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Old 04-17-2014, 09:42 AM   #29
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Originally Posted by GenoMax View Post
With LSF, not setting the -Xmx flag is leading to default allocation of 4G (at least on our cluster, things may be set up differently at other locations) which results in Java running out of heap space. I am also not using exclusive nodes option so far and it seems to be working fine.
Hmm, thanks for testing. Sounds like LSF is setting the ulimit too low, probably for 1 slot no matter how many slots you reserve, I'm guessing.

BTW: The latest code for BBMap (32.06) seems to have shell script files in DOS format (wasn't the case before on previous versions).
Thanks for noticing that; I've uploaded a new version 32.07 which fixes it. They work fine for me but some versions of bash can't process DOS encoding.

By the way - I forgot to mention it, but I added the phiX reference and truseq adapters to the /resources/ directory, for use with BBDuk.
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