view test-data/res_files/report.txt @ 74:fe3a93edb210 draft default tip

planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit b10ab97380b0f2f5850138b9ddc03cd6afae1a9d
author brasset_jensen
date Fri, 30 Sep 2022 14:46:12 +0000
parents 11708af40030
children
line wrap: on
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Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35115.dat_symlink.fa
Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35114.dat_symlink.fa
Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35112.dat_symlink.fa
Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35113.dat_symlink.fa
Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35116.dat_symlink.fa
Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35118.dat_symlink.fa
Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35111.dat_symlink.fa
-----------------------------
bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35115.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/dataset_35773_18-29.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35115.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/dataset_35773_18-29.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam'
Parsing /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam file
	reads: 4610
	mappers: 3968
	unique mappers: 3963
-----------------------------
----------------------------
Create subgroups:
fastq_in: fastq_dir/reads-sample-small.fastq_all_mappers.fastq
directory_out: /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/
mismatches: 0
mismatches TE: 3
-----------------------------
bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35116.dat_symlink.fa' 'fastq_dir/reads-sample-small.fastq_all_mappers.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35116.dat_symlink.fa /dev/stdin 'fastq_dir/reads-sample-small.fastq_all_mappers.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.sam'
	reads: 3968
	mappers: 9
	unmapped: 3959
-----------------------------
-----------------------------
bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35112.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs_rejected.fastq' 2> 'CPzbhiix_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35112.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs_rejected.fastq' 2> 'CPzbhiix_samse.err' > 'CPzbhiix'
	reads: 3959
	mappers: 850
	unmapped: 3109
-----------------------------
-----------------------------
bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35114.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/rRNAs_rejected.fastq' 2> 'ACwrrvou_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35114.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/rRNAs_rejected.fastq' 2> 'ACwrrvou_samse.err' > 'ACwrrvou'
	reads: 3109
	mappers: 21
	unmapped: 3088
-----------------------------
-----------------------------
bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35113.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/rRNAs_rejected.fastq' 2> 'AJabugdx_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35113.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/rRNAs_rejected.fastq' 2> 'AJabugdx_samse.err' > 'AJabugdx'
	reads: 3088
	mappers: 8
	unmapped: 3080
-----------------------------
-----------------------------
bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35118.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/transcripts.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35118.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/transcripts.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/transcripts.sam'
	reads: 3080
	mappers: 227
	unmapped: 2853
-----------------------------
-----------------------------
bwa aln -t 8 -n 3 '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35111.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/rejected_transcripts.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/TEs.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35111.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/rejected_transcripts.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/TEs.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/TEs.sam'
	reads: 2853
	mappers: 2678
	unmapped: 175
-----------------------------
** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq started, pid: 22278
-----------------------------
bwa aln -t 8 -n 3 '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35111.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35111.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs.sam'
-----------------------------
bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35118.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35118.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts.sam'
-----------------------------
bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35115.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/dataset_35115.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome.sam'
** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.fastq started, pid: 22279
** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/miRNAs.fastq just finished with PID 22279 and exit code: 0
** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/siRNAs.fastq started, pid: 22405
** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq just finished with PID 22278 and exit code: 0
** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/piRNAs.fastq started, pid: 22464
** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/siRNAs.fastq just finished with PID 22405 and exit code: 0
** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/piRNAs.fastq just finished with PID 22464 and exit code: 0
ping_pong_partners /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups//piRNAs/TEs.sam /data/galaxy/galaxy-server/database/jobs_directory/015/15799/dataset_35827_files/reads-sample-small.fastq/subgroups/PPPartners/
Fastq fork : /data/galaxy/galaxy-server/database/files/035/dataset_35773.dat started, pid: 22106
Fastq fork /data/galaxy/galaxy-server/database/files/035/dataset_35773.dat just finished with PID 22106 and exit code: 0
Job done!