singularity, error on creating temp files

[aheravi]

Hi all, I'm trying to run your tool using the singularity image and getting the below error. Could you please comment on that? I don't have permission to write on the reference folder and need a running parameter(s) to avoid creating a file/folder on the reference folder. I tried a couple like --TMP_DIR and --singularity_cache with no luck.

Thanks, Ali

my running command:

singularity exec gridss_latest.sif virusbreakend --workingdir test --kraken2db /virusbreakenddb --output $lib.virusbreakend.vcf --reference /hg38_no_alt/genome/fasta/hg38_no_alt.fa test.bam

Error:

Fri Oct  6 19:45:19 PDT 2023: Running GRIDSS steps: setupreference,
mkdir: cannot create directory '/hg38_no_alt/genome/fasta/hg38_no_alt.fa.tmp.gridsslock': Permission denied
Fri Oct  6 19:45:19 PDT 2023: Multiple instances of setupreference cannot be run concurrently. Aborting due to existence of /hg38_no_alt/genome/fasta/hg38_no_alt.fa.tmp.gridsslock