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Steven Sutcliffe
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
| To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.36.jar | ||
| TrimmomaticPE: Started with arguments: | ||
| /home/ssutclif/scratch/collab_project/raw_reads/SRR828645_1.fastq /home/ssutclif/scratch/collab_project/raw_reads/SRR828645_2.fastq output_SRR828645_1_paired.fastq output_SRR828645_1_unpaired.fastq output_SRR828645_2_paired.fastq output_SRR828645_2_unpaired.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 | ||
| java.io.FileNotFoundException: /scratch/ssutclif/collab_project/trimmed_reads/TruSeq3-PE.fa (No such file or directory) | ||
| at java.io.FileInputStream.open0(Native Method) | ||
| at java.io.FileInputStream.open(FileInputStream.java:195) | ||
| at java.io.FileInputStream.<init>(FileInputStream.java:138) | ||
| at org.usadellab.trimmomatic.fasta.FastaParser.parse(FastaParser.java:54) | ||
| at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:110) | ||
| at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:71) | ||
| at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32) | ||
| at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59) | ||
| at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:536) | ||
| at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80) | ||
| Quality encoding detected as phred33 | ||
| Input Read Pairs: 10750017 Both Surviving: 8912486 (82.91%) Forward Only Surviving: 589170 (5.48%) Reverse Only Surviving: 587152 (5.46%) Dropped: 661209 (6.15%) | ||
| TrimmomaticPE: Completed successfully | ||
| TrimmomaticPE: Started with arguments: | ||
| /home/ssutclif/scratch/collab_project/raw_reads/SRR828660_1.fastq /home/ssutclif/scratch/collab_project/raw_reads/SRR828660_2.fastq output_SRR828660_1_paired.fastq output_SRR828660_1_unpaired.fastq output_SRR828660_2_paired.fastq output_SRR828660_2_unpaired.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 | ||
| java.io.FileNotFoundException: /scratch/ssutclif/collab_project/trimmed_reads/TruSeq3-PE.fa (No such file or directory) | ||
| at java.io.FileInputStream.open0(Native Method) | ||
| at java.io.FileInputStream.open(FileInputStream.java:195) | ||
| at java.io.FileInputStream.<init>(FileInputStream.java:138) | ||
| at org.usadellab.trimmomatic.fasta.FastaParser.parse(FastaParser.java:54) | ||
| at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:110) | ||
| at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:71) | ||
| at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32) | ||
| at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59) | ||
| at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:536) | ||
| at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80) | ||
| Quality encoding detected as phred33 | ||
| Input Read Pairs: 17158723 Both Surviving: 14489319 (84.44%) Forward Only Surviving: 959036 (5.59%) Reverse Only Surviving: 755481 (4.40%) Dropped: 954887 (5.57%) | ||
| TrimmomaticPE: Completed successfully | ||
| TrimmomaticPE: Started with arguments: | ||
| /home/ssutclif/scratch/collab_project/raw_reads/SRR828661_1.fastq /home/ssutclif/scratch/collab_project/raw_reads/SRR828661_2.fastq output_SRR828661_1_paired.fastq output_SRR828661_1_unpaired.fastq output_SRR828661_2_paired.fastq output_SRR828661_2_unpaired.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 | ||
| java.io.FileNotFoundException: /scratch/ssutclif/collab_project/trimmed_reads/TruSeq3-PE.fa (No such file or directory) | ||
| at java.io.FileInputStream.open0(Native Method) | ||
| at java.io.FileInputStream.open(FileInputStream.java:195) | ||
| at java.io.FileInputStream.<init>(FileInputStream.java:138) | ||
| at org.usadellab.trimmomatic.fasta.FastaParser.parse(FastaParser.java:54) | ||
| at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:110) | ||
| at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:71) | ||
| at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32) | ||
| at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59) | ||
| at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:536) | ||
| at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80) | ||
| Quality encoding detected as phred33 | ||
| Input Read Pairs: 12181686 Both Surviving: 9601441 (78.82%) Forward Only Surviving: 732334 (6.01%) Reverse Only Surviving: 883314 (7.25%) Dropped: 964597 (7.92%) | ||
| TrimmomaticPE: Completed successfully |
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| #!/bin/bash | ||
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| #SBATCH --time=10:00:00 | ||
| #SBATCH --mem=40G | ||
| #SBATCH --cpus-per-task=16 | ||
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| module load trimmomatic/0.36 | ||
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| raw_dic=../../0_RawData/0_Bacteria_Reads | ||
| #Note make sure reads are unzipped | ||
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| java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.36.jar PE $raw_dic/SRR828645_1.fastq \ | ||
| $raw_dic/SRR828645_2.fastq output_SRR828645_1_paired.fastq \ | ||
| output_SRR828645_1_unpaired.fastq output_SRR828645_2_paired.fastq \ | ||
| output_SRR828645_2_unpaired.fastq \ | ||
| ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 | ||
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| java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.36.jar PE $raw_dic/SRR828660_1.fastq \ | ||
| $raw_dic/SRR828660_2.fastq output_SRR828660_1_paired.fastq \ | ||
| output_SRR828660_1_unpaired.fastq output_SRR828660_2_paired.fastq \ | ||
| output_SRR828660_2_unpaired.fastq \ | ||
| ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 | ||
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| java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.36.jar PE $raw_dic/SRR828661_1.fastq \ | ||
| $raw_dic/SRR828661_2.fastq output_SRR828661_1_paired.fastq \ | ||
| output_SRR828661_1_unpaired.fastq output_SRR828661_2_paired.fastq \ | ||
| output_SRR828661_2_unpaired.fastq \ | ||
| ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 | ||
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