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 tarmri.
-For Cell Ranger versions 3.1 and earlier, the script will be located here:
cellranger-x.y.z/cellranger-cs/x.y.z/tenkit/bin/tarmri
-For versions 4.0 and above, the script can be located from here:
cellranger-x.y.z/bin/tenkit/tarmri
The invocation command for this tool is either usingcellranger 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:
cellranger-x.y.z/cellranger-cs/x.y.z/tenkit/bin/tarmri path/to/run1
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 cellranger-x.y.z/bin/tenkit/tarmri
You can then use below command for uploading the logs to our server.
cellranger upload your@email.edu 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.
Products: All
Last Updated: June 2023