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Known problems

HuggingFace ClamAV false positive:

Problem: HuggingFace runs an automatic ClamAV routine to detect viruses. In the past this has lead to false positives on .h5ad files.

Solution: Load the h5ad file into a notebook, convert the adata.X to a sparse matrix with adata.X = sp.csr_matrix(adata.X). This will solve the problem most of the time, you can check if the file is still flagged by running clamscan $FILE.