[E::hts_open] fail to open file

[trl]

Hello, when I try to use "jgi_summarize_bam_contig_depths" with more than 1021 bam-files I get for each additional file this error:

[E::hts_open] fail to open file 'plant18984.bam' ...

Is there any file limitation?

Best Robin

[Rob Egan]

I haven't tried that many files, but 1021 is an odd threshold and seems to indicate to me that your computer has a limit of 1024 open files (including STDIN, STDOUT and STDERR). Check the ulimit on # of open files:

Our systems have a limit of 4096

ulimit -n 4096

If yours is limited to 1024, have your systems administrator increase the limit.

[trl]

Thanks a lot, problem solved!