Plugin error from diversity: QIIME 2021.4

[saidhinub (Dhinoth KumarB)]

Dear Team,

I just installed the latest QIIME2 version using ubuntu 20.04 LTS in WSL2. I was trying the "Moving pictures" tutorial to check if the installation working properly. At the Alpha and beta diversity analysis stage I am running in to the following error.

"Plugin error from diversity:

[('/tmp/qiime2-archive-37dumjet/81242a89-b421-4fa8-9858-26df8ce1b39f/data/feature-table.biom', '/tmp/qiime2-archive-zeujrk6z/d25377eb-8730-4d57-bf86-452a2ef5cbf3/data/feature-table.biom', "[Errno 13] Permission denied: '/tmp/qiime2-archive-37dumjet/81242a89-b421-4fa8-9858-26df8ce1b39f/data/feature-table.biom' -> '/tmp/qiime2-archive-zeujrk6z/d25377eb-8730-4d57-bf86-452a2ef5cbf3/data/feature-table.biom'")]

Debug info has been saved to /tmp/qiime2-q2cli-err-mxn8zm9n.log"

the log file has the following message.
"/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/sklearn/metrics/pairwise.py:1776: DataConversionWarning: Data was converted to boolean for metric jaccard
warnings.warn(msg, DataConversionWarning)
/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.012488721124875216 and the largest is 3.591392193348517.
warn(
/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.012972069562952403 and the largest is 2.4367036221169256.
warn(
/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.018973045082089985 and the largest is 3.159951574009762.
warn(
Traceback (most recent call last):
File "/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 244, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 512, in callable_executor
aliased_result = output._alias(prov)
File "/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/result.py", line 162, in _alias
alias._archiver = archive.Archiver.from_data(
File "/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 316, in from_data
Format.write(rec, type, format, data_initializer, provenance_capture)
File "/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/core/archive/format/v5.py", line 20, in write
super().write(archive_record, type, format, data_initializer,
File "/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/core/archive/format/v1.py", line 18, in write
super().write(archive_record, type, format, data_initializer,
File "/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/core/archive/format/v0.py", line 62, in write
data_initializer(data_dir)
File "/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/result.py", line 157, in clone_original
shutil.copytree(str(self._archiver.data_dir), str(into),
File "/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/shutil.py", line 557, in copytree
return _copytree(entries=entries, src=src, dst=dst, symlinks=symlinks,
File "/home/dhinothb/miniconda3/envs/qiime2-2021.4/lib/python3.8/shutil.py", line 513, in _copytree
raise Error(errors)
shutil.Error: [('/tmp/qiime2-archive-4s9no9s9/bb891194-6c2c-42f9-8c81-924037306b5c/data/feature-table.biom', '/tmp/qiime2-archive-gjq55yzf/aa1376ec-9b13-42ba-85b0-e321ce8deca5/data/feature-table.biom', "[Errno 13] Permission denied: '/tmp/qiime2-archive-4s9no9s9/bb891194-6c2c-42f9-8c81-924037306b5c/data/feature-table.biom' -> '/tmp/qiime2-archive-gjq55yzf/aa1376ec-9b13-42ba-85b0-e321ce8deca5/data/feature-table.biom'")]"

PLease help me to rectify this.

Thanks

[lizgehret]

Hi @saidhinub, welcome to the forum!

This looks like it may be a permissions issue related to your /tmp folder. I ran through the Moving Pictures tutorial on my end using QIIME 2 2021.4 (on OSX) and didn't run into any permission errors on my end.

Can you share the output of ls -lF / | grep tmp? This will show what permissions your /tmp directory has. You can then try running chmod 1777 /tmp to see if that fixes the issue. For further details, please see this stack overflow post:

What are correct permissions for /tmp ? I unintentionally set it all public recursively

Hopefully this will resolve the issue!

[saidhinub (Dhinoth KumarB)]

@lizgehret

ls -lF / | grep tmp

Hi Lizgehret,

Thanks for responding. Please see the permission status of /tmp. I already tried the chmod 1777 / tmp and it didn't resolve the issue.

drwxrwxrwx 1 root root 512 Jul 1 15:48 tmp/.

Thanks

[saidhinub (Dhinoth KumarB)]

This looks to be an issue with the diversity package and the WSL based Ubuntu. I tried running the demo using the virtual box and it went on fine with out any glitch. The rest of the work flow is also fine, just the diversity step doesn't work.

Thanks

Regards
BDK

[lizgehret]

Hi BDK,

Thanks for the follow-up! I'm glad you were able to get this working using VirtualBox. This is a good solution that I'd say will most likely be your easiest way forward - but in case this comes up for you again using WSL, I'd also recommend double checking that you are operating as an administrator (both on Windows and within WSL). You could also try using sudo to see if that is a feasible workaround (we've seen this work for some other folks as well who have run into similar permissions issues on WSL).

If you do find anything else that works for you within WSL moving forward, we'd greatly appreciate it if you could share those findings with us!

Cheers,
Liz