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PengNi / ccsmeth

Detecting DNA methylation from PacBio CCS reads
BSD 3-Clause Clear License
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setting temp folder for samtools #28

Closed drramki-chop closed 2 years ago

drramki-chop commented 2 years ago

I am running this in a shared HPC environment. Looks like the samtools is using /tmp and it has limited space. I am aware there is a --tmp-dir setting for samtools. I do not see how to set it up for the CCSmeth pipeline (environment variable?)

Thanks for your help.

==stderr: samtools sort: fail to open "/tmp/samtools.3547891.6686.tmp.0000.bam": No such file or directory terminate called after throwing an instance of 'PacBio::Utility::AlarmException' /bin/sh: line 1: 3547891 Aborted (core dumped) pbmm2 align --preset HIFI -j 8 --sort

drramki-chop commented 2 years ago

setting the TMPDIR environment variable seems to solve the problem.