- edited description
[E::hts_open] fail to open file
Issue #42
resolved
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
Comments (4)
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reporter -
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.
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reporter Thanks a lot, problem solved!
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- changed status to resolved
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