Mapping failed because of application errors

How To MapMyCells
1

Hi! I am really excited to use this tool but have been encountering issues at the last stage of the analysis and receiving a “Mapping Failed. Mapping algorithm failed because of application errors.”
Here is the requested info:

  • Operating system and web browser: Windows 11 and Chrome
  • Run ID: 1697776005895-695f859a-5df9-4a1e-8fab-97eb3aab835e
  • Information on the data: This is mouse snRNAseq data generated using a combinatorial indexing approach (sciRNAseq). The minimal h5ad was generated in R with just the cell-by-gene table. Column names are ENSEMBL IDs (e.g. ENSMUSG00000051951) and row names are cell barcodes. The AnnData object n_obs x n_vars = 50000 x 22004 with a total size of 327.4MB.
  • Instructions on how to reproduce the issue: I uploaded the h5ad to the site and am using the 10x Whole Mouse Brain as the reference taxonomy and hierarchical mapping as the mapping algorithm. The job proceeds through ‘input file validation’ and ‘algorithm run’, but errors during the ‘Mapping completed’ step.
    Any suggestions would be greatly appreciated! Thanks.
2

Hi,

It looks like your h5ad file contains negative gene expression values (minimum value is -7). This is a problem for our algorithm as we assume that the inputs are raw counts which we then convert to log2(counts per million + 1). Obviously, the log2 is not going to handle -7 very well.

Hope this isn’t an absolute show stopper for you.

Cheers,

Scott Daniel

3

Thanks for catching that. I fixed it and got it work, thanks for your help!