Redirecting ABySS temp directory

[thh32]

Basically I am filling my temp directory whilst running ABySS and due to running on a server am unable to increase the size of my temp dir but would be able to provide it with a large area if I can redirect which directory ABySS uses. I have seen online people are saying to use the -T option however this doesn't seem to exist/work in the version I am using (abyss/1.3.7). I have attempted putting the -T option at every point in the submission file but always fails. Any help anyone can provide would be greatly appreciated.

Many thanks,
Thomas Hitch

[peromhc]

in bash you can change the location of TMP like this:

export TMPDIR=/path/to/your/tmp

Set TMP before you execute ABySS, and you should be OK to go.

[thh32]

@peromhc I have tried your solution but Abyss failed again and the error file stated

Building the suffix array...
Building the suffix array...
Building the suffix array...
Building the Burrows-Wheeler transform...
Building the character occurrence table...
Building the Burrows-Wheeler transform...
Building the Burrows-Wheeler transform...
Building the character occurrence table...
Building the character occurrence table...
Mateless          0
Unaligned   5004524  41.3%
Singleton   2508903  20.7%
FR          2159292  17.8%
RF              307  0.00253%
FF              887  0.00732%
Different   2437470  20.1%
Total      12111383
Mateless          0
Unaligned   4868853  25.9%
Singleton   4053627  21.5%
FR          3480448  18.5%
RF              321  0.00171%
FF              708  0.00376%
Different   6418481  34.1%
Total      18822438
sort: write failed: /tmp/725829.1.large.q/sortQGku1s: No space left on device
error: no @SQ records in the SAM header
make: *** [L002-3.dist] Error 1
make: *** Deleting file `L002-3.dist'
make: *** Waiting for unfinished jobs....
Mateless          0
Unaligned   4817815  25.8%
Singleton   4157786  22.3%
FR          3414023  18.3%
RF              275  0.00147%
FF              650  0.00348%
Different   6260889  33.6%
Total      18651438

[westerman]

Could you show us your EXPORT command followed by your ABySS command? If done properly then the program 'sort' (which ABySS is using) should not point to '/tmp'.

[thh32]

I used the command in the wrong place, now it works. I had put the export command separate to my submission script, when export command was put into the submission file it redirected the tmpdir and works fine.

Thanks alot,

Tom