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Could not find the CellO resources directory called
'resources' in '/mnt/b0/compbio-ebs-01/igr/d0/220317_000000/130'. Will download resources to current
directory.
Running command: curl http://deweylab.biostat.wisc.edu/cell_type_classification/resources_v2.0.0.tar.gz > /mnt/b0/compbio-ebs-01/igr/d0/220317_000000/130/resources_v2.0.0.tar.gz
Running command: tar -C /mnt/b0/compbio-ebs-01/igr/d0/220317_000000/130 -zxf resources_v2.0.0.tar.gz
Running command: rm /mnt/b0/compbio-ebs-01/igr/d0/220317_000000/130/resources_v2.0.0.tar.gz
Checking if any pre-trained model is compatible with this input dataset...
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
<ipython-input-45-2570c77cb08a> in <module>
4 #sc.pp.neighbors(adata0a, n_neighbors=15)
5 #sc.tl.leiden(adata0a, resolution=2.0)
----> 6 cello.scanpy_cello(adata0a,
7 clust_key='leiden',
8 rsrc_loc='/mnt/b0/compbio-ebs-01/igr/d0/220317_000000/130',
/usr/local/lib/python3.9/site-packages/cello/scanpy_cello.py in cello(adata, clust_key, rsrc_loc, algo, out_prefix, model_file, log_dir, term_ids, remove_anatomical_subterms)
127 else:
128 # Load or train a model
--> 129 mod = ce._retrieve_pretrained_model(adata, algo, rsrc_loc)
130 if mod is None:
131 mod = ce.train_model(
/usr/local/lib/python3.9/site-packages/cello/cello.py in _retrieve_pretrained_model(ad, algo, rsrc_loc)
329 model_fname
330 )
--> 331 with open(model_f, 'rb') as f:
332 mod = dill.load(f)
333 feats = mod.classifier.features
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/b0/compbio-ebs-01/igr/d0/220317_000000/130/resources/trained_models/ir.dill'
Could somebody offer some guidance?
Thank you.
Ivan
The text was updated successfully, but these errors were encountered:
My apologies for the trouble. I just fixed the bug. If you re-install CellO via pip install -U cello-classify, then the new version should hopefully work now. Let me know if you still experience an issue.
I'm getting the same error. I downloaded the resources and unpacked with:
wget https://deweylab.biostat.wisc.edu/cell_type_classification/resources_v2.0.0.tar.gz; tar -xvf resources_v2.0.0.tar.gz
which gives me the following output:
x resources/
x resources/gene_metadata/
x resources/trained_models/
x resources/README
x resources/training_set/
x resources/training_set/labels.json
x resources/training_set/experiment_to_study.json
x resources/training_set/experiment_to_tags.json
x resources/training_set/log_tpm.h5: truncated gzip input
tar: Error exit delayed from previous errors.
and the following files:
ls resources/*
resources/README
resources/gene_metadata:
resources/trained_models:
resources/training_set:
experiment_to_study.json experiment_to_tags.json labels.json log_tpm.h5
I installed cello-classify v 2.1.1 in my conda env with pip:
Hello everyone.
I just installed the latest cello-classify version with pip. Version 2.0.3. Installation went fine.
When I try to use it, I get an error.
I execute this cell in a JupyterLab notebook:
and this is the error:
Could somebody offer some guidance?
Thank you.
Ivan
The text was updated successfully, but these errors were encountered: