I’m getting an error when I try to run the core metrics for phylogentic. Here is the code I am using:

qiime diversity core-metrics-phylogenetic
–i-phylogeny rooted-tree.qza
–i-table suziTable.qza
–p-sampling-depth 3200
–m-metadata-file hong-metadata.txt
–output-dir core-metrics-results

I created my tree using the instructions from the moving pictures tutorial here:

This is the error I am getting:

Plugin error from diversity:

[Errno 13] Permission denied: ‘/tmp/qiime2-provenance-b8dabsr0’ -> ‘/tmp/qiime2-archive-7tj7g459/886192a6-d9ac-41c3-9fec-45367e1a35f1/provenance’

Debug info has been saved to /tmp/qiime2-q2cli-err-su9ye8h3.log

Let me know if you need any additional information to be able to figure out where I have gone wrong. Thank you!

Hey there @sthansen!

This isn’t an error from QIIME 2, this is a filesystem permission error - the user you are running QIIME 2 as doesn’t have permission to write to the temporary directory. Are you using an institutional cluster? If so, check with them on this, something seems strange to me about not having permission for that.

Thank you for the help! I believe I have figured out what the issue was. Thank you!

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It would be helpful for future users of the forum to know what you did to solve your problem - if you get a chance to share here that would be great!

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In my case, it was because I was starting from the wrong directory. It was trying to access a directory via a path that made it seem like I was trying to access files I did not have authorization to access. Once I started from the directory, it worked.


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