output/shovill/Lactococcus/shovill.log Version 1
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
SEEK ID: https://fairdomhub.org/documents/2573?version=1
Filename:
output/shovill/Lactococcus/shovill.log
Format: Plain text document
Size: 492 KB
[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.
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Created: 12th Nov 2021 at 23:20
Last updated: 12th Nov 2021 at 23:20
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Version 1 (earliest) Created 12th Nov 2021 at 23:20 by Marko Petek
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https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
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National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
Advanced Projects list for this Document with search and filtering
This project’s main objective was to identify novel Colorado potato beetle gene targets for the development of specific RNAi insecticides and further validate prospective targets using transcriptomics. The work included gene selection, establishment of double-stranded RNA (dsRNA) production methodology and the evaluation of dsRNAs’ insecticidal potential in CPB feeding laboratory and field trials.
Programme: NIBSys
Public web page: http://projects.nib.si/rnainval/
Start date: 1st Nov 2014
End date: 31st Oct 2017
Advanced Investigations list for this Document with search and filtering
Short Name: 03_Omics Title: Omics analysis of RNAi response in CPB Description: Transcriptomics and metagenome changes upon feeding CPB larvae with dsRNA Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_01_ns-dsRNA_trans, _S_02_metagenome_resp
Assays: _A_01-DNAisol, _A_01_RNA-Seq_dsEGFP-NGS, _A_02-DNASeq, _A_02_CLC-RNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _I_03_Omics-files, _S_01_ns-dsRNA_trans-files, _S_02_metagenome_resp-files
Advanced Studies list for this Document with search and filtering
Short Name: 02_metagenome_resp Title: CPB gut microbiome response to dsRNA feeding Description: Response of CPB gut microbiome to dsRNA feeding on the level of microbe abundance Raw Data: pISA Study creation date: 2021-01-15 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_03_Omics
Assays: _A_01-DNAisol, _A_02-DNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _S_02_metagenome_resp-files
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Short Name: 06_extr_bact-assembly Assay Class: DRY Assay Type: assembly Title: De novo genome assembly of bacteria Description: De novo genome assembly of bacteria from rcf-extracted shotgun metagenomics reads pISA Assay creation date: 2021-01-16 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_03_Omics
Study: _S_02_metagenome_resp
