cell ranger reanalyze makes loupe file with "Invalid File Format"

[jeffpkamp]

I am feeding an h5 file into cellranger reanalyze. The program completes without any errors and I don't see any errors in the logs, but when I try to open the cloupe file made by it I get the error message:

"Loupeserver encountered an error: invalid file format"

can you advise me on troubleshooting the problem?

[evolvedmicrobe]

This usually indicates that reanalyze was run with an input file that wasn't produced by Cell Ranger, was your input matrix modified after running Cell Ranger?

[jeffpkamp]

Yes, we have normalized several sets or visium data and I am using cellranger reanalyzed to make the loupe files from a modified h5 file. I'm not asking for you to support this, just hoping you could point me toward where I might find the problem, since the error message is not informative and I didn't see any problems in the logs.

[jeffpkamp]

Okay, so I tested reanalyze out with an h5 file that I haven't modified, and I am getting the same error when trying to open the loupe file.

I am running reanalyzed like this:

cellranger reanalyze --id re_test --matrix "./corrected_A7384/SpaceRanger/19938X4/outs/filtered_feature_bc_matrix.h5"

[evolvedmicrobe]

The issue is that spaceranger data is not supported in cellranger reanalyze, this is an interesting use case though, and there may be some features coming out soon (not committed to yet), that will enable you to do this.

[jeffpkamp]

I found the problem. I was running cellranger 5.0. I ran it with the newest cellranger available at 10x's website, 7.1 and it worked with both the control and modified data.