Cellranger gives error
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
and
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