ValueError: Found array with 0 feature(s) (shape=(2, 0)) while a minimum of 1 is required.

[pcantalupo]

Hi , I'm testing the pipeline with 200K reads from 1 sample. I got the following error:

Skip filtering by dispersion since number of variables are less than `n_top_genes`.
Traceback (most recent call last):
  File "/opt/scvelo_analysis.py", line 65, in <module>
    main(args.alevin_h5ad_file)
  File "/opt/scvelo_analysis.py", line 26, in main
    sc.pp.pca(adata, n_comps=50)
  File "/usr/local/lib/python3.8/dist-packages/scanpy/preprocessing/_pca.py", line 200, in pca
    output = _pca_with_sparse(
  File "/usr/local/lib/python3.8/dist-packages/scanpy/preprocessing/_pca.py", line 268, in _pca_with_sparse
    X = check_array(X, accept_sparse=['csr', 'csc'])
  File "/usr/local/lib/python3.8/dist-packages/sklearn/utils/validation.py", line 72, in inner_f
    return f(**kwargs)
  File "/usr/local/lib/python3.8/dist-packages/sklearn/utils/validation.py", line 658, in check_array
    raise ValueError("Found array with %d feature(s) (shape=%s) while"
ValueError: Found array with 0 feature(s) (shape=(2, 0)) while a minimum of 1 is required.
INFO [job scvelo_analysis] Max memory used: 157MiB
ERROR [job scvelo_analysis] Job error:
("Error collecting output for parameter 'annotated_h5ad_file': steps/scvelo-analysis.cwl:18:7: Did not find output file with glob pattern: '['scvelo_annotated.h5ad']'.", {})
WARNING [job scvelo_analysis] completed permanentFail
ERROR [step scvelo_analysis] Output is missing expected field file:///Users/pgc92/projects/hubmap/salmon-rnaseq/pipeline.cwl#scvelo_analysis/annotated_h5ad_file
ERROR [step scvelo_analysis] Output is missing expected field file:///Users/pgc92/projects/hubmap/salmon-rnaseq/pipeline.cwl#scvelo_analysis/annotated_zarr_dir
ERROR [step scvelo_analysis] Output is missing expected field file:///Users/pgc92/projects/hubmap/salmon-rnaseq/pipeline.cwl#scvelo_analysis/embedding_grid_plot
ERROR [step scvelo_analysis] Output is missing expected field file:///Users/pgc92/projects/hubmap/salmon-rnaseq/pipeline.cwl#scvelo_analysis/embedding_stream_plot
WARNING [step scvelo_analysis] completed permanentFail