bbduk truncated fastq file according to FastQC - help?

Question

[lintonf]

I was able to succeessfully remove adapters from my PE 150bp x 2 reads using bbduk.sh, but I kept seeing that I had a long string of Gs in my R2 sequences (~ 0.1% of my R2 reads).

I reran the original fastq files with bbduk to remove the string of Gs, and this worked for most of my PE files except for one pair.

When I ran this trimmed set of PE reads through FastQC (after bbduk), I received an error that said:

Failed to process file EA_Pool-POW_1-1a_S28_L001_R1_CLEANEST.fastq
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: Ran out of data in the middle of a fastq entry.  Your file is probably truncated
    at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:179)
    at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125)
    at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:77)
    at java.lang.Thread.run(Thread.java:722)

Has anyone encountered this issue before with output fastqs from bbduk?

Should I just not worry about the ~0.1% of GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG kmers in my R2 reads?

Thank you!

Answer 1

[swbarnes2]

I'd start by rerunning the trimming; it might have just randomly stopped.

Honestly, a string of G's isn't going to align to anything, so it's not going to do anything bad if you leave them in.

[lintonf]

That was my thought, and it's such a low % of the R2 reads. Thanks for the input!

[Ram]

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