I am trying to run cellranger but I get fastq permission denied error

fi1d18@RBGO-Server2:/opt$ cellranger-atac count --id test --reference refdata-cellranger-arc-GRCh38-2020-A-2.0.0 --fastqs /data/fi1d18/Downloads/FASTQ_scATAC/ --chemistry ARC-v1
error: couldn't open MRO file
    Caused by: Permission denied (os error 13)

I have added the path by

export PATH=/opt/cellranger-atac-2.0.0:$PATH

And by vim I have also added the path

fi1d18@RBGO-Server2:/opt$ vim ~/.bashrc

Any help please?

  • $\begingroup$ Does your user have permission to read inside opt ? mro are configurations files used and read by cellranger during each steps. If they cannot be access, then the pipeline should fail. $\endgroup$
    – fra
    May 6, 2021 at 8:00

1 Answer 1


Two of those command line parameters should be accessible locations (see here). Could you please add the output of the following commands:

ls -l /data/fi1d18/Downloads/FASTQ_scATAC/ | head


ls -l refdata-cellranger-arc-GRCh38-2020-A-2.0.0 | head

I suspect that the refdata link should be an absolute path, rather than a relative path, i.e. something like this:

cellranger-atac count --id test --reference /opt/refdata-cellranger-arc-GRCh38-2020-A-2.0.0 --fastqs /data/fi1d18/Downloads/FASTQ_scATAC/ --chemistry ARC-v1

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