Besides the log file, how else can we check progress in Mothur?


I am using a Linux server (132 GB RAM), set up by our IT support to run Mothur.

For the step cluster.split, Mothur has been running for over 2 days and the Mothur interface hasn’t changed a bit since this morning. I know it’s still running since I can see there is 1 Mothur job currently running on the server.
Does Mothur have some kind of progress indicator that I can watch to track the progress: how much is done; how much longer the wait is…

On a related note, I used to be able to include the “processors=8” option in cluster.split to have 8 Mothur jobs running simultaneously. This time, however, there is only 1 Mothur job even when I specified “processors=8”. Any thoughts on why?

Thank you!


Hi spll,

It would be helpful to see the exact command you are running with cluster.split. I also suspect that you only have one group. Can you run count.groups(count=????) where you give it the name of your count file? If you can post the output to the screen for that command we can take a look.



Thank you Pat! My answers to your questions are listed below. Could you still comment on if Mothur has some kind of progress indicator that we can watch to track the progress?

The cluster.split command: cluster.split (fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table,, splitmethod=classify, taxlevel=6, cutoff=0.03, processors=8)

Here is the output after I run count.groups:


Thanks - the first step is splitting the files up and this might take a bit of time. Do you see any files being produced in your directory?

Can you tell me what you get when you run …

grep -c "^>" stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta

I suspect you have a lot of uniques - what region did you sequence and with what chemistry?


Hi Pat, I got 397554 when I run the grep command.
Although not sure what to make of this number 397554, I already read your blog post and know the problem I encounter has to do with high error rates in my data.

Unfortunately I won’t be able to re-run the ngs using a shorter amplicon. Whatever I get from this data set will be it. At this point, I will see if our IT support can install Mothur on a more powerful server for me. We don’t have a contract with Amazon.

So is it true that there is no way for users to track progresses in Mothur (except checking the log file)? I am really curious about this. Thank you!


If you run ls -lth in the directory where you are outputting your files, you should see the files growing over time.