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)
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Could you run your BAM through Picard's ValidateSam, and let us know the version of FastQC you're using? Looks like a bug :/
OP is using a fastq file with FastQC :-)
@mehar: Can you show us the output of
head -4 reverse.fastqso we can confirm the file is actually in fastq format?Oh yeah, 'reverse.fastq' - perhaps I need another coffee :)
Also try counting the number of lines in the file:
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] :
The number this gives should be equivalent to the number of lines in file divided by 4 if correctly formatted.