i have fastq file , i'm able run fastqc program analyse file. when use trim_galore, fastqc (or fastqc option in trim_galore) not working anymore.
$ fastqc ./sub1_val_1.fq.gz this output:
started analysis of sub1_val_1.fq.gz analysis complete sub1_val_1.fq.gz failed process file sub1_val_1.fq.gz java.lang.arrayindexoutofboundsexception: -1 @ uk.ac.babraham.fastqc.modules.sequencelengthdistribution.calculatedistribution(sequencelengthdistribution.java:100) @ uk.ac.babraham.fastqc.modules.sequencelengthdistribution.raiseserror(sequencelengthdistribution.java:184) @ uk.ac.babraham.fastqc.report.htmlreportarchive.startdocument(htmlreportarchive.java:336) @ uk.ac.babraham.fastqc.report.htmlreportarchive.<init>(htmlreportarchive.java:84) @ uk.ac.babraham.fastqc.analysis.offlinerunner.analysiscomplete(offlinerunner.java:155) @ uk.ac.babraham.fastqc.analysis.analysisrunner.run(analysisrunner.java:110) @ java.lang.thread.run(thread.java:695) is failed process file error because version not correct between trim_galore , fastqc?
i found this, wasn't helpful.
i'm using fastqc v0.11.5 , trim_galore v0.4.1.
i subsetted library (reads in paired-end) using this:
seqtk sample -s100 ./srr2937435_1.fastq.gz 10000 | gzip > sub1.fastq.gz seqtk sample -s100 ./srr2937435_2.fastq.gz 10000 | gzip > sub2.fastq.gz the sub1_val_1.fq.gz file after passing sub1.fastq.gz trim_galore. fastqc sub1.fastq.gz working.
note: suggested posted on biostars.org.
i found answer: have uncompress it. probably, trim_galore working tar.gz , not fastq.gz.
gzip -d -k sub1.fastq.gz > sub1.fastq y # accept overwrite gzip -d -k sub2.fastq.gz > sub2.fastq y # accept overwrite trim_galore --illumina --paired --fastqc sub1.fastq sub2.fastq 
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