Plugin error from diversity to get alpha and beta diversity

hi everyone!
Im trying to make alpha and beta diversity but when i run the following:

qiime diversity core-metrics-phylogenetic
--i-phylogeny diversity/rooted_tree.qza
--i-table ft_norm.qza
--m-metadata-file manifest.tsv
--p-sampling-depth 70

it delivers the following:

Plugin error from diversity:

  Command '['faithpd', '-i', '/tmp/qiime2-archive-ejg1vpg5/b9610ce0-1b41-47f6-8d53-db8ffbf5805b/data/feature-table.biom', '-t', '/tmp/qiime2-archive-l2v5o3n_/9cd2f4a3-3e36-428c-a4a5-d7645fa37ec4/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-kt9qqyrl']' returned non-zero exit status 1.

See above for debug info.

How can i solve it?


Hi @kevin_SalOrt,

It doesn't look like you included the full error log (the additional error messaging that is produced when including the --verbose flag in your command) - but the first thing that I am seeing without looking at that is the following line in your command:


It looks like this might be a typo for the following parameter:


Make sure there is a space between that command and the name of the directory you would like to send unspecified results to.

If that doesn't solve the problem, please re-run the full command with the --verbose flag and copy/paste the entire terminal output in your response. Thanks! :lizard:


thanks! it looks like it was the space because when I added it, I got no problem


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