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!

(Colin J Brislawn) #2

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!

(Matthew Ryan Dillon) #4

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: