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.
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.
