c2997108/centos6:2-flye-2.4.2-release-3 centos:centos6
using docker
+ set -o pipefail
++ find input_1/
++ egrep '[.]f(ast|)q$'
+ cat input_1/output.sickle.fastq
+ docker run -v /data/user2/work/84:/data/user2/work/84 -w /data/user2/work/84 -u root -i --rm c2997108/centos6:2-flye-2.4.2-release-3 flye --nano-raw all.fastq --out-dir output --threads 8 --genome-size 10M
[2019-09-06 08:54:36] INFO: Starting Flye 2.4.2-release
[2019-09-06 08:54:36] INFO: >>>STAGE: configure
[2019-09-06 08:54:36] INFO: Configuring run
[2019-09-06 08:54:36] INFO: Total read length: 65381103
[2019-09-06 08:54:36] INFO: Input genome size: 10000000
[2019-09-06 08:54:36] INFO: Estimated coverage: 6
[2019-09-06 08:54:36] INFO: Reads N50/N90: 28370 / 8124
[2019-09-06 08:54:36] INFO: Minimum overlap set to 5000
[2019-09-06 08:54:36] INFO: Selected k-mer size: 15
[2019-09-06 08:54:36] INFO: >>>STAGE: assembly
[2019-09-06 08:54:36] INFO: Assembling disjointigs
[2019-09-06 08:54:37] INFO: Reading sequences
[2019-09-06 08:54:37] INFO: Generating solid k-mer index
[2019-09-06 08:54:55] INFO: Counting k-mers (1/2):
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2019-09-06 08:54:57] INFO: Counting k-mers (2/2):
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2019-09-06 08:55:00] 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 08:55:00] INFO: Filling index table
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2019-09-06 08:55:05] INFO: Extending reads
[2019-09-06 08:55:43] INFO: Overlap-based coverage: 10
[2019-09-06 08:55:43] INFO: Median overlap divergence: 0.120416
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2019-09-06 08:56:02] INFO: Assembled 69 disjointigs
[2019-09-06 08:56:02] INFO: Generating sequence
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2019-09-06 08:56:47] INFO: >>>STAGE: consensus
[2019-09-06 08:56:47] INFO: Running Minimap2
[2019-09-06 08:57:01] INFO: Computing consensus
[2019-09-06 08:57:41] INFO: Alignment error rate: 0.163103812516
[2019-09-06 08:57:41] INFO: >>>STAGE: repeat
[2019-09-06 08:57:41] INFO: Building and resolving repeat graph
[2019-09-06 08:57:41] INFO: Reading sequences
[2019-09-06 08:57:41] INFO: Building repeat graph
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2019-09-06 08:58:28] INFO: Median overlap divergence: 0.138254
[2019-09-06 08:58:28] INFO: Aligning reads to the graph
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2019-09-06 08:59:00] INFO: Aligned read sequence: 64258546 / 65381103 (0.982831)
[2019-09-06 08:59:00] INFO: Median overlap divergence: 0.0893004
[2019-09-06 08:59:00] INFO: Mean edge coverage: 13
[2019-09-06 08:59:00] INFO: Resolving repeats
[2019-09-06 08:59:01] INFO: >>>STAGE: trestle
[2019-09-06 08:59:01] INFO: Simple unbridged repeats: 0
[2019-09-06 08:59:01] INFO: Resolved: 0
[2019-09-06 08:59:01] INFO: >>>STAGE: contigger
[2019-09-06 08:59:01] INFO: Generating contigs
[2019-09-06 08:59:01] INFO: Reading sequences
[2019-09-06 08:59:02] INFO: Generated 20 contigs
[2019-09-06 08:59:02] INFO: >>>STAGE: polishing
[2019-09-06 08:59:02] INFO: Polishing genome (1/1)
[2019-09-06 08:59:02] INFO: Running minimap2
[2019-09-06 08:59:10] INFO: Separating alignment into bubbles
[2019-09-06 08:59:42] INFO: Alignment error rate: 0.161113900819
[2019-09-06 08:59:42] INFO: Correcting bubbles
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2019-09-06 09:01:18] INFO: >>>STAGE: finalize
[2019-09-06 09:01:18] INFO: Assembly statistics:

	Total length:	4689029
	Fragments:	16
	Fragments N50:	4588463
	Largest frg:	4588463
	Scaffolds:	0
	Mean coverage:	14

[2019-09-06 09:01:18] INFO: Final assembly: /data/user2/work/84/output/assembly.fasta
+ rm -f all.fastq
+ 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/84:/data/user2/work/84 -w /data/user2/work/84 -u root -i --rm centos:centos6 chmod -R a=rXw .
+ echo 0
+ exit