Thanks @mentorwan!
I’m very strongly suspecting that /spin1/scratch is a network mounted file share. It looks like we are having issues with shutil.rmtree() (a part of the Python standard library) and it doesn’t seem to be “allowed” to delete the files (which is it’s only job).
I have an idea for how we might be able to confirm this:
I’m guessing you have a metadata file that we can use qiime metadata tabulate on (which will make this test fast).
I’d like to try it two different ways, one way:
qiime metadata tabulate --m-input-file <your file> --o-visualization doesntmatter.qzv
(I would expect to see the same errors as above)
Then we can run it again, but this time setting up a different temporary directory:
mkdir $HOME/delete-this-later
(this will be our new /spin1/scratch/ywan)
TMPDIR=$HOME/delete-this-later qiime metadata tabulate --m-input-file <your file> --o-visualization doesntmatter.qzv
(this will change TMPDIR for only this command)
If you do not see an error, then it definitely has to do with what /spin1/scratch is.
However, if you do see the same error, then it’s a little inconclusive as your home directory may also be mounted the same way (pretty common), or there is still something more fundamentally wrong (and I have no idea what that might be yet).
I’d also like to see what
ls $HOME/delete-this-later
says after you have run the above (it should be empty).
Thanks again for you assistance in debugging this! I really appreciate it!