Question: My run failed and didn't automatically generate the mri.tgz file that 10x support generally asks for. Can I generate this file manually?
Answer: Yes, you can generate the .mri.tgz file. The Cell Ranger and Space Ranger pipelines has an utility tool called
-For Cell Ranger versions 3.1 and earlier, the script will be located here:
-For versions 4.0 and above, the script can be located from here:
The invocation command for this tool is either using
cellranger tarmri, or using
spaceranger tarmri. To use
tarmri to generate a .mri.tgz file for a failed run, call
tarmri and give it the path to the failed pipestance. You run it by giving it the output directory named after the value of "--id=" in the cellranger or spaceranger command line.
For example, if
--id=run1 in your cellranger command line then your tarmri command would look like this:
where x.y.z is the Cell Ranger version 3.1 or earlier. For versions 4.0 and above, you can make use of the path
You can then use below command for uploading the logs to our server.
cellranger upload email@example.com path/to/log.mri.tgz
The .mri.tgz file contains a number of logs (including error messages, status reports, and information about the system) that are useful for trouble-shooting failures. The .mri.tgz file does not contain sequence data or analysis outputs.
Last Updated: June 2023