FastQC contaminant line error

Question

[jmah]

I'm running FastQC on a set of raw fq reads that were generated by NextSeq. On some files, but not all, I get the error "Expected 2 sections for contaminant line but got 1 from Illumina Paired End”. It looks like it originates from the contaminant finder module (see here: https://github.com/csf-ngs/fastqc/blob/master/uk/ac/bbsrc/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java). However, I've never specified the contaminants option and this error does not come up for other files, despite being run in exactly the same way. Any ideas?

Thanks for your help!

[GenoMax]

Following is only a vague suggestion but something to look at while you wait for a more informed response.

Sounds like your data may have been trimmed on the instrument (or in BaseSpace) and I wonder if the reads may now be out of order, if one of the reads from a pair was discarded during trimming.

Can you do a quick check on the file pairs to see if you have the same number of reads in both R1/R2. If not, you would need to fix that by using repair.sh from BBMap suite.

[jmah]

Huh! I didn't know the instrument or BaseSpace could trim reads. However, it looks like there are the same number of reads in R1/R2. Thanks for the suggestion. I'll check that now each time I get reads back from an instrument.