Good afternoon! I am using Qiime2 in a conda env and ran the beta-rarefaction plug-in:
qiime diversity beta-rarefaction
I would get the error message:
Plugin error from diversity:
Command '['ssu', '-i', '/var/folders/ff/1kk8pp_x6xq9jk3pkmnty9w40000gn/T/qiime2/marlydmejia/data/8332f6cf-72d4-4eca-a8ef-ee85a4516a31/data/feature-table.biom', '-t', '/var/folders/ff/1kk8pp_x6xq9jk3pkmnty9w40000gn/T/qiime2/marlydmejia/data/bc681fc9-3a54-48b7-9143-434a11a5a94c/data/tree.nwk', '-m', 'weighted_normalized', '-o', '/var/folders/ff/1kk8pp_x6xq9jk3pkmnty9w40000gn/T/q2-LSMatFormat-rtnbsu1n']' returned non-zero exit status 1.
Using verbose, we also saw:
Compute failed in one_off: Table observation IDs are not a subset of the tree tips. This error can also be triggered if a node name contains a single quote (this is unlikely). Traceback (most recent call last):
The table above had been feature-filtered (also exported and re-imported into qiime), so we tried running with an un-exported, minimally filtered table and still got the error. We then ran a smaller sample-filtered table (4 samples) that went through the process. When we opened the tree and saw many single-quotes, so we left that alone and pursued computational or mismatched causes of error. We tried using "export UNIFRAC_USE_GPU=N" and another computer to no avail. Finally, we found that there was a mismatch in features where the ID VOUX01000001 was not in the tree and therefore caused an error when I used the weighted_normalized_unifrac method. I had created my taxonomy file out of my table using:
qiime greengenes2 taxonomy-from-table
and, upon exporting my taxonomy into a tsv, saw that the feature ID corresponded to an unspecific call.
It made sense in my mind that it would not by in the tree. Once I removed this ID found in 10 samples at less than 0.1 frequency, the phylogenetic tree could be used for generation of the appropriate output files. It was odd because I had previously run the "qiime diversity core-metrics-phylogenetic" with the 2022.10.phylogeny.asv.nwk.qza and got a bunch of output files where distances ranged 0 - 400s. *I actually started with the 2022.10.phylogeny.asv.nwk.qza in beta-rarefaction and then thought it wasn't working because it didn't match the md5 taxonomy file I used. Switching between phylogeny.asv or .md5 still gave me the error.
Is this something that can be fixed in taxonomy so that it doesn't lead to this mismatching? Or can it be stated as a warning for users to remove calls that would not end up on a tree?
Thank you so much for your time!