Hi,
I have a pipeline where I am aligning several SRR files with cellranger. An example accession where I am having trouble is GSM6432155 which has accessions SRR SRR20829090 to SRR20829093. When I am aligning what appears to be some of the larger accessions I get the the error which has been discussed in this github page (https://github.com/10XGenomics/cellranger/issues/114). This conclusion was that this is due to insufficient disc space allocated to cellranger. I am running cellranger on a spartan HPC and I was hoping someone could please tell me how determine how much disc space is allocated to cellranger?
I am running cellranger in my /scratch and I have used 2843GB out of 5002GB. I am having particular trouble with SRR20829090 and I have tried re-downloading the sample with no success.
Thanks!
Have you contacted 10x via their github or via support e-mail? They'll probably be the best source of information on this
While you may be running in
/scratchit is possible that your cluster may be set up to use some temporary space where the intermediate files are being written to. You may be running out of space there. You may want to check with your local cluster admins. The cellranger/workflow manager log files should have clues for this.