monitoring mothur's progress

How do you guys recommend monitoring that mothur is still working on some of these huge commands? I’m running Ubuntu 11.10 and am just watching system process with htop but that just shows that mothur is maxing out 3 of my processors. How do you check that it hasn’t crashed? I’m running chimera.uchime on a 1M+ fasta and will let it run as long as it needs but also don’t want to be sitting here for weeks only to find that it crashed Monday, if you know what I mean.

(ps sorry if this isn’t in the correct area of the forum)

So many of the commands - including uclust show output to indicate progress. Is this showing anything?

This is all I’ve seen, it hasn’t added anything new since Tuesday morning.

mothur > mothur > chimera.uchime(fasta=bac.unique.good.filter.unique.fasta, name=bac.unique.good.filter.names, group=bac.pick.groups, processors=5)

uchime by Robert C. Edgar
This code is donated to the public domain.

Checking sequences from bac.unique.good.filter.unique.fasta …
[ERROR]: Could not open bac.unique.good.filter.unique.uchime.chimeraBP241
[ERROR]: Could not open bac.unique.good.filter.unique.uchime.chimera25573.tempSL167
[ERROR]: Could not open bac.unique.good.filter.unique.uchime.chimera25572.tempOL334

The [ERROR] messages would be a good sign that something is wrong :slight_smile: I’d kill it and start again. Sometimes flakey things happen or people don’t have the correct write permissions.


so [ERROR] is always fatal? Kill a command if I see that?

Generally speaking, yes.