diff --git a/1_Bacteria/0_QC_Reads/slurm-43794039.out b/1_Bacteria/0_QC_Reads/slurm-43794039.out deleted file mode 100644 index 5459b32..0000000 --- a/1_Bacteria/0_QC_Reads/slurm-43794039.out +++ /dev/null @@ -1,49 +0,0 @@ -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.(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.(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.(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 diff --git a/1_Bacteria/0_QC_Reads/trimming_script.sh b/1_Bacteria/0_QC_Reads/trimming_script.sh deleted file mode 100644 index 1b5094d..0000000 --- a/1_Bacteria/0_QC_Reads/trimming_script.sh +++ /dev/null @@ -1,29 +0,0 @@ -#!/bin/bash - -#SBATCH --time=10:00:00 -#SBATCH --mem=40G -#SBATCH --cpus-per-task=16 - -module load trimmomatic/0.36 - -raw_dic=../../0_RawData/0_Bacteria_Reads -#Note make sure reads are unzipped - -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 - -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 - -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 -