Galaxy- Combining 2 Queries

Question

[Bdv]

hi I tried to combine 2 queries in galaxy and received the following error:

sort: write failed: /tmp/sortKHo9Wg: No space left on device join: invalid file number in field spec: `-1'

How this can be fixed? I worked on 454 data and created a SAM file there, then filtered for the reads which aligned only once to the genome and then, according to the tutorial, tried to combine the quries and to leave only those raws in the SAM file which are also found in the filtered file (and thus occur only once), this is when I received the error. Many thanks!

[Sean Davis]

The error seems pretty specific--the server running the query is out of tmp space. Looks like you probably want to write to the galaxy support email list?

[Madelaine Gogol]

• http://lists.bx.psu.edu/listinfo/galaxy-user
• http://lists.bx.psu.edu/listinfo/galaxy-dev

[Zhidkov]

I think when you filtering SAM file on certain field (in your case mapped unique), obtained file (with unique reads only) is still in SAM format. In addition today I received several times a message that public Galaxy was down, so try to perform your analysis again.

Answer 1

[Ketil]

Using 'sort' and 'join' seems like a plausible way to do what you describe.

The 'sort' command can use quite a bit of temporary disk space. The /tmp partition is small in some setups (sometimes just using a tmpfs ramdisk), so this can be overridden by setting $TMPDIR or using the -T option to point to a temporary directory with more available space.

If this is something Galaxy is doing, it probably needs to be fixed there.

Answer 2

[Geparada]

are you using galaxy on the cloud or the public server?

I often use galaxy at the public server and I had that error one time. A way to continue with your workflow, is cloning only the active that are not deleted of your history, and try to run your process again.

If you aren't using the public server. Just use a bigger store device.

Good luck!