Closed ekernf01 closed 2 years ago
I wonder if this is https://github.com/theislab/anndata/issues/287 . I will see if there is a fix there.
Yes, it is. Fixed by using a newer version of anndata, available from conda-forge but not bioconda.
conda install "anndata>=0.7" -c conda-forge
I'm converting an h5ad file to seurat and I get the error in the title. The h5ad file is from the kallisto|bustools pipeline, but I can't share it because it contains unpublished data. I also can't find publicly available example output from kb, but if you think it would help, I can try to generate some. For context, I provide:
conda list
I'm not familiar with the h5ad specification. Do you think this is a problem with the file, or maybe some version incompatibility? Thanks!
Versions
Python packages from conda list
python_packages.txt
R packages from renv lockfile
renv.lock.txt
Traceback