At least on our system (Ubuntu based), sending a SIGTERM, or possibly a HUP to mothur can cause all of the procs to go defunct, leaving as many zombies as there were threads in mothur. it would be really great if I didn’t have to killall -9 if I cancel a job using mothur on a job scheduled system.
As an associated issue, it would be EXCEPTIONAL if, when running Mothur in interactive mode, it would catch CTRL+C and cancel the currently running command, rather than drop out of mothur entirely.
after troubleshooting, first item should be deleted, replaced with:
when running in batch mode, perhaps mothur should EXIT when previous command is going to cause mass hysteria on part of later commands?
in this case:
make.contigs() with misnamed input files will run to completion, and cause some sort of threading nightmare, once it gets to later steps in the batch…
Thanks for bringing this issue to our attention. The catch for CTRL+C in mothur is designed to let you bail out of a command not an instance of mothur. We added this feature thinking about interactive mode where you may want to exit a command after noticing an error, but would want to continue using mothur. It doesn’t work well in batch or script mode because bailing out of a command usually forces the following commands to error out. We are always looking for ways to make mothur more user friendly. I will add this feature request to our list.