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Hi there,
First off, I'd like to say thank you for making this wonderful tool!
I'm having an issue where I am trying to run MapMyCells using the code from this repo, and I am trying to do so with the online 10x Whole Mouse Brain taxonomy (CCN20230722) that is used on the MapMyCells website. I am also trying to do so programmatically so I don't have to use the otherwise unwieldy command line expression to run it. My python code to perform a test run looks like this (I am also using the sample mouse brain h5ad file provided on the website to test it out):
However, I am getting the following error, and I can't seem to figure out what is causing it:
Traceback (most recent call last):
File "/Users/ariandjahed/LocalRepos/SharedRepos/Bonsai_SpatialTranscriptomics/mapmycells_data/test_with_local_repo/mapmycellstest.py", line 26, in <module>
mapping_runner.run()
File "/Users/ariandjahed/LocalRepos/Other/cell_type_mapper/src/cell_type_mapper/cli/from_specified_markers.py", line 71, in run
run_mapping(
File "/Users/ariandjahed/LocalRepos/Other/cell_type_mapper/src/cell_type_mapper/cli/from_specified_markers.py", line 144, in run_mapping
output = _run_mapping(
^^^^^^^^^^^^^
File "/Users/ariandjahed/LocalRepos/Other/cell_type_mapper/src/cell_type_mapper/cli/from_specified_markers.py", line 310, in _run_mapping
create_marker_cache_from_specified_markers(
File "/Users/ariandjahed/LocalRepos/Other/cell_type_mapper/src/cell_type_mapper/type_assignment/marker_cache_v2.py", line 115, in create_marker_cache_from_specified_markers
marker_lookup = validate_marker_lookup(
^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/ariandjahed/LocalRepos/Other/cell_type_mapper/src/cell_type_mapper/type_assignment/marker_cache_v2.py", line 775, in validate_marker_lookup
raise RuntimeError(error_msg)
RuntimeError: After comparing query data to reference data, no valid marker genes could be found at any level in the taxonomy.
Example of genes in query set:
['2900052N01Rik', '4930509J09Rik', '9330158H04Rik', 'A630012P03Rik', 'A830036E02Rik']
What would you advise? Any help would be appreciated.
Thank you so much in advance!
The text was updated successfully, but these errors were encountered:
Hi there,
First off, I'd like to say thank you for making this wonderful tool!
I'm having an issue where I am trying to run MapMyCells using the code from this repo, and I am trying to do so with the online 10x Whole Mouse Brain taxonomy (CCN20230722) that is used on the MapMyCells website. I am also trying to do so programmatically so I don't have to use the otherwise unwieldy command line expression to run it. My python code to perform a test run looks like this (I am also using the sample mouse brain h5ad file provided on the website to test it out):
However, I am getting the following error, and I can't seem to figure out what is causing it:
What would you advise? Any help would be appreciated.
Thank you so much in advance!
The text was updated successfully, but these errors were encountered: