Closed AlcaArctica closed 5 months ago
Hi Alca,
I encountered the same issue. Did you find the solution for it? Thanks,
Hi, I think this is a general singularity issue, not really a samplesheet one. Did you already use any other nf-core pipeline with singularity ?
linked to #180
Description of the bug
I am getting a sample sheet error with the following sample sheet:
The error may be related to https://github.com/nf-core/hic/issues/152, but as there is only one line in my sample sheet it seems unlikely.
Another potential problem could be that our system does not have file locks. However, I thought I took care of that by using the
-w /tmp/
flag. (/tmp/
does have file locks!). Any other idea what I could try?Perhaps singularity is missing some bind? (because of the message
/tmp/1c/167b78c8be41694d24c476732df8e2 doesn't exist in container
) Is it possible to specify a singularity bind? I cant use docker, as we cannot install docker on our system.Command used and terminal output
Relevant files
No response
System information
nextflow version 23.04.4.5881 openjdk 17.0.8-internal 2023-07-18 HPC Singularity Linux nextflow pull nf-core/hic Checking nf-core/hic ... Already-up-to-date - revision: fe4ac65631 [master]