shovill: test-data/shovill_std

author	iuc
date	Fri, 16 Sep 2022 14:39:43 +0000
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children

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8 ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	1 [shovill] Hello piemari
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	2 [shovill] You ran: /home/piemari/apps/conda/envs/metaphlan/bin/shovill --outdir ../shovill_bam/ --cpus 8 --ram 4 --R1 ../mutant_R1.fastq --R2 ../mutant_R2.fastq --namefmt contig%05d --depth 100 --keepfiles --minlen 0 --mincov 2 --assembler spades --force
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	3 [shovill] This is shovill 1.1.0
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	4 [shovill] Written by Torsten Seemann
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	5 [shovill] Homepage is https://github.com/tseemann/shovill
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	6 [shovill] Operating system is linux
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	7 [shovill] Perl version is v5.32.1
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	8 [shovill] Machine has 32 CPU cores and 251.66 GB RAM
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	9 [shovill] Using bwa - /home/piemari/apps/conda/envs/metaphlan/bin/bwa \| Version: 0.7.17-r1188
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	10 [shovill] Using flash - /home/piemari/apps/conda/envs/metaphlan/bin/flash \| FLASH v1.2.11
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	11 [shovill] Using java - /home/piemari/apps/conda/envs/metaphlan/bin/java \| openjdk version "11.0.1" 2018-10-16 LTS
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	12 [shovill] Using kmc - /home/piemari/apps/conda/envs/metaphlan/bin/kmc \| K-Mer Counter (KMC) ver. 3.2.1 (2022-01-04)
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	13 [shovill] Using lighter - /home/piemari/apps/conda/envs/metaphlan/bin/lighter \| Lighter v1.1.2
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	14 [shovill] Using megahit - /home/piemari/apps/conda/envs/metaphlan/bin/megahit \| MEGAHIT v1.2.9
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	15 [shovill] Using megahit_toolkit - /home/piemari/apps/conda/envs/metaphlan/bin/megahit_toolkit \| v1.2.9
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	16 [shovill] Using pigz - /home/piemari/apps/conda/envs/metaphlan/bin/pigz \| pigz 2.6
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	17 [shovill] Using pilon - /home/piemari/apps/conda/envs/metaphlan/bin/pilon \| Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	18 [shovill] Using samclip - /home/piemari/apps/conda/envs/metaphlan/bin/samclip \| samclip 0.4.0
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	19 [shovill] Using samtools - /home/piemari/apps/conda/envs/metaphlan/bin/samtools \| Version: 1.15 (using htslib 1.14)
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	20 [shovill] Using seqtk - /home/piemari/apps/conda/envs/metaphlan/bin/seqtk \| Version: 1.3-r106
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	21 [shovill] Using skesa - /home/piemari/apps/conda/envs/metaphlan/bin/skesa \| SKESA 2.4.0
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	22 [shovill] Using spades.py - /home/piemari/apps/conda/envs/metaphlan/bin/spades.py \| SPAdes genome assembler v3.14.1
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	23 [shovill] Using trimmomatic - /home/piemari/apps/conda/envs/metaphlan/bin/trimmomatic \| 0.39
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	24 [shovill] Using velvetg - /home/piemari/apps/conda/envs/metaphlan/bin/velvetg \| Version 1.2.10
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	25 [shovill] Using velveth - /home/piemari/apps/conda/envs/metaphlan/bin/velveth \| Version 1.2.10
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	26 [shovill] Found spades version: 003014000
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	27 [shovill] Will use spades 003014000 options: --isolate and --merged
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	28 [shovill] Forced overwrite of existing --outdir ../shovill_bam/
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	29 [shovill] Using tempdir: /tmp
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	30 [shovill] Changing into folder: /home/piemari/shovill_bam
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	31 [shovill] Collecting raw read statistics with 'seqtk'
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	32 [shovill] Running: seqtk fqchk -q3 \/home\/piemari\/mutant_R1\.fastq >/tmp/1MILzK1fer 2>&1 \| sed 's/^/[seqtk] /' \| tee -a shovill.log
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	33 [shovill] Read stats: max_len = 150
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	34 [shovill] Read stats: min_len = 150
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	35 [shovill] Read stats: total_bp = 300000
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	36 [shovill] Read stats: avg_len = 150
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	37 [shovill] Estimating genome size by counting unqiue 21-mers > frequency 10
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	38 [shovill] Running: kmc -sm -m2 -t8 -k21 -ci10 \/home\/piemari\/mutant_R1\.fastq /tmp/_n_4cOtiee/kmc /tmp/_n_4cOtiee 2>&1 \| sed 's/^/[kmc] /' \| tee -a shovill.log
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	39 [kmc] **
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	40 [kmc] Stage 1: 0% Stage 1: 100%
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	41 [kmc] Stage 2: 0% Stage 2: 84% Stage 2: 90% Stage 2: 94% Stage 2: 96% Stage 2: 98% Stage 2: 99% Stage 2: 100%
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	42 [kmc]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	43 [kmc]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	44 [kmc] 1st stage: 0.08264s
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	45 [kmc] 2nd stage: 0.104849s
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	46 [kmc] 3rd stage: 0.002521s
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	47 [kmc] Total : 0.19001s
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	48 [kmc] Tmp size : 0MB
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	49 [kmc] Tmp size strict memory : 0MB
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	50 [kmc] Tmp total: 0MB
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	51 [kmc]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	52 [kmc] Stats:
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	53 [kmc] No. of k-mers below min. threshold : 34495
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	54 [kmc] No. of k-mers above max. threshold : 0
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	55 [kmc] No. of unique k-mers : 35683
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	56 [kmc] No. of unique counted k-mers : 1188
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	57 [kmc] Total no. of k-mers : 130000
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	58 [kmc] Total no. of reads : 1000
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	59 [kmc] Total no. of super-k-mers : 18576
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	60 [shovill] Using genome size 1188 bp
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	61 [shovill] Estimated sequencing depth: 252 x
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	62 [shovill] Subsampling reads by factor 0.397 to get from 252x to 100x
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	63 [shovill] Running: seqtk sample \/home\/piemari\/mutant_R1\.fastq 0.397 \| pigz --fast -c -p 8 > R1.sub.fq.gz 2>&1 \| sed 's/^/[seqtk] /' \| tee -a shovill.log
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	64 [shovill] Running: seqtk sample \/home\/piemari\/mutant_R2\.fastq 0.397 \| pigz --fast -c -p 8 > R2.sub.fq.gz 2>&1 \| sed 's/^/[seqtk] /' \| tee -a shovill.log
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	65 [shovill] Appending -Xmx4g to _JAVA_OPTIONS
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	66 [shovill] Running: ln -sf R1\.sub\.fq\.gz R1.fq.gz 2>&1 \| sed 's/^/[ln] /' \| tee -a shovill.log
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	67 [shovill] Running: ln -sf R2\.sub\.fq\.gz R2.fq.gz 2>&1 \| sed 's/^/[ln] /' \| tee -a shovill.log
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	68 [shovill] Average read length looks like 150 bp
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	69 [shovill] Automatically setting --minlen to 75
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	70 [shovill] Setting k-mer range to (31 .. 112)
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	71 [shovill] Estimated K-mers: 31 51 71 91 111 [kn=5, ks=20, kmin=31, kmax=112]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	72 [shovill] Using kmers: 31,51,71,91,111
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	73 [shovill] Correcting reads with 'Lighter'
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	74 [shovill] Running: lighter -od . -r R1.fq.gz -r R2.fq.gz -K 32 1188 -t 8 -maxcor 1 2>&1 \| sed 's/^/[lighter] /' \| tee -a shovill.log
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	75 [lighter] [2022-05-04 12:29:31] =============Start====================
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	76 [lighter] [2022-05-04 12:29:31] Scanning the input files to infer alpha(sampling rate)
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	77 [lighter] [2022-05-04 12:29:31] Average coverage is 103.535 and alpha is 0.068
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	78 [lighter] [2022-05-04 12:29:31] Bad quality threshold is "1"
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	79 [lighter] [2022-05-04 12:29:32] Finish sampling kmers
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	80 [lighter] [2022-05-04 12:29:32] Bloom filter A's false positive rate: 0.264464
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	81 [lighter] [2022-05-04 12:29:32] Finish storing trusted kmers
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	82 [lighter] [2022-05-04 12:29:32] Finish error correction
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	83 [lighter] Processed 820 reads:
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	84 [lighter] 48 are error-free
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	85 [lighter] Corrected 1731 bases(2.242228 corrections for reads with errors)
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	86 [lighter] Trimmed 0 reads with average trimmed bases 0.000000
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	87 [lighter] Discard 0 reads
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	88 [shovill] Overlapping/stitching PE reads with 'FLASH'
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	89 [shovill] Running: flash -m 20 -M 150 -d . -o flash -z -t 8 R1.cor.fq.gz R2.cor.fq.gz 2>&1 \| sed 's/^//' \| tee -a shovill.log
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	90 [FLASH] Starting FLASH v1.2.11
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	91 [FLASH] Fast Length Adjustment of SHort reads
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	92 [FLASH]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	93 [FLASH] Input files:
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	94 [FLASH] R1.cor.fq.gz
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	95 [FLASH] R2.cor.fq.gz
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	96 [FLASH]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	97 [FLASH] Output files:
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	98 [FLASH] ./flash.extendedFrags.fastq.gz
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	99 [FLASH] ./flash.notCombined_1.fastq.gz
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	100 [FLASH] ./flash.notCombined_2.fastq.gz
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	101 [FLASH] ./flash.hist
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	102 [FLASH] ./flash.histogram
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	103 [FLASH]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	104 [FLASH] Parameters:
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	105 [FLASH] Min overlap: 20
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	106 [FLASH] Max overlap: 150
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	107 [FLASH] Max mismatch density: 0.250000
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	108 [FLASH] Allow "outie" pairs: false
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	109 [FLASH] Cap mismatch quals: false
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	110 [FLASH] Combiner threads: 8
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	111 [FLASH] Input format: FASTQ, phred_offset=33
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	112 [FLASH] Output format: FASTQ, phred_offset=33, gzip
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	113 [FLASH]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	114 [FLASH] Starting reader and writer threads
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	115 [FLASH] Starting 8 combiner threads
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	116 [FLASH] Processed 410 read pairs
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	117 [FLASH]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	118 [FLASH] Read combination statistics:
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	119 [FLASH] Total pairs: 410
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	120 [FLASH] Combined pairs: 387
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	121 [FLASH] Uncombined pairs: 23
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	122 [FLASH] Percent combined: 94.39%
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	123 [FLASH]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	124 [FLASH] Writing histogram files.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	125 [FLASH]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	126 [FLASH] FLASH v1.2.11 complete!
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	127 [FLASH] 0.022 seconds elapsed
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	128 [shovill] Assembling reads with 'spades'
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	129 [shovill] Running: spades.py -1 flash.notCombined_1.fastq.gz -2 flash.notCombined_2.fastq.gz --isolate --threads 8 --memory 4 -o spades --tmp-dir /tmp -k 31,51,71,91,111 --merged flash.extendedFrags.fastq.gz 2>&1 \| sed 's/^/[spades] /' \| tee -a shovill.log
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	130 [spades] Command line: /home/piemari/apps/conda/envs/metaphlan/bin/spades.py -1 /home/piemari/shovill_bam/flash.notCombined_1.fastq.gz -2 /home/piemari/shovill_bam/flash.notCombined_2.fastq.gz --isolate --threads 8 --memory 4 -o /home/piemari/shovill_bam/spades --tmp-dir /tmp -k 31,51,71,91,111 --merged /home/piemari/shovill_bam/flash.extendedFrags.fastq.gz
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	131 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	132 [spades] System information:
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	133 [spades] SPAdes version: 3.14.1
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	134 [spades] Python version: 3.7.12
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	135 [spades] OS: Linux-3.10.0-1160.62.1.el7.x86_64-x86_64-with-centos-7.9.2009-Core
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	136 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	137 [spades] Output dir: /home/piemari/shovill_bam/spades
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	138 [spades] Mode: ONLY assembling (without read error correction)
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	139 [spades] Debug mode is turned OFF
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	140 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	141 [spades] Dataset parameters:
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	142 [spades] Isolate mode
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	143 [spades] Reads:
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	144 [spades] Library number: 1, library type: paired-end
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	145 [spades] orientation: fr
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	146 [spades] left reads: ['/home/piemari/shovill_bam/flash.notCombined_1.fastq.gz']
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	147 [spades] right reads: ['/home/piemari/shovill_bam/flash.notCombined_2.fastq.gz']
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	148 [spades] interlaced reads: not specified
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	149 [spades] single reads: not specified
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	150 [spades] merged reads: ['/home/piemari/shovill_bam/flash.extendedFrags.fastq.gz']
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	151 [spades] Assembly parameters:
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	152 [spades] k: [31, 51, 71, 91, 111]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	153 [spades] Repeat resolution is enabled
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	154 [spades] Mismatch careful mode is turned OFF
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	155 [spades] MismatchCorrector will be SKIPPED
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	156 [spades] Coverage cutoff is turned OFF
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	157 [spades] Other parameters:
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	158 [spades] Dir for temp files: /tmp
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	159 [spades] Threads: 8
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	160 [spades] Memory limit (in Gb): 4
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	161 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	162 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	163 [spades] ======= SPAdes pipeline started. Log can be found here: /home/piemari/shovill_bam/spades/spades.log
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	164 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	165 [spades] /home/piemari/shovill_bam/flash.notCombined_1.fastq.gz: max reads length: 150
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	166 [spades] /home/piemari/shovill_bam/flash.notCombined_2.fastq.gz: max reads length: 150
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	167 [spades] Files with merged reads were ignored.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	168 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	169 [spades] Reads length: 150
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	170 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	171 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	172 [spades] ===== Before start started.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	173 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	174 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	175 [spades] ===== Assembling started.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	176 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	177 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	178 [spades] ===== K31 started.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	179 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	180 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	181 [spades] == Running: /home/piemari/apps/conda/envs/metaphlan/bin/spades-core /home/piemari/shovill_bam/spades/K31/configs/config.info /home/piemari/shovill_bam/spades/K31/configs/isolate_mode.info
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	182 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	183 [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is tmp_contigs.fasta
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	184 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K31/configs/config.info
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	185 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K31/configs/isolate_mode.info
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	186 [spades] 0:00:00.000 4M / 10M INFO General (memory_limit.cpp : 49) Memory limit set to 4 Gb
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	187 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	188 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 86) Maximum k-mer length: 128
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	189 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 87) Assembling dataset (/home/piemari/shovill_bam/spades/dataset.info) with K=31
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	190 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 8
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	191 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 194) SPAdes started
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	192 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	193 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	194 [spades] 0:00:00.000 4M / 10M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	195 [spades] 0:00:00.002 4M / 12M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while)
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	196 [spades] 0:00:00.002 4M / 12M INFO General (read_converter.cpp : 73) Converting paired reads
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	197 [spades] 0:00:00.009 71M / 71M INFO General (binary_converter.cpp : 111) 23 reads written
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	198 [spades] 0:00:00.009 47M / 47M INFO General (read_converter.cpp : 81) Converting single reads
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	199 [spades] 0:00:00.011 57M / 57M INFO General (binary_converter.cpp : 111) 0 reads written
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	200 [spades] 0:00:00.011 57M / 57M INFO General (read_converter.cpp : 87) Converting merged reads
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	201 [spades] 0:00:00.017 77M / 77M INFO General (binary_converter.cpp : 111) 387 reads written
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	202 [spades] 0:00:00.022 17M / 40M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	203 [spades] 0:00:00.026 17M / 40M INFO General (construction.cpp : 150) Max read length 280
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	204 [spades] 0:00:00.026 17M / 40M INFO General (construction.cpp : 153) Max read length without merged 150
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	205 [spades] 0:00:00.026 17M / 40M INFO General (construction.cpp : 156) Average read length 193.032
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	206 [spades] 0:00:00.026 17M / 40M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	207 [spades] 0:00:00.026 17M / 40M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 64 files using 8 threads. This might take a while.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	208 [spades] 0:00:00.026 17M / 40M INFO General (file_limit.hpp : 32) Open file limit set to 131072
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	209 [spades] 0:00:00.027 17M / 40M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166615 Gb
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	210 [spades] 0:00:00.027 17M / 40M INFO General (kmer_splitters.hpp : 97) Using cell size of 349417
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	211 [spades] 0:00:00.100 71M / 560M INFO General (kmer_splitters.hpp : 293) Used 866 reads
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	212 [spades] 0:00:00.100 71M / 560M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	213 [spades] 0:00:00.111 71M / 560M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7283 kmers in total.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	214 [spades] 0:00:00.111 71M / 560M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	215 [spades] 0:00:00.114 71M / 560M INFO General (stage.cpp : 113) PROCEDURE == Extension index construction
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	216 [spades] 0:00:00.114 71M / 560M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	217 [spades] 0:00:00.114 71M / 560M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	218 [spades] 0:00:00.115 71M / 560M INFO General (file_limit.hpp : 32) Open file limit set to 131072
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	219 [spades] 0:00:00.115 71M / 560M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166468 Gb
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	220 [spades] 0:00:00.115 71M / 560M INFO General (kmer_splitters.hpp : 97) Using cell size of 174554
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	221 [spades] 0:00:00.188 2G / 2G INFO General (kmer_splitters.hpp : 364) Processed 7283 kmers
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	222 [spades] 0:00:00.188 2G / 2G INFO General (kmer_splitters.hpp : 369) Used 7283 kmers.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	223 [spades] 0:00:00.212 85M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	224 [spades] 0:00:00.236 85M / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7222 kmers in total.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	225 [spades] 0:00:00.236 85M / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	226 [spades] 0:00:00.241 85M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	227 [spades] 0:00:00.264 86M / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	228 [spades] 0:00:00.266 86M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 12384 bytes occupied (13.7181 bits per kmer).
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	229 [spades] 0:00:00.266 86M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	230 [spades] 0:00:00.273 86M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	231 [spades] 0:00:00.274 86M / 2G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	232 [spades] 0:00:00.274 86M / 2G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K)
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	233 [spades] 0:00:00.274 86M / 2G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	234 [spades] 0:00:00.279 86M / 2G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 96
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	235 [spades] 0:00:00.284 86M / 2G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 97
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	236 [spades] 0:00:00.284 86M / 2G INFO Early tip clipping (early_simplification.hpp : 30) 2642 32-mers were removed by early tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	237 [spades] 0:00:00.285 86M / 2G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	238 [spades] 0:00:00.285 86M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	239 [spades] 0:00:00.287 86M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 186 sequences extracted
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	240 [spades] 0:00:00.288 86M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	241 [spades] 0:00:00.289 86M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	242 [spades] 0:00:00.290 86M / 2G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM)
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	243 [spades] 0:00:00.290 86M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	244 [spades] 0:00:00.290 86M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	245 [spades] 0:00:00.301 87M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 7864 bytes occupied (8.6382 bits per kmer).
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	246 [spades] 0:00:00.301 87M / 2G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	247 [spades] 0:00:00.310 87M / 2G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	248 [spades] 0:00:00.314 87M / 2G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	249 [spades] 0:00:00.314 87M / 2G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 2
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	250 [spades] 0:00:00.315 87M / 2G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 60
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	251 [spades] 0:00:00.315 87M / 2G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 60. Coverage mad: 7.413
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	252 [spades] 0:00:00.315 87M / 2G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	253 [spades] 0:00:00.324 87M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	254 [spades] 0:00:00.349 87M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	255 [spades] 0:00:00.414 87M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	256 [spades] 0:00:00.501 87M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	257 [spades] 0:00:00.540 87M / 2G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 56.9644. Fitted coverage std. dev: 9.10691
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	258 [spades] 0:00:00.540 87M / 2G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	259 [spades] 0:00:00.541 87M / 2G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 39
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	260 [spades] 0:00:00.541 87M / 2G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 29
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	261 [spades] 0:00:00.541 87M / 2G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 1104
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	262 [spades] 0:00:00.541 87M / 2G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 56.9644
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	263 [spades] 0:00:00.541 87M / 2G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 29
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	264 [spades] 0:00:00.542 87M / 2G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	265 [spades] 0:00:00.542 87M / 2G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	266 [spades] 0:00:00.542 87M / 2G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	267 [spades] 0:00:00.542 87M / 2G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	268 [spades] 0:00:00.542 87M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	269 [spades] 0:00:00.545 87M / 2G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	270 [spades] 0:00:00.545 87M / 2G INFO StageManager (stage.cpp : 166) STAGE == Simplification
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	271 [spades] 0:00:00.546 87M / 2G INFO General (simplification.cpp : 383) Graph simplification started
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	272 [spades] 0:00:00.546 87M / 2G INFO General (graph_simplification.hpp : 643) Creating parallel br instance
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	273 [spades] 0:00:00.546 87M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	274 [spades] 0:00:00.546 87M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	275 [spades] 0:00:00.550 87M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	276 [spades] 0:00:00.550 87M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	277 [spades] 0:00:00.557 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 60 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	278 [spades] 0:00:00.557 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	279 [spades] 0:00:00.559 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	280 [spades] 0:00:00.560 84M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	281 [spades] 0:00:00.560 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	282 [spades] 0:00:00.560 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	283 [spades] 0:00:00.561 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	284 [spades] 0:00:00.561 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	285 [spades] 0:00:00.561 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	286 [spades] 0:00:00.561 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	287 [spades] 0:00:00.562 84M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	288 [spades] 0:00:00.562 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	289 [spades] 0:00:00.562 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	290 [spades] 0:00:00.562 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	291 [spades] 0:00:00.562 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	292 [spades] 0:00:00.563 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	293 [spades] 0:00:00.563 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	294 [spades] 0:00:00.563 84M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	295 [spades] 0:00:00.563 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	296 [spades] 0:00:00.563 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	297 [spades] 0:00:00.564 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	298 [spades] 0:00:00.564 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	299 [spades] 0:00:00.564 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	300 [spades] 0:00:00.564 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	301 [spades] 0:00:00.564 84M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	302 [spades] 0:00:00.564 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	303 [spades] 0:00:00.565 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	304 [spades] 0:00:00.565 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	305 [spades] 0:00:00.565 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	306 [spades] 0:00:00.565 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	307 [spades] 0:00:00.565 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	308 [spades] 0:00:00.566 84M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	309 [spades] 0:00:00.566 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	310 [spades] 0:00:00.566 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	311 [spades] 0:00:00.566 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	312 [spades] 0:00:00.566 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	313 [spades] 0:00:00.567 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	314 [spades] 0:00:00.567 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	315 [spades] 0:00:00.567 84M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	316 [spades] 0:00:00.567 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	317 [spades] 0:00:00.567 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	318 [spades] 0:00:00.568 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	319 [spades] 0:00:00.568 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	320 [spades] 0:00:00.568 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	321 [spades] 0:00:00.568 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	322 [spades] 0:00:00.568 84M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	323 [spades] 0:00:00.568 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	324 [spades] 0:00:00.569 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	325 [spades] 0:00:00.569 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	326 [spades] 0:00:00.569 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	327 [spades] 0:00:00.569 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	328 [spades] 0:00:00.569 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	329 [spades] 0:00:00.570 84M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	330 [spades] 0:00:00.570 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	331 [spades] 0:00:00.570 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	332 [spades] 0:00:00.570 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	333 [spades] 0:00:00.570 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	334 [spades] 0:00:00.571 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	335 [spades] 0:00:00.571 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	336 [spades] 0:00:00.571 84M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	337 [spades] 0:00:00.571 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	338 [spades] 0:00:00.571 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	339 [spades] 0:00:00.571 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	340 [spades] 0:00:00.572 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	341 [spades] 0:00:00.572 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	342 [spades] 0:00:00.572 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	343 [spades] 0:00:00.572 84M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	344 [spades] 0:00:00.572 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	345 [spades] 0:00:00.575 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	346 [spades] 0:00:00.575 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	347 [spades] 0:00:00.576 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	348 [spades] 0:00:00.576 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	349 [spades] 0:00:00.576 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	350 [spades] 0:00:00.576 84M / 2G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	351 [spades] 0:00:00.576 84M / 2G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	352 [spades] 0:00:00.577 84M / 2G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	353 [spades] 0:00:00.577 84M / 2G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	354 [spades] 0:00:00.577 84M / 2G INFO General (graph_simplification.hpp : 643) Creating parallel br instance
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	355 [spades] 0:00:00.577 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	356 [spades] 0:00:00.578 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	357 [spades] 0:00:00.578 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	358 [spades] 0:00:00.578 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	359 [spades] 0:00:00.578 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	360 [spades] 0:00:00.579 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	361 [spades] 0:00:00.579 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	362 [spades] 0:00:00.579 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	363 [spades] 0:00:00.579 84M / 2G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	364 [spades] 0:00:00.579 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	365 [spades] 0:00:00.580 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 1 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	366 [spades] 0:00:00.580 84M / 2G INFO General (simplification.cpp : 496) Counting average coverage
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	367 [spades] 0:00:00.580 84M / 2G INFO General (simplification.cpp : 502) Average coverage = 55.1872
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	368 [spades] 0:00:00.580 84M / 2G INFO StageManager (stage.cpp : 166) STAGE == Contig Output
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	369 [spades] 0:00:00.583 84M / 2G INFO General (read_converter.cpp : 102) Outputting contigs to /home/piemari/shovill_bam/spades/K31/simplified_contigs
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	370 [spades] 0:00:00.585 84M / 2G INFO General (binary_converter.cpp : 111) 1 reads written
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	371 [spades] 0:00:00.589 84M / 2G INFO General (pipeline.cpp : 259) SPAdes finished
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	372 [spades] 0:00:00.590 84M / 2G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 0 seconds
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	373 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	374 [spades] ===== K31 finished.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	375 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	376 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	377 [spades] ===== K51 started.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	378 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	379 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	380 [spades] == Running: /home/piemari/apps/conda/envs/metaphlan/bin/spades-core /home/piemari/shovill_bam/spades/K51/configs/config.info /home/piemari/shovill_bam/spades/K51/configs/isolate_mode.info
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	381 [spades]
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	382 [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /home/piemari/shovill_bam/spades/K31/simplified_contigs
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	383 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K51/configs/config.info
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	384 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K51/configs/isolate_mode.info
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	385 [spades] 0:00:00.000 4M / 10M INFO General (memory_limit.cpp : 49) Memory limit set to 4 Gb
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	386 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	387 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 86) Maximum k-mer length: 128
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	388 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 87) Assembling dataset (/home/piemari/shovill_bam/spades/dataset.info) with K=51
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	389 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 8
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	390 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 194) SPAdes started
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	391 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	392 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	393 [spades] 0:00:00.000 4M / 10M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	394 [spades] 0:00:00.001 4M / 12M INFO General (read_converter.cpp : 53) Binary reads detected
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	395 [spades] 0:00:00.002 4M / 14M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	396 [spades] 0:00:00.002 4M / 14M INFO General (construction.cpp : 115) Contigs from previous K will be used: /home/piemari/shovill_bam/spades/K31/simplified_contigs
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	397 [spades] 0:00:00.007 4M / 14M INFO General (construction.cpp : 150) Max read length 280
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	398 [spades] 0:00:00.007 4M / 14M INFO General (construction.cpp : 153) Max read length without merged 150
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	399 [spades] 0:00:00.007 4M / 14M INFO General (construction.cpp : 156) Average read length 193.032
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	400 [spades] 0:00:00.007 4M / 14M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	401 [spades] 0:00:00.007 4M / 14M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 64 files using 8 threads. This might take a while.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	402 [spades] 0:00:00.007 4M / 14M INFO General (file_limit.hpp : 32) Open file limit set to 131072
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	403 [spades] 0:00:00.007 4M / 14M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166632 Gb
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	404 [spades] 0:00:00.007 4M / 14M INFO General (kmer_splitters.hpp : 97) Using cell size of 174726
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	405 [spades] 0:00:00.085 84M / 556M INFO General (kmer_splitters.hpp : 293) Used 868 reads
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	406 [spades] 0:00:00.085 84M / 556M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	407 [spades] 0:00:00.102 84M / 556M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8238 kmers in total.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	408 [spades] 0:00:00.102 84M / 556M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	409 [spades] 0:00:00.106 84M / 556M INFO General (stage.cpp : 113) PROCEDURE == Extension index construction
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	410 [spades] 0:00:00.106 84M / 556M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	411 [spades] 0:00:00.106 84M / 556M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	412 [spades] 0:00:00.106 84M / 556M INFO General (file_limit.hpp : 32) Open file limit set to 131072
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	413 [spades] 0:00:00.106 84M / 556M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166509 Gb
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	414 [spades] 0:00:00.107 84M / 556M INFO General (kmer_splitters.hpp : 97) Using cell size of 87298
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	415 [spades] 0:00:00.181 2G / 2G INFO General (kmer_splitters.hpp : 364) Processed 8238 kmers
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	416 [spades] 0:00:00.181 2G / 2G INFO General (kmer_splitters.hpp : 369) Used 8238 kmers.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	417 [spades] 0:00:00.203 97M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	418 [spades] 0:00:00.220 97M / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8201 kmers in total.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	419 [spades] 0:00:00.221 97M / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	420 [spades] 0:00:00.226 97M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	421 [spades] 0:00:00.252 92M / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	422 [spades] 0:00:00.253 92M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 12872 bytes occupied (12.5565 bits per kmer).
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	423 [spades] 0:00:00.254 92M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	424 [spades] 0:00:00.257 92M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	425 [spades] 0:00:00.258 92M / 2G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	426 [spades] 0:00:00.258 92M / 2G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K)
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	427 [spades] 0:00:00.259 92M / 2G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	428 [spades] 0:00:00.263 92M / 2G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 115
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	429 [spades] 0:00:00.268 92M / 2G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 116
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	430 [spades] 0:00:00.268 92M / 2G INFO Early tip clipping (early_simplification.hpp : 30) 3952 52-mers were removed by early tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	431 [spades] 0:00:00.268 92M / 2G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	432 [spades] 0:00:00.269 92M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	433 [spades] 0:00:00.272 92M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 118 sequences extracted
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	434 [spades] 0:00:00.273 92M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	435 [spades] 0:00:00.274 92M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	436 [spades] 0:00:00.274 92M / 2G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM)
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	437 [spades] 0:00:00.275 92M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	438 [spades] 0:00:00.275 92M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	439 [spades] 0:00:00.286 92M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 8280 bytes occupied (8.04079 bits per kmer).
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	440 [spades] 0:00:00.286 92M / 2G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while.
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	441 [spades] 0:00:00.294 92M / 2G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	442 [spades] 0:00:00.297 92M / 2G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	443 [spades] 0:00:00.297 92M / 2G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 2
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	444 [spades] 0:00:00.297 92M / 2G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 51
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	445 [spades] 0:00:00.298 92M / 2G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 51. Coverage mad: 7.413
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	446 [spades] 0:00:00.298 92M / 2G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	447 [spades] 0:00:00.306 92M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	448 [spades] 0:00:00.326 92M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	449 [spades] 0:00:00.371 92M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	450 [spades] 0:00:00.392 92M / 2G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 48.7323. Fitted coverage std. dev: 7.8967
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	451 [spades] 0:00:00.392 92M / 2G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	452 [spades] 0:00:00.393 92M / 2G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 33
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	453 [spades] 0:00:00.393 92M / 2G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 25
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	454 [spades] 0:00:00.393 92M / 2G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 1099
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	455 [spades] 0:00:00.393 92M / 2G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 48.7323
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	456 [spades] 0:00:00.393 92M / 2G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 25
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	457 [spades] 0:00:00.394 92M / 2G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	458 [spades] 0:00:00.394 92M / 2G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	459 [spades] 0:00:00.394 92M / 2G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	460 [spades] 0:00:00.394 92M / 2G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	461 [spades] 0:00:00.394 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	462 [spades] 0:00:00.397 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	463 [spades] 0:00:00.397 92M / 2G INFO StageManager (stage.cpp : 166) STAGE == Simplification
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	464 [spades] 0:00:00.398 92M / 2G INFO General (simplification.cpp : 383) Graph simplification started
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	465 [spades] 0:00:00.398 92M / 2G INFO General (graph_simplification.hpp : 643) Creating parallel br instance
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	466 [spades] 0:00:00.398 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	467 [spades] 0:00:00.399 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	468 [spades] 0:00:00.399 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	469 [spades] 0:00:00.399 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	470 [spades] 0:00:00.401 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 40 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	471 [spades] 0:00:00.402 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	472 [spades] 0:00:00.402 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	473 [spades] 0:00:00.402 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	474 [spades] 0:00:00.403 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	475 [spades] 0:00:00.403 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	476 [spades] 0:00:00.403 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	477 [spades] 0:00:00.404 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	478 [spades] 0:00:00.404 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	479 [spades] 0:00:00.404 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	480 [spades] 0:00:00.405 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	481 [spades] 0:00:00.405 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	482 [spades] 0:00:00.405 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	483 [spades] 0:00:00.405 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	484 [spades] 0:00:00.405 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	485 [spades] 0:00:00.405 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	486 [spades] 0:00:00.406 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	487 [spades] 0:00:00.406 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	488 [spades] 0:00:00.406 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	489 [spades] 0:00:00.406 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	490 [spades] 0:00:00.406 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	491 [spades] 0:00:00.406 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	492 [spades] 0:00:00.407 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	493 [spades] 0:00:00.407 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	494 [spades] 0:00:00.407 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	495 [spades] 0:00:00.407 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	496 [spades] 0:00:00.407 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	497 [spades] 0:00:00.407 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	498 [spades] 0:00:00.408 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	499 [spades] 0:00:00.408 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445 iuc parents: diff changeset	500 [spades] 0:00:00.408 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

8

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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1 [shovill] Hello piemari

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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2 [shovill] You ran: /home/piemari/apps/conda/envs/metaphlan/bin/shovill --outdir ../shovill_bam/ --cpus 8 --ram 4 --R1 ../mutant_R1.fastq --R2 ../mutant_R2.fastq --namefmt contig%05d --depth 100 --keepfiles --minlen 0 --mincov 2 --assembler spades --force

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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3 [shovill] This is shovill 1.1.0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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4 [shovill] Written by Torsten Seemann

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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5 [shovill] Homepage is https://github.com/tseemann/shovill

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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6 [shovill] Operating system is linux

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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7 [shovill] Perl version is v5.32.1

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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8 [shovill] Machine has 32 CPU cores and 251.66 GB RAM

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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9 [shovill] Using bwa - /home/piemari/apps/conda/envs/metaphlan/bin/bwa | Version: 0.7.17-r1188

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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10 [shovill] Using flash - /home/piemari/apps/conda/envs/metaphlan/bin/flash | FLASH v1.2.11

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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11 [shovill] Using java - /home/piemari/apps/conda/envs/metaphlan/bin/java | openjdk version "11.0.1" 2018-10-16 LTS

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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12 [shovill] Using kmc - /home/piemari/apps/conda/envs/metaphlan/bin/kmc | K-Mer Counter (KMC) ver. 3.2.1 (2022-01-04)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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13 [shovill] Using lighter - /home/piemari/apps/conda/envs/metaphlan/bin/lighter | Lighter v1.1.2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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14 [shovill] Using megahit - /home/piemari/apps/conda/envs/metaphlan/bin/megahit | MEGAHIT v1.2.9

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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15 [shovill] Using megahit_toolkit - /home/piemari/apps/conda/envs/metaphlan/bin/megahit_toolkit | v1.2.9

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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16 [shovill] Using pigz - /home/piemari/apps/conda/envs/metaphlan/bin/pigz | pigz 2.6

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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17 [shovill] Using pilon - /home/piemari/apps/conda/envs/metaphlan/bin/pilon | Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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18 [shovill] Using samclip - /home/piemari/apps/conda/envs/metaphlan/bin/samclip | samclip 0.4.0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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19 [shovill] Using samtools - /home/piemari/apps/conda/envs/metaphlan/bin/samtools | Version: 1.15 (using htslib 1.14)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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20 [shovill] Using seqtk - /home/piemari/apps/conda/envs/metaphlan/bin/seqtk | Version: 1.3-r106

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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21 [shovill] Using skesa - /home/piemari/apps/conda/envs/metaphlan/bin/skesa | SKESA 2.4.0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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22 [shovill] Using spades.py - /home/piemari/apps/conda/envs/metaphlan/bin/spades.py | SPAdes genome assembler v3.14.1

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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23 [shovill] Using trimmomatic - /home/piemari/apps/conda/envs/metaphlan/bin/trimmomatic | 0.39

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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24 [shovill] Using velvetg - /home/piemari/apps/conda/envs/metaphlan/bin/velvetg | Version 1.2.10

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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25 [shovill] Using velveth - /home/piemari/apps/conda/envs/metaphlan/bin/velveth | Version 1.2.10

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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26 [shovill] Found spades version: 003014000

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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27 [shovill] Will use spades 003014000 options: --isolate and --merged

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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28 [shovill] Forced overwrite of existing --outdir ../shovill_bam/

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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29 [shovill] Using tempdir: /tmp

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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30 [shovill] Changing into folder: /home/piemari/shovill_bam

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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31 [shovill] Collecting raw read statistics with 'seqtk'

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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32 [shovill] Running: seqtk fqchk -q3 \/home\/piemari\/mutant_R1\.fastq >/tmp/1MILzK1fer 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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33 [shovill] Read stats: max_len = 150

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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34 [shovill] Read stats: min_len = 150

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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35 [shovill] Read stats: total_bp = 300000

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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36 [shovill] Read stats: avg_len = 150

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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37 [shovill] Estimating genome size by counting unqiue 21-mers > frequency 10

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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38 [shovill] Running: kmc -sm -m2 -t8 -k21 -ci10 \/home\/piemari\/mutant_R1\.fastq /tmp/_n_4cOtiee/kmc /tmp/_n_4cOtiee 2>&1 | sed 's/^/[kmc] /' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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39 [kmc] **

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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40 [kmc] Stage 1: 0% Stage 1: 100%

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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41 [kmc] Stage 2: 0% Stage 2: 84% Stage 2: 90% Stage 2: 94% Stage 2: 96% Stage 2: 98% Stage 2: 99% Stage 2: 100%

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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42 [kmc]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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43 [kmc]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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44 [kmc] 1st stage: 0.08264s

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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45 [kmc] 2nd stage: 0.104849s

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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46 [kmc] 3rd stage: 0.002521s

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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47 [kmc] Total : 0.19001s

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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diff changeset

48 [kmc] Tmp size : 0MB

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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49 [kmc] Tmp size strict memory : 0MB

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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50 [kmc] Tmp total: 0MB

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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51 [kmc]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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52 [kmc] Stats:

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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53 [kmc] No. of k-mers below min. threshold : 34495

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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54 [kmc] No. of k-mers above max. threshold : 0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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55 [kmc] No. of unique k-mers : 35683

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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56 [kmc] No. of unique counted k-mers : 1188

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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57 [kmc] Total no. of k-mers : 130000

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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58 [kmc] Total no. of reads : 1000

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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59 [kmc] Total no. of super-k-mers : 18576

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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60 [shovill] Using genome size 1188 bp

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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61 [shovill] Estimated sequencing depth: 252 x

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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62 [shovill] Subsampling reads by factor 0.397 to get from 252x to 100x

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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63 [shovill] Running: seqtk sample \/home\/piemari\/mutant_R1\.fastq 0.397 | pigz --fast -c -p 8 > R1.sub.fq.gz 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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64 [shovill] Running: seqtk sample \/home\/piemari\/mutant_R2\.fastq 0.397 | pigz --fast -c -p 8 > R2.sub.fq.gz 2>&1 | sed 's/^/[seqtk] /' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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65 [shovill] Appending -Xmx4g to _JAVA_OPTIONS

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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66 [shovill] Running: ln -sf R1\.sub\.fq\.gz R1.fq.gz 2>&1 | sed 's/^/[ln] /' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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67 [shovill] Running: ln -sf R2\.sub\.fq\.gz R2.fq.gz 2>&1 | sed 's/^/[ln] /' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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68 [shovill] Average read length looks like 150 bp

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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69 [shovill] Automatically setting --minlen to 75

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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70 [shovill] Setting k-mer range to (31 .. 112)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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71 [shovill] Estimated K-mers: 31 51 71 91 111 [kn=5, ks=20, kmin=31, kmax=112]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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72 [shovill] Using kmers: 31,51,71,91,111

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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73 [shovill] Correcting reads with 'Lighter'

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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74 [shovill] Running: lighter -od . -r R1.fq.gz -r R2.fq.gz -K 32 1188 -t 8 -maxcor 1 2>&1 | sed 's/^/[lighter] /' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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75 [lighter] [2022-05-04 12:29:31] =============Start====================

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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76 [lighter] [2022-05-04 12:29:31] Scanning the input files to infer alpha(sampling rate)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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77 [lighter] [2022-05-04 12:29:31] Average coverage is 103.535 and alpha is 0.068

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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78 [lighter] [2022-05-04 12:29:31] Bad quality threshold is "1"

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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79 [lighter] [2022-05-04 12:29:32] Finish sampling kmers

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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80 [lighter] [2022-05-04 12:29:32] Bloom filter A's false positive rate: 0.264464

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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81 [lighter] [2022-05-04 12:29:32] Finish storing trusted kmers

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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82 [lighter] [2022-05-04 12:29:32] Finish error correction

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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83 [lighter] Processed 820 reads:

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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84 [lighter] 48 are error-free

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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85 [lighter] Corrected 1731 bases(2.242228 corrections for reads with errors)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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86 [lighter] Trimmed 0 reads with average trimmed bases 0.000000

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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87 [lighter] Discard 0 reads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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88 [shovill] Overlapping/stitching PE reads with 'FLASH'

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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89 [shovill] Running: flash -m 20 -M 150 -d . -o flash -z -t 8 R1.cor.fq.gz R2.cor.fq.gz 2>&1 | sed 's/^//' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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90 [FLASH] Starting FLASH v1.2.11

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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91 [FLASH] Fast Length Adjustment of SHort reads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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92 [FLASH]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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93 [FLASH] Input files:

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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94 [FLASH] R1.cor.fq.gz

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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95 [FLASH] R2.cor.fq.gz

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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96 [FLASH]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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97 [FLASH] Output files:

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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98 [FLASH] ./flash.extendedFrags.fastq.gz

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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99 [FLASH] ./flash.notCombined_1.fastq.gz

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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100 [FLASH] ./flash.notCombined_2.fastq.gz

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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101 [FLASH] ./flash.hist

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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102 [FLASH] ./flash.histogram

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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103 [FLASH]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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104 [FLASH] Parameters:

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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105 [FLASH] Min overlap: 20

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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106 [FLASH] Max overlap: 150

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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107 [FLASH] Max mismatch density: 0.250000

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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108 [FLASH] Allow "outie" pairs: false

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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109 [FLASH] Cap mismatch quals: false

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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110 [FLASH] Combiner threads: 8

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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111 [FLASH] Input format: FASTQ, phred_offset=33

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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112 [FLASH] Output format: FASTQ, phred_offset=33, gzip

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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113 [FLASH]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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114 [FLASH] Starting reader and writer threads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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115 [FLASH] Starting 8 combiner threads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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116 [FLASH] Processed 410 read pairs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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117 [FLASH]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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118 [FLASH] Read combination statistics:

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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119 [FLASH] Total pairs: 410

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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120 [FLASH] Combined pairs: 387

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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121 [FLASH] Uncombined pairs: 23

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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122 [FLASH] Percent combined: 94.39%

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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123 [FLASH]

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124 [FLASH] Writing histogram files.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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125 [FLASH]

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126 [FLASH] FLASH v1.2.11 complete!

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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127 [FLASH] 0.022 seconds elapsed

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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128 [shovill] Assembling reads with 'spades'

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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129 [shovill] Running: spades.py -1 flash.notCombined_1.fastq.gz -2 flash.notCombined_2.fastq.gz --isolate --threads 8 --memory 4 -o spades --tmp-dir /tmp -k 31,51,71,91,111 --merged flash.extendedFrags.fastq.gz 2>&1 | sed 's/^/[spades] /' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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130 [spades] Command line: /home/piemari/apps/conda/envs/metaphlan/bin/spades.py -1 /home/piemari/shovill_bam/flash.notCombined_1.fastq.gz -2 /home/piemari/shovill_bam/flash.notCombined_2.fastq.gz --isolate --threads 8 --memory 4 -o /home/piemari/shovill_bam/spades --tmp-dir /tmp -k 31,51,71,91,111 --merged /home/piemari/shovill_bam/flash.extendedFrags.fastq.gz

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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131 [spades]

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132 [spades] System information:

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133 [spades] SPAdes version: 3.14.1

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134 [spades] Python version: 3.7.12

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135 [spades] OS: Linux-3.10.0-1160.62.1.el7.x86_64-x86_64-with-centos-7.9.2009-Core

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136 [spades]

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137 [spades] Output dir: /home/piemari/shovill_bam/spades

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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138 [spades] Mode: ONLY assembling (without read error correction)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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139 [spades] Debug mode is turned OFF

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140 [spades]

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141 [spades] Dataset parameters:

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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142 [spades] Isolate mode

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143 [spades] Reads:

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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144 [spades] Library number: 1, library type: paired-end

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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145 [spades] orientation: fr

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146 [spades] left reads: ['/home/piemari/shovill_bam/flash.notCombined_1.fastq.gz']

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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147 [spades] right reads: ['/home/piemari/shovill_bam/flash.notCombined_2.fastq.gz']

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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148 [spades] interlaced reads: not specified

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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149 [spades] single reads: not specified

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150 [spades] merged reads: ['/home/piemari/shovill_bam/flash.extendedFrags.fastq.gz']

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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151 [spades] Assembly parameters:

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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152 [spades] k: [31, 51, 71, 91, 111]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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153 [spades] Repeat resolution is enabled

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154 [spades] Mismatch careful mode is turned OFF

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155 [spades] MismatchCorrector will be SKIPPED

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156 [spades] Coverage cutoff is turned OFF

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157 [spades] Other parameters:

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158 [spades] Dir for temp files: /tmp

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159 [spades] Threads: 8

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160 [spades] Memory limit (in Gb): 4

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161 [spades]

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162 [spades]

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163 [spades] ======= SPAdes pipeline started. Log can be found here: /home/piemari/shovill_bam/spades/spades.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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164 [spades]

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165 [spades] /home/piemari/shovill_bam/flash.notCombined_1.fastq.gz: max reads length: 150

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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166 [spades] /home/piemari/shovill_bam/flash.notCombined_2.fastq.gz: max reads length: 150

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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167 [spades] Files with merged reads were ignored.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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168 [spades]

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169 [spades] Reads length: 150

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170 [spades]

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171 [spades]

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172 [spades] ===== Before start started.

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173 [spades]

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174 [spades]

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175 [spades] ===== Assembling started.

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176 [spades]

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177 [spades]

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178 [spades] ===== K31 started.

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179 [spades]

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180 [spades]

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181 [spades] == Running: /home/piemari/apps/conda/envs/metaphlan/bin/spades-core /home/piemari/shovill_bam/spades/K31/configs/config.info /home/piemari/shovill_bam/spades/K31/configs/isolate_mode.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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182 [spades]

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183 [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is tmp_contigs.fasta

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184 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K31/configs/config.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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185 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K31/configs/isolate_mode.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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186 [spades] 0:00:00.000 4M / 10M INFO General (memory_limit.cpp : 49) Memory limit set to 4 Gb

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187 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A

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188 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 86) Maximum k-mer length: 128

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189 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 87) Assembling dataset (/home/piemari/shovill_bam/spades/dataset.info) with K=31

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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190 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 8

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191 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 194) SPAdes started

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192 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion

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193 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0

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194 [spades] 0:00:00.000 4M / 10M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion

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195 [spades] 0:00:00.002 4M / 12M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while)

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196 [spades] 0:00:00.002 4M / 12M INFO General (read_converter.cpp : 73) Converting paired reads

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197 [spades] 0:00:00.009 71M / 71M INFO General (binary_converter.cpp : 111) 23 reads written

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198 [spades] 0:00:00.009 47M / 47M INFO General (read_converter.cpp : 81) Converting single reads

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199 [spades] 0:00:00.011 57M / 57M INFO General (binary_converter.cpp : 111) 0 reads written

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200 [spades] 0:00:00.011 57M / 57M INFO General (read_converter.cpp : 87) Converting merged reads

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201 [spades] 0:00:00.017 77M / 77M INFO General (binary_converter.cpp : 111) 387 reads written

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202 [spades] 0:00:00.022 17M / 40M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction

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203 [spades] 0:00:00.026 17M / 40M INFO General (construction.cpp : 150) Max read length 280

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204 [spades] 0:00:00.026 17M / 40M INFO General (construction.cpp : 153) Max read length without merged 150

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205 [spades] 0:00:00.026 17M / 40M INFO General (construction.cpp : 156) Average read length 193.032

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206 [spades] 0:00:00.026 17M / 40M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting

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207 [spades] 0:00:00.026 17M / 40M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 64 files using 8 threads. This might take a while.

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208 [spades] 0:00:00.026 17M / 40M INFO General (file_limit.hpp : 32) Open file limit set to 131072

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209 [spades] 0:00:00.027 17M / 40M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166615 Gb

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210 [spades] 0:00:00.027 17M / 40M INFO General (kmer_splitters.hpp : 97) Using cell size of 349417

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211 [spades] 0:00:00.100 71M / 560M INFO General (kmer_splitters.hpp : 293) Used 866 reads

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212 [spades] 0:00:00.100 71M / 560M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

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213 [spades] 0:00:00.111 71M / 560M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7283 kmers in total.

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214 [spades] 0:00:00.111 71M / 560M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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215 [spades] 0:00:00.114 71M / 560M INFO General (stage.cpp : 113) PROCEDURE == Extension index construction

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216 [spades] 0:00:00.114 71M / 560M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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217 [spades] 0:00:00.114 71M / 560M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while.

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218 [spades] 0:00:00.115 71M / 560M INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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219 [spades] 0:00:00.115 71M / 560M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166468 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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220 [spades] 0:00:00.115 71M / 560M INFO General (kmer_splitters.hpp : 97) Using cell size of 174554

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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221 [spades] 0:00:00.188 2G / 2G INFO General (kmer_splitters.hpp : 364) Processed 7283 kmers

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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222 [spades] 0:00:00.188 2G / 2G INFO General (kmer_splitters.hpp : 369) Used 7283 kmers.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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223 [spades] 0:00:00.212 85M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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224 [spades] 0:00:00.236 85M / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 7222 kmers in total.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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225 [spades] 0:00:00.236 85M / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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226 [spades] 0:00:00.241 85M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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227 [spades] 0:00:00.264 86M / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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228 [spades] 0:00:00.266 86M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 12384 bytes occupied (13.7181 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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229 [spades] 0:00:00.266 86M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers

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230 [spades] 0:00:00.273 86M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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231 [spades] 0:00:00.274 86M / 2G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping

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232 [spades] 0:00:00.274 86M / 2G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K)

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233 [spades] 0:00:00.274 86M / 2G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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234 [spades] 0:00:00.279 86M / 2G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 96

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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235 [spades] 0:00:00.284 86M / 2G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 97

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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236 [spades] 0:00:00.284 86M / 2G INFO Early tip clipping (early_simplification.hpp : 30) 2642 32-mers were removed by early tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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237 [spades] 0:00:00.285 86M / 2G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph

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238 [spades] 0:00:00.285 86M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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239 [spades] 0:00:00.287 86M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 186 sequences extracted

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240 [spades] 0:00:00.288 86M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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241 [spades] 0:00:00.289 86M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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242 [spades] 0:00:00.290 86M / 2G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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243 [spades] 0:00:00.290 86M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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244 [spades] 0:00:00.290 86M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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245 [spades] 0:00:00.301 87M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 7864 bytes occupied (8.6382 bits per kmer).

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246 [spades] 0:00:00.301 87M / 2G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while.

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247 [spades] 0:00:00.310 87M / 2G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM

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248 [spades] 0:00:00.314 87M / 2G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding

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249 [spades] 0:00:00.314 87M / 2G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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250 [spades] 0:00:00.315 87M / 2G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 60

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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251 [spades] 0:00:00.315 87M / 2G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 60. Coverage mad: 7.413

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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252 [spades] 0:00:00.315 87M / 2G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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253 [spades] 0:00:00.324 87M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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254 [spades] 0:00:00.349 87M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4

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255 [spades] 0:00:00.414 87M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8

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256 [spades] 0:00:00.501 87M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16

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257 [spades] 0:00:00.540 87M / 2G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 56.9644. Fitted coverage std. dev: 9.10691

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258 [spades] 0:00:00.540 87M / 2G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1

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259 [spades] 0:00:00.541 87M / 2G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 39

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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260 [spades] 0:00:00.541 87M / 2G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 29

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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261 [spades] 0:00:00.541 87M / 2G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 1104

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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262 [spades] 0:00:00.541 87M / 2G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 56.9644

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263 [spades] 0:00:00.541 87M / 2G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 29

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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264 [spades] 0:00:00.542 87M / 2G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0

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265 [spades] 0:00:00.542 87M / 2G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification

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266 [spades] 0:00:00.542 87M / 2G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning

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267 [spades] 0:00:00.542 87M / 2G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled

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268 [spades] 0:00:00.542 87M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover

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269 [spades] 0:00:00.545 87M / 2G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times

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270 [spades] 0:00:00.545 87M / 2G INFO StageManager (stage.cpp : 166) STAGE == Simplification

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271 [spades] 0:00:00.546 87M / 2G INFO General (simplification.cpp : 383) Graph simplification started

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272 [spades] 0:00:00.546 87M / 2G INFO General (graph_simplification.hpp : 643) Creating parallel br instance

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273 [spades] 0:00:00.546 87M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1

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274 [spades] 0:00:00.546 87M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

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275 [spades] 0:00:00.550 87M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

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276 [spades] 0:00:00.550 87M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

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277 [spades] 0:00:00.557 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 60 times

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278 [spades] 0:00:00.557 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

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279 [spades] 0:00:00.559 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 3 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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280 [spades] 0:00:00.560 84M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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281 [spades] 0:00:00.560 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

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282 [spades] 0:00:00.560 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

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354 [spades] 0:00:00.577 84M / 2G INFO General (graph_simplification.hpp : 643) Creating parallel br instance

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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355 [spades] 0:00:00.577 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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356 [spades] 0:00:00.578 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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357 [spades] 0:00:00.578 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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358 [spades] 0:00:00.578 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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359 [spades] 0:00:00.578 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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360 [spades] 0:00:00.579 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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361 [spades] 0:00:00.579 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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362 [spades] 0:00:00.579 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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363 [spades] 0:00:00.579 84M / 2G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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364 [spades] 0:00:00.579 84M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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365 [spades] 0:00:00.580 84M / 2G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 1 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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366 [spades] 0:00:00.580 84M / 2G INFO General (simplification.cpp : 496) Counting average coverage

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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367 [spades] 0:00:00.580 84M / 2G INFO General (simplification.cpp : 502) Average coverage = 55.1872

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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368 [spades] 0:00:00.580 84M / 2G INFO StageManager (stage.cpp : 166) STAGE == Contig Output

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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369 [spades] 0:00:00.583 84M / 2G INFO General (read_converter.cpp : 102) Outputting contigs to /home/piemari/shovill_bam/spades/K31/simplified_contigs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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370 [spades] 0:00:00.585 84M / 2G INFO General (binary_converter.cpp : 111) 1 reads written

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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371 [spades] 0:00:00.589 84M / 2G INFO General (pipeline.cpp : 259) SPAdes finished

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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372 [spades] 0:00:00.590 84M / 2G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 0 seconds

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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373 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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374 [spades] ===== K31 finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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375 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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376 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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377 [spades] ===== K51 started.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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378 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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379 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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380 [spades] == Running: /home/piemari/apps/conda/envs/metaphlan/bin/spades-core /home/piemari/shovill_bam/spades/K51/configs/config.info /home/piemari/shovill_bam/spades/K51/configs/isolate_mode.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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381 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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382 [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /home/piemari/shovill_bam/spades/K31/simplified_contigs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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383 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K51/configs/config.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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384 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K51/configs/isolate_mode.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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385 [spades] 0:00:00.000 4M / 10M INFO General (memory_limit.cpp : 49) Memory limit set to 4 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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386 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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387 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 86) Maximum k-mer length: 128

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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388 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 87) Assembling dataset (/home/piemari/shovill_bam/spades/dataset.info) with K=51

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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389 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 8

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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390 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 194) SPAdes started

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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391 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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392 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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393 [spades] 0:00:00.000 4M / 10M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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394 [spades] 0:00:00.001 4M / 12M INFO General (read_converter.cpp : 53) Binary reads detected

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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395 [spades] 0:00:00.002 4M / 14M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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396 [spades] 0:00:00.002 4M / 14M INFO General (construction.cpp : 115) Contigs from previous K will be used: /home/piemari/shovill_bam/spades/K31/simplified_contigs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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397 [spades] 0:00:00.007 4M / 14M INFO General (construction.cpp : 150) Max read length 280

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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398 [spades] 0:00:00.007 4M / 14M INFO General (construction.cpp : 153) Max read length without merged 150

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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399 [spades] 0:00:00.007 4M / 14M INFO General (construction.cpp : 156) Average read length 193.032

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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400 [spades] 0:00:00.007 4M / 14M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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401 [spades] 0:00:00.007 4M / 14M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 64 files using 8 threads. This might take a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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402 [spades] 0:00:00.007 4M / 14M INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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403 [spades] 0:00:00.007 4M / 14M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166632 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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404 [spades] 0:00:00.007 4M / 14M INFO General (kmer_splitters.hpp : 97) Using cell size of 174726

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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405 [spades] 0:00:00.085 84M / 556M INFO General (kmer_splitters.hpp : 293) Used 868 reads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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406 [spades] 0:00:00.085 84M / 556M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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407 [spades] 0:00:00.102 84M / 556M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8238 kmers in total.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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408 [spades] 0:00:00.102 84M / 556M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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409 [spades] 0:00:00.106 84M / 556M INFO General (stage.cpp : 113) PROCEDURE == Extension index construction

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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410 [spades] 0:00:00.106 84M / 556M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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411 [spades] 0:00:00.106 84M / 556M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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412 [spades] 0:00:00.106 84M / 556M INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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413 [spades] 0:00:00.106 84M / 556M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166509 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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414 [spades] 0:00:00.107 84M / 556M INFO General (kmer_splitters.hpp : 97) Using cell size of 87298

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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415 [spades] 0:00:00.181 2G / 2G INFO General (kmer_splitters.hpp : 364) Processed 8238 kmers

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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416 [spades] 0:00:00.181 2G / 2G INFO General (kmer_splitters.hpp : 369) Used 8238 kmers.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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417 [spades] 0:00:00.203 97M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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418 [spades] 0:00:00.220 97M / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8201 kmers in total.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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419 [spades] 0:00:00.221 97M / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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420 [spades] 0:00:00.226 97M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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421 [spades] 0:00:00.252 92M / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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422 [spades] 0:00:00.253 92M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 12872 bytes occupied (12.5565 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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423 [spades] 0:00:00.254 92M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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424 [spades] 0:00:00.257 92M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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425 [spades] 0:00:00.258 92M / 2G INFO General (stage.cpp : 113) PROCEDURE == Early tip clipping

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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426 [spades] 0:00:00.258 92M / 2G INFO General (construction.cpp : 293) Early tip clipper length bound set as (RL - K)

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427 [spades] 0:00:00.259 92M / 2G INFO Early tip clipping (early_simplification.hpp : 28) Early tip clipping

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428 [spades] 0:00:00.263 92M / 2G INFO Early tip clipping (early_simplification.hpp : 63) #tipped junctions: 115

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429 [spades] 0:00:00.268 92M / 2G INFO Early tip clipping (early_simplification.hpp : 74) Clipped tips: 116

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430 [spades] 0:00:00.268 92M / 2G INFO Early tip clipping (early_simplification.hpp : 30) 3952 52-mers were removed by early tip clipper

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431 [spades] 0:00:00.268 92M / 2G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph

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432 [spades] 0:00:00.269 92M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths

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433 [spades] 0:00:00.272 92M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 118 sequences extracted

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434 [spades] 0:00:00.273 92M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops

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435 [spades] 0:00:00.274 92M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected

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436 [spades] 0:00:00.274 92M / 2G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM)

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437 [spades] 0:00:00.275 92M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

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438 [spades] 0:00:00.275 92M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

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439 [spades] 0:00:00.286 92M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 8280 bytes occupied (8.04079 bits per kmer).

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440 [spades] 0:00:00.286 92M / 2G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while.

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441 [spades] 0:00:00.294 92M / 2G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM

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442 [spades] 0:00:00.297 92M / 2G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding

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443 [spades] 0:00:00.297 92M / 2G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 2

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444 [spades] 0:00:00.297 92M / 2G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 51

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445 [spades] 0:00:00.298 92M / 2G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 51. Coverage mad: 7.413

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446 [spades] 0:00:00.298 92M / 2G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model

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447 [spades] 0:00:00.306 92M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2

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448 [spades] 0:00:00.326 92M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4

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449 [spades] 0:00:00.371 92M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8

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450 [spades] 0:00:00.392 92M / 2G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 48.7323. Fitted coverage std. dev: 7.8967

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451 [spades] 0:00:00.392 92M / 2G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1

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452 [spades] 0:00:00.393 92M / 2G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 33

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453 [spades] 0:00:00.393 92M / 2G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 25

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454 [spades] 0:00:00.393 92M / 2G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 1099

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455 [spades] 0:00:00.393 92M / 2G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 48.7323

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456 [spades] 0:00:00.393 92M / 2G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 25

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457 [spades] 0:00:00.394 92M / 2G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0

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458 [spades] 0:00:00.394 92M / 2G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification

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459 [spades] 0:00:00.394 92M / 2G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning

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460 [spades] 0:00:00.394 92M / 2G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled

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461 [spades] 0:00:00.394 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover

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462 [spades] 0:00:00.397 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times

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463 [spades] 0:00:00.397 92M / 2G INFO StageManager (stage.cpp : 166) STAGE == Simplification

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464 [spades] 0:00:00.398 92M / 2G INFO General (simplification.cpp : 383) Graph simplification started

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465 [spades] 0:00:00.398 92M / 2G INFO General (graph_simplification.hpp : 643) Creating parallel br instance

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466 [spades] 0:00:00.398 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1

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467 [spades] 0:00:00.399 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

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468 [spades] 0:00:00.399 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

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469 [spades] 0:00:00.399 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

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470 [spades] 0:00:00.401 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 40 times

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471 [spades] 0:00:00.402 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

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472 [spades] 0:00:00.402 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

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473 [spades] 0:00:00.402 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2

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474 [spades] 0:00:00.403 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

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475 [spades] 0:00:00.403 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

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476 [spades] 0:00:00.403 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

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478 [spades] 0:00:00.404 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

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480 [spades] 0:00:00.405 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3

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487 [spades] 0:00:00.406 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4

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494 [spades] 0:00:00.407 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5

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508 [spades] 0:00:00.409 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7

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522 [spades] 0:00:00.411 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9

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529 [spades] 0:00:00.413 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10

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532 [spades] 0:00:00.413 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

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534 [spades] 0:00:00.413 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

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536 [spades] 0:00:00.414 92M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11

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539 [spades] 0:00:00.416 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

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543 [spades] 0:00:00.417 92M / 2G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup

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544 [spades] 0:00:00.418 92M / 2G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification

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545 [spades] 0:00:00.418 92M / 2G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled

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546 [spades] 0:00:00.418 92M / 2G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled

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547 [spades] 0:00:00.419 92M / 2G INFO General (graph_simplification.hpp : 643) Creating parallel br instance

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548 [spades] 0:00:00.419 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

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550 [spades] 0:00:00.420 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

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554 [spades] 0:00:00.421 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

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556 [spades] 0:00:00.421 92M / 2G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges

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557 [spades] 0:00:00.422 92M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges

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558 [spades] 0:00:00.422 92M / 2G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 2 times

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559 [spades] 0:00:00.422 92M / 2G INFO General (simplification.cpp : 496) Counting average coverage

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560 [spades] 0:00:00.423 92M / 2G INFO General (simplification.cpp : 502) Average coverage = 47.8689

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561 [spades] 0:00:00.423 92M / 2G INFO StageManager (stage.cpp : 166) STAGE == Contig Output

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562 [spades] 0:00:00.424 92M / 2G INFO General (read_converter.cpp : 102) Outputting contigs to /home/piemari/shovill_bam/spades/K51/simplified_contigs

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563 [spades] 0:00:00.426 92M / 2G INFO General (binary_converter.cpp : 111) 1 reads written

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564 [spades] 0:00:00.433 92M / 2G INFO General (pipeline.cpp : 259) SPAdes finished

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565 [spades] 0:00:00.433 92M / 2G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 0 seconds

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566 [spades]

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567 [spades] ===== K51 finished.

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568 [spades]

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569 [spades]

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570 [spades] ===== K71 started.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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571 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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572 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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573 [spades] == Running: /home/piemari/apps/conda/envs/metaphlan/bin/spades-core /home/piemari/shovill_bam/spades/K71/configs/config.info /home/piemari/shovill_bam/spades/K71/configs/isolate_mode.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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574 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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575 [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /home/piemari/shovill_bam/spades/K51/simplified_contigs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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576 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K71/configs/config.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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577 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K71/configs/isolate_mode.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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578 [spades] 0:00:00.000 4M / 10M INFO General (memory_limit.cpp : 49) Memory limit set to 4 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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579 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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580 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 86) Maximum k-mer length: 128

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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581 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 87) Assembling dataset (/home/piemari/shovill_bam/spades/dataset.info) with K=71

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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582 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 8

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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583 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 194) SPAdes started

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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584 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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585 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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586 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 218) Will need read mapping, kmer mapper will be attached

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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587 [spades] 0:00:00.000 4M / 10M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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588 [spades] 0:00:00.001 4M / 12M INFO General (read_converter.cpp : 53) Binary reads detected

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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589 [spades] 0:00:00.001 4M / 14M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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590 [spades] 0:00:00.001 4M / 14M INFO General (construction.cpp : 115) Contigs from previous K will be used: /home/piemari/shovill_bam/spades/K51/simplified_contigs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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591 [spades] 0:00:00.006 4M / 14M INFO General (construction.cpp : 150) Max read length 280

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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592 [spades] 0:00:00.006 4M / 14M INFO General (construction.cpp : 153) Max read length without merged 150

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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593 [spades] 0:00:00.006 4M / 14M INFO General (construction.cpp : 156) Average read length 193.032

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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594 [spades] 0:00:00.006 4M / 14M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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595 [spades] 0:00:00.006 4M / 14M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 64 files using 8 threads. This might take a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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596 [spades] 0:00:00.007 4M / 14M INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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597 [spades] 0:00:00.007 4M / 14M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166632 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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598 [spades] 0:00:00.007 4M / 14M INFO General (kmer_splitters.hpp : 97) Using cell size of 116484

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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599 [spades] 0:00:00.088 81M / 554M INFO General (kmer_splitters.hpp : 293) Used 868 reads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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600 [spades] 0:00:00.088 81M / 554M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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601 [spades] 0:00:00.100 83M / 554M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8725 kmers in total.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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602 [spades] 0:00:00.100 83M / 554M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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603 [spades] 0:00:00.104 83M / 554M INFO General (stage.cpp : 113) PROCEDURE == Extension index construction

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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604 [spades] 0:00:00.104 83M / 554M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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605 [spades] 0:00:00.104 83M / 554M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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606 [spades] 0:00:00.104 83M / 554M INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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607 [spades] 0:00:00.104 83M / 554M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166542 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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608 [spades] 0:00:00.104 83M / 554M INFO General (kmer_splitters.hpp : 97) Using cell size of 58210

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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609 [spades] 0:00:00.177 2G / 2G INFO General (kmer_splitters.hpp : 364) Processed 8725 kmers

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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610 [spades] 0:00:00.177 2G / 2G INFO General (kmer_splitters.hpp : 369) Used 8725 kmers.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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611 [spades] 0:00:00.200 89M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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612 [spades] 0:00:00.218 89M / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8713 kmers in total.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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613 [spades] 0:00:00.218 89M / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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614 [spades] 0:00:00.224 89M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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615 [spades] 0:00:00.249 87M / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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616 [spades] 0:00:00.251 87M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 13120 bytes occupied (12.0464 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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617 [spades] 0:00:00.251 87M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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618 [spades] 0:00:00.254 87M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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619 [spades] 0:00:00.255 87M / 2G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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620 [spades] 0:00:00.255 87M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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621 [spades] 0:00:00.260 87M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 308 sequences extracted

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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622 [spades] 0:00:00.266 87M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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623 [spades] 0:00:00.271 87M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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624 [spades] 0:00:00.280 87M / 2G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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625 [spades] 0:00:00.281 87M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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626 [spades] 0:00:00.281 87M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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627 [spades] 0:00:00.294 87M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 8536 bytes occupied (7.8267 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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628 [spades] 0:00:00.294 87M / 2G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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629 [spades] 0:00:00.300 87M / 2G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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630 [spades] 0:00:00.307 87M / 2G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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631 [spades] 0:00:00.308 87M / 2G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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632 [spades] 0:00:00.308 87M / 2G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 44

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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633 [spades] 0:00:00.308 87M / 2G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 44. Coverage mad: 7.413

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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634 [spades] 0:00:00.308 87M / 2G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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635 [spades] 0:00:00.315 87M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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636 [spades] 0:00:00.334 87M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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637 [spades] 0:00:00.377 87M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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638 [spades] 0:00:00.421 87M / 2G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 40.9755. Fitted coverage std. dev: 6.3525

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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639 [spades] 0:00:00.421 87M / 2G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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640 [spades] 0:00:00.421 87M / 2G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 28

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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641 [spades] 0:00:00.421 87M / 2G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 21

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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642 [spades] 0:00:00.422 87M / 2G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 1088

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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643 [spades] 0:00:00.422 87M / 2G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 40.9755

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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644 [spades] 0:00:00.422 87M / 2G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 21

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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645 [spades] 0:00:00.422 87M / 2G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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646 [spades] 0:00:00.423 87M / 2G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer

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647 [spades] 0:00:00.423 87M / 2G INFO General (graph_pack.hpp : 105) Index refill

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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648 [spades] 0:00:00.423 87M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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649 [spades] 0:00:00.423 87M / 2G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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650 [spades] 0:00:00.424 87M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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651 [spades] 0:00:00.424 87M / 2G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166486 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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652 [spades] 0:00:00.424 87M / 2G INFO General (kmer_splitters.hpp : 97) Using cell size of 58191

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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653 [spades] 0:00:00.513 2G / 2G INFO General (edge_index_builders.hpp : 82) Used 616 sequences.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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654 [spades] 0:00:00.531 94M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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655 [spades] 0:00:00.562 94M / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8725 kmers in total.

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656 [spades] 0:00:00.563 94M / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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657 [spades] 0:00:00.568 94M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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658 [spades] 0:00:00.586 89M / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.

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659 [spades] 0:00:00.588 89M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 13104 bytes occupied (12.0151 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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660 [spades] 0:00:00.588 89M / 2G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.

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661 [spades] 0:00:00.592 89M / 2G INFO General (edge_index.hpp : 92) Index refilled

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662 [spades] 0:00:00.595 89M / 2G INFO General (gap_closer.cpp : 147) Preparing shift maps

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663 [spades] 0:00:00.596 89M / 2G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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664 [spades] 0:00:00.598 89M / 2G INFO General (gap_closer.cpp : 126) Used 23 paired reads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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665 [spades] 0:00:00.598 89M / 2G INFO General (gap_closer.cpp : 128) Merging paired indices

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666 [spades] 0:00:00.598 89M / 2G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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667 [spades] 0:00:00.599 89M / 2G INFO GapCloser (gap_closer.cpp : 364) Closing short gaps complete: filled 0 gaps after checking 0 candidates

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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668 [spades] 0:00:00.599 89M / 2G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification

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669 [spades] 0:00:00.599 89M / 2G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning

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670 [spades] 0:00:00.600 89M / 2G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled

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671 [spades] 0:00:00.600 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover

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672 [spades] 0:00:00.600 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times

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673 [spades] 0:00:00.600 89M / 2G INFO StageManager (stage.cpp : 166) STAGE == Simplification

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674 [spades] 0:00:00.601 89M / 2G INFO General (simplification.cpp : 383) Graph simplification started

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675 [spades] 0:00:00.601 89M / 2G INFO General (graph_simplification.hpp : 643) Creating parallel br instance

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676 [spades] 0:00:00.601 89M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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677 [spades] 0:00:00.601 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

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678 [spades] 0:00:00.603 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 128 times

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679 [spades] 0:00:00.603 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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680 [spades] 0:00:00.607 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 19 times

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681 [spades] 0:00:00.607 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

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682 [spades] 0:00:00.609 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

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683 [spades] 0:00:00.609 89M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2

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684 [spades] 0:00:00.609 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

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685 [spades] 0:00:00.610 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

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686 [spades] 0:00:00.610 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

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687 [spades] 0:00:00.610 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

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688 [spades] 0:00:00.610 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

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689 [spades] 0:00:00.611 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

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690 [spades] 0:00:00.611 89M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3

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691 [spades] 0:00:00.611 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

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692 [spades] 0:00:00.611 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

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693 [spades] 0:00:00.611 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

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694 [spades] 0:00:00.612 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

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695 [spades] 0:00:00.612 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

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696 [spades] 0:00:00.612 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

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697 [spades] 0:00:00.612 89M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 4

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698 [spades] 0:00:00.612 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

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699 [spades] 0:00:00.612 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

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700 [spades] 0:00:00.613 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

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701 [spades] 0:00:00.613 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

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702 [spades] 0:00:00.613 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

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704 [spades] 0:00:00.613 89M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 5

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705 [spades] 0:00:00.613 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

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707 [spades] 0:00:00.614 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

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711 [spades] 0:00:00.614 89M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 6

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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712 [spades] 0:00:00.615 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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713 [spades] 0:00:00.615 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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714 [spades] 0:00:00.615 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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715 [spades] 0:00:00.615 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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716 [spades] 0:00:00.615 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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717 [spades] 0:00:00.615 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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718 [spades] 0:00:00.616 89M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 7

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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719 [spades] 0:00:00.616 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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720 [spades] 0:00:00.616 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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721 [spades] 0:00:00.616 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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722 [spades] 0:00:00.616 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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723 [spades] 0:00:00.617 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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724 [spades] 0:00:00.617 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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725 [spades] 0:00:00.617 89M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 8

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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726 [spades] 0:00:00.617 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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727 [spades] 0:00:00.617 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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728 [spades] 0:00:00.617 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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730 [spades] 0:00:00.618 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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731 [spades] 0:00:00.618 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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732 [spades] 0:00:00.618 89M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 9

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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733 [spades] 0:00:00.618 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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734 [spades] 0:00:00.618 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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735 [spades] 0:00:00.619 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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736 [spades] 0:00:00.619 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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737 [spades] 0:00:00.619 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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738 [spades] 0:00:00.619 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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739 [spades] 0:00:00.619 89M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 10

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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740 [spades] 0:00:00.619 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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741 [spades] 0:00:00.620 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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742 [spades] 0:00:00.620 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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743 [spades] 0:00:00.620 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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744 [spades] 0:00:00.620 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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745 [spades] 0:00:00.620 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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746 [spades] 0:00:00.620 89M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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747 [spades] 0:00:00.621 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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748 [spades] 0:00:00.623 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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749 [spades] 0:00:00.623 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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750 [spades] 0:00:00.623 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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751 [spades] 0:00:00.623 89M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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752 [spades] 0:00:00.624 89M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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753 [spades] 0:00:00.624 89M / 2G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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754 [spades] 0:00:00.624 89M / 2G INFO General (graph_pack.hpp : 105) Index refill

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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755 [spades] 0:00:00.625 89M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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756 [spades] 0:00:00.625 89M / 2G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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757 [spades] 0:00:00.625 89M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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758 [spades] 0:00:00.626 89M / 2G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166471 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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759 [spades] 0:00:00.626 89M / 2G INFO General (kmer_splitters.hpp : 97) Using cell size of 58185

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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760 [spades] 0:00:00.681 2G / 2G INFO General (edge_index_builders.hpp : 82) Used 14 sequences.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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761 [spades] 0:00:00.688 100M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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762 [spades] 0:00:00.704 100M / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1720 kmers in total.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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763 [spades] 0:00:00.704 100M / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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764 [spades] 0:00:00.709 100M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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765 [spades] 0:00:00.728 100M / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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766 [spades] 0:00:00.729 100M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10088 bytes occupied (46.9209 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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767 [spades] 0:00:00.730 100M / 2G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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768 [spades] 0:00:00.733 100M / 2G INFO General (edge_index.hpp : 92) Index refilled

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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769 [spades] 0:00:00.735 100M / 2G INFO General (gap_closer.cpp : 147) Preparing shift maps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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770 [spades] 0:00:00.735 100M / 2G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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771 [spades] 0:00:00.738 100M / 2G INFO General (gap_closer.cpp : 126) Used 23 paired reads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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772 [spades] 0:00:00.739 100M / 2G INFO General (gap_closer.cpp : 128) Merging paired indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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773 [spades] 0:00:00.739 100M / 2G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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774 [spades] 0:00:00.739 100M / 2G INFO GapCloser (gap_closer.cpp : 364) Closing short gaps complete: filled 0 gaps after checking 0 candidates

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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775 [spades] 0:00:00.743 100M / 2G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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776 [spades] 0:00:00.744 100M / 2G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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777 [spades] 0:00:00.744 100M / 2G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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778 [spades] 0:00:00.744 100M / 2G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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779 [spades] 0:00:00.744 100M / 2G INFO General (graph_simplification.hpp : 643) Creating parallel br instance

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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780 [spades] 0:00:00.745 100M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

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781 [spades] 0:00:00.748 100M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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782 [spades] 0:00:00.748 100M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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783 [spades] 0:00:00.753 100M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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784 [spades] 0:00:00.753 100M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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785 [spades] 0:00:00.760 100M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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786 [spades] 0:00:00.761 100M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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787 [spades] 0:00:00.766 100M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

788 [spades] 0:00:00.766 100M / 2G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

789 [spades] 0:00:00.766 100M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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790 [spades] 0:00:00.770 100M / 2G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 6 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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791 [spades] 0:00:00.770 100M / 2G INFO General (simplification.cpp : 496) Counting average coverage

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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792 [spades] 0:00:00.770 100M / 2G INFO General (simplification.cpp : 502) Average coverage = 39.6025

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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793 [spades] 0:00:00.770 100M / 2G INFO StageManager (stage.cpp : 166) STAGE == Contig Output

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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794 [spades] 0:00:00.771 100M / 2G INFO General (read_converter.cpp : 102) Outputting contigs to /home/piemari/shovill_bam/spades/K71/simplified_contigs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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795 [spades] 0:00:00.775 100M / 2G INFO General (binary_converter.cpp : 111) 1 reads written

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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796 [spades] 0:00:00.780 100M / 2G INFO General (pipeline.cpp : 259) SPAdes finished

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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797 [spades] 0:00:00.781 100M / 2G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 0 seconds

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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798 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

799 [spades] ===== K71 finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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800 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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801 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

802 [spades] ===== K91 started.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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803 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

804 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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805 [spades] == Running: /home/piemari/apps/conda/envs/metaphlan/bin/spades-core /home/piemari/shovill_bam/spades/K91/configs/config.info /home/piemari/shovill_bam/spades/K91/configs/isolate_mode.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

806 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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807 [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /home/piemari/shovill_bam/spades/K71/simplified_contigs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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808 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K91/configs/config.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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809 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K91/configs/isolate_mode.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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810 [spades] 0:00:00.000 4M / 10M INFO General (memory_limit.cpp : 49) Memory limit set to 4 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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811 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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812 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 86) Maximum k-mer length: 128

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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813 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 87) Assembling dataset (/home/piemari/shovill_bam/spades/dataset.info) with K=91

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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814 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 8

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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815 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 194) SPAdes started

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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816 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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817 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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818 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 218) Will need read mapping, kmer mapper will be attached

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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819 [spades] 0:00:00.000 4M / 10M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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820 [spades] 0:00:00.002 4M / 12M INFO General (read_converter.cpp : 53) Binary reads detected

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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821 [spades] 0:00:00.003 4M / 16M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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822 [spades] 0:00:00.003 4M / 16M INFO General (construction.cpp : 115) Contigs from previous K will be used: /home/piemari/shovill_bam/spades/K71/simplified_contigs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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823 [spades] 0:00:00.014 4M / 16M INFO General (construction.cpp : 150) Max read length 280

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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824 [spades] 0:00:00.014 4M / 16M INFO General (construction.cpp : 153) Max read length without merged 150

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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825 [spades] 0:00:00.014 4M / 16M INFO General (construction.cpp : 156) Average read length 193.032

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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826 [spades] 0:00:00.014 4M / 16M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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827 [spades] 0:00:00.014 4M / 16M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 64 files using 8 threads. This might take a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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828 [spades] 0:00:00.014 4M / 16M INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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829 [spades] 0:00:00.014 4M / 16M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166632 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

830 [spades] 0:00:00.015 4M / 16M INFO General (kmer_splitters.hpp : 97) Using cell size of 116484

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

831 [spades] 0:00:00.092 83M / 554M INFO General (kmer_splitters.hpp : 293) Used 868 reads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

832 [spades] 0:00:00.092 83M / 554M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

833 [spades] 0:00:00.104 83M / 554M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8793 kmers in total.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

834 [spades] 0:00:00.105 83M / 554M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

835 [spades] 0:00:00.108 83M / 554M INFO General (stage.cpp : 113) PROCEDURE == Extension index construction

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

836 [spades] 0:00:00.108 83M / 554M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

837 [spades] 0:00:00.108 83M / 554M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

838 [spades] 0:00:00.108 83M / 554M INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

839 [spades] 0:00:00.108 83M / 554M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166534 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

840 [spades] 0:00:00.108 83M / 554M INFO General (kmer_splitters.hpp : 97) Using cell size of 58208

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

841 [spades] 0:00:00.181 2G / 2G INFO General (kmer_splitters.hpp : 364) Processed 8793 kmers

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

842 [spades] 0:00:00.181 2G / 2G INFO General (kmer_splitters.hpp : 369) Used 8793 kmers.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

843 [spades] 0:00:00.204 98M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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844 [spades] 0:00:00.221 98M / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8798 kmers in total.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

845 [spades] 0:00:00.221 98M / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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846 [spades] 0:00:00.227 98M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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847 [spades] 0:00:00.250 96M / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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848 [spades] 0:00:00.252 96M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 13136 bytes occupied (11.9445 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

849 [spades] 0:00:00.252 96M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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850 [spades] 0:00:00.256 96M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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851 [spades] 0:00:00.256 96M / 2G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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852 [spades] 0:00:00.256 96M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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853 [spades] 0:00:00.262 96M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 294 sequences extracted

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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854 [spades] 0:00:00.263 96M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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855 [spades] 0:00:00.264 96M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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856 [spades] 0:00:00.265 96M / 2G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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857 [spades] 0:00:00.265 96M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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858 [spades] 0:00:00.265 96M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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859 [spades] 0:00:00.276 97M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 8576 bytes occupied (7.80257 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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860 [spades] 0:00:00.276 97M / 2G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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861 [spades] 0:00:00.280 97M / 2G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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862 [spades] 0:00:00.282 97M / 2G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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863 [spades] 0:00:00.282 97M / 2G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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864 [spades] 0:00:00.283 97M / 2G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 32

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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865 [spades] 0:00:00.283 97M / 2G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 33. Coverage mad: 5.9304

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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866 [spades] 0:00:00.283 97M / 2G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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867 [spades] 0:00:00.289 97M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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868 [spades] 0:00:00.304 97M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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869 [spades] 0:00:00.356 97M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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870 [spades] 0:00:00.392 97M / 2G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 33.4369. Fitted coverage std. dev: 4.99367

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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871 [spades] 0:00:00.392 97M / 2G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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872 [spades] 0:00:00.393 97M / 2G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 23

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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873 [spades] 0:00:00.393 97M / 2G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 17

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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874 [spades] 0:00:00.393 97M / 2G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 1078

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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875 [spades] 0:00:00.393 97M / 2G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 33.4369

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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876 [spades] 0:00:00.393 97M / 2G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 17

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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877 [spades] 0:00:00.393 97M / 2G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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878 [spades] 0:00:00.394 97M / 2G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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879 [spades] 0:00:00.394 97M / 2G INFO General (graph_pack.hpp : 105) Index refill

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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880 [spades] 0:00:00.394 97M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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881 [spades] 0:00:00.394 97M / 2G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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882 [spades] 0:00:00.394 97M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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883 [spades] 0:00:00.395 97M / 2G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166468 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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884 [spades] 0:00:00.395 97M / 2G INFO General (kmer_splitters.hpp : 97) Using cell size of 58184

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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885 [spades] 0:00:00.459 2G / 2G INFO General (edge_index_builders.hpp : 82) Used 588 sequences.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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886 [spades] 0:00:00.476 113M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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887 [spades] 0:00:00.494 113M / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8793 kmers in total.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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888 [spades] 0:00:00.495 113M / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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889 [spades] 0:00:00.501 113M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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890 [spades] 0:00:00.521 113M / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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891 [spades] 0:00:00.523 113M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 13144 bytes occupied (11.9586 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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892 [spades] 0:00:00.523 113M / 2G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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893 [spades] 0:00:00.527 113M / 2G INFO General (edge_index.hpp : 92) Index refilled

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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894 [spades] 0:00:00.529 113M / 2G INFO General (gap_closer.cpp : 147) Preparing shift maps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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895 [spades] 0:00:00.529 113M / 2G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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896 [spades] 0:00:00.532 113M / 2G INFO General (gap_closer.cpp : 126) Used 23 paired reads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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897 [spades] 0:00:00.532 113M / 2G INFO General (gap_closer.cpp : 128) Merging paired indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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898 [spades] 0:00:00.533 113M / 2G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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899 [spades] 0:00:00.533 113M / 2G INFO GapCloser (gap_closer.cpp : 364) Closing short gaps complete: filled 0 gaps after checking 0 candidates

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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900 [spades] 0:00:00.537 113M / 2G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification

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901 [spades] 0:00:00.538 113M / 2G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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902 [spades] 0:00:00.538 113M / 2G INFO General (graph_simplification.hpp : 671) Flanking coverage based disconnection disabled

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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903 [spades] 0:00:00.538 113M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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904 [spades] 0:00:00.543 113M / 2G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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905 [spades] 0:00:00.543 113M / 2G INFO StageManager (stage.cpp : 166) STAGE == Simplification

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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906 [spades] 0:00:00.544 113M / 2G INFO General (simplification.cpp : 383) Graph simplification started

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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907 [spades] 0:00:00.544 113M / 2G INFO General (graph_simplification.hpp : 643) Creating parallel br instance

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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908 [spades] 0:00:00.544 113M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 1

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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909 [spades] 0:00:00.545 113M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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910 [spades] 0:00:00.549 113M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 132 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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911 [spades] 0:00:00.550 113M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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912 [spades] 0:00:00.555 113M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 8 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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913 [spades] 0:00:00.555 113M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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914 [spades] 0:00:00.558 113M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

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915 [spades] 0:00:00.559 113M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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916 [spades] 0:00:00.559 113M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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917 [spades] 0:00:00.559 113M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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918 [spades] 0:00:00.560 113M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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919 [spades] 0:00:00.560 113M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

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920 [spades] 0:00:00.560 113M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

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921 [spades] 0:00:00.561 113M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

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922 [spades] 0:00:00.561 113M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 3

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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923 [spades] 0:00:00.561 113M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

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924 [spades] 0:00:00.561 113M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

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987 [spades] 0:00:00.578 113M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

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992 [spades] 0:00:00.641 2G / 2G INFO General (edge_index_builders.hpp : 82) Used 26 sequences.

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993 [spades] 0:00:00.649 121M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

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994 [spades] 0:00:00.665 121M / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 2088 kmers in total.

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995 [spades] 0:00:00.665 121M / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

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996 [spades] 0:00:00.670 121M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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997 [spades] 0:00:00.688 121M / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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998 [spades] 0:00:00.689 121M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10200 bytes occupied (39.0805 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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999 [spades] 0:00:00.690 121M / 2G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1000 [spades] 0:00:00.693 121M / 2G INFO General (edge_index.hpp : 92) Index refilled

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1001 [spades] 0:00:00.695 121M / 2G INFO General (gap_closer.cpp : 147) Preparing shift maps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1002 [spades] 0:00:00.696 121M / 2G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1003 [spades] 0:00:00.698 121M / 2G INFO General (gap_closer.cpp : 126) Used 23 paired reads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1004 [spades] 0:00:00.699 121M / 2G INFO General (gap_closer.cpp : 128) Merging paired indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1005 [spades] 0:00:00.699 121M / 2G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1006 [spades] 0:00:00.699 121M / 2G INFO GapCloser (gap_closer.cpp : 364) Closing short gaps complete: filled 0 gaps after checking 0 candidates

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1007 [spades] 0:00:00.703 121M / 2G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1008 [spades] 0:00:00.704 121M / 2G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1009 [spades] 0:00:00.704 121M / 2G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1010 [spades] 0:00:00.705 121M / 2G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1011 [spades] 0:00:00.705 121M / 2G INFO General (graph_simplification.hpp : 643) Creating parallel br instance

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1012 [spades] 0:00:00.705 121M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1013 [spades] 0:00:00.708 121M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1014 [spades] 0:00:00.709 121M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1015 [spades] 0:00:00.713 121M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1016 [spades] 0:00:00.714 121M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1017 [spades] 0:00:00.718 121M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1018 [spades] 0:00:00.719 121M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1019 [spades] 0:00:00.720 121M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1020 [spades] 0:00:00.720 121M / 2G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1021 [spades] 0:00:00.721 121M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1022 [spades] 0:00:00.722 121M / 2G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 12 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1023 [spades] 0:00:00.722 121M / 2G INFO General (simplification.cpp : 496) Counting average coverage

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1024 [spades] 0:00:00.723 121M / 2G INFO General (simplification.cpp : 502) Average coverage = 31.9224

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1025 [spades] 0:00:00.723 121M / 2G INFO StageManager (stage.cpp : 166) STAGE == Contig Output

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1026 [spades] 0:00:00.724 121M / 2G INFO General (read_converter.cpp : 102) Outputting contigs to /home/piemari/shovill_bam/spades/K91/simplified_contigs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1027 [spades] 0:00:00.727 121M / 2G INFO General (binary_converter.cpp : 111) 1 reads written

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1028 [spades] 0:00:00.732 121M / 2G INFO General (pipeline.cpp : 259) SPAdes finished

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1029 [spades] 0:00:00.733 121M / 2G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 0 seconds

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1030 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1031 [spades] ===== K91 finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1032 [spades]

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1033 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1034 [spades] ===== K111 started.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1035 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1036 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1037 [spades] == Running: /home/piemari/apps/conda/envs/metaphlan/bin/spades-core /home/piemari/shovill_bam/spades/K111/configs/config.info /home/piemari/shovill_bam/spades/K111/configs/isolate_mode.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1038 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1039 [spades] WARNING: Try to use logger before create one. Level=INFO. Message=Additional contigs is /home/piemari/shovill_bam/spades/K91/simplified_contigs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1040 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K111/configs/config.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1041 [spades] 0:00:00.000 4M / 9M INFO General (main.cpp : 75) Loaded config from /home/piemari/shovill_bam/spades/K111/configs/isolate_mode.info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1042 [spades] 0:00:00.000 4M / 10M INFO General (memory_limit.cpp : 49) Memory limit set to 4 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1043 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 85) Starting SPAdes, built from N/A, git revision N/A

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1044 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 86) Maximum k-mer length: 128

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1045 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 87) Assembling dataset (/home/piemari/shovill_bam/spades/dataset.info) with K=111

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1046 [spades] 0:00:00.000 4M / 10M INFO General (main.cpp : 88) Maximum # of threads to use (adjusted due to OMP capabilities): 8

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1047 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 194) SPAdes started

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1048 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 201) Starting from stage: read_conversion

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1049 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 207) Two-step RR enabled: 0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1050 [spades] 0:00:00.000 4M / 10M INFO General (pipeline.cpp : 218) Will need read mapping, kmer mapper will be attached

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1051 [spades] 0:00:00.000 4M / 10M INFO StageManager (stage.cpp : 166) STAGE == Binary Read Conversion

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1052 [spades] 0:00:00.001 4M / 12M INFO General (read_converter.cpp : 53) Binary reads detected

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1053 [spades] 0:00:00.002 4M / 16M INFO StageManager (stage.cpp : 166) STAGE == de Bruijn graph construction

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1054 [spades] 0:00:00.002 4M / 16M INFO General (construction.cpp : 115) Contigs from previous K will be used: /home/piemari/shovill_bam/spades/K91/simplified_contigs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1055 [spades] 0:00:00.007 4M / 16M INFO General (construction.cpp : 150) Max read length 280

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1056 [spades] 0:00:00.007 4M / 16M INFO General (construction.cpp : 153) Max read length without merged 150

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1057 [spades] 0:00:00.007 4M / 16M INFO General (construction.cpp : 156) Average read length 193.032

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1058 [spades] 0:00:00.007 4M / 16M INFO General (stage.cpp : 113) PROCEDURE == k+1-mer counting

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1059 [spades] 0:00:00.007 4M / 16M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 64 files using 8 threads. This might take a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1060 [spades] 0:00:00.007 4M / 16M INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1061 [spades] 0:00:00.007 4M / 16M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166632 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1062 [spades] 0:00:00.007 4M / 16M INFO General (kmer_splitters.hpp : 97) Using cell size of 87363

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1063 [spades] 0:00:00.085 83M / 552M INFO General (kmer_splitters.hpp : 293) Used 868 reads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1064 [spades] 0:00:00.085 83M / 552M INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1065 [spades] 0:00:00.101 83M / 552M INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8451 kmers in total.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1066 [spades] 0:00:00.101 83M / 552M INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1067 [spades] 0:00:00.105 83M / 552M INFO General (stage.cpp : 113) PROCEDURE == Extension index construction

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1068 [spades] 0:00:00.105 83M / 552M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1069 [spades] 0:00:00.105 83M / 552M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1070 [spades] 0:00:00.105 83M / 552M INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1071 [spades] 0:00:00.105 83M / 552M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166533 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1072 [spades] 0:00:00.105 83M / 552M INFO General (kmer_splitters.hpp : 97) Using cell size of 43655

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1073 [spades] 0:00:00.179 2G / 2G INFO General (kmer_splitters.hpp : 364) Processed 8451 kmers

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1074 [spades] 0:00:00.180 2G / 2G INFO General (kmer_splitters.hpp : 369) Used 8451 kmers.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1075 [spades] 0:00:00.203 97M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1076 [spades] 0:00:00.220 99M / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8478 kmers in total.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1077 [spades] 0:00:00.220 99M / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1078 [spades] 0:00:00.226 99M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1079 [spades] 0:00:00.250 96M / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1080 [spades] 0:00:00.252 96M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 12992 bytes occupied (12.2595 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1081 [spades] 0:00:00.252 96M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1082 [spades] 0:00:00.257 96M / 2G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1083 [spades] 0:00:00.258 96M / 2G INFO General (stage.cpp : 113) PROCEDURE == Condensing graph

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1084 [spades] 0:00:00.258 96M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1085 [spades] 0:00:00.263 97M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 272 sequences extracted

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1086 [spades] 0:00:00.264 97M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1087 [spades] 0:00:00.265 97M / 2G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1088 [spades] 0:00:00.266 97M / 2G INFO General (stage.cpp : 113) PROCEDURE == Filling coverage indices (PHM)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1089 [spades] 0:00:00.266 97M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1090 [spades] 0:00:00.267 97M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1091 [spades] 0:00:00.280 97M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 8376 bytes occupied (7.929 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1092 [spades] 0:00:00.280 97M / 2G INFO General (construction.cpp : 429) Collecting k-mer coverage information from reads, this takes a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1093 [spades] 0:00:00.284 97M / 2G INFO General (construction.cpp : 549) Filling coverage and flanking coverage from PHM

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1094 [spades] 0:00:00.290 97M / 2G INFO StageManager (stage.cpp : 166) STAGE == EC Threshold Finding

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1095 [spades] 0:00:00.291 97M / 2G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1096 [spades] 0:00:00.291 97M / 2G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 28

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1097 [spades] 0:00:00.291 97M / 2G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 28. Coverage mad: 5.9304

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1098 [spades] 0:00:00.291 97M / 2G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1099 [spades] 0:00:00.297 97M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1100 [spades] 0:00:00.310 97M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1101 [spades] 0:00:00.342 97M / 2G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1102 [spades] 0:00:00.373 97M / 2G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 26.1152. Fitted coverage std. dev: 4.16511

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1103 [spades] 0:00:00.373 97M / 2G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.999998

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1104 [spades] 0:00:00.374 97M / 2G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 18

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1105 [spades] 0:00:00.374 97M / 2G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 14

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1106 [spades] 0:00:00.374 97M / 2G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 1059

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1107 [spades] 0:00:00.374 97M / 2G INFO General (genomic_info_filler.cpp : 53) Mean coverage was calculated as 26.1152

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1108 [spades] 0:00:00.374 97M / 2G INFO General (genomic_info_filler.cpp : 68) EC coverage threshold value was calculated as 14

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1109 [spades] 0:00:00.374 97M / 2G INFO General (genomic_info_filler.cpp : 69) Trusted kmer low bound: 0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1110 [spades] 0:00:00.375 97M / 2G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1111 [spades] 0:00:00.375 97M / 2G INFO General (graph_pack.hpp : 105) Index refill

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1112 [spades] 0:00:00.375 97M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1113 [spades] 0:00:00.375 97M / 2G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1114 [spades] 0:00:00.375 97M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1115 [spades] 0:00:00.376 97M / 2G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166477 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1116 [spades] 0:00:00.376 97M / 2G INFO General (kmer_splitters.hpp : 97) Using cell size of 43640

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1117 [spades] 0:00:00.444 2G / 2G INFO General (edge_index_builders.hpp : 82) Used 544 sequences.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1118 [spades] 0:00:00.465 105M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1119 [spades] 0:00:00.487 105M / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 8451 kmers in total.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1120 [spades] 0:00:00.487 105M / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1121 [spades] 0:00:00.493 105M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1122 [spades] 0:00:00.513 106M / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1123 [spades] 0:00:00.515 106M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 12976 bytes occupied (12.2835 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1124 [spades] 0:00:00.515 106M / 2G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1125 [spades] 0:00:00.518 106M / 2G INFO General (edge_index.hpp : 92) Index refilled

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1126 [spades] 0:00:00.524 106M / 2G INFO General (gap_closer.cpp : 147) Preparing shift maps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1127 [spades] 0:00:00.525 106M / 2G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1128 [spades] 0:00:00.527 106M / 2G INFO General (gap_closer.cpp : 126) Used 23 paired reads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1129 [spades] 0:00:00.527 106M / 2G INFO General (gap_closer.cpp : 128) Merging paired indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1130 [spades] 0:00:00.527 106M / 2G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1131 [spades] 0:00:00.528 106M / 2G INFO GapCloser (gap_closer.cpp : 364) Closing short gaps complete: filled 0 gaps after checking 0 candidates

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1132 [spades] 0:00:00.528 106M / 2G INFO StageManager (stage.cpp : 166) STAGE == Raw Simplification

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1133 [spades] 0:00:00.529 106M / 2G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1134 [spades] 0:00:00.529 106M / 2G INFO General (simplification.cpp : 63) Most init cleaning disabled on main iteration

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1135 [spades] 0:00:00.530 106M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1136 [spades] 0:00:00.530 106M / 2G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1137 [spades] 0:00:00.530 106M / 2G INFO StageManager (stage.cpp : 166) STAGE == Simplification

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1139 [spades] 0:00:00.531 106M / 2G INFO General (graph_simplification.hpp : 643) Creating parallel br instance

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1208 [spades] 0:00:00.550 106M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1209 [spades] 0:00:00.550 106M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1210 [spades] 0:00:00.550 106M / 2G INFO General (simplification.cpp : 388) PROCEDURE == Simplification cycle, iteration 11

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1211 [spades] 0:00:00.551 106M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1212 [spades] 0:00:00.553 106M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1213 [spades] 0:00:00.554 106M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1214 [spades] 0:00:00.558 106M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1215 [spades] 0:00:00.559 106M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1216 [spades] 0:00:00.564 106M / 2G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1217 [spades] 0:00:00.568 106M / 2G INFO StageManager (stage.cpp : 166) STAGE == Gap Closer

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1218 [spades] 0:00:00.569 106M / 2G INFO General (graph_pack.hpp : 105) Index refill

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1219 [spades] 0:00:00.569 106M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1220 [spades] 0:00:00.569 106M / 2G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 128 files using 8 threads. This might take a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1221 [spades] 0:00:00.570 106M / 2G INFO General (file_limit.hpp : 32) Open file limit set to 131072

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1222 [spades] 0:00:00.570 106M / 2G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.166454 Gb

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1223 [spades] 0:00:00.570 106M / 2G INFO General (kmer_splitters.hpp : 97) Using cell size of 43635

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1224 [spades] 0:00:00.631 2G / 2G INFO General (edge_index_builders.hpp : 82) Used 64 sequences.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1225 [spades] 0:00:00.641 119M / 2G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1226 [spades] 0:00:00.656 119M / 2G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 3182 kmers in total.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1227 [spades] 0:00:00.656 119M / 2G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1228 [spades] 0:00:00.661 119M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1229 [spades] 0:00:00.681 119M / 2G INFO General (kmer_index_builder.hpp : 150) Merging final buckets.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1230 [spades] 0:00:00.682 119M / 2G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10600 bytes occupied (26.6499 bits per kmer).

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1231 [spades] 0:00:00.683 119M / 2G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1232 [spades] 0:00:00.686 119M / 2G INFO General (edge_index.hpp : 92) Index refilled

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1233 [spades] 0:00:00.689 119M / 2G INFO General (gap_closer.cpp : 147) Preparing shift maps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1234 [spades] 0:00:00.689 119M / 2G INFO General (gap_closer.cpp : 107) Processing paired reads (takes a while)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1235 [spades] 0:00:00.691 119M / 2G INFO General (gap_closer.cpp : 126) Used 23 paired reads

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1236 [spades] 0:00:00.692 119M / 2G INFO General (gap_closer.cpp : 128) Merging paired indices

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1237 [spades] 0:00:00.692 119M / 2G INFO GapCloser (gap_closer.cpp : 332) Closing short gaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1238 [spades] 0:00:00.693 119M / 2G INFO GapCloser (gap_closer.cpp : 364) Closing short gaps complete: filled 0 gaps after checking 0 candidates

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1239 [spades] 0:00:00.693 119M / 2G INFO StageManager (stage.cpp : 166) STAGE == Simplification Cleanup

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1240 [spades] 0:00:00.694 119M / 2G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1241 [spades] 0:00:00.694 119M / 2G INFO General (graph_simplification.hpp : 456) Disconnection of relatively low covered edges disabled

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1242 [spades] 0:00:00.694 119M / 2G INFO General (graph_simplification.hpp : 493) Complex tip clipping disabled

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1243 [spades] 0:00:00.695 119M / 2G INFO General (graph_simplification.hpp : 643) Creating parallel br instance

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1244 [spades] 0:00:00.695 119M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1245 [spades] 0:00:00.695 119M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1246 [spades] 0:00:00.696 119M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1247 [spades] 0:00:00.696 119M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1248 [spades] 0:00:00.697 119M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1249 [spades] 0:00:00.697 119M / 2G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1250 [spades] 0:00:00.697 119M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1251 [spades] 0:00:00.698 119M / 2G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1252 [spades] 0:00:00.698 119M / 2G INFO General (simplification.cpp : 343) Disrupting self-conjugate edges

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1253 [spades] 0:00:00.698 119M / 2G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1254 [spades] 0:00:00.700 119M / 2G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 31 times

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1255 [spades] 0:00:00.701 119M / 2G INFO General (simplification.cpp : 496) Counting average coverage

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1256 [spades] 0:00:00.701 119M / 2G INFO General (simplification.cpp : 502) Average coverage = 25.1649

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1257 [spades] 0:00:00.701 119M / 2G INFO StageManager (stage.cpp : 166) STAGE == Mismatch Correction

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1258 [spades] 0:00:00.701 119M / 2G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 1220 kmers to process

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1259 [spades] 0:00:00.702 119M / 2G INFO General (graph_pack.hpp : 115) Normalizing done

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1260 [spades] 0:00:00.714 119M / 2G INFO General (mismatch_shall_not_pass.hp: 195) Finished collecting potential mismatches positions

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1261 [spades] 0:00:00.714 119M / 2G INFO General (mismatch_shall_not_pass.hp: 310) All edges processed

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1262 [spades] 0:00:00.715 119M / 2G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1263 [spades] 0:00:00.715 119M / 2G INFO StageManager (stage.cpp : 166) STAGE == Contig Output

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1264 [spades] 0:00:00.716 119M / 2G INFO General (contig_output.hpp : 21) Outputting contigs to /home/piemari/shovill_bam/spades/K111/before_rr.fasta

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1265 [spades] 0:00:00.719 119M / 2G INFO General (contig_output_stage.cpp : 146) Writing GFA graph to /home/piemari/shovill_bam/spades/K111/assembly_graph_after_simplification.gfa

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1266 [spades] 0:00:00.719 119M / 2G INFO StageManager (stage.cpp : 166) STAGE == Paired Information Counting

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1267 [spades] 0:00:00.719 119M / 2G INFO General (graph_pack.hpp : 113) Normalizing k-mer map. Total 1220 kmers to process

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1268 [spades] 0:00:00.720 119M / 2G INFO General (graph_pack.hpp : 115) Normalizing done

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1269 [spades] 0:00:00.720 119M / 2G INFO General (pair_info_count.cpp : 322) Min edge length for estimation: 1140

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1270 [spades] 0:00:00.720 119M / 2G INFO General (pair_info_count.cpp : 333) Estimating insert size for library #0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1271 [spades] 0:00:00.720 119M / 2G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1272 [spades] 0:00:00.763 263M / 2G INFO General (pair_info_count.cpp : 39) Selecting usual mapper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1273 [spades] 0:00:00.967 263M / 2G INFO General (sequence_mapper_notifier.h: 94) Total 410 reads processed

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1274 [spades] 0:00:01.259 263M / 2G INFO General (pair_info_count.cpp : 208) Edge pairs: 2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1275 [spades] 0:00:01.261 263M / 2G INFO General (pair_info_count.cpp : 210) 334 paired reads (81.4634% of all) aligned to long edges

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1276 [spades] 0:00:01.263 119M / 2G INFO General (pair_info_count.cpp : 352) Insert size = 201.347, deviation = 42.1646, left quantile = 150, right quantile = 261, read length = 150

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1277 [spades] 0:00:01.263 119M / 2G INFO General (pair_info_count.cpp : 373) Filtering data for library #0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1278 [spades] 0:00:01.266 119M / 2G INFO General (pair_info_count.cpp : 39) Selecting usual mapper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1279 [spades] 0:00:01.268 119M / 2G INFO General (sequence_mapper_notifier.h: 94) Total 410 reads processed

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1280 [spades] 0:00:01.268 119M / 2G INFO General (pair_info_count.cpp : 385) Mapping library #0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1281 [spades] 0:00:01.269 119M / 2G INFO General (pair_info_count.cpp : 387) Mapping paired reads (takes a while)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1282 [spades] 0:00:01.269 119M / 2G INFO General (pair_info_count.cpp : 285) Left insert size quantile 150, right insert size quantile 261, filtering threshold 2, rounding threshold 0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1283 [spades] 0:00:01.277 119M / 2G INFO General (pair_info_count.cpp : 39) Selecting usual mapper

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1284 [spades] 0:00:01.280 119M / 2G INFO General (sequence_mapper_notifier.h: 94) Total 410 reads processed

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1285 [spades] 0:00:01.283 119M / 2G INFO StageManager (stage.cpp : 166) STAGE == Distance Estimation

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1286 [spades] 0:00:01.283 119M / 2G INFO General (distance_estimation.cpp : 174) Processing library #0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1287 [spades] 0:00:01.284 119M / 2G INFO General (distance_estimation.cpp : 150) Weight Filter Done

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1288 [spades] 0:00:01.284 119M / 2G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1289 [spades] 0:00:01.286 119M / 2G INFO General (distance_estimation.cpp : 35) Filtering info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1290 [spades] 0:00:01.287 119M / 2G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1291 [spades] 0:00:01.287 119M / 2G INFO General (pair_info_filters.hpp : 263) Done filtering

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1292 [spades] 0:00:01.287 119M / 2G INFO General (distance_estimation.cpp : 157) Refining clustered pair information

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1293 [spades] 0:00:01.287 119M / 2G INFO General (distance_estimation.cpp : 159) The refining of clustered pair information has been finished

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1294 [spades] 0:00:01.288 119M / 2G INFO General (distance_estimation.cpp : 161) Improving paired information

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1295 [spades] 0:00:01.288 119M / 2G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1296 [spades] 0:00:01.289 119M / 2G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1297 [spades] 0:00:01.289 119M / 2G INFO General (distance_estimation.cpp : 104) Filling scaffolding index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1298 [spades] 0:00:01.290 119M / 2G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1299 [spades] 0:00:01.290 119M / 2G INFO General (distance_estimation.cpp : 35) Filtering info

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1300 [spades] 0:00:01.290 119M / 2G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1301 [spades] 0:00:01.291 119M / 2G INFO General (pair_info_filters.hpp : 263) Done filtering

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1302 [spades] 0:00:01.291 119M / 2G INFO General (distance_estimation.cpp : 183) Clearing raw paired index

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1303 [spades] 0:00:01.291 119M / 2G INFO StageManager (stage.cpp : 166) STAGE == Repeat Resolving

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1304 [spades] 0:00:01.291 119M / 2G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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diff changeset

1305 [spades] 0:00:01.292 119M / 2G INFO General (launcher.cpp : 538) ExSPAnder repeat resolving tool started

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1306 [spades] 0:00:01.293 119M / 2G INFO General (launcher.cpp : 404) Creating main extenders, unique edge length = 2000

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1307 [spades] 0:00:01.293 119M / 2G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #0 is 25.1649

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1308 [spades] 0:00:01.293 119M / 2G INFO General (extenders_logic.cpp : 311) Estimated coverage of library #0 is 25.1649

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1309 [spades] 0:00:01.294 119M / 2G INFO General (extenders_logic.cpp : 519) Using 1 paired-end library

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1310 [spades] 0:00:01.294 119M / 2G INFO General (extenders_logic.cpp : 520) Using 1 paired-end scaffolding library

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1311 [spades] 0:00:01.294 119M / 2G INFO General (extenders_logic.cpp : 521) Using 0 single read libraries

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1312 [spades] 0:00:01.294 119M / 2G INFO General (launcher.cpp : 432) Total number of extenders is 3

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1313 [spades] 0:00:01.294 119M / 2G INFO General (launcher.cpp : 244) Finalizing paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1314 [spades] 0:00:01.295 119M / 2G INFO General (launcher.cpp : 246) Deduplicating paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1315 [spades] 0:00:01.295 119M / 2G INFO General (launcher.cpp : 250) Paths deduplicated

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1316 [spades] 0:00:01.295 119M / 2G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1317 [spades] 0:00:01.295 119M / 2G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1318 [spades] 0:00:01.295 119M / 2G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1319 [spades] 0:00:01.295 119M / 2G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1320 [spades] 0:00:01.296 119M / 2G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1321 [spades] 0:00:01.296 119M / 2G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1322 [spades] 0:00:01.296 119M / 2G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1323 [spades] 0:00:01.296 119M / 2G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1324 [spades] 0:00:01.296 119M / 2G INFO General (launcher.cpp : 267) Paths finalized

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1325 [spades] 0:00:01.296 119M / 2G INFO General (launcher.cpp : 439) Closing gaps in paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1326 [spades] 0:00:01.297 119M / 2G INFO General (launcher.cpp : 467) Gap closing completed

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1327 [spades] 0:00:01.297 119M / 2G INFO General (launcher.cpp : 296) Traversing tandem repeats

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1328 [spades] 0:00:01.297 119M / 2G INFO General (launcher.cpp : 306) Traversed 0 loops

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1329 [spades] 0:00:01.297 119M / 2G INFO General (launcher.cpp : 244) Finalizing paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1330 [spades] 0:00:01.297 119M / 2G INFO General (launcher.cpp : 246) Deduplicating paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1331 [spades] 0:00:01.298 119M / 2G INFO General (launcher.cpp : 250) Paths deduplicated

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1332 [spades] 0:00:01.298 119M / 2G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1333 [spades] 0:00:01.298 119M / 2G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1334 [spades] 0:00:01.298 119M / 2G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1335 [spades] 0:00:01.298 119M / 2G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1336 [spades] 0:00:01.298 119M / 2G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1337 [spades] 0:00:01.299 119M / 2G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1338 [spades] 0:00:01.299 119M / 2G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1339 [spades] 0:00:01.299 119M / 2G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1340 [spades] 0:00:01.299 119M / 2G INFO General (launcher.cpp : 267) Paths finalized

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1341 [spades] 0:00:01.299 119M / 2G INFO General (launcher.cpp : 596) ExSPAnder repeat resolving tool finished

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1342 [spades] 0:00:01.299 119M / 2G INFO StageManager (stage.cpp : 166) STAGE == Contig Output

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1343 [spades] 0:00:01.300 119M / 2G INFO General (contig_output.hpp : 21) Outputting contigs to /home/piemari/shovill_bam/spades/K111/before_rr.fasta

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1344 [spades] 0:00:01.302 119M / 2G INFO General (contig_output_stage.cpp : 146) Writing GFA graph to /home/piemari/shovill_bam/spades/K111/assembly_graph_with_scaffolds.gfa

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1345 [spades] 0:00:01.302 119M / 2G INFO General (contig_output_stage.cpp : 160) Outputting FastG graph to /home/piemari/shovill_bam/spades/K111/assembly_graph.fastg

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1346 [spades] 0:00:01.304 119M / 2G INFO General (contig_output_stage.cpp : 190) Breaking scaffolds

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1347 [spades] 0:00:01.304 119M / 2G INFO General (contig_output_stage.cpp : 95) Outputting contigs to /home/piemari/shovill_bam/spades/K111/final_contigs.fasta

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1348 [spades] 0:00:01.306 119M / 2G INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /home/piemari/shovill_bam/spades/K111/final_contigs.paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

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1349 [spades] 0:00:01.307 119M / 2G INFO General (contig_output_stage.cpp : 95) Outputting contigs to /home/piemari/shovill_bam/spades/K111/scaffolds.fasta

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1350 [spades] 0:00:01.308 119M / 2G INFO General (contig_output_stage.cpp : 101) Outputting FastG paths to /home/piemari/shovill_bam/spades/K111/scaffolds.paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1351 [spades] 0:00:01.310 119M / 2G INFO General (contig_output_stage.cpp : 108) Populating GFA with scaffold paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1352 [spades] 0:00:01.312 119M / 2G INFO General (pipeline.cpp : 259) SPAdes finished

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1353 [spades] 0:00:01.313 116M / 2G INFO General (main.cpp : 107) Assembling time: 0 hours 0 minutes 1 seconds

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1354 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1355 [spades] ===== K111 finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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diff changeset

1356 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1357 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1358 [spades] ===== Copy files started.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1359 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1360 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1361 [spades] == Running: /home/piemari/apps/conda/envs/metaphlan/bin/python /home/piemari/apps/conda/envs/metaphlan/share/spades/spades_pipeline/scripts/copy_files.py /home/piemari/shovill_bam/spades/K111/before_rr.fasta /home/piemari/shovill_bam/spades/before_rr.fasta /home/piemari/shovill_bam/spades/K111/assembly_graph_after_simplification.gfa /home/piemari/shovill_bam/spades/assembly_graph_after_simplification.gfa /home/piemari/shovill_bam/spades/K111/final_contigs.fasta /home/piemari/shovill_bam/spades/contigs.fasta /home/piemari/shovill_bam/spades/K111/first_pe_contigs.fasta /home/piemari/shovill_bam/spades/first_pe_contigs.fasta /home/piemari/shovill_bam/spades/K111/strain_graph.gfa /home/piemari/shovill_bam/spades/strain_graph.gfa /home/piemari/shovill_bam/spades/K111/scaffolds.fasta /home/piemari/shovill_bam/spades/scaffolds.fasta /home/piemari/shovill_bam/spades/K111/scaffolds.paths /home/piemari/shovill_bam/spades/scaffolds.paths /home/piemari/shovill_bam/spades/K111/assembly_graph_with_scaffolds.gfa /home/piemari/shovill_bam/spades/assembly_graph_with_scaffolds.gfa /home/piemari/shovill_bam/spades/K111/assembly_graph.fastg /home/piemari/shovill_bam/spades/assembly_graph.fastg /home/piemari/shovill_bam/spades/K111/final_contigs.paths /home/piemari/shovill_bam/spades/contigs.paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1362 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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diff changeset

1363 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1364 [spades] ===== Copy files finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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diff changeset

1365 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1366 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1367 [spades] ===== Assembling finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1368 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1369 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1370 [spades] ===== Breaking scaffolds started.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1371 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1372 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1373 [spades] == Running: /home/piemari/apps/conda/envs/metaphlan/bin/python /home/piemari/apps/conda/envs/metaphlan/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /home/piemari/shovill_bam/spades/scaffolds.fasta --misc_dir /home/piemari/shovill_bam/spades/misc --threshold_for_breaking_scaffolds 3

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1374 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1375 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1376 [spades] ===== Breaking scaffolds finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1377 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1378 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1379 [spades] ===== Terminate started.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1380 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1381 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1382 [spades] ===== Terminate finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1383 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1384 [spades] * Assembled contigs are in /home/piemari/shovill_bam/spades/contigs.fasta

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1385 [spades] * Assembled scaffolds are in /home/piemari/shovill_bam/spades/scaffolds.fasta

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1386 [spades] * Paths in the assembly graph corresponding to the contigs are in /home/piemari/shovill_bam/spades/contigs.paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1387 [spades] * Paths in the assembly graph corresponding to the scaffolds are in /home/piemari/shovill_bam/spades/scaffolds.paths

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1388 [spades] * Assembly graph is in /home/piemari/shovill_bam/spades/assembly_graph.fastg

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1389 [spades] * Assembly graph in GFA format is in /home/piemari/shovill_bam/spades/assembly_graph_with_scaffolds.gfa

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1390 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1391 [spades] ======= SPAdes pipeline finished.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1392 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1393 [spades] SPAdes log can be found here: /home/piemari/shovill_bam/spades/spades.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1394 [spades]

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1395 [spades] Thank you for using SPAdes!

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1396 [shovill] Checking for assembly errors in spades.fasta

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1397 [shovill] Running: bwa index spades.fasta 2>&1 | sed 's/^/[bwa-index] /' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1398 [bwa-index] [bwa_index] Pack FASTA... 0.00 sec

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1399 [bwa-index] [bwa_index] Construct BWT for the packed sequence...

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1400 [bwa-index] [bwa_index] 0.00 seconds elapse.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1401 [bwa-index] [bwa_index] Update BWT... 0.00 sec

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1402 [bwa-index] [bwa_index] Pack forward-only FASTA... 0.00 sec

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1403 [bwa-index] [bwa_index] Construct SA from BWT and Occ... 0.00 sec

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1404 [bwa-index] [main] Version: 0.7.17-r1188

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1405 [bwa-index] [main] CMD: bwa index spades.fasta

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1406 [bwa-index] [main] Real time: 0.012 sec; CPU: 0.004 sec

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1407 [shovill] Running: samtools faidx spades.fasta 2>&1 | sed 's/^/[faidx] /' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1408 [shovill] Running: (bwa mem -v 3 -x intractg -t 8 spades.fasta R1.fq.gz R2.fq.gz | samclip --ref spades.fasta.fai | samtools sort --threads 2 -m 1024m --reference spades.fasta -T /tmp -o shovill.bam) 2>&1 | sed 's/^/[bwa+samtools-sort] /' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1409 [bwa+samtools-sort] [M::bwa_idx_load_from_disk] read 0 ALT contigs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1410 [bwa+samtools-sort] [M::process] read 820 sequences (123000 bp)...

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1411 [bwa+samtools-sort] [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 410, 0, 0)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1412 [bwa+samtools-sort] [M::mem_pestat] skip orientation FF as there are not enough pairs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1413 [bwa+samtools-sort] [M::mem_pestat] analyzing insert size distribution for orientation FR...

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1414 [bwa+samtools-sort] [M::mem_pestat] (25, 50, 75) percentile: (163, 197, 230)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1415 [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (29, 364)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1416 [bwa+samtools-sort] [M::mem_pestat] mean and std.dev: (200.81, 42.23)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1417 [bwa+samtools-sort] [M::mem_pestat] low and high boundaries for proper pairs: (1, 431)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1418 [bwa+samtools-sort] [M::mem_pestat] skip orientation RF as there are not enough pairs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1419 [bwa+samtools-sort] [M::mem_pestat] skip orientation RR as there are not enough pairs

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1420 [bwa+samtools-sort] [M::mem_process_seqs] Processed 820 reads in 0.101 CPU sec, 0.021 real sec

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1421 [bwa+samtools-sort] [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1422 [bwa+samtools-sort] [samclip] Loading: spades.fasta.fai

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1423 [bwa+samtools-sort] [samclip] Found 1 sequences in spades.fasta.fai

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1424 [bwa+samtools-sort] [main] Version: 0.7.17-r1188

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1425 [bwa+samtools-sort] [main] CMD: bwa mem -v 3 -x intractg -t 8 spades.fasta R1.fq.gz R2.fq.gz

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1426 [bwa+samtools-sort] [main] Real time: 0.053 sec; CPU: 0.107 sec

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1427 [bwa+samtools-sort] [samclip] Total SAM records 820, removed 63, allowed 123, passed 757

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1428 [bwa+samtools-sort] [samclip] Header contained 2 lines

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1429 [bwa+samtools-sort] [samclip] Done.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1430 [bwa+samtools-sort] [bam_sort_core] merging from 0 files and 2 in-memory blocks...

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1431 [shovill] Running: samtools index shovill.bam 2>&1 | sed 's/^/[samtools-index] /' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1432 [shovill] Correcting errors in spades.fasta

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1433 [shovill] Running: pilon --genome spades.fasta --frags shovill.bam --minmq 60 --minqual 3 --fix bases --output pilon --threads 8 --changes --mindepth 0.25 2>&1 | sed 's/^/[pilon] /' | tee -a shovill.log

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1434 [pilon] Picked up _JAVA_OPTIONS: -Xmx4g

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1435 [pilon] Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1436 [pilon] --threads argument no longer supported; ignoring!

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1437 [pilon] Genome: spades.fasta

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1438 [pilon] Fixing snps, indels

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1439 [pilon] Input genome size: 1251

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1440 [pilon] Processing NODE_1_length_1251_cov_25.164912:1-1251

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1441 [pilon] frags shovill.bam: coverage 79

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1442 [pilon] Total Reads: 757, Coverage: 79, minDepth: 20

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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1443 [pilon] Confirmed 1152 of 1251 bases (92,09%)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

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1444 [pilon] Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1445 [pilon] NODE_1_length_1251_cov_25.164912:1-1251 log:

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1446 [pilon] Finished processing NODE_1_length_1251_cov_25.164912:1-1251

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1447 [pilon] Writing NODE_1_length_1251_cov_25.164912:1-1251 changes to pilon.changes

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1448 [pilon] Writing updated NODE_1_length_1251_cov_25.164912_pilon to pilon.fasta

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1449 [pilon] Mean frags coverage: 79

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1450 [pilon] Mean total coverage: 79

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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diff changeset

1451 [shovill] Repaired 0 contigs from spades.fasta at 0 positions.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

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1452 [shovill] Assembly is 1251, estimated genome size was 1188 (+5.30%)

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1453 [shovill] Using genome graph file 'spades/assembly_graph_with_scaffolds.gfa' => 'contigs.gfa'

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1454 [shovill] Walltime used: 0 min 10 sec

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1455 [shovill] Results in: /home/piemari/shovill_bam

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1456 [shovill] Final assembly graph: /home/piemari/shovill_bam/contigs.gfa

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1457 [shovill] Final assembly contigs: /home/piemari/shovill_bam/contigs.fa

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1458 [shovill] It contains 1 (min=75) contigs totalling 1251 bp.

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

parents:

diff changeset

1459 [shovill] Have a suggestion for shovill? Tell me at https://github.com/tseemann/shovill/issues

ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445

iuc

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diff changeset

1460 [shovill] Done.

Mercurial > repos > iuc > shovill

annotate test-data/shovill_std_log @ 8:ad80238462c1 draft