Question: Vg gamsort temporary folder
gravatar for arunkumarramrsh
9 weeks ago by
arunkumarramrsh10 wrote:

Hi, I was trying to use vg gamsort to sort and index the gam file so as to use vg chunk later. I get the following error when I run gamsort

[E::bgzf_flush] File write failed (wrong size)

[E::bgzf_flush] File write failed (wrong size)

terminate called without an active exception

I think this is because it is running out of space in the temporary directory. I am not sure where this tmp directory is or if I have access to it, as I work in a shared cluster. Is there a way to specific the tmp directory as it is possible for vg index? I got the same error while running vg index but was able to rectify it using the -b option. While vg index allows indexing of a sorted gam file, mine comes directly from vg map so don't think it is sorted.


vg vg gamsort • 120 views
ADD COMMENTlink modified 9 weeks ago by Jouni Sirén90 • written 9 weeks ago by arunkumarramrsh10
gravatar for Jouni Sirén
9 weeks ago by
Jouni Sirén90
UCSC Genomics Institute
Jouni Sirén90 wrote:

vg gamsort, as well as most other vg commands, takes the temporary directory from environment variables. The primary variable is TMPDIR, but vg also checks a number of other variables (TMP, TEMP, TEMPDIR, USERPROFILE) if that has not been set. If everything else fails, vg falls back to /tmp.

The main exception are temporary files created by external libraries. We try to make the libraries use the same directory vg uses, but that's not always possible.

ADD COMMENTlink written 9 weeks ago by Jouni Sirén90

Thanks! changing the environment variables did the trick!

ADD REPLYlink written 9 weeks ago by arunkumarramrsh10
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