Error while dereplicating sequences

Hello, everyone!

I’m trying to dereplicate my filtered sequences in QIIME2 2019.4 (in Virtual Box). The commands were as follow:

qiime quality-filter q-score joined
–i-demux Felipe-Imported-Joined.qza
–p-min-quality 30
–p-min-length-fraction 0.8
–o-filtered-sequences Felipe-Filtered.qza
–o-filter-stats Felipe-Filtered-Stats.qza

qiime vsearch dereplicate-sequences
–i-sequences Felipe-Filtered.qza
–o-dereplicated-table Felipe-Derep-FeatTable.qza
–o-dereplicated-sequences Felipe-Derep-RepSeqs.qza

I tried this command three times already. The first time I got an error message that said something about RAM memory, but now I only get this error message:

Plugin error from vsearch:
Command ‘[‘vsearch’, ‘–derep_fulllength’, ‘/tmp/q2-QIIME1DemuxDirFmt-7727i0vt/seqs.fna’, ‘–output’, ‘/tmp/q2-DNAFASTAFormat-__os03dd’, ‘–relabel_sha1’, ‘–relabel_keep’, ‘–uc’, ‘/tmp/tmpdbc0cl4p’, ‘–qmask’, ‘none’, ‘–xsize’]’ died with <Signals.SIGKILL: 9>.
Debug info has been saved to /tmp/qiime2-q2cli-err-gmgmxrtl.log

I couldn’t find this .log about the debug info, I’m sorry.
Thanks for the help!

Forgot to say that I’m trying to run these commands in parallel to Deblur so I can compare both outputs. I already have the Feature Table and Feature Data [Sequences] outputs from Deblur.

Yep, this looks like a memory error. We do not see memory errors usually with either of these commands but this is probably a contributing factor:

Try running one at a time and/or closing down other applications on your computer that may be using up large amounts of memory.

The actions you are running are not very memory-intensive, so this is a matter of low system resources — at the end of the day this could be a hardware limitation.

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Hi, @Nicholas_Bokulich,

thanks for the answer. Sorry, I didn’t express myself right. I’m not running both commands in parallel, I’m running one at a time. I just meant I want to do both and compare them, Deblur is already done, but I cannot go forward with the dereplicate-sequences step so I can do open-reference OTU clustering.

I see, I believe my laptop 2GB will not be enough. How do I raise my RAM in Virtual Box? Anyway, I’ll try to get hold of a better computer with greater RAM.

Thank you :smiley:

please see the virtual box manual. The default setting may be very low.

Good luck!

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