From dfa2d3fdc59bd9a93be029156eb7f7e94bfc4f7f Mon Sep 17 00:00:00 2001 From: Steven Sutcliffe Date: Thu, 28 Apr 2022 07:00:17 -0700 Subject: [PATCH] added QC w/trimmomatic --- 1_Bacteria/0_QC_Reads/slurm-43794039.out | 49 ++++++++++++++++++++++++ 1_Bacteria/0_QC_Reads/trimming_script.sh | 29 ++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 1_Bacteria/0_QC_Reads/slurm-43794039.out create mode 100644 1_Bacteria/0_QC_Reads/trimming_script.sh diff --git a/1_Bacteria/0_QC_Reads/slurm-43794039.out b/1_Bacteria/0_QC_Reads/slurm-43794039.out new file mode 100644 index 0000000..5459b32 --- /dev/null +++ b/1_Bacteria/0_QC_Reads/slurm-43794039.out @@ -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.(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 new file mode 100644 index 0000000..1b5094d --- /dev/null +++ b/1_Bacteria/0_QC_Reads/trimming_script.sh @@ -0,0 +1,29 @@ +#!/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 +