How do I get help with a failed mkfastq run?

Question: How do I get help with a failed mkfastq run?

Answer: Please do the following:

1. Please upload the tarball in your output directory (with the file extension mri.tgz) using the upload tool (in this example for Cell Ranger):
   
   cellranger upload youremail@institution.edu jobid.mri.tgz
   
   ...where jobid is what you input into the --id option of mkfastq (if not specified, defaults to the name of the flowcell). This tarball contains numerous diagnostic logs that we can use for debugging.
   
   
2. Please email support@10xgenomics.com with the following:
   - The exact command line you used.
   - The sample sheet that you used.
   - The RunInfo.xml and runParameters.xml files from your BCL directory.
   - The kind of libraries you are demultiplexing (including chemistry).
   - The DemuxSummaryF1L1.txt file from the output Stats folder. There should be one such file for each lane.