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hammerlab / biokepi

Bioinformatics Ketrew Pipelines
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NetMHC temp directory can't be on mounted NFS #467

Closed julia326 closed 7 years ago

julia326 commented 7 years ago

Otherwise it runs into issues when trying to clean up after itself and removing temp directories:

Segmentation fault (core dumped)
rm: cannot remove '/pgv-results/biokepi-coco-work/toolkit-coco/netmhc-tools/tmp/tmpqZd1O7/.nfs000000000008febe00000843': Device or resource busy
rm: cannot remove '/pgv-results/biokepi-coco-work/toolkit-coco/netmhc-tools/tmp/tmpqZd1O7/.nfs000000000008febf00000841': Device or resource busy
rm: cannot remove '/pgv-results/biokepi-coco-work/toolkit-coco/netmhc-tools/tmp/tmpqZd1O7/.nfs000000000008fec000000842': Device or resource busy
rm: cannot remove '/pgv-results/biokepi-coco-work/toolkit-coco/netmhc-tools/tmp/tmpqZd1O7/.nfs000000000008fec100000844': Device or resource busy
COULD NOT REMOVE TEMPORARY DIRECTORY /pgv-results/biokepi-coco-work/toolkit-coco/netmhc-tools/tmp/tmpqZd1O7
PROBABLY ON MOUNTED FILE SYSTEM!

This fails silently (ish) by failing to return a bunch of predictions. To avoid, make sure that TMPDIR is set to something local.