Mercurial > repos > brasset_jensen > srnapipe
comparison test-data/res_files/report.txt @ 61:9185ca0a7b43 draft
Updated package according to recommendations.
| author | pierre.pouchin |
|---|---|
| date | Wed, 16 Jan 2019 08:18:13 -0500 |
| parents | |
| children | 11708af40030 |
comparison
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| 60:9645d995fb3c | 61:9185ca0a7b43 |
|---|---|
| 1 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa | |
| 2 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35114.dat_symlink.fa | |
| 3 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35112.dat_symlink.fa | |
| 4 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35113.dat_symlink.fa | |
| 5 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35116.dat_symlink.fa | |
| 6 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa | |
| 7 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35111.dat_symlink.fa | |
| 8 ----------------------------- | |
| 9 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' | |
| 10 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 | |
| 11 reads: 45570 | |
| 12 mappers: 39040 | |
| 13 unique mappers: 38991 | |
| 14 ----------------------------- | |
| 15 ---------------------------- | |
| 16 Create subgroups: | |
| 17 fastq_in: fastq_dir/reads-sample-small.fastq_all_mappers.fastq | |
| 18 directory_out: /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/ | |
| 19 mismatches: 0 | |
| 20 mismatches TE: 3 | |
| 21 ----------------------------- | |
| 22 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' | |
| 23 reads: 39040 | |
| 24 mappers: 63 | |
| 25 unmapped: 38977 | |
| 26 ----------------------------- | |
| 27 ----------------------------- | |
| 28 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' | |
| 29 reads: 38977 | |
| 30 mappers: 8170 | |
| 31 unmapped: 30807 | |
| 32 ----------------------------- | |
| 33 ----------------------------- | |
| 34 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' | |
| 35 reads: 30807 | |
| 36 mappers: 196 | |
| 37 unmapped: 30611 | |
| 38 ----------------------------- | |
| 39 ----------------------------- | |
| 40 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' | |
| 41 reads: 30611 | |
| 42 mappers: 81 | |
| 43 unmapped: 30530 | |
| 44 ----------------------------- | |
| 45 ----------------------------- | |
| 46 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' | |
| 47 reads: 30530 | |
| 48 mappers: 2247 | |
| 49 unmapped: 28283 | |
| 50 ----------------------------- | |
| 51 ----------------------------- | |
| 52 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' | |
| 53 reads: 28283 | |
| 54 mappers: 26344 | |
| 55 unmapped: 1939 | |
| 56 ----------------------------- | |
| 57 ** 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 | |
| 58 ----------------------------- | |
| 59 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' | |
| 60 ----------------------------- | |
| 61 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' | |
| 62 ----------------------------- | |
| 63 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' | |
| 64 ** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq started, pid: 14244 | |
| 65 ** 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 | |
| 66 ** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/siRNAs.fastq started, pid: 14405 | |
| 67 ** 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 | |
| 68 ** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/piRNAs.fastq started, pid: 14463 | |
| 69 ** 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 | |
| 70 ** 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 | |
| 71 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/ | |
| 72 Fastq fork : /data/galaxy/galaxy-server/database/files/035/dataset_35117.dat started, pid: 14070 | |
| 73 Fastq fork /data/galaxy/galaxy-server/database/files/035/dataset_35117.dat just finished with PID 14070 and exit code: 0 | |
| 74 Job done! |