One thing I tried was "qiime toots export | biom convert --to-tsv" for the table.qza FeatureTable[frequency] and checked the resultant table.tsv for Na's. There were none.
The big question is whether this is a bug or something wrong with my data? Should I remove the controls from the table prior to submitting it to beta-diversity calculation? Thanks a million.
Sorry to hear things aren't working for you :(. Can you help us help you by preparing a small minimum working example? And please pare it down to the minimum commands required to reproduce the error. Thanks!
The problem is caused by sample DNAfreewater6 --- it has no observations at all (check out your table summary viz). You can filter that out by updating your filter-samples command above to include --p-min-frequency 1, which will drop any samples with no observations in it.
Keep us posted!
thermokarst
(Matthew Ryan Dillon)
unassigned thermokarst
#6
Could there be a line somewhere in the code that would tell the user that this was the sample causing the problem? If not, I’ll just have to check my samples from now on and make sure there are none with 0 features. Thanks again.
thermokarst
(Matthew Ryan Dillon)
assigned thermokarst
#8
I suppose so, but technically the error is originating outside of QIIME 2 (that was coming from scikit-bio). This isn’t usually a problem for most folks, since they usually provide a rarefied feature table, which will not include any zero-sequence samples.
With that said, we would certainly appreciate a contribution to add this error check, if you’re interested!
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thermokarst
(Matthew Ryan Dillon)
unassigned thermokarst
#10