demux emp-paired killed, QIIME 2 version 2020.2

Hello. I am trying to demultiplex my sequences using the following command:

qiime demux emp-paired
–i-seqs emp-paired-end-sequences.qza
–m-barcodes-file [insert barcode file name].txt
–m-barcodes-column barcode-sequence
–o-per-sample-sequences demux.qza
–o-error-correction-details demux-details.qza

I have not been getting an error message. Instead, after 30 minutes(?), it is killed.

I am using VirtualBox (6.0.22) with QIIME 2 version 2020.2. I am using 4 processors and 12 GB of RAM. The file has about 90 samples. Prior to attempting demux, I imported the samples with qiime tools import.

Is this file too large for my system? Thank you in advance for your help.

Welcome to the forum, @mfkirk!
Thanks for putting together such a detailed post. This situation is not uncommon, and I suspect you’re right (this is likely an out-of-memory error), but there are other things that could be happening.

What is the actual error message? Does it indicate a SIGKILL? These are often OOM errors, but could be caused by other things too (e.g. your computer misbehaving when it goes to sleep, etc).

Here are some things you can do to troubleshoot/work around the issue. Definitely check that your VM is provisioned the way that you expect before doing anything else.

Looking forward:

  • There are other memory-intensive commands you’ll run into during your analysis. Many of them have parameters that let you reduce memory needs, “chunking” your data, or reducing the size of some computational widget to make make things go easier on your ram. Keep an eye out for these in the docs.
  • If you run into other issues, check out the forum’s search :mag: feature. Most common problems have been treated at length here, and it may take you less time to find an answer than to write up a new post.

Good luck!
Chris :snail:

Thank you Chris! I increased RAM and the number of processors and it appears to have worked. I appreciate your time and the extra tips. I will definitely keep those in mind as I move forward. Thank you again!

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Glad everything worked out, @mfkirk! Happy :qiime2:-ing

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