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Trimmomatic: option to use filenames.
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12
data/modules/trimmomatic/issue_864/180518_mATAC_t10_1_trimmomatic.err
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807201 | ||
| TrimmomaticPE: Started with arguments: | ||
| -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog | ||
| Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' | ||
| ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences | ||
| Quality encoding detected as phred33 | ||
| Input Read Pairs: 68758964 Both Surviving: 68738356 (99.97%) Forward Only Surviving: 4329 (0.01%) Reverse Only Surviving: 6139 (0.01%) Dropped: 10140 (0.01%) | ||
| TrimmomaticPE: Completed successfully |
12 changes: 12 additions & 0 deletions
12
data/modules/trimmomatic/issue_864/180518_mATAC_t11_1_trimmomatic.err
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23820432 | ||
| TrimmomaticPE: Started with arguments: | ||
| -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog | ||
| Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' | ||
| ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences | ||
| Quality encoding detected as phred33 | ||
| Input Read Pairs: 36757610 Both Surviving: 36747933 (99.97%) Forward Only Surviving: 2407 (0.01%) Reverse Only Surviving: 3687 (0.01%) Dropped: 3583 (0.01%) | ||
| TrimmomaticPE: Completed successfully |
12 changes: 12 additions & 0 deletions
12
data/modules/trimmomatic/issue_864/180518_mATAC_t12_1_trimmomatic.err
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807210 | ||
| TrimmomaticPE: Started with arguments: | ||
| -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog | ||
| Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' | ||
| ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences | ||
| Quality encoding detected as phred33 | ||
| Input Read Pairs: 22377822 Both Surviving: 22368123 (99.96%) Forward Only Surviving: 4068 (0.02%) Reverse Only Surviving: 5630 (0.03%) Dropped: 1 (0.00%) | ||
| TrimmomaticPE: Completed successfully |
12 changes: 12 additions & 0 deletions
12
data/modules/trimmomatic/issue_864/180518_mATAC_t1_1_trimmomatic.err
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807202 | ||
| TrimmomaticPE: Started with arguments: | ||
| -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog | ||
| Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' | ||
| ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences | ||
| Quality encoding detected as phred33 | ||
| Input Read Pairs: 22377822 Both Surviving: 22368011 (99.96%) Forward Only Surviving: 4745 (0.02%) Reverse Only Surviving: 5065 (0.02%) Dropped: 1 (0.00%) | ||
| TrimmomaticPE: Completed successfully |
12 changes: 12 additions & 0 deletions
12
data/modules/trimmomatic/issue_864/180518_mATAC_t3_1_trimmomatic.err
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807206 | ||
| TrimmomaticPE: Started with arguments: | ||
| -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog | ||
| Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' | ||
| ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences | ||
| Quality encoding detected as phred33 | ||
| Input Read Pairs: 68777345 Both Surviving: 68767299 (99.99%) Forward Only Surviving: 1952 (0.00%) Reverse Only Surviving: 3622 (0.01%) Dropped: 4472 (0.01%) | ||
| TrimmomaticPE: Completed successfully |
12 changes: 12 additions & 0 deletions
12
data/modules/trimmomatic/issue_864/180518_mATAC_t4_1_trimmomatic.err
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807214 | ||
| TrimmomaticPE: Started with arguments: | ||
| -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog | ||
| Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' | ||
| ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences | ||
| Quality encoding detected as phred33 | ||
| Input Read Pairs: 58558991 Both Surviving: 58544996 (99.98%) Forward Only Surviving: 3031 (0.01%) Reverse Only Surviving: 4723 (0.01%) Dropped: 6241 (0.01%) | ||
| TrimmomaticPE: Completed successfully |
12 changes: 12 additions & 0 deletions
12
data/modules/trimmomatic/issue_864/180518_mATAC_t5_1_trimmomatic.err
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807212 | ||
| TrimmomaticPE: Started with arguments: | ||
| -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog | ||
| Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' | ||
| ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences | ||
| Quality encoding detected as phred33 | ||
| Input Read Pairs: 91645932 Both Surviving: 91623858 (99.98%) Forward Only Surviving: 3779 (0.00%) Reverse Only Surviving: 6136 (0.01%) Dropped: 12159 (0.01%) | ||
| TrimmomaticPE: Completed successfully |
12 changes: 12 additions & 0 deletions
12
data/modules/trimmomatic/issue_864/180518_mATAC_t6_1_trimmomatic.err
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807219 | ||
| TrimmomaticPE: Started with arguments: | ||
| -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog | ||
| Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' | ||
| ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences | ||
| Quality encoding detected as phred33 | ||
| Input Read Pairs: 58633103 Both Surviving: 58625158 (99.99%) Forward Only Surviving: 1983 (0.00%) Reverse Only Surviving: 3642 (0.01%) Dropped: 2320 (0.00%) | ||
| TrimmomaticPE: Completed successfully |
12 changes: 12 additions & 0 deletions
12
data/modules/trimmomatic/issue_864/180518_mATAC_t8_1_trimmomatic.err
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807217 | ||
| TrimmomaticPE: Started with arguments: | ||
| -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog | ||
| Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' | ||
| ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences | ||
| Quality encoding detected as phred33 | ||
| Input Read Pairs: 16990806 Both Surviving: 16986783 (99.98%) Forward Only Surviving: 847 (0.00%) Reverse Only Surviving: 1584 (0.01%) Dropped: 1592 (0.01%) | ||
| TrimmomaticPE: Completed successfully |
12 changes: 12 additions & 0 deletions
12
data/modules/trimmomatic/issue_864/180518_mATAC_t9_1_trimmomatic.err
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| Picked up _JAVA_OPTIONS: -Xmx8000m -Djava.io.tmpdir=/tmp/23807221 | ||
| TrimmomaticPE: Started with arguments: | ||
| -threads 8 fastq_r1.fastqsanger.gz fastq_r2.fastqsanger.gz fastq_out_r1_paired.fastqsanger.gz fastq_out_r1_unpaired.fastqsanger.gz fastq_out_r2_paired.fastqsanger.gz fastq_out_r2_unpaired.fastqsanger.gz ILLUMINACLIP:/g/funcgen/galaxy-production/database/dependencies/_conda/envs/__trimmomatic@0.36/share/trimmomatic-0.36-3/adapters/NexteraPE-PE.fa:1:30:4:2:true MINLEN:20 TRAILING:3 -trimlog trimlog | ||
| Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' | ||
| Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' | ||
| ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences | ||
| Quality encoding detected as phred33 | ||
| Input Read Pairs: 56406356 Both Surviving: 56379957 (99.95%) Forward Only Surviving: 3801 (0.01%) Reverse Only Surviving: 15581 (0.03%) Dropped: 7017 (0.01%) | ||
| TrimmomaticPE: Completed successfully |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| trimmomatic: | ||
| s_name_filenames: true |