sambamba depth -- open too many files

biod / sambamba

Tools for working with SAM/BAM data

http://thebird.nl/blog/D_Dragon.html

GNU General Public License v2.0

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sambamba depth -- open too many files #377

Closed YPGG1234 closed 5 years ago

YPGG1234 commented 5 years ago

hi,everyone, i meet a problem when i use “sambamba depth” to handle a bam file.It reports “ _sambamba-depth: Cannot open or create file 'XXX_cleandedup.bam' : Too many open files”. There is only one bam file and i had already dedup with Picard，but when i use “sambamba depth”,it works wrong.I had test “sambamba depth” with other bam files,there are all run correctly.I don't know why.Can somebody help me?

pjotrp commented 5 years ago

Check open files with https://www.cyberciti.biz/faq/howto-linux-get-list-of-open-files/. Linux often allows for 1024 open files. You can increase that.

YPGG1234 commented 5 years ago

Thank you for your answer,but I'm not root user.I split bed file to many small files,and use ulimit -Sn 4096 to increase the open files number,finally it works right.