Biostar Test Site

This is site is used for testing only. Visit: https://www.biostars.org to ask a question.

Vg gamsort temporary folder
1
1
Entering edit mode
12 months ago

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.

Thanks!

vg vg gamsort • 303 views
ADD COMMENT
1
Entering edit mode
12 months ago
Jouni Sirén ▴ 130

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 COMMENT
0
Entering edit mode

Thanks! changing the environment variables did the trick!

ADD REPLY

Login before adding your answer.

Traffic: 239 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6