CODEWITHSUNDEEP
unixbioinformaticsfastafastq
M. Beausoleil
M. Beausoleil

Reputation: 3557

Why is FastQC not working after using Trim galore?

I have a FASTQ file and I'm able to run the FASTQC program to analyse the file. but when I use trim_galore, FASTQC (or the FASTQC option in trim_galore) is not working anymore. 

$ fastqc ./sub1_val_1.fq.gz

This is the output: 

Started analysis of sub1_val_1.fq.gz
Analysis complete for sub1_val_1.fq.gz
Failed to process file sub1_val_1.fq.gz
java.lang.ArrayIndexOutOfBoundsException: -1
    at uk.ac.babraham.FastQC.Modules.SequenceLengthDistribution.calculateDistribution(SequenceLengthDistribution.java:100)
    at uk.ac.babraham.FastQC.Modules.SequenceLengthDistribution.raisesError(SequenceLengthDistribution.java:184)
    at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:336)
    at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
    at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:155)
    at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)
    at java.lang.Thread.run(Thread.java:695)

Is the Failed to process file an error because the version is not correct between trim_galore and FastQC?

I found this, but that wasn't that helpful.

I'm using FastQC v0.11.5 and trim_galore v0.4.1.

I subsetted a 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 was after passing sub1.fastq.gz into trim_galore. FastQC with sub1.fastq.gz is working.

Note: As suggested posted on biostars.org.

Upvotes: 0

Views: 713

Answers (1)

M. Beausoleil
M. Beausoleil

Reputation: 3557

I found the answer: You have to uncompress it. Probably, trim_galore is only working with tar.gz and not fastq.gz. 

gzip -d -k sub1.fastq.gz > sub1.fastq
y # to accept to overwrite
gzip -d -k sub2.fastq.gz > sub2.fastq
y # to accept to overwrite

trim_galore  --illumina --paired --fastqc sub1.fastq sub2.fastq

Upvotes: 1

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