Pre-clustering, 40 days in the wilderness?

So Ive been running the pre-cluster for almost 7 days. When Im not using my laptop for anything else the CPU runs at about 40% and Mothur takes up almost all of that.

Since initiating the command the laptop has not been shut down, only locked though it likely went into standby overnight. Im not sure if the processing ability differs between locked and standby but Im only using two processors as I have a maximum of four and if I use all four, the command will be carried out but the program crashes upon generation of results.

My question is, is i possible to know whether the command is still being processed or is it a case of wait and see? All I have to go on is a lack of error notification.

Thanks in advance!


Are you running it on a mac or linux? If so you could use the top command line tool and see if it is still running. Alternatively, if you’re using windows, there should be an app that looks at what the CPU is doing.

Hi Pschloss, thanks for the reply and the suggestion. Its much appreciated.

Yeah, Im using windows; are you talking about task manager?

Ive been using the processes/performances monitor which shows that mothur is taking up almost all of the CPU function and, according to the details tab, is still running normally. What I was looking for is an independent indicator in Mothur which confirms that its still working.

Im currently working the mothur tutorial and I want to know that everything is working fine before I start plugging my data in, rather than waiting 7+ days to find that it stopped working three days ago because it was in standby over night. Of course the .exe window has no options so Im guessing Im doing all I can already.

Are you currently running the stability dataset in the MiSeq SOP or your own data? If it’s your own data, could you tell us how many unique sequences and groups you have?

When you look in your directory, do you see any files with ‘precluster’ in the name? Does it look like it’s getting updated periodically? Do you have any files ending in ‘map’?

Sorry for all the questions :slight_smile:

Hej Pat. Thanks for your time. No apology necessary. I appreciate the help!

Yes, Im running the stability files in MiSeq SOP. I wanted to ensure that I could get through the tutorial before I used our data. And the results so far are good but there has been no precluster or pre.cluster files generated nor have there been any files containing or ending in ‘map’.


It should work pretty fast. I run it in the workshops as stated in the wiki page and it pushes right through. Maybe kill it and start again? You might also get the latest greatest version while you’re at it.

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