Mercurial > repos > brasset_jensen > srnapipe
view test-data/res_files/report.txt @ 72:b140b740f828 draft
"planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit e90f8c18f63f21f99b1a0fc9c381290f3fd31e16"
| author | brasset_jensen |
|---|---|
| date | Tue, 30 Jun 2020 06:38:36 -0400 |
| parents | 11708af40030 |
| children |
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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!