Core -metrics -phylogenetics


Please assist, I ran qiime diversity core-metrics-phylogenetic --i-table tablej.qza --i-phylogeny rooted-tree.qza --p-sampling-depth 1450 --m-metadata-metadata.tsv --output-dir core-diversity

and the error I got is * Plugin error from diversity* /var/tmp/pbs.1640270.sched01/q2-AlphaDiversityFormat-uajsgvd1 is not a(n) AlphaDiversityFormat file

Thanks in advance for your help

Hi @kedi,

That’d odd, I think the most likely situation is the alpha diversity is being returned as empty data which is then written as an empty file, which the AlphaDiversityFormat dislikes.

That said, I don’t know why that would be happening, is it possible any of the IDs don’t match between either the metadata, table, or phylogeny? Or perhaps the sampling depth is too high (although I really doubt that’s the issue).

If you didn’t mind sharing your data, I could have a look at it, so you could send me a DM with links to it or if they are small enough, upload directly in the DM.

Hi @ embolyen

Thanks , sorted turned out the input file was wrong.


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