Question: How do I get help with a failed mkfastq run?
Answer: Please do the following:
- 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 firstname.lastname@example.org jobid.mri.tgz
jobidis what you input into the
mkfastq(if not specified, defaults to the name of the flowcell). This tarball contains numerous diagnostic logs that we can use for debugging.
- Please email email@example.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.