open file limits and bcl2fastq

I was trying to demultiplex a MiSeq run with the Illumina utility `bcl2fastq` today and got the error “too many open files (24)”.

As it turns out, if you have more than about 250 samples in your run, the utility will open > 1024 file handles to do its processing (2x for R1, R2, then maybe indexes? not sure). 1024 files is the default limit on a lot of Linux systems for a particular process; however, you can get around it very easily by setting `ulimit -n 4000` or some other number. You do not need to be root to do this, so I think it’s a per-user thing and will likely be reset once you log out.




One thought on “open file limits and bcl2fastq

  1. Hi,
    thanks, this was helpfull. I guess the bcl files must also be openend although I don’t know how much at a time.

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