Hi
Hello
I am running “Moving Pictures” tutorial from Qiime2, but when using the command:
qiime diversity alpha-rarefaction
--i-table table.qza
--i-phylogeny rooted-tree.qza
--p-max-depth 4000
--m-metadata-file sample-metadata.tsv
--o-visualization alpha-rarefaction.qzv
It shows me the following error:
Plugin error from diversity:
[Errno 13] Permission denied: '/tmp/qiime2-provenance-ir2epxax' -> '/tmp/qiime2/liseth/processes/1000-1711937712.96@liseth/4db3d772-7a82-4231-8911-2e894b447efe.4961683935190916441/4db3d772-7a82-4231-8911-2e894b447efe/provenance'
Debug info has been saved to /tmp/qiime2-q2cli-err-9nv95z07.log
This using qiime 2 version 2024.2. This using qiime 2 version 2024.2 with ubuntu 22.04 WSL 1 on Windows
The error file is this:
Traceback (most recent call last):
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 581, in _execute_action
results = action(**arguments)
File "", line 2, in alpha_rarefaction
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 615, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py", line 375, in alpha_rarefaction
data = _compute_rarefaction_data(table, min_depth, max_depth,
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2_diversity/_alpha/_visualizer.py", line 299, in _compute_rarefaction_data
rt, = rarefy_method(feature_table, depth)
File "", line 2, in rarefy
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/context.py", line 143, in deferred_action
return action_obj._bind(
File "", line 2, in rarefy
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 583, in callable_executor
self.signature.coerce_given_outputs(output_views, output_types,
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/core/type/signature.py", line 492, in coerce_given_outputs
output = self._create_output_artifact(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/core/type/signature.py", line 516, in _create_output_artifact
artifact = qiime2.sdk.Artifact._from_view(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/result.py", line 367, in _from_view
artifact._archiver = archive.Archiver.from_data(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 409, in from_data
Format.write(rec, type, format, data_initializer,
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/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/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/core/archive/format/v1.py", line 25, in write
provenance_capture.finalize(
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/core/archive/provenance.py", line 507, in finalize
raise err
File "/home/liseth/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/core/archive/provenance.py", line 500, in finalize
os.rename(self.path, final_path)
PermissionError: [Errno 13] Permission denied: '/tmp/qiime2-provenance-ir2epxax' -> '/tmp/qiime2/liseth/processes/1000-1711937712.96@liseth/4db3d772-7a82-4231-8911-2e894b447efe.4961683935190916441/4db3d772-7a82-4231-8911-2e894b447efe/provenance'
I searched the forum for the solution to this problem and ran the commands:
stat /tmp
File: /tmp
Size: 512 Blocks: 0 IO Block: 512 directory
Device: 2h/2d Inode: 3096224744491815 Links: 1
Access: (1777/drwxrwxrwt) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 2024-03-31 20:39:20.491252100 -0500
Modify: 2024-03-31 20:39:20.491252100 -0500
Change: 2024-03-31 20:39:20.491252100 -0500
Birth: -
stat /tmp/qiime2/
File: /tmp/qiime2/
Size: 512 Blocks: 0 IO Block: 512 directory
Device: 2h/2d Inode: 14918173765795189 Links: 1
Access: (1777/drwxrwxrwt) Uid: ( 1000/ liseth) Gid: ( 1000/ liseth)
Access: 2024-03-31 19:14:17.180829800 -0500
Modify: 2024-03-29 20:14:27.780345900 -0500
Change: 2024-03-29 20:14:27.780345900 -0500
Birth: -
stat /tmp/qiime2/liseth
File: /tmp/qiime2/liseth
Size: 512 Blocks: 0 IO Block: 512 directory
Device: 2h/2d Inode: 36310271995738091 Links: 1
Access: (0755/drwxr-xr-x) Uid: ( 1000/ liseth) Gid: ( 1000/ liseth)
Access: 2024-03-31 21:08:08.181100200 -0500
Modify: 2024-03-31 21:08:08.181100200 -0500
Change: 2024-03-31 21:08:08.181100200 -0500
Birth: -
stat /tmp -f
File: "/tmp"
ID: 100000000 Namelen: 255 Type: wslfs
Block size: 4096 Fundamental block size: 4096
Blocks: Total: 58319608 Free: 9630811 Available: 9630811
Inodes: Total: 999 Free: 1000000
I don't know what's happening and I haven't been able to solve the problem. I am new to the program and would greatly appreciate any help. The truth is I have seen several answers to similar questions and I have executed some commands but this problem does not solve