Error during run about solo HOT 4 CLOSED

Hi there,

Could you tell me what sort of file type you are feeding into solo? Is it a loom, h5ad, or 10x cell ranger output?

It seems like the singlet_scvi_data.X data type isn't a dense np.array, so if you want a quick fix you could do this yourself by ensuring the input expression matrix is a dense np.array but Solo should coerce this for you.

Let me know the file type you are using and input gene expression object type, so I can replicate it on my end and fix the issue or better yet if you can you could share the file with me. I know that's not always possible though.

Best
Nick

from solo.

Thanks Nick,

I am using the 10x cells ranger outputs (V2 and V3). I haven't QC filtered the data and I suspect that may be contributing to the error? Let me know if you can replicate the error

I'll implement a QC step and retry to see if that solves the issue. Let me know if you identify and resolve the issue on your end in the meantime.

Cheers,
Drew

from solo.

@drneavin This issue should be fixed if you install from master. Let me know if its not resolved by reopening this issue

from solo.

Any way that this could be updated for the pip install method? I am installing this in a singularity bucket and am receiving the following error when I try to install from github:

Warning: Permanently added 'github.com,13.237.44.5' (RSA) to the list of known hosts.
[email protected]: Permission denied (publickey).
fatal: Could not read from remote repository.

However, installation works well with pip install solo-sc.

Thanks,
Drew

from solo.