running fastqc after trim_galore

Question

[josebenitez2009]

Hi everybody, good day

Running this command :

./trim_galore -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA  -q 20 --rrbs  --stringency 5 --phred64  --paired --length 20 S14_R1.fastqc S14_R2.fastqc --path_to_cutadapt /usr/bin/cutadapt --fastqc

When begin to run FastQC the machine give the next error :

Analysis complete for S14_R1.fastqc_val_1.fq
Failed to process file S14_R1.fastqc_val_1.fq
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:745)

  >>> Now running FastQC on the validated data S14_R2.fastqc_val_2.fq<<<

Started analysis of S14_R2.fastqc_val_2.fq
Analysis complete for S14_R2.fastqc_val_2.fq
Failed to process file S14_R2.fastqc_val_2.fq
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:745)
Deleting both intermediate output files S14_R1.fastqc_trimmed.fq and S14_R2.fastqc_trimmed.fq

Any idea to resolve this welcome.

Thanks in advanced & regards,

Answer 1

[Brian Bushnell]

Sounds like a bug. Are you using the latest version?

Alternatively, you will get substantially better adapter-trimming using BBDuk.

Answer 2

[josebenitez2009]

Thanks for your answer.

Yes I'm using the last fastQC version.

And about BBDuk, I do not know what it is, I'm going to know now.

Regards.

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing comments to keep threads logically organized.