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Mismatch dtype for diff_expr.py #248

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tsigalko2003 opened this issue Jun 8, 2022 · 0 comments
Open

Mismatch dtype for diff_expr.py #248

tsigalko2003 opened this issue Jun 8, 2022 · 0 comments

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@tsigalko2003
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We are running de-analysis of a h5ad file, it worked for many datasets but we found this bug for some specific cases. The issue is reproducible with multiple OS/docker container.
The error message details are:

File "/root/miniconda3/bin/cirro", line 8, in
sys.exit(main())
File "/root/miniconda3/lib/python3.9/site-packages/cirrocumulus/main.py", line 20, in main
cmd.main(command_args)
File "/root/miniconda3/lib/python3.9/site-packages/cirrocumulus/prepare_data.py", line 354, in main
prepare_data.execute()
File "/root/miniconda3/lib/python3.9/site-packages/cirrocumulus/prepare_data.py", line 193, in execute
pg.de_analysis(dataset, cluster=field,
File "/root/miniconda3/lib/python3.9/site-packages/pegasusio/decorators.py", line 12, in wrapper_timer
result = func(*args, **kwargs)
File "/root/miniconda3/lib/python3.9/site-packages/pegasus/tools/diff_expr.py", line 495, in de_analysis
df = _de_test(X, cluster_labels, gene_names, n_jobs, t, fisher, temp_folder, verbose)
File "/root/miniconda3/lib/python3.9/site-packages/pegasus/tools/diff_expr.py", line 56, in _de_test
data, indices, indptr = csr_to_csc(X.data, X.indices, X.indptr, X.shape[0], X.shape[1], ords)
File "ext_modules/diff_expr_utils.pyx", line 22, in pegasus.cylib.de_utils.__pyx_fuse_1_1csr_to_csc
ValueError: Buffer dtype mismatch, expected 'const float' but got 'double'

We are running on python3.9, pegasusio 0.6.1 ( we had also tried lower version but the same issue.) The dataset comes from public source https://atlas.kpmp.org/api/v1/file/download/9b26dec2-d40a-4fbd-8fc1-73be3d7aeba5/c798e11b-bbde-45dd-bd91-487f27c93f8f_WashU-UCSD_HuBMAP_KPMP-Biopsy_10X-R_12032021.h5Seurat. We had converted the h5Seurat into h5ad by seurat-disk (https://mojaveazure.github.io/seurat-disk/reference/LoadH5Seurat.html).

Thanks,
Tao

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