_length_49877_cov_50.484283_pilon to pilon.fasta [pilon] Writing NODE_15_length_46866_cov_57.877548:1-46866 changes to pilon.changes [pilon] Writing updated NODE_15_length_46866_cov_57.877548_pilon to pilon.fasta [pilon] Writing NODE_16_length_46293_cov_41.603699:1-46293 changes to pilon.changes [pilon] Writing updated NODE_16_length_46293_cov_41.603699_pilon to pilon.fasta [pilon] Writing NODE_17_length_44083_cov_45.462877:1-44083 changes to pilon.changes [pilon] Writing updated NODE_17_length_44083_cov_45.462877_pilon to pilon.fasta [pilon] Writing NODE_18_length_42551_cov_59.168065:1-42551 changes to pilon.changes [pilon] Writing updated NODE_18_length_42551_cov_59.168065_pilon to pilon.fasta [pilon] Writing NODE_19_length_39822_cov_45.950329:1-39822 changes to pilon.changes [pilon] Writing updated NODE_19_length_39822_cov_45.950329_pilon to pilon.fasta [pilon] Writing NODE_20_length_35358_cov_60.026733:1-35358 changes to pilon.changes [pilon] Writing updated NODE_20_length_35358_cov_60.026733_pilon to pilon.fasta [pilon] Writing NODE_21_length_31170_cov_46.522207:1-31170 changes to pilon.changes [pilon] Writing updated NODE_21_length_31170_cov_46.522207_pilon to pilon.fasta [pilon] Writing NODE_22_length_30560_cov_31.999310:1-30560 changes to pilon.changes [pilon] Writing updated NODE_22_length_30560_cov_31.999310_pilon to pilon.fasta [pilon] Writing NODE_23_length_30082_cov_39.311572:1-30082 changes to pilon.changes [pilon] Writing updated NODE_23_length_30082_cov_39.311572_pilon to pilon.fasta [pilon] Writing NODE_24_length_27859_cov_33.842022:1-27859 changes to pilon.changes [pilon] Writing updated NODE_24_length_27859_cov_33.842022_pilon to pilon.fasta [pilon] Writing NODE_25_length_27770_cov_54.426345:1-27770 changes to pilon.changes [pilon] Writing updated NODE_25_length_27770_cov_54.426345_pilon to pilon.fasta [pilon] Writing NODE_26_length_26480_cov_58.159604:1-26480 changes to pilon.changes [pilon] Writing updated NODE_26_length_26480_cov_58.159604_pilon to pilon.fasta [pilon] Writing NODE_27_length_26025_cov_36.316553:1-26025 changes to pilon.changes [pilon] Writing updated NODE_27_length_26025_cov_36.316553_pilon to pilon.fasta [pilon] Writing NODE_28_length_24965_cov_56.849863:1-24965 changes to pilon.changes [pilon] Writing updated NODE_28_length_24965_cov_56.849863_pilon to pilon.fasta [pilon] Writing NODE_29_length_23079_cov_32.276941:1-23079 changes to pilon.changes [pilon] Writing updated NODE_29_length_23079_cov_32.276941_pilon to pilon.fasta [pilon] Writing NODE_30_length_21392_cov_39.908984:1-21392 changes to pilon.changes [pilon] Writing updated NODE_30_length_21392_cov_39.908984_pilon to pilon.fasta [pilon] Writing NODE_31_length_20808_cov_55.769710:1-20808 changes to pilon.changes [pilon] Writing updated NODE_31_length_20808_cov_55.769710_pilon to pilon.fasta [pilon] Writing NODE_32_length_15314_cov_32.797341:1-15314 changes to pilon.changes [pilon] Writing updated NODE_32_length_15314_cov_32.797341_pilon to pilon.fasta [pilon] Writing NODE_33_length_15095_cov_57.026579:1-15095 changes to pilon.changes [pilon] Writing updated NODE_33_length_15095_cov_57.026579_pilon to pilon.fasta [pilon] Writing NODE_34_length_14248_cov_60.176329:1-14248 changes to pilon.changes [pilon] Writing updated NODE_34_length_14248_cov_60.176329_pilon to pilon.fasta [pilon] Writing NODE_35_length_12911_cov_38.730023:1-12911 changes to pilon.changes [pilon] Writing updated NODE_35_length_12911_cov_38.730023_pilon to pilon.fasta [pilon] Writing NODE_36_length_12840_cov_38.927353:1-12840 changes to pilon.changes [pilon] Writing updated NODE_36_length_12840_cov_38.927353_pilon to pilon.fasta [pilon] Writing NODE_37_length_10469_cov_56.914090:1-10469 changes to pilon.changes [pilon] Writing updated NODE_37_length_10469_cov_56.914090_pilon to pilon.fasta [pilon] Writing NODE_38_length_10396_cov_58.472895:1-10396 changes to pilon.changes [pilon] Writing updated NODE_38_length_10396_cov_58.472895_pilon to pilon.fasta [pilon] Writing NODE_39_length_9867_cov_55.174123:1-9867 changes to pilon.changes [pilon] Writing updated NODE_39_length_9867_cov_55.174123_pilon to pilon.fasta [pilon] Writing NODE_40_length_9694_cov_24.666876:1-9694 changes to pilon.changes [pilon] Writing updated NODE_40_length_9694_cov_24.666876_pilon to pilon.fasta [pilon] Writing NODE_41_length_8710_cov_29.313308:1-8710 changes to pilon.changes [pilon] Writing updated NODE_41_length_8710_cov_29.313308_pilon to pilon.fasta [pilon] Writing NODE_42_length_8186_cov_24.711345:1-8186 changes to pilon.changes [pilon] Writing updated NODE_42_length_8186_cov_24.711345_pilon to pilon.fasta [pilon] Writing NODE_43_length_8142_cov_39.854632:1-8142 changes to pilon.changes [pilon] Writing updated NODE_43_length_8142_cov_39.854632_pilon to pilon.fasta [pilon] Writing NODE_44_length_7802_cov_49.704596:1-7802 changes to pilon.changes [pilon] Writing updated NODE_44_length_7802_cov_49.704596_pilon to pilon.fasta [pilon] Writing NODE_45_length_7758_cov_75.902580:1-7758 changes to pilon.changes [pilon] Writing updated NODE_45_length_7758_cov_75.902580_pilon to pilon.fasta [pilon] Writing NODE_46_length_7733_cov_93.546506:1-7733 changes to pilon.changes [pilon] Writing updated NODE_46_length_7733_cov_93.546506_pilon to pilon.fasta [pilon] Writing NODE_47_length_7733_cov_84.630321:1-7733 changes to pilon.changes [pilon] Writing updated NODE_47_length_7733_cov_84.630321_pilon to pilon.fasta [pilon] Writing NODE_48_length_7076_cov_77.874191:1-7076 changes to pilon.changes [pilon] Writing updated NODE_48_length_7076_cov_77.874191_pilon to pilon.fasta [pilon] Writing NODE_49_length_6704_cov_20.519064:1-6704 changes to pilon.changes [pilon] Writing updated NODE_49_length_6704_cov_20.519064_pilon to pilon.fasta [pilon] Writing NODE_50_length_6535_cov_104.265513:1-6535 changes to pilon.changes [pilon] Writing updated NODE_50_length_6535_cov_104.265513_pilon to pilon.fasta [pilon] Writing NODE_51_length_6463_cov_45.929360:1-6463 changes to pilon.changes [pilon] Writing updated NODE_51_length_6463_cov_45.929360_pilon to pilon.fasta [pilon] Writing NODE_52_length_6347_cov_31.040315:1-6347 changes to pilon.changes [pilon] Writing updated NODE_52_length_6347_cov_31.040315_pilon to pilon.fasta [pilon] Writing NODE_53_length_6284_cov_72.995457:1-6284 changes to pilon.changes [pilon] Writing updated NODE_53_length_6284_cov_72.995457_pilon to pilon.fasta [pilon] Writing NODE_54_length_6183_cov_101.750742:1-6183 changes to pilon.changes [pilon] Writing updated NODE_54_length_6183_cov_101.750742_pilon to pilon.fasta [pilon] Writing NODE_55_length_5916_cov_40.733563:1-5916 changes to pilon.changes [pilon] Writing updated NODE_55_length_5916_cov_40.733563_pilon to pilon.fasta [pilon] Writing NODE_56_length_5882_cov_44.708210:1-5882 changes to pilon.changes [pilon] Writing updated NODE_56_length_5882_cov_44.708210_pilon to pilon.fasta [pilon] Writing NODE_57_length_5712_cov_85.235736:1-5712 changes to pilon.changes [pilon] Writing updated NODE_57_length_5712_cov_85.235736_pilon to pilon.fasta [pilon] Writing NODE_58_length_5431_cov_55.347646:1-5431 changes to pilon.changes [pilon] Writing updated NODE_58_length_5431_cov_55.347646_pilon to pilon.fasta [pilon] Writing NODE_59_length_5253_cov_47.182970:1-5253 changes to pilon.changes [pilon] Writing updated NODE_59_length_5253_cov_47.182970_pilon to pilon.fasta [pilon] Writing NODE_60_length_5155_cov_242.537942:1-5155 changes to pilon.changes [pilon] Writing updated NODE_60_length_5155_cov_242.537942_pilon to pilon.fasta [pilon] Writing NODE_61_length_4876_cov_50.439327:1-4876 changes to pilon.changes [pilon] Writing updated NODE_61_length_4876_cov_50.439327_pilon to pilon.fasta [pilon] Writing NODE_62_length_4112_cov_71.900276:1-4112 changes to pilon.changes [pilon] Writing updated NODE_62_length_4112_cov_71.900276_pilon to pilon.fasta [pilon] Writing NODE_63_length_4055_cov_60.968480:1-4055 changes to pilon.changes [pilon] Writing updated NODE_63_length_4055_cov_60.968480_pilon to pilon.fasta [pilon] Writing NODE_64_length_3915_cov_22.312335:1-3915 changes to pilon.changes [pilon] Writing updated NODE_64_length_3915_cov_22.312335_pilon to pilon.fasta [pilon] Writing NODE_65_length_3859_cov_46.880150:1-3859 changes to pilon.changes [pilon] Writing updated NODE_65_length_3859_cov_46.880150_pilon to pilon.fasta [pilon] Writing NODE_66_length_3739_cov_17.781371:1-3739 changes to pilon.changes [pilon] Writing updated NODE_66_length_3739_cov_17.781371_pilon to pilon.fasta [pilon] Writing NODE_67_length_3657_cov_25.732466:1-3657 changes to pilon.changes [pilon] Writing updated NODE_67_length_3657_cov_25.732466_pilon to pilon.fasta [pilon] Writing NODE_68_length_3622_cov_34.099400:1-3622 changes to pilon.changes [pilon] Writing updated NODE_68_length_3622_cov_34.099400_pilon to pilon.fasta [pilon] Writing NODE_69_length_3592_cov_82.280035:1-3592 changes to pilon.changes [pilon] Writing updated NODE_69_length_3592_cov_82.280035_pilon to pilon.fasta [pilon] Writing NODE_70_length_3576_cov_37.180318:1-3576 changes to pilon.changes [pilon] Writing updated NODE_70_length_3576_cov_37.180318_pilon to pilon.fasta [pilon] Writing NODE_71_length_3531_cov_97.446921:1-3531 changes to pilon.changes [pilon] Writing updated NODE_71_length_3531_cov_97.446921_pilon to pilon.fasta [pilon] Writing NODE_72_length_3116_cov_62.176962:1-3116 changes to pilon.changes [pilon] Writing updated NODE_72_length_3116_cov_62.176962_pilon to pilon.fasta [pilon] Writing NODE_73_length_2986_cov_46.962653:1-2986 changes to pilon.changes [pilon] Writing updated NODE_73_length_2986_cov_46.962653_pilon to pilon.fasta [pilon] Writing NODE_74_length_2878_cov_68.913674:1-2878 changes to pilon.changes [pilon] Writing updated NODE_74_length_2878_cov_68.913674_pilon to pilon.fasta [pilon] Writing NODE_75_length_2783_cov_52.388805:1-2783 changes to pilon.changes [pilon] Writing updated NODE_75_length_2783_cov_52.388805_pilon to pilon.fasta [pilon] Writing NODE_76_length_2733_cov_59.843798:1-2733 changes to pilon.changes [pilon] Writing updated NODE_76_length_2733_cov_59.843798_pilon to pilon.fasta [pilon] Writing NODE_77_length_2670_cov_38.073754:1-2670 changes to pilon.changes [pilon] Writing updated NODE_77_length_2670_cov_38.073754_pilon to pilon.fasta [pilon] Writing NODE_78_length_2608_cov_79.446723:1-2608 changes to pilon.changes [pilon] Writing updated NODE_78_length_2608_cov_79.446723_pilon to pilon.fasta [pilon] Writing NODE_79_length_2601_cov_68.245161:1-2601 changes to pilon.changes [pilon] Writing updated NODE_79_length_2601_cov_68.245161_pilon to pilon.fasta [pilon] Writing NODE_80_length_2567_cov_16.834015:1-2567 changes to pilon.changes [pilon] Writing updated NODE_80_length_2567_cov_16.834015_pilon to pilon.fasta [pilon] Writing NODE_81_length_2552_cov_73.875771:1-2552 changes to pilon.changes [pilon] Writing updated NODE_81_length_2552_cov_73.875771_pilon to pilon.fasta [pilon] Writing NODE_82_length_2490_cov_154.097087:1-2490 changes to pilon.changes [pilon] Writing updated NODE_82_length_2490_cov_154.097087_pilon to pilon.fasta [pilon] Writing NODE_83_length_2465_cov_20.519625:1-2465 changes to pilon.changes [pilon] Writing updated NODE_83_length_2465_cov_20.519625_pilon to pilon.fasta [pilon] Writing NODE_84_length_2374_cov_57.449179:1-2374 changes to pilon.changes [pilon] Writing updated NODE_84_length_2374_cov_57.449179_pilon to pilon.fasta [pilon] Writing NODE_85_length_2357_cov_15.264311:1-2357 changes to pilon.changes [pilon] Writing updated NODE_85_length_2357_cov_15.264311_pilon to pilon.fasta [pilon] Writing NODE_86_length_2317_cov_51.236339:1-2317 changes to pilon.changes [pilon] Writing updated NODE_86_length_2317_cov_51.236339_pilon to pilon.fasta [pilon] Writing NODE_87_length_2289_cov_12.089022:1-2289 changes to pilon.changes [pilon] Writing updated NODE_87_length_2289_cov_12.089022_pilon to pilon.fasta [pilon] Writing NODE_88_length_2287_cov_22.660203:1-2287 changes to pilon.changes [pilon] Writing updated NODE_88_length_2287_cov_22.660203_pilon to pilon.fasta [pilon] Writing NODE_89_length_2274_cov_72.618672:1-2274 changes to pilon.changes [pilon] Writing updated NODE_89_length_2274_cov_72.618672_pilon to pilon.fasta [pilon] Writing NODE_90_length_2262_cov_28.539468:1-2262 changes to pilon.changes [pilon] Writing updated NODE_90_length_2262_cov_28.539468_pilon to pilon.fasta [pilon] Writing NODE_91_length_2143_cov_108.869931:1-2143 changes to pilon.changes [pilon] Writing updated NODE_91_length_2143_cov_108.869931_pilon to pilon.fasta [pilon] Writing NODE_92_length_2104_cov_28.162885:1-2104 changes to pilon.changes [pilon] Writing updated NODE_92_length_2104_cov_28.162885_pilon to pilon.fasta [pilon] Writing NODE_93_length_2099_cov_55.472700:1-2099 changes to pilon.changes [pilon] Writing updated NODE_93_length_2099_cov_55.472700_pilon to pilon.fasta [pilon] Writing NODE_94_length_2082_cov_25.812851:1-2082 changes to pilon.changes [pilon] Writing updated NODE_94_length_2082_cov_25.812851_pilon to pilon.fasta [pilon] Writing NODE_95_length_2039_cov_45.280501:1-2039 changes to pilon.changes [pilon] Writing updated NODE_95_length_2039_cov_45.280501_pilon to pilon.fasta [pilon] Writing NODE_96_length_1995_cov_24.163821:1-1995 changes to pilon.changes [pilon] Writing updated NODE_96_length_1995_cov_24.163821_pilon to pilon.fasta [pilon] Writing NODE_97_length_1959_cov_80.442329:1-1959 changes to pilon.changes [pilon] Writing updated NODE_97_length_1959_cov_80.442329_pilon to pilon.fasta [pilon] Writing NODE_98_length_1834_cov_40.031524:1-1834 changes to pilon.changes [pilon] Writing updated NODE_98_length_1834_cov_40.031524_pilon to pilon.fasta [pilon] Writing NODE_99_length_1833_cov_48.651285:1-1833 changes to pilon.changes [pilon] Writing updated NODE_99_length_1833_cov_48.651285_pilon to pilon.fasta [pilon] Writing NODE_100_length_1813_cov_10.894208:1-1813 changes to pilon.changes [pilon] Writing updated NODE_100_length_1813_cov_10.894208_pilon to pilon.fasta [pilon] Writing NODE_101_length_1806_cov_38.067062:1-1806 changes to pilon.changes [pilon] Writing updated NODE_101_length_1806_cov_38.067062_pilon to pilon.fasta [pilon] Writing NODE_102_length_1806_cov_36.555490:1-1806 changes to pilon.changes [pilon] Writing updated NODE_102_length_1806_cov_36.555490_pilon to pilon.fasta [pilon] Writing NODE_103_length_1802_cov_38.196312:1-1802 changes to pilon.changes [pilon] Writing updated NODE_103_length_1802_cov_38.196312_pilon to pilon.fasta [pilon] Writing NODE_104_length_1747_cov_218.543050:1-1747 changes to pilon.changes [pilon] Writing updated NODE_104_length_1747_cov_218.543050_pilon to pilon.fasta [pilon] Writing NODE_105_length_1741_cov_30.058025:1-1741 changes to pilon.changes [pilon] Writing updated NODE_105_length_1741_cov_30.058025_pilon to pilon.fasta [pilon] Writing NODE_106_length_1728_cov_76.780336:1-1728 changes to pilon.changes [pilon] Writing updated NODE_106_length_1728_cov_76.780336_pilon to pilon.fasta [pilon] Writing NODE_107_length_1726_cov_25.937695:1-1726 changes to pilon.changes [pilon] Writing updated NODE_107_length_1726_cov_25.937695_pilon to pilon.fasta [pilon] Writing NODE_108_length_1714_cov_37.838669:1-1714 changes to pilon.changes [pilon] Writing updated NODE_108_length_1714_cov_37.838669_pilon to pilon.fasta [pilon] Writing NODE_109_length_1679_cov_70.392169:1-1679 changes to pilon.changes [pilon] Writing updated NODE_109_length_1679_cov_70.392169_pilon to pilon.fasta [pilon] Writing NODE_110_length_1656_cov_16.851466:1-1656 changes to pilon.changes [pilon] Writing updated NODE_110_length_1656_cov_16.851466_pilon to pilon.fasta [pilon] Writing NODE_111_length_1650_cov_59.013080:1-1650 changes to pilon.changes [pilon] Writing updated NODE_111_length_1650_cov_59.013080_pilon to pilon.fasta [pilon] Writing NODE_112_length_1628_cov_69.434638:1-1628 changes to pilon.changes [pilon] Writing updated NODE_112_length_1628_cov_69.434638_pilon to pilon.fasta [pilon] Writing NODE_113_length_1627_cov_51.319389:1-1627 changes to pilon.changes [pilon] Writing updated NODE_113_length_1627_cov_51.319389_pilon to pilon.fasta [pilon] Writing NODE_114_length_1609_cov_188.451613:1-1609 changes to pilon.changes [pilon] Writing updated NODE_114_length_1609_cov_188.451613_pilon to pilon.fasta [pilon] Writing NODE_115_length_1571_cov_35.100690:1-1571 changes to pilon.changes [pilon] Writing updated NODE_115_length_1571_cov_35.100690_pilon to pilon.fasta [pilon] Writing NODE_116_length_1516_cov_34.746953:1-1516 changes to pilon.changes [pilon] Writing updated NODE_116_length_1516_cov_34.746953_pilon to pilon.fasta [pilon] Writing NODE_117_length_1440_cov_20.257013:1-1440 changes to pilon.changes [pilon] Writing updated NODE_117_length_1440_cov_20.257013_pilon to pilon.fasta [pilon] Writing NODE_118_length_1421_cov_76.483077:1-1421 changes to pilon.changes [pilon] Writing updated NODE_118_length_1421_cov_76.483077_pilon to pilon.fasta [pilon] Writing NODE_119_length_1411_cov_37.088372:1-1411 changes to pilon.changes [pilon] Writing updated NODE_119_length_1411_cov_37.088372_pilon to pilon.fasta [pilon] Writing NODE_120_length_1386_cov_60.144664:1-1386 changes to pilon.changes [pilon] Writing updated NODE_120_length_1386_cov_60.144664_pilon to pilon.fasta [pilon] Writing NODE_121_length_1384_cov_89.728424:1-1384 changes to pilon.changes [pilon] Writing updated NODE_121_length_1384_cov_89.728424_pilon to pilon.fasta [pilon] Writing NODE_122_length_1374_cov_22.642458:1-1374 changes to pilon.changes [pilon] Writing updated NODE_122_length_1374_cov_22.642458_pilon to pilon.fasta [pilon] Writing NODE_123_length_1353_cov_37.403409:1-1353 changes to pilon.changes [pilon] Writing updated NODE_123_length_1353_cov_37.403409_pilon to pilon.fasta [pilon] Writing NODE_124_length_1253_cov_836.028269:1-1253 changes to pilon.changes [pilon] Writing updated NODE_124_length_1253_cov_836.028269_pilon to pilon.fasta [pilon] Writing NODE_125_length_1220_cov_36.185623:1-1220 changes to pilon.changes [pilon] Writing updated NODE_125_length_1220_cov_36.185623_pilon to pilon.fasta [pilon] Writing NODE_126_length_1205_cov_19.812731:1-1205 changes to pilon.changes [pilon] Writing updated NODE_126_length_1205_cov_19.812731_pilon to pilon.fasta [pilon] Writing NODE_127_length_1177_cov_57.232008:1-1177 changes to pilon.changes [pilon] Writing updated NODE_127_length_1177_cov_57.232008_pilon to pilon.fasta [pilon] Writing NODE_128_length_1169_cov_43.748092:1-1169 changes to pilon.changes [pilon] Writing updated NODE_128_length_1169_cov_43.748092_pilon to pilon.fasta [pilon] Writing NODE_129_length_1166_cov_30.761722:1-1166 changes to pilon.changes [pilon] Writing updated NODE_129_length_1166_cov_30.761722_pilon to pilon.fasta [pilon] Writing NODE_130_length_1139_cov_49.474460:1-1139 changes to pilon.changes [pilon] Writing updated NODE_130_length_1139_cov_49.474460_pilon to pilon.fasta [pilon] Writing NODE_131_length_1124_cov_29.725823:1-1124 changes to pilon.changes [pilon] Writing updated NODE_131_length_1124_cov_29.725823_pilon to pilon.fasta [pilon] Writing NODE_132_length_1066_cov_25.722751:1-1066 changes to pilon.changes [pilon] Writing updated NODE_132_length_1066_cov_25.722751_pilon to pilon.fasta [pilon] Writing NODE_133_length_1052_cov_121.211600:1-1052 changes to pilon.changes [pilon] Writing updated NODE_133_length_1052_cov_121.211600_pilon to pilon.fasta [pilon] Writing NODE_134_length_1048_cov_49.237325:1-1048 changes to pilon.changes [pilon] Writing updated NODE_134_length_1048_cov_49.237325_pilon to pilon.fasta [pilon] Writing NODE_135_length_1040_cov_38.381937:1-1040 changes to pilon.changes [pilon] Writing updated NODE_135_length_1040_cov_38.381937_pilon to pilon.fasta [pilon] Writing NODE_136_length_1033_cov_25.697368:1-1033 changes to pilon.changes [pilon] Writing updated NODE_136_length_1033_cov_25.697368_pilon to pilon.fasta [pilon] Writing NODE_137_length_1026_cov_61.611050:1-1026 changes to pilon.changes [pilon] Writing updated NODE_137_length_1026_cov_61.611050_pilon to pilon.fasta [pilon] Writing NODE_138_length_1019_cov_47.689310:1-1019 changes to pilon.changes [pilon] Writing updated NODE_138_length_1019_cov_47.689310_pilon to pilon.fasta [pilon] Writing NODE_139_length_1002_cov_7.601589:1-1002 changes to pilon.changes [pilon] Writing updated NODE_139_length_1002_cov_7.601589_pilon to pilon.fasta [pilon] Writing NODE_140_length_975_cov_31.407494:1-975 changes to pilon.changes [pilon] Writing updated NODE_140_length_975_cov_31.407494_pilon to pilon.fasta [pilon] Writing NODE_141_length_949_cov_35.725845:1-949 changes to pilon.changes [pilon] Writing updated NODE_141_length_949_cov_35.725845_pilon to pilon.fasta [pilon] Writing NODE_142_length_937_cov_46.539216:1-937 changes to pilon.changes [pilon] Writing updated NODE_142_length_937_cov_46.539216_pilon to pilon.fasta [pilon] Writing NODE_143_length_934_cov_14.063961:1-934 changes to pilon.changes [pilon] Writing updated NODE_143_length_934_cov_14.063961_pilon to pilon.fasta [pilon] Writing NODE_144_length_927_cov_12.808933:1-927 changes to pilon.changes [pilon] Writing updated NODE_144_length_927_cov_12.808933_pilon to pilon.fasta [pilon] Writing NODE_145_length_924_cov_9.550436:1-924 changes to pilon.changes [pilon] Writing updated NODE_145_length_924_cov_9.550436_pilon to pilon.fasta [pilon] Writing NODE_146_length_908_cov_26.869123:1-908 changes to pilon.changes [pilon] Writing updated NODE_146_length_908_cov_26.869123_pilon to pilon.fasta [pilon] Writing NODE_147_length_906_cov_1448.536306:1-906 changes to pilon.changes [pilon] Writing updated NODE_147_length_906_cov_1448.536306_pilon to pilon.fasta [pilon] Writing NODE_148_length_891_cov_14.910390:1-891 changes to pilon.changes [pilon] Writing updated NODE_148_length_891_cov_14.910390_pilon to pilon.fasta [pilon] Writing NODE_149_length_874_cov_133.118194:1-874 changes to pilon.changes [pilon] Writing updated NODE_149_length_874_cov_133.118194_pilon to pilon.fasta [pilon] Writing NODE_150_length_873_cov_4.017287:1-873 changes to pilon.changes [pilon] Writing updated NODE_150_length_873_cov_4.017287_pilon to pilon.fasta [pilon] Writing NODE_151_length_867_cov_4.878016:1-867 changes to pilon.changes [pilon] Writing updated NODE_151_length_867_cov_4.878016_pilon to pilon.fasta [pilon] Writing NODE_152_length_852_cov_10.299590:1-852 changes to pilon.changes [pilon] Writing updated NODE_152_length_852_cov_10.299590_pilon to pilon.fasta [pilon] Writing NODE_153_length_849_cov_50.174451:1-849 changes to pilon.changes [pilon] Writing updated NODE_153_length_849_cov_50.174451_pilon to pilon.fasta [pilon] Writing NODE_154_length_842_cov_28.624133:1-842 changes to pilon.changes [pilon] Writing updated NODE_154_length_842_cov_28.624133_pilon to pilon.fasta [pilon] Writing NODE_155_length_842_cov_21.274619:1-842 changes to pilon.changes [pilon] Writing updated NODE_155_length_842_cov_21.274619_pilon to pilon.fasta [pilon] Writing NODE_156_length_836_cov_14.065734:1-836 changes to pilon.changes [pilon] Writing updated NODE_156_length_836_cov_14.065734_pilon to pilon.fasta [pilon] Writing NODE_157_length_836_cov_10.777622:1-836 changes to pilon.changes [pilon] Writing updated NODE_157_length_836_cov_10.777622_pilon to pilon.fasta [pilon] Writing NODE_158_length_834_cov_27.249649:1-834 changes to pilon.changes [pilon] Writing updated NODE_158_length_834_cov_27.249649_pilon to pilon.fasta [pilon] Writing NODE_159_length_821_cov_11.877143:1-821 changes to pilon.changes [pilon] Writing updated NODE_159_length_821_cov_11.877143_pilon to pilon.fasta [pilon] Writing NODE_160_length_807_cov_16.803207:1-807 changes to pilon.changes [pilon] Writing updated NODE_160_length_807_cov_16.803207_pilon to pilon.fasta [pilon] Writing NODE_161_length_799_cov_16.939528:1-799 changes to pilon.changes [pilon] Writing updated NODE_161_length_799_cov_16.939528_pilon to pilon.fasta [pilon] Writing NODE_162_length_798_cov_6.648449:1-798 changes to pilon.changes [pilon] Writing updated NODE_162_length_798_cov_6.648449_pilon to pilon.fasta [pilon] Writing NODE_163_length_789_cov_9.603293:1-789 changes to pilon.changes [pilon] Writing updated NODE_163_length_789_cov_9.603293_pilon to pilon.fasta [pilon] Writing NODE_164_length_789_cov_8.868263:1-789 changes to pilon.changes [pilon] Writing updated NODE_164_length_789_cov_8.868263_pilon to pilon.fasta [pilon] Writing NODE_165_length_774_cov_8.341501:1-774 changes to pilon.changes [pilon] Writing updated NODE_165_length_774_cov_8.341501_pilon to pilon.fasta [pilon] Writing NODE_166_length_766_cov_21.088372:1-766 changes to pilon.changes [pilon] Writing updated NODE_166_length_766_cov_21.088372_pilon to pilon.fasta [pilon] Writing NODE_167_length_759_cov_6.311912:1-759 changes to pilon.changes [pilon] Writing updated NODE_167_length_759_cov_6.311912_pilon to pilon.fasta [pilon] Writing NODE_168_length_736_cov_8.320325:1-736 changes to pilon.changes [pilon] Writing updated NODE_168_length_736_cov_8.320325_pilon to pilon.fasta [pilon] Writing NODE_169_length_736_cov_6.398374:1-736 changes to pilon.changes [pilon] Writing updated NODE_169_length_736_cov_6.398374_pilon to pilon.fasta [pilon] Writing NODE_170_length_735_cov_3.469055:1-735 changes to pilon.changes [pilon] Writing updated NODE_170_length_735_cov_3.469055_pilon to pilon.fasta [pilon] Writing NODE_171_length_730_cov_29.178982:1-730 changes to pilon.changes [pilon] Writing updated NODE_171_length_730_cov_29.178982_pilon to pilon.fasta [pilon] Writing NODE_172_length_725_cov_2.814570:1-725 changes to pilon.changes [pilon] Writing updated NODE_172_length_725_cov_2.814570_pilon to pilon.fasta [pilon] Writing NODE_173_length_719_cov_31.735786:1-719 changes to pilon.changes [pilon] Writing updated NODE_173_length_719_cov_31.735786_pilon to pilon.fasta [pilon] Writing NODE_174_length_718_cov_5.661642:1-718 changes to pilon.changes [pilon] Writing updated NODE_174_length_718_cov_5.661642_pilon to pilon.fasta [pilon] Writing NODE_175_length_712_cov_36.543147:1-712 changes to pilon.changes [pilon] Writing updated NODE_175_length_712_cov_36.543147_pilon to pilon.fasta [pilon] Writing NODE_176_length_705_cov_6.952055:1-705 changes to pilon.changes [pilon] Writing updated NODE_176_length_705_cov_6.952055_pilon to pilon.fasta [pilon] Writing NODE_177_length_701_cov_7.705172:1-701 changes to pilon.changes [pilon] Writing updated NODE_177_length_701_cov_7.705172_pilon to pilon.fasta [pilon] Writing NODE_178_length_695_cov_3.146341:1-695 changes to pilon.changes [pilon] Writing updated NODE_178_length_695_cov_3.146341_pilon to pilon.fasta [pilon] Writing NODE_179_length_690_cov_6.340949:1-690 changes to pilon.changes [pilon] Writing updated NODE_179_length_690_cov_6.340949_pilon to pilon.fasta [pilon] Writing NODE_180_length_675_cov_8.315884:1-675 changes to pilon.changes [pilon] Writing updated NODE_180_length_675_cov_8.315884_pilon to pilon.fasta [pilon] Writing NODE_181_length_662_cov_5.432532:1-662 changes to pilon.changes [pilon] Writing updated NODE_181_length_662_cov_5.432532_pilon to pilon.fasta [pilon] Writing NODE_182_length_661_cov_3.612963:1-661 changes to pilon.changes [pilon] Writing updated NODE_182_length_661_cov_3.612963_pilon to pilon.fasta [pilon] Writing NODE_183_length_632_cov_2.011742:1-632 changes to pilon.changes [pilon] Writing updated NODE_183_length_632_cov_2.011742_pilon to pilon.fasta [pilon] Writing NODE_184_length_629_cov_1.885827:1-629 changes to pilon.changes [pilon] Writing updated NODE_184_length_629_cov_1.885827_pilon to pilon.fasta [pilon] Writing NODE_185_length_624_cov_6.166998:1-624 changes to pilon.changes [pilon] Writing updated NODE_185_length_624_cov_6.166998_pilon to pilon.fasta [pilon] Writing NODE_186_length_622_cov_5.117764:1-622 changes to pilon.changes [pilon] Writing updated NODE_186_length_622_cov_5.117764_pilon to pilon.fasta [pilon] Writing NODE_187_length_603_cov_1.628631:1-603 changes to pilon.changes [pilon] Writing updated NODE_187_length_603_cov_1.628631_pilon to pilon.fasta [pilon] Writing NODE_188_length_597_cov_5.487395:1-597 changes to pilon.changes [pilon] Writing updated NODE_188_length_597_cov_5.487395_pilon to pilon.fasta [pilon] Writing NODE_189_length_591_cov_32.878723:1-591 changes to pilon.changes [pilon] Writing updated NODE_189_length_591_cov_32.878723_pilon to pilon.fasta [pilon] Writing NODE_190_length_587_cov_135.416309:1-587 changes to pilon.changes [pilon] Writing updated NODE_190_length_587_cov_135.416309_pilon to pilon.fasta [pilon] Writing NODE_191_length_587_cov_3.429185:1-587 changes to pilon.changes [pilon] Writing updated NODE_191_length_587_cov_3.429185_pilon to pilon.fasta [pilon] Writing NODE_192_length_581_cov_15.104348:1-581 changes to pilon.changes [pilon] Writing updated NODE_192_length_581_cov_15.104348_pilon to pilon.fasta [pilon] Writing NODE_193_length_574_cov_28.719647:1-574 changes to pilon.changes [pilon] Writing updated NODE_193_length_574_cov_28.719647_pilon to pilon.fasta [pilon] Writing NODE_194_length_560_cov_0.615034:1-560 changes to pilon.changes [pilon] Writing updated NODE_194_length_560_cov_0.615034_pilon to pilon.fasta [pilon] Writing NODE_195_length_542_cov_10.425178:1-542 changes to pilon.changes [pilon] Writing updated NODE_195_length_542_cov_10.425178_pilon to pilon.fasta [pilon] Writing NODE_196_length_538_cov_1.561151:1-538 changes to pilon.changes [pilon] Writing updated NODE_196_length_538_cov_1.561151_pilon to pilon.fasta [pilon] Writing NODE_197_length_500_cov_1.817942:1-500 changes to pilon.changes [pilon] Writing updated NODE_197_length_500_cov_1.817942_pilon to pilon.fasta [pilon] Writing NODE_198_length_491_cov_1.945946:1-491 changes to pilon.changes [pilon] Writing updated NODE_198_length_491_cov_1.945946_pilon to pilon.fasta [pilon] Writing NODE_199_length_468_cov_1.409222:1-468 changes to pilon.changes [pilon] Writing updated NODE_199_length_468_cov_1.409222_pilon to pilon.fasta [pilon] Writing NODE_200_length_446_cov_0.784615:1-446 changes to pilon.changes [pilon] Writing updated NODE_200_length_446_cov_0.784615_pilon to pilon.fasta [pilon] Writing NODE_201_length_432_cov_1.257235:1-432 changes to pilon.changes [pilon] Writing updated NODE_201_length_432_cov_1.257235_pilon to pilon.fasta [pilon] Writing NODE_202_length_416_cov_0.738983:1-416 changes to pilon.changes [pilon] Writing updated NODE_202_length_416_cov_0.738983_pilon to pilon.fasta [pilon] Writing NODE_203_length_414_cov_0.467577:1-414 changes to pilon.changes [pilon] Writing updated NODE_203_length_414_cov_0.467577_pilon to pilon.fasta [pilon] Writing NODE_204_length_413_cov_52.547945:1-413 changes to pilon.changes [pilon] Writing updated NODE_204_length_413_cov_52.547945_pilon to pilon.fasta [pilon] Writing NODE_205_length_410_cov_1.574394:1-410 changes to pilon.changes [pilon] Writing updated NODE_205_length_410_cov_1.574394_pilon to pilon.fasta [pilon] Writing NODE_206_length_409_cov_48.888889:1-409 changes to pilon.changes [pilon] Writing updated NODE_206_length_409_cov_48.888889_pilon to pilon.fasta [pilon] Writing NODE_207_length_409_cov_0.402778:1-409 changes to pilon.changes [pilon] Writing updated NODE_207_length_409_cov_0.402778_pilon to pilon.fasta [pilon] Writing NODE_208_length_408_cov_1.515679:1-408 changes to pilon.changes [pilon] Writing updated NODE_208_length_408_cov_1.515679_pilon to pilon.fasta [pilon] Writing NODE_209_length_408_cov_0.881533:1-408 changes to pilon.changes [pilon] Writing updated NODE_209_length_408_cov_0.881533_pilon to pilon.fasta [pilon] Writing NODE_210_length_408_cov_0.634146:1-408 changes to pilon.changes [pilon] Writing updated NODE_210_length_408_cov_0.634146_pilon to pilon.fasta [pilon] Writing NODE_211_length_406_cov_0.407018:1-406 changes to pilon.changes [pilon] Writing updated NODE_211_length_406_cov_0.407018_pilon to pilon.fasta [pilon] Writing NODE_212_length_405_cov_1.049296:1-405 changes to pilon.changes [pilon] Writing updated NODE_212_length_405_cov_1.049296_pilon to pilon.fasta [pilon] Writing NODE_213_length_403_cov_105.060284:1-403 changes to pilon.changes [pilon] Writing updated NODE_213_length_403_cov_105.060284_pilon to pilon.fasta [pilon] Writing NODE_214_length_403_cov_1.078014:1-403 changes to pilon.changes [pilon] Writing updated NODE_214_length_403_cov_1.078014_pilon to pilon.fasta [pilon] Writing NODE_215_length_403_cov_0.411348:1-403 changes to pilon.changes [pilon] Writing updated NODE_215_length_403_cov_0.411348_pilon to pilon.fasta [pilon] Writing NODE_216_length_403_cov_0.166667:1-403 changes to pilon.changes [pilon] Writing updated NODE_216_length_403_cov_0.166667_pilon to pilon.fasta [pilon] Writing NODE_217_length_387_cov_28.992481:1-387 changes to pilon.changes [pilon] Writing updated NODE_217_length_387_cov_28.992481_pilon to pilon.fasta [pilon] Writing NODE_218_length_377_cov_119.761719:1-377 changes to pilon.changes [pilon] Writing updated NODE_218_length_377_cov_119.761719_pilon to pilon.fasta [pilon] Writing NODE_219_length_357_cov_65.419492:1-357 changes to pilon.changes [pilon] Writing updated NODE_219_length_357_cov_65.419492_pilon to pilon.fasta [pilon] Writing NODE_220_length_355_cov_31.337607:1-355 changes to pilon.changes [pilon] Writing updated NODE_220_length_355_cov_31.337607_pilon to pilon.fasta [pilon] Writing NODE_221_length_354_cov_58.403433:1-354 changes to pilon.changes [pilon] Writing updated NODE_221_length_354_cov_58.403433_pilon to pilon.fasta [pilon] Writing NODE_222_length_349_cov_125.583333:1-349 changes to pilon.changes [pilon] Writing updated NODE_222_length_349_cov_125.583333_pilon to pilon.fasta [pilon] Writing NODE_223_length_347_cov_54.097345:1-347 changes to pilon.changes [pilon] Writing updated NODE_223_length_347_cov_54.097345_pilon to pilon.fasta [pilon] Writing NODE_224_length_307_cov_59.037634:1-307 changes to pilon.changes [pilon] Writing updated NODE_224_length_307_cov_59.037634_pilon to pilon.fasta [pilon] Writing NODE_225_length_306_cov_22.772973:1-306 changes to pilon.changes [pilon] Writing updated NODE_225_length_306_cov_22.772973_pilon to pilon.fasta [pilon] Writing NODE_226_length_296_cov_28.394286:1-296 changes to pilon.changes [pilon] Writing updated NODE_226_length_296_cov_28.394286_pilon to pilon.fasta [pilon] Writing NODE_227_length_286_cov_58.272727:1-286 changes to pilon.changes [pilon] Writing updated NODE_227_length_286_cov_58.272727_pilon to pilon.fasta [pilon] Writing NODE_228_length_270_cov_38.838926:1-270 changes to pilon.changes [pilon] Writing updated NODE_228_length_270_cov_38.838926_pilon to pilon.fasta [pilon] Writing NODE_229_length_261_cov_73.464286:1-261 changes to pilon.changes [pilon] Writing updated NODE_229_length_261_cov_73.464286_pilon to pilon.fasta [pilon] Writing NODE_230_length_243_cov_92.778689:1-243 changes to pilon.changes [pilon] Writing updated NODE_230_length_243_cov_92.778689_pilon to pilon.fasta [pilon] Writing NODE_231_length_243_cov_58.229508:1-243 changes to pilon.changes [pilon] Writing updated NODE_231_length_243_cov_58.229508_pilon to pilon.fasta [pilon] Writing NODE_232_length_243_cov_56.196721:1-243 changes to pilon.changes [pilon] Writing updated NODE_232_length_243_cov_56.196721_pilon to pilon.fasta [pilon] Writing NODE_233_length_243_cov_42.450820:1-243 changes to pilon.changes [pilon] Writing updated NODE_233_length_243_cov_42.450820_pilon to pilon.fasta [pilon] Writing NODE_234_length_242_cov_40.925620:1-242 changes to pilon.changes [pilon] Writing updated NODE_234_length_242_cov_40.925620_pilon to pilon.fasta [pilon] Writing NODE_235_length_241_cov_54.466667:1-241 changes to pilon.changes [pilon] Writing updated NODE_235_length_241_cov_54.466667_pilon to pilon.fasta [pilon] Writing NODE_236_length_240_cov_167.823529:1-240 changes to pilon.changes [pilon] Writing updated NODE_236_length_240_cov_167.823529_pilon to pilon.fasta [pilon] Writing NODE_237_length_240_cov_52.882353:1-240 changes to pilon.changes [pilon] Writing updated NODE_237_length_240_cov_52.882353_pilon to pilon.fasta [pilon] Writing NODE_238_length_239_cov_52.855932:1-239 changes to pilon.changes [pilon] Writing updated NODE_238_length_239_cov_52.855932_pilon to pilon.fasta [pilon] Writing NODE_239_length_239_cov_29.288136:1-239 changes to pilon.changes [pilon] Writing updated NODE_239_length_239_cov_29.288136_pilon to pilon.fasta [pilon] Writing NODE_240_length_238_cov_50.128205:1-238 changes to pilon.changes [pilon] Writing updated NODE_240_length_238_cov_50.128205_pilon to pilon.fasta [pilon] Writing NODE_241_length_232_cov_65.252252:1-232 changes to pilon.changes [pilon] Writing updated NODE_241_length_232_cov_65.252252_pilon to pilon.fasta [pilon] Writing NODE_242_length_222_cov_59.168317:1-222 changes to pilon.changes [pilon] Writing updated NODE_242_length_222_cov_59.168317_pilon to pilon.fasta [pilon] Writing NODE_243_length_132_cov_2.636364:1-132 changes to pilon.changes [pilon] Writing updated NODE_243_length_132_cov_2.636364_pilon to pilon.fasta [pilon] Writing NODE_244_length_124_cov_87.000000:1-124 changes to pilon.changes [pilon] Writing updated NODE_244_length_124_cov_87.000000_pilon to pilon.fasta [pilon] Writing NODE_245_length_122_cov_6136.000000:1-122 changes to pilon.changes [pilon] Writing updated NODE_245_length_122_cov_6136.000000_pilon to pilon.fasta [pilon] Mean frags coverage: 143 [pilon] Mean total coverage: 143 [shovill] Repaired 1 contigs from spades.fasta at 1 positions. [shovill] Removing low coverage contig (< 2 x): NODE_184_length_629_cov_1.885827_pilon [shovill] Removing low coverage contig (< 2 x): NODE_187_length_603_cov_1.628631_pilon [shovill] Removing low coverage contig (< 2 x): NODE_194_length_560_cov_0.615034_pilon [shovill] Removing low coverage contig (< 2 x): NODE_196_length_538_cov_1.561151_pilon [shovill] Removing low coverage contig (< 2 x): NODE_197_length_500_cov_1.817942_pilon [shovill] Removing low coverage contig (< 2 x): NODE_198_length_491_cov_1.945946_pilon [shovill] Removing low coverage contig (< 2 x): NODE_199_length_468_cov_1.409222_pilon [shovill] Removing low coverage contig (< 2 x): NODE_200_length_446_cov_0.784615_pilon [shovill] Removing low coverage contig (< 2 x): NODE_201_length_432_cov_1.257235_pilon [shovill] Removing low coverage contig (< 2 x): NODE_202_length_416_cov_0.738983_pilon [shovill] Removing low coverage contig (< 2 x): NODE_203_length_414_cov_0.467577_pilon [shovill] Removing low coverage contig (< 2 x): NODE_205_length_410_cov_1.574394_pilon [shovill] Removing low coverage contig (< 2 x): NODE_207_length_409_cov_0.402778_pilon [shovill] Removing low coverage contig (< 2 x): NODE_208_length_408_cov_1.515679_pilon [shovill] Removing low coverage contig (< 2 x): NODE_210_length_408_cov_0.634146_pilon [shovill] Removing low coverage contig (< 2 x): NODE_209_length_408_cov_0.881533_pilon [shovill] Removing low coverage contig (< 2 x): NODE_211_length_406_cov_0.407018_pilon [shovill] Removing low coverage contig (< 2 x): NODE_212_length_405_cov_1.049296_pilon [shovill] Removing low coverage contig (< 2 x): NODE_215_length_403_cov_0.411348_pilon [shovill] Removing low coverage contig (< 2 x): NODE_214_length_403_cov_1.078014_pilon [shovill] Removing low coverage contig (< 2 x): NODE_216_length_403_cov_0.166667_pilon [shovill] Removing short contig (< 200 bp): NODE_243_length_132_cov_2.636364_pilon [shovill] Removing short contig (< 200 bp): NODE_244_length_124_cov_87.000000_pilon [shovill] Removing short contig (< 200 bp): NODE_245_length_122_cov_6136.000000_pilon [shovill] Assembly is 2531811, estimated genome size was 3000000 (-15.61%) [shovill] Using genome graph file 'spades/assembly_graph_with_scaffolds.gfa' => 'contigs.gfa' [shovill] Walltime used: 8 min 4 sec [shovill] Results in: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus [shovill] Final assembly graph: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/contigs.gfa [shovill] Final assembly contigs: /DATB/markop/CPB/CPB_rcf_DNAseq/shovill/Lactococcus/contigs.fa [shovill] It contains 221 (min=200) contigs totalling 2531811 bp. [shovill] The shovill manual is at https://github.com/tseemann/shovill/blob/master/README.md [shovill] Done.