Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error with command qiime qemistree make-hierarchy #157

Open
anani-a-missinou opened this issue Dec 14, 2023 · 3 comments
Open

Error with command qiime qemistree make-hierarchy #157

anani-a-missinou opened this issue Dec 14, 2023 · 3 comments

Comments

@anani-a-missinou
Copy link

Hi dear developers,

I was very excited to use your tools, everything was fine until I got this error from running qemistree make-hierarchy

I also try to run this command with your file from the tutorial, but I get the same error. I will send you the details of the error in the hope that you understand where it comes from.

(qiime2-shotgun-2023.9) $ qiime qemistree make-hierarchy --i-csi-results features_pacs_pos_fingerprints.qza --i-feature-tables features_pacs_pos-table_hdf5.qza --o-tree features_pacs_pos-qemistree.qza --o-feature-table features_pacs_pos-table-hashed.qza --o-feature-data features_pacs_pos-data.qza
Plugin error from qemistree:

[Errno 2] No such file or directory: '/tmp/qiime2/amissinou/data/d5b2035f-8a82-471f-b757-31724593ff2e/data/csi-output'

Debug info has been saved to /tmp/qiime2-q2cli-err-9gxctqzh.log
(qiime2-shotgun-2023.9) $ more /tmp/qiime2-q2cli-err-9gxctqzh.log
Traceback (most recent call last):
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/q2cli/commands.py", line 581, in _execute_action
results = action(**arguments)
File "", line 2, in make_hierarchy
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in callable_executor
output_views = self._callable(**view_args)
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/q2_qemistree/_hierarchy.py", line 118, in make_hierarchy
collated_fps, smiles = process_csi_results(csi_result, None, metric)
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/q2_qemistree/_process_fingerprint.py", line 88, in process_csi_results
collated_fps = collate_fingerprint(csi_result, metric)
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/q2_qemistree/_process_fingerprint.py", line 28, in collate_fingerprint
fpfoldrs = os.listdir(csi_result)
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/qiime2/amissinou/data/d5b2035f-8a82-471f-b757-31724593ff2e/data/csi-output'

Thank you for your help

@anani-a-missinou
Copy link
Author

(qiime2-shotgun-2023.9) $ mkdir -p /tmp/qiime2/amissinou/data/d5b2035f-8a82-471f-b757-31724593ff2e/data/csi-output
(qiime2-shotgun-2023.9) $ qiime qemistree make-hierarchy --i-csi-results features_pacs_pos_fingerprints.qza --i-feature-tables features_pacs_pos-table_hdf5.qza --o-tree features_pacs_pos-qemistree.qza --o-feature-table features_pacs_pos-table-hashed.qza --o-feature-data features_pacs_pos-data.qza
Traceback (most recent call last):
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 118, in _get_versions
with self.open(self.VERSION_FILE) as fh:
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 248, in open
return open(os.path.join(self.path, relpath))
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/qiime2/amissinou/data/d5b2035f-8a82-471f-b757-31724593ff2e/VERSION'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/q2cli/util.py", line 488, in _load_input_file
artifact = qiime2.sdk.Result.load(fp)
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/sdk/result.py", line 76, in load
archiver = cache._load_uuid(peek.uuid)
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/cache.py", line 955, in _load_uuid
return Archiver.load_raw(path, self)
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 385, in load_raw
archive = cls.get_archive(filepath)
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 320, in get_archive
archive = _NoOpArchive(filepath)
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 92, in init
self.version, self.framework_version = self._get_versions()
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 128, in _get_versions
raise ValueError("Archive does not contain a correctly formatted"
ValueError: Archive does not contain a correctly formatted VERSION file.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/q2cli/click/type.py", line 116, in _convert_input
result, error = q2cli.util._load_input(value)
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/q2cli/util.py", line 397, in _load_input
artifact, error = _load_input_file(fp)
File "/home/amissinou/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/q2cli/util.py", line 494, in _load_input_file
raise ValueError(
ValueError: It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'CSIFolder' and format 'CSIDirFmt'

There was a problem loading 'features_pacs_pos_fingerprints.qza' as an artifact:

It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'CSIFolder' and format 'CSIDirFmt'

See above for debug info.

(qiime2-shotgun-2023.9) $ qiime tools peek features_pacs_pos_fingerprints.qza

UUID: d5b2035f-8a82-471f-b757-31724593ff2e
Type: CSIFolder
Data format: CSIDirFmt

@anupriyatripathi
Copy link
Collaborator

anupriyatripathi commented Dec 14, 2023 via email

@anani-a-missinou
Copy link
Author

Ok, thank you @anupriyatripathi for your response.

@helenamrusso, I appreciate your help.

Thank you

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants