Failed to process file in fastqc

Question

[mehar.27march]

i run fastqc of merged file of trimmomatic result and found the se error...

[yasmin@login3 Metagenomics]$ fastqc reverse.fastq Started analysis of reverse.fastq Analysis complete for reverse.fastq Failed to process file reverse.fastq java.lang.ArrayIndexOutOfBoundsException: -1 at uk.ac.babraham.FastQC.Modules.SequenceLengthDistribution.calculateDis tribution(SequenceLengthDistribution.java:100) at uk.ac.babraham.FastQC.Modules.SequenceLengthDistribution.raisesError( SequenceLengthDistribution.java:184) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLRepo rtArchive.java:336) at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchi ve.java:84) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(Offline Runner.java:155) at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java :110) at java.lang.Thread.run(Thread.java:679)

[John]

Could you run your BAM through Picard's ValidateSam, and let us know the version of FastQC you're using? Looks like a bug :/

[GenoMax]

OP is using a fastq file with FastQC :-)

@mehar: Can you show us the output of head -4 reverse.fastq so we can confirm the file is actually in fastq format?

[John]

Oh yeah, 'reverse.fastq' - perhaps I need another coffee :)

[Tonor]

Also try counting the number of lines in the file:

wc -l reverse.fastq

The number of lines outputted should be divisible by 4 if in correct fastq format. You can also check the number of reads, replace "NB500959" with whatever text your reads all start [typically the machine name for Illumina such as M01234 for a MiSeq; or SRR for files downloaded from SRA] :

grep "^@NB500101" | wc -l

The number this gives should be equivalent to the number of lines in file divided by 4 if correctly formatted.