Tmp directory for `qiime dada2 denoise-paired`

Is there a way to specify the temporary directory location for qiime dada2 denoise-paired? During an error, the command writes to /tmp/ by default. This is a problem when the job is run on a SGE compute cluster, since the /tmp/ directory differs between the cluster node that the job ran on versus the /tmp/ of the job submit host (the server where the qsub job was submitted from). This causes a lot of confusion with members of my lab who check the /tmp/ in the submit host, but they don’t know which cluster node the job was run on, so they don’t know which /tmp/ actually contains the log file. I don’t see any parameter for qiime dada2 denoise-paired to specify the tmp directory. Is there a global variable that can be set (eg., QIIME2_TMP=/path/to/my/temp_dir/)?

Hey @nick-youngblut,

There is!
You can use the “standard” TMPDIR environment variable. QIIME 2 should respect that (and any plugins which don’t we would like to have a word with :wink: )

2 Likes

Great! Thanks for the help!

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.