I’m running Qiime2-2018.11 on a 16S dataset of 288 samples, sequenced on a Miseq. Here is my pipeline: https://github.com/scottdaniel/TagSequencingPipeline/blob/master/qiime2/qiime2_pipeline.bash
The code runs up to the point of
qiime diversity beta-phylogenetic (line 243) where it stops and spits out an error:
Plugin error from diversity:
Data must be symmetric and cannot contain NaNs. Debug info has been saved to /tmp/qiime2-q2cli-err-8uujpowz.log
I attached the error log even though it wasn’t that informative. error-log-for-beta-phylogenetic.txt (1.5 KB)
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.