1- downloaded the FASTQ file, cellranger 3 and the reference genome GRCh38-3.0.0 into one directory in cluster computer
2- untag the FASTQ files.
3- ran the argument for the RNA FASTQ first:
2) The --id option will be used to create the output directory (also for the library id) so make sure to keep the fastq files in a different directory than the current working directory or use a different id. You are using pbmc_1k_protein_v3_fastqs for id option as well as the raw file.
3) If 2 is not the case check the current working directory is there is a new pbmc_1k_protein_v3_fastqs created and share the contents of _log file.
Okay I figured it out for mine I think. So the "samplename" portion of the fastq can't have underscores. I changed mine to TestSampleA8_S3_L001_R2_001.fastq.gz instead of a longer underscore separated name and its working now. Let me know if that works for you.
How is the software supposed to understand which sample you want to look at with "pbmc1k"? There are no samples in there with names like pbmc1K_S1_L001...
Did you try
cellranger count --help
?Yes, I didn't see any problem with my argument
Doesn't run
means what exactly?It doesn't give errors but nothing happens and it takes me back to the command line. It only shows this:
I am running into the exact same problem. Test run was successful etc. @ATpoint did you ever figure out the issue?
seems to me that sample needs 2 hyphens, too: