Vsearch closed-reference clustering terminated automatically when running

Hi, I am new to QIIME and QIIME2. I met a problem when running the vsearch closed-reference clustering with the Greengene 97_otus.qza as reference. The task seems could run normally at the beginning, but it just got terminated itself after about 20 min.
Here is the commend line I used:

qiime vsearch cluster-features-closed-reference
–i-table table.qza
–i-sequences rep-seqs.qza
–i-reference-sequences 97_otus-GG.qza
–p-perc-identity 0.97
–o-clustered-table table-cr-97.qza
–o-clustered-sequences rep-seqs-cr-97.qza
–o-unmatched-sequences unmatched-cr-97.qza

After about 20min’s waiting, the word ‘Terminated’ appeared and no output is generated.

Anyone can tell me what is happening? Thank you so much!

Hello Lea,

Welcome to the Qiime 2 forums! Let's see if we can answer your question. :qiime2:

This seems like a mystery... let's look for clues! :mag: :face_with_monocle:

Are their any outputs at all? Log files? Empty files?

Does it always terminate after 20 minutes?

What kind of computer are you running this on? If this is a server or compute cluster, perhaps the command was canceled by a admin? I've had that happen to me before.

Let me know what you find!


Hi colin, thank you for your reply. For the closed-reference-clustering, it always terminated after ~20min with no output at all. But strange thing is that the same input file seems work well with the open-reference-clustering (at least there are output files that looks normal…)
I am running on a compute cluster.

Thank you again for your kind help!

Are you running out of disk space? In particular, your tmp directory might be filling up. This would be a good question to run by your sysadmin, BTW. Otherwise, please either re-rerun with the --verbose flag, or, attach the error log here - thanks!

:qiime2: :t_rex:

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