Please help me fix plugin error while making 16S taxonomy .qzv file

I am trying to create a 16S taxonomy visualization from a .qza file and have encountered a plugin error that I have trouble understanding. Please help!

I am running qiime 2 - 11.2020 on a cluster.

Here are the commands and errors:

]$ qiime metadata tabulate --m-input-file 16S-taxonomy.qza --o-visualization 16S-taxonomy.qzv --verbose

/share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/site-packages/ijson/backends/init.py:22: UserWarning: Cannot determine yajl version, assuming <1.0.12
warnings.warn(‘Cannot determine yajl version, assuming <1.0.12’)
Traceback (most recent call last):
File “/share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/site-packages/q2cli/commands.py”, line 329, in call
results = action(**arguments)
File “”, line 2, in tabulate
File “/share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 452, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File “/share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/site-packages/q2_metadata/_tabulate.py”, line 36, in tabulate
context={‘table’: table, ‘page_size’: page_size})
File “/share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/site-packages/q2templates/_templates.py”, line 41, in render
shutil.copy2(os.path.join(template_data, ‘base.html’), temp_dir.name)
File “/share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/shutil.py”, line 264, in copy2
copystat(src, dst, follow_symlinks=follow_symlinks)
File “/share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/shutil.py”, line 229, in copystat
_copyxattr(src, dst, follow_symlinks=follow)
File “/share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/shutil.py”, line 164, in _copyxattr
value = os.getxattr(src, name, follow_symlinks=follow_symlinks)
OSError: [Errno 22] Invalid argument: ‘/share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/site-packages/q2templates/templates/base.html’

Plugin error from metadata:

[Errno 22] Invalid argument: ‘/share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/site-packages/q2templates/templates/base.html’

See above for debug info.

Thank you for your time!

Hi @abhisheknaik211! Welcome to the forum! :wave:

It looks like there is something going on with your conda installation. Let’s see if we can get this sorted out!

Can you share the output of these commands? Make sure your qiime2 environment is activated first.

  • env
  • conda info
  • conda list
  • ls -al /share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/site-packages/q2templates/templates/base.html

Thank you for your help Andrew!

Here are the outputs you requested:

env: env.txt (11.7 KB)

conda info and conda list: conda info, conda list.txt (32.6 KB)

$ ls -al /share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/site-packages/q2templates/templates/base.html
-rw-rw-r-- 2 share root 1330 Dec 5 15:53 /share/pkg/condas/2018-05-11/envs/qiime2-2020.11/lib/python3.6/site-packages/q2templates/templates/base.html

1 Like

Hi @abhisheknaik211,

Sorry for the delay!

I think there is something funky going on with file permissions either with the temporary directory that QIIME 2 is using or in the location that QIIME 2 is installed. I noticed there is no TMPDIR variable defined in your environment. One thing you might try is to set the TMPDIR environment variable to a directory that you have write permissions for, eg, export TMPDIR=/tmp and then try running your command.

Are you running something like module load on a shared cluster to use QIIME 2?

If you have the option of starting over from scratch with a brand new QIIME 2 installation, I would definitely recommend that.