Number of reads does not match!

[Richard]

Hi,

I'm having the same issue as someone had last year (https://groups.google.com/forum/#!topic/pear-users/ovaK3kxVgtw), where I get the following error:

1 Problem, number of reads does not match! n1 = 0 n2 = 115740

Aborted (core dumped)

Like in the previous thread, PEAR works for some files but not all. The number of reads is equal in both files (e.g. 9476732 for the files used that generated the error above) and, unlike in the previous discussion, all my reads are the same length: 125bp. Full file paths are used.

Any ideas how I get resolve this issue?

Many thanks,

Richard

[Joshua Herr]

Hi Richard, 

Sorry to hear about your issue.  I'm not a PEAR developer, but, like the other example you linked, it doesn't seem to be a PEAR issue here.  Something is wrong with your files or how you are calling on them.  It could be any number of things causing this. 

Your first file is not being read or is being read but PEAR does not recognize the sequence data.  This means you could have an incorrect path or a naming error.  You mention that for both files the number of reads does not match what your error output is.  

I would check your fastq files for data integrity -- it's possible that a file (or both) was "damaged" somewhere along the line.  Do you have a MD5 sum from your sequencing provider to check against the files?

Without being there in person, this is a really hard error to troubleshoot via a listserve.  If you can trial and error troubleshoot on your own, as well as seek out local help, this could be best.  Feel free to contact me if you have questions and I can see what I can do to help.  The exact command and exact error message you received would help greatly.

Best of luck.  Cheers ~ josh  

Joshua R. Herr, Ph.D. | Michigan State University

Department of Microbiology & Molecular Genetics | 6173 Biomedical Physical Sciences Building  | East Lansing, MI, 48823, USA

joshuaherr.com | joshua...@gmail.com | cellular: 503.880.3131

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[Richard]

Thanks Josh. I was using a subset of fastq files, created using Biopython. Although I can't see how this would interfere with PEAR, my simple solution has been to merge the raw files first then subset the merged fastqs afterwards.

Cheers,

Richard