Lon Blauvelt
Lon Blauvelt
Is there anything particular to the nodes not being assigned? Like, are they partitioned differently, or are fulfilling a GPU requirement? Or are all nodes created equal? Toil does try...
@diekhans Hmmm... actually tracking the `tmp` dir usage would be useful. I'll look into it.
It looks like this is because we use `check_call` and the default of printing `stdout` directly in the call: https://github.com/DataBiosphere/toil/blob/a20dc7e59b722a2282a3f8cb8b811488e0e56edb/src/toil/lib/accelerators.py#L37 I'll make a PR to fix this. Thanks for reporting...
PR is here: https://github.com/DataBiosphere/toil/pull/5307
@mr-c Hmmm... will ask management if they've added blocks for some reason.
@mr-c I'm told nothing was changed on our end. Maybe a different jira login or the ticket was so new that the link had some latency?
Toil issues should now explicitly be viewable by anyone logged into jira.
@KeteSakharova Running this for me on your provided files seems to work on python3.6 locally? I did not attempt it on `--batchSystem LSF`, but running it on python3.6 might fix...
@KeteSakharova Sorry for the delayed response. Could you check the log file? I believe, in this case, it is: `/scratch/node-cfc331eb-7973-4fe6-9824-cb01db67d7c2-4c851d71-4470-427d-930d-37533136b43e/tmpdg4eoeec/worker_log.txt` Adding the option `--debugWorker` may also help. Not sure exactly...
@arostamianfar I don't have a minimum list unfortunately. @tthyer I'd be very interested in your results. Please keep us updated and thank you for experimenting. :)