Too many open files error when using giggle to build the index

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Changson Wan

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Mar 12, 2018, 11:08:29 AM3/12/18

to giggle

Hi,

I am using the tool giggle and indexing 1000 bed files. Those bed files have been sort and bgzipped. And now I am facing the problem that the giggle says "giggle: Could not open file 'bed_gz/36573_peaks.bed.gz': Too many open files". I don't know how can I deal with the error.

Thank you!

Changson Wan

Ryan Layer

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Mar 12, 2018, 11:11:07 AM3/12/18

to Changson Wan, giggle

Try

ulimit -Sn 16384

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