I'm trying to run Trimmomatic on some shotgun sequencing paired end files and while most of them are working (so I know the code isn't the problem), a handful of files are unable to be run. I ran this code:
java -jar /scratch/g/jkirby/trimmomatic-0.39/trimmomatic-0.39.jar PE /scratch/g/jkirby/Landon_WGS_reanalysis/Figure_8/00_RAW_sequences/LTH2584Risp_108_R1.fastq.gz /scratch/g/jkirby/Landon_WGS_reanalysis/Figure_8/00_RAW_sequences/LTH2584Risp_108_R2.fastq.gz /scratch/g/jkirby/Landon_WGS_reanalysis/mouse_removal/LTH2584Risp_108_trimmed_R1.fastq.gz /scratch/g/jkirby/Landon_WGS_reanalysis/mouse_removal/LTH2584Risp_108_untrimmed_R1.fastq.gz /scratch/g/jkirby/Landon_WGS_reanalysis/mouse_removal/LTH2584Risp_108_trimmed_R2.fastq.gz /scratch/g/jkirby/Landon_WGS_reanalysis/mouse_removal/LTH2584Risp_108_untrimmed_R2.fastq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36
And keep getting this error from Trimmomatic: Exception in thread "main" java.lang.RuntimeException: Invalid FASTQ name line: followed by a bunch of dark symbols with question marks inside for several hundred (or possibly several thousand) lines.
A second file resulted in a similar error but the problematic line was completely different:
Exception in thread "main" java.lang.RuntimeException: Invalid FASTQ comment line: GCCTCAGCTCCGGGATGTGCTTCATCAGATGGATAAAGGAATTTAGCCAAAGGCTACTTTTGTGGTGAACAGCGGGACAGGGTTGCATTTGAATTATGTCCAGACTCAGCCGGTTCCCATCTACACGCAGAACCAGCACTATCTGAAGGAG
Clearly the error is with the fastq files but I'm not sure if there's a way to fix them?
java -jar /scratch/g/jkirby/trimmomatic-0.39/trimmomatic-0.39.jar PE /scratch/g/jkirby/Landon_WGS_reanalysis/Figure_8/00_RAW_sequences/LTH2584Risp_108_R1.fastq.gz /scratch/g/jkirby/Landon_WGS_reanalysis/Figure_8/00_RAW_sequences/LTH2584Risp_108_R2.fastq.gz /scratch/g/jkirby/Landon_WGS_reanalysis/mouse_removal/LTH2584Risp_108_trimmed_R1.fastq.gz /scratch/g/jkirby/Landon_WGS_reanalysis/mouse_removal/LTH2584Risp_108_untrimmed_R1.fastq.gz /scratch/g/jkirby/Landon_WGS_reanalysis/mouse_removal/LTH2584Risp_108_trimmed_R2.fastq.gz /scratch/g/jkirby/Landon_WGS_reanalysis/mouse_removal/LTH2584Risp_108_untrimmed_R2.fastq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36
And keep getting this error from Trimmomatic: Exception in thread "main" java.lang.RuntimeException: Invalid FASTQ name line: followed by a bunch of dark symbols with question marks inside for several hundred (or possibly several thousand) lines.
A second file resulted in a similar error but the problematic line was completely different:
Exception in thread "main" java.lang.RuntimeException: Invalid FASTQ comment line: GCCTCAGCTCCGGGATGTGCTTCATCAGATGGATAAAGGAATTTAGCCAAAGGCTACTTTTGTGGTGAACAGCGGGACAGGGTTGCATTTGAATTATGTCCAGACTCAGCCGGTTCCCATCTACACGCAGAACCAGCACTATCTGAAGGAG
Clearly the error is with the fastq files but I'm not sure if there's a way to fix them?