pre.cluster "Could not open X.outputNames.temp" error

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cryomics
Posts: 4
Joined: Wed Mar 30, 2016 1:59 am

pre.cluster "Could not open X.outputNames.temp" error

Post by cryomics » Sun Jun 18, 2017 10:26 pm

I'm running mothur 1.39.5 on a cluster with 72 threads across 3 nodes and am having some trouble with the temp files not being found during the pre.cluster stage. I get a bunch of errors like this...

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[ERROR]: Could not open 66838.outputNames.temp
[ERROR]: Could not open 66839.outputNames.temp
[ERROR]: Could not open 66840.outputNames.temp
...
and when I do summary.seqs on the resulting files, I get a "file mismatch detected" error.

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[ERROR]: Your count file contains 1275926 unique sequences, but your fasta file contains 135805. File mismatch detected, quitting command.
I'm not even sure where to start in troubleshooting this, anyone have suggestions? Thanks

pschloss
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Re: pre.cluster "Could not open X.outputNames.temp" error

Post by pschloss » Mon Jun 19, 2017 7:35 am

Can you try running with 8 processors?

cryomics
Posts: 4
Joined: Wed Mar 30, 2016 1:59 am

Re: pre.cluster "Could not open X.outputNames.temp" error

Post by cryomics » Mon Jun 19, 2017 4:09 pm

Thanks -- it finished with 8 processors. Are some commands more susceptible to this than others? Is 8 the maximum suggested threads to run mothur on? thanks

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