script: nanopore~flye-sickle_se "$scriptdir"/nanopore~sickle_se
centos:centos6 quay.io/biocontainers/fastqc:0.11.8--1 quay.io/biocontainers/flye:2.4--py27ha92aebf_0 quay.io/biocontainers/sickle-trim:1.33--ha92aebf_4
using docker
+ set -o pipefail
+ bash /data/user2/work/81/nanopore~sickle_se -c 8 -m 67108864 -s '-t sanger -q 15 -l 2000' input_1/
centos:centos6 quay.io/biocontainers/fastqc:0.11.8--1 quay.io/biocontainers/flye:2.4--py27ha92aebf_0 quay.io/biocontainers/sickle-trim:1.33--ha92aebf_4
using docker
+ set -o pipefail
++ find input_1//
++ egrep '[.]f(ast|)q$'
+ cat input_1//out-20171105_1126_171105_Loman_Ecoli.fastq
+ docker run -v /data/user2/work/81:/data/user2/work/81 -w /data/user2/work/81 -u root -i --rm quay.io/biocontainers/fastqc:0.11.8--1 fastqc -t 8 --extract input.fastq
Started analysis of input.fastq
Approx 5% complete for input.fastq
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Approx 20% complete for input.fastq
Approx 35% complete for input.fastq
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Approx 55% complete for input.fastq
Approx 70% complete for input.fastq
Approx 80% complete for input.fastq
Approx 95% complete for input.fastq
Analysis complete for input.fastq
+ rm -f input.fastq
+ xargs -I '{}' -P 8 bash -c '{}'
++ find input_1//
++ egrep '[.]f(ast|)q$'
+ for i in '`find $input_1/|egrep "[.]f(ast|)q$"`'
+ echo docker run -v '$PWD:$PWD' -w '$PWD' -u root -i --rm quay.io/biocontainers/sickle-trim:1.33--ha92aebf_4 sickle se -f input_1//out-20171105_1126_171105_Loman_Ecoli.fastq -o input_1//out-20171105_1126_171105_Loman_Ecoli.fastq.sickle -t sanger -q 15 -l 2000

FastQ records kept: 4961
FastQ records discarded: 4388

+ cat input_1//out-20171105_1126_171105_Loman_Ecoli.fastq.sickle
+ docker run -v /data/user2/work/81:/data/user2/work/81 -w /data/user2/work/81 -u root -i --rm quay.io/biocontainers/fastqc:0.11.8--1 fastqc -t 8 --extract output.sickle.fastq
Started analysis of output.sickle.fastq
Approx 10% complete for output.sickle.fastq
Approx 30% complete for output.sickle.fastq
Approx 55% complete for output.sickle.fastq
Approx 75% complete for output.sickle.fastq
Analysis complete for output.sickle.fastq
+ rm -f input_1/out-20171105_1126_171105_Loman_Ecoli.fastq.sickle
+ post_processing
+ '[' 2 = 1 ']'
+ exit
+ docker run -v /data/user2/work/81:/data/user2/work/81 -w /data/user2/work/81 -u root -i --rm quay.io/biocontainers/flye:2.4--py27ha92aebf_0 flye --nano-raw output.sickle.fastq --out-dir output.flye --threads 8 --genome-size 10M
[2019-09-06 08:49:43] INFO: Starting Flye 2.4-release
[2019-09-06 08:49:43] INFO: >>>STAGE: configure
[2019-09-06 08:49:43] INFO: Configuring run
[2019-09-06 08:49:43] INFO: Input genome size: 10000000
[2019-09-06 08:49:43] INFO: Estimated coverage: 7
[2019-09-06 08:49:43] INFO: Reads N50/N90: 25366 / 5928
[2019-09-06 08:49:43] INFO: Minimum overlap set to 5000
[2019-09-06 08:49:43] INFO: Selected k-mer size: 15
[2019-09-06 08:49:43] INFO: >>>STAGE: assembly
[2019-09-06 08:49:43] INFO: Assembling reads
[2019-09-06 08:49:43] INFO: Reading sequences
[2019-09-06 08:49:43] INFO: Generating solid k-mer index
[2019-09-06 08:50:01] INFO: Counting kmers (1/2):
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[2019-09-06 08:50:02] INFO: Counting kmers (2/2):
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[2019-09-06 08:50:06] WARNING: Unable to separate erroneous k-mers from solid k-mers. Possible reasons: 
	(1) Incorrect expected assembly size parameter 
	(2) Highly uneven coverage of the assembly 
	(3) Running with error-corrected reads in raw reads mode
	Assembly will continue, but results might not be optimal
[2019-09-06 08:50:06] INFO: Filling index table
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[2019-09-06 08:50:11] INFO: Extending reads
[2019-09-06 08:50:53] INFO: Overlap-based coverage: 11
[2019-09-06 08:50:53] INFO: Median overlap divergence: 0.119044
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[2019-09-06 08:51:14] INFO: Assembled 26 draft contigs
[2019-09-06 08:51:14] INFO: Generating contig sequences
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[2019-09-06 08:51:54] INFO: >>>STAGE: consensus
[2019-09-06 08:51:54] INFO: Running Minimap2
[2019-09-06 08:52:06] INFO: Computing consensus
[2019-09-06 08:53:34] INFO: Alignment error rate: 0.17155453639
[2019-09-06 08:53:34] INFO: >>>STAGE: repeat
[2019-09-06 08:53:34] INFO: Building and resolving repeat graph
[2019-09-06 08:53:34] INFO: Reading sequences
[2019-09-06 08:53:34] INFO: Building repeat graph
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[2019-09-06 08:54:06] INFO: Median overlap divergence: 0.119365
[2019-09-06 08:54:06] INFO: Aligning reads to the graph
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[2019-09-06 08:54:37] INFO: Aligned read sequence: 64646194 / 65381103 (0.98876)
[2019-09-06 08:54:37] INFO: Median overlap divergence: 0.0813888
[2019-09-06 08:54:38] INFO: Mean edge coverage: 14
[2019-09-06 08:54:38] INFO: Resolving repeats
[2019-09-06 08:54:38] INFO: >>>STAGE: trestle
[2019-09-06 08:54:38] INFO: Simple unbridged repeats: 0
[2019-09-06 08:54:38] INFO: Resolved: 0
[2019-09-06 08:54:38] INFO: >>>STAGE: contigger
[2019-09-06 08:54:38] INFO: Generating contigs
[2019-09-06 08:54:38] INFO: Reading sequences
[2019-09-06 08:54:39] INFO: Generated 5 contigs
[2019-09-06 08:54:39] INFO: >>>STAGE: polishing
[2019-09-06 08:54:39] INFO: Polishing genome (1/1)
[2019-09-06 08:54:39] INFO: Running minimap2
[2019-09-06 08:54:45] INFO: Separating alignment into bubbles
[2019-09-06 08:56:21] INFO: Alignment error rate: 0.152418908582
[2019-09-06 08:56:21] INFO: Correcting bubbles
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[2019-09-06 08:57:45] INFO: >>>STAGE: finalize
[2019-09-06 08:57:45] INFO: Assembly statistics:

	Total length:	4703774
	Contigs:	5
	Scaffolds:	5
	Scaffolds N50:	4655002
	Largest scf:	4655002
	Mean coverage:	14

[2019-09-06 08:57:45] INFO: Final assembly: /data/user2/work/81/output.flye/scaffolds.fasta
+ post_processing
+ '[' 1 = 1 ']'
+ '[' 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' = 'docker run -v $PWD:$PWD -w $PWD -u root -i --rm ' ']'
+ docker run -v /data/user2/work/81:/data/user2/work/81 -w /data/user2/work/81 -u root -i --rm centos:centos6 chmod -R a=rXw .
+ echo 0
+ exit