MapMyCells task stuck at "Input file validated" step for many hours without progressing

How To MapMyCells
1

Hello,

I’m encountering a persistent issue with the MapMyCells tool: my mapping task has been stuck at the Input file validated stage for several hours, even though the page showed an ETA of 5 minutes when I submitted it. The progress never advances to the “Algorithm run” step, and no error message is displayed.

Task details

  • Reference Taxonomy: 10x Whole Mouse Brain (CCN20230722)
  • Mapping Algorithm: Hierarchical Mapping
  • Input: h5ad file of mouse hippocampal snRNA-seq data
  • Submission date: Oct 9, 2026

Troubleshooting I have tried

  • Refreshed the task page multiple times
  • Re-uploaded and resubmitted the file once; the issue reoccurs exactly the same way
  • Verified that the h5ad file uses standard mouse gene symbols and meets the input requirements

Could the team help check whether this is a server-side issue, or if there is a format problem with my data that is blocking the pipeline? I can provide more file details or logs if needed.

Thank you for your help!

2

Hi Mike9!

Thanks for the detailed report, and sorry for the trouble. I’m an engineer at the Allen Institute and can confirm this was a server-side problem, not an issue with your data. Your file format and gene symbols were fine.

On Oct 8 we deployed an earlier version of an infrastructure change whose fix was already prepared and awaiting release. That earlier version left the compute that runs mapping jobs unable to start new work, so tasks submitted in that window stalled after input validation. The fix went out on the morning of Oct 11, and mapping jobs are running normally again.

We’re aware of the gap in our release process that allowed this, and we’re working to make sure it doesn’t occur again.

Tasks that stalled during that window won’t resume on their own, so please resubmit your file. If it gets stuck again or fails, reply here with the task ID and submission time and we’ll look into it right away.