Trouble with "feature-table group"

Hi! I am having an issue with the feature-table group command in Qiime2 (ver. 2017.12). Specifically, I have two sequencing runs that I am trying to merge, summing adding the OTU counts for some re-sequenced samples from run #2 using the indexes from run #1. I have successfully merged the two table.qza, ref-seqs.qza, and mapping files, and I have created a new column in the mapping file that identifies each sample by its proper index from run #1.

Then I execute the following command:

qiime feature-table group \
--i-table merged-table.qza \
--p-axis sample \
--m-metadata-file merged-map.txt \
--m-metadata-category "run1_id" \
--p-mode sum \
--o-grouped-table grouped-table.qza \

This command, while not killed, does not finish in 2 hours on a compute node with 16g of memory (which seems entirely sufficient). Do you have any idea what could be going wrong?

Hi @wsano! I’d expect the command to have finished within 2 hours and having 16GB at its disposal. How many samples and features are in merged-table.qza? To find that out, you can run qiime feature-table summarize. We haven’t performance benchmarked the feature-table group method, so you may have discovered a performance bug.

Another option is to share your data files with me (merged-table.qza and merged-map.txt) so that I can try to reproduce the issue locally. You can send those files to me via a Direct Message on the forum, Dropbox, Google Drive, etc. Thanks!

Hi! Thanks for the response. merged-table.qza has a total of 43 samples and 451 features, which again doesn’t seem like enough to cause a problem given my experience with qiimes other functionality. I will send you my data files via dm.

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Thanks for sending the files @wsano!

I agree, that’s not a large number of samples or features.

Can you please send me merged-table.qza? I need the .qza file to reproduce this locally (you sent me a .qzv file, which is a visualization, and I’m not able to recreate the feature table from the visualization). Thanks!

Thanks for the .qza @wsano! Using a native QIIME 2 2017.12 installation on Ubuntu, the command completed successfully within 3-4 seconds.

I noticed your command has a trailing backslash character (\) after the final option:

--o-grouped-table grouped-table.qza \

If a command line ends with a backslash, the shell (e.g. bash) will wait for further input before executing the command. My hunch is that the command never ran. Can you try rerunning your command without the trailing backslash character?

qiime feature-table group \
--i-table merged-table.qza \
--p-axis sample \
--m-metadata-file merged-map.txt \
--m-metadata-category "run1_id" \
--p-mode sum \
--o-grouped-table grouped-table.qza

Thanks!

It worked! Thanks for the fix.

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