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bcgsc / tigmint

⛓ Correct misassemblies using linked AND long reads
https://bcgsc.github.io/tigmint/
GNU General Public License v3.0
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Changing /tmp location #34

Closed ilaydabozan closed 4 years ago

ilaydabozan commented 4 years ago

Hello, I'm running tigmint-make tigmint draft=myassembly reads=myreads command in ORCA docker environment. I got this error;

[E::bgzf_close] File write failed
[E::bgzf_flush] File write failed (wrong size)
[E::bgzf_close] File write failed
[E::bgzf_flush] File write failed (wrong size)
[E::bgzf_close] File write failed
[E::bgzf_flush] File write failed (wrong size)
[E::bgzf_close] File write failed
samtools sort: failed to create temporary file "/tmp/myassembly.myreads.sortbx.bam.PVwtv6.0136.bam": No space left on device
samtools sort: failed to create temporary file "/tmp/myassembly.myreads.sortbx.bam.PVwtv6.0137.bam": No space left on device

I believe this is due to my filesystem not having enough memory in the /tmp directory. Is there a way to reassign the temporary directory to another location?

Thank you, Ilayda

lcoombe commented 4 years ago

Hi Ilayda,

Try setting your TMPDIR variable (ie. export TMPDIR=<other dir>). That should lead the temporary files to be created in the directory of your choice vs. in /tmp by default.

Hope that helps! Lauren

ilaydabozan commented 4 years ago

Thank you so much, Lauren, for the quick response. I will try it out shortly and let you know.

Best, Ilayda

ilaydabozan commented 4 years ago

Hi Lauren,

Thank you for your response. I was able to change the TMPDIR to a directory with more memory allocations and Tigmint ran perfectly fine.

Best, Ilayda

lcoombe commented 4 years ago

Excellent - I'm glad that fixed the issue!