Mercurial > repos > brasset_jensen > srnapipe
view test-data/res_files/report.txt @ 62:e6c4f3e96e47 draft
planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 87e0c95b4d0d1954e81247c31a8f74c5d87c7f9e
| author | pierre.pouchin |
|---|---|
| date | Thu, 17 Jan 2019 09:56:52 -0500 |
| parents | 9185ca0a7b43 |
| children | 11708af40030 |
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Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35114.dat_symlink.fa Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35112.dat_symlink.fa Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35113.dat_symlink.fa Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35116.dat_symlink.fa Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35111.dat_symlink.fa ----------------------------- bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/dataset_35117_18-29.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/dataset_35117_18-29.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam' Parsing /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam file reads: 45570 mappers: 39040 unique mappers: 38991 ----------------------------- ---------------------------- Create subgroups: fastq_in: fastq_dir/reads-sample-small.fastq_all_mappers.fastq directory_out: /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/ mismatches: 0 mismatches TE: 3 ----------------------------- bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35116.dat_symlink.fa' 'fastq_dir/reads-sample-small.fastq_all_mappers.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_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/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.sam' reads: 39040 mappers: 63 unmapped: 38977 ----------------------------- ----------------------------- bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35112.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs_rejected.fastq' 2> 'SLupcxhh_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35112.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs_rejected.fastq' 2> 'SLupcxhh_samse.err' > 'SLupcxhh' reads: 38977 mappers: 8170 unmapped: 30807 ----------------------------- ----------------------------- bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35114.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/rRNAs_rejected.fastq' 2> 'LCcdxnpg_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35114.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/rRNAs_rejected.fastq' 2> 'LCcdxnpg_samse.err' > 'LCcdxnpg' reads: 30807 mappers: 196 unmapped: 30611 ----------------------------- ----------------------------- bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35113.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/rRNAs_rejected.fastq' 2> 'KAehfkzc_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35113.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/rRNAs_rejected.fastq' 2> 'KAehfkzc_samse.err' > 'KAehfkzc' reads: 30611 mappers: 81 unmapped: 30530 ----------------------------- ----------------------------- bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/transcripts.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/transcripts.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/transcripts.sam' reads: 30530 mappers: 2247 unmapped: 28283 ----------------------------- ----------------------------- bwa aln -t 8 -n 3 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35111.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/rejected_transcripts.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/TEs.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35111.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/rejected_transcripts.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/TEs.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/TEs.sam' reads: 28283 mappers: 26344 unmapped: 1939 ----------------------------- ** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq started, pid: 14243 ----------------------------- bwa aln -t 8 -n 3 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35111.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35111.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs.sam' ----------------------------- bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts.sam' ----------------------------- bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome.sam' ** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq started, pid: 14244 ** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq just finished with PID 14244 and exit code: 0 ** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/siRNAs.fastq started, pid: 14405 ** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq just finished with PID 14243 and exit code: 0 ** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/piRNAs.fastq started, pid: 14463 ** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/siRNAs.fastq just finished with PID 14405 and exit code: 0 ** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/piRNAs.fastq just finished with PID 14463 and exit code: 0 ping_pong_partners /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups//piRNAs/TEs.sam /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/PPPartners/ Fastq fork : /data/galaxy/galaxy-server/database/files/035/dataset_35117.dat started, pid: 14070 Fastq fork /data/galaxy/galaxy-server/database/files/035/dataset_35117.dat just finished with PID 14070 and exit code: 0 Job done!