Error with command qiime qemistree make-hierarchy #157
Comments
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(qiime2-shotgun-2023.9) $ mkdir -p /tmp/qiime2/amissinou/data/d5b2035f-8a82-471f-b757-31724593ff2e/data/csi-output During handling of the above exception, another exception occurred: Traceback (most recent call last): The above exception was the direct cause of the following exception: Traceback (most recent call last): 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 |
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@Mannochio Russo, Helena ***@***.***> might have used
this recently and could likely help!
Anupriya Tripathi
Principal AI Scientist, Genentech <https://www.gene.com/>
…On Thu, 14 Dec 2023 at 01:33, Anani Amegan MISSINOU < ***@***.***> wrote:
*(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
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Ok, thank you @anupriyatripathi for your response. @helenamrusso, I appreciate your help. Thank you |
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
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