Mercurial > repos > brasset_jensen > srnapipe

annotate test-data/res_files/report.txt @ 61:9185ca0a7b43 draft

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Updated package according to recommendations.
author pierre.pouchin
date Wed, 16 Jan 2019 08:18:13 -0500
parents
children 11708af40030
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
61
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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1 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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2 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35114.dat_symlink.fa
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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3 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35112.dat_symlink.fa
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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4 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35113.dat_symlink.fa
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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5 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35116.dat_symlink.fa
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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6 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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7 Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35111.dat_symlink.fa
9185ca0a7b43 Updated package according to recommendations.
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8 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
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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'
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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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
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11 reads: 45570
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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12 mappers: 39040
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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13 unique mappers: 38991
9185ca0a7b43 Updated package according to recommendations.
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14 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
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15 ----------------------------
9185ca0a7b43 Updated package according to recommendations.
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16 Create subgroups:
9185ca0a7b43 Updated package according to recommendations.
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17 fastq_in: fastq_dir/reads-sample-small.fastq_all_mappers.fastq
9185ca0a7b43 Updated package according to recommendations.
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18 directory_out: /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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19 mismatches: 0
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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20 mismatches TE: 3
9185ca0a7b43 Updated package according to recommendations.
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21 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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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'
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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23 reads: 39040
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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24 mappers: 63
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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25 unmapped: 38977
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26 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
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27 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
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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'
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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29 reads: 38977
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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30 mappers: 8170
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pierre.pouchin
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31 unmapped: 30807
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32 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
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33 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
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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'
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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35 reads: 30807
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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36 mappers: 196
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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37 unmapped: 30611
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38 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
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39 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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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'
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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41 reads: 30611
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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42 mappers: 81
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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43 unmapped: 30530
9185ca0a7b43 Updated package according to recommendations.
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44 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
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45 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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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'
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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47 reads: 30530
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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48 mappers: 2247
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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49 unmapped: 28283
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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50 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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51 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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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'
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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53 reads: 28283
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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54 mappers: 26344
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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55 unmapped: 1939
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56 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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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
9185ca0a7b43 Updated package according to recommendations.
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58 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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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'
9185ca0a7b43 Updated package according to recommendations.
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60 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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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'
9185ca0a7b43 Updated package according to recommendations.
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62 -----------------------------
9185ca0a7b43 Updated package according to recommendations.
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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'
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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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
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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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
9185ca0a7b43 Updated package according to recommendations.
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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
9185ca0a7b43 Updated package according to recommendations.
pierre.pouchin
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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
9185ca0a7b43 Updated package according to recommendations.
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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
9185ca0a7b43 Updated package according to recommendations.
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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
9185ca0a7b43 Updated package according to recommendations.
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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
9185ca0a7b43 Updated package according to recommendations.
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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/
9185ca0a7b43 Updated package according to recommendations.
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72 Fastq fork : /data/galaxy/galaxy-server/database/files/035/dataset_35117.dat started, pid: 14070
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73 Fastq fork /data/galaxy/galaxy-server/database/files/035/dataset_35117.dat just finished with PID 14070 and exit code: 0
9185ca0a7b43 Updated package according to recommendations.
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74 Job done!