Error with command qiime qemistree make-hierarchy

[anani-a-missinou]

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]

(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]

@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

— Reply to this email directly, view it on GitHub https://github.com/biocore/q2-qemistree/issues/157#issuecomment-1855494082, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD6ULPOYDGQSAULBRI2ACDLYJLBYNAVCNFSM6AAAAABAUPYIF6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJVGQ4TIMBYGI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[anani-a-missinou]

Ok, thank you @anupriyatripathi for your response.

@helenamrusso, I appreciate your help.

Thank you