- A Linux cluster
- globally installed SLURM 18.08.7.1
- globally installed singularity 3.4.1+
- installed snakemake 5.19.3 (eg. in an anaconda environment)
- Sauron: There is a strange issue with RepeatMasker. For some reason it does not run. ReapearMasking with TanTan works fine.
- Sauron: I have had many jobs failing due to a singularity error:
FATAL: container creation failed: failed to resolved session directory
. This does not occur on VSC. From the extended message:Activating singularity image /cl_tmp/reslph/projects/xylographa_fun/.snakemake/singularity/195cc8bdbe1d3f304062822f8f4f06ce.simg FATAL: container creation failed: failed to resolved session directory /usertmp/singularity/mnt/session: lstat /tmp/singularity: no such file or directory
I assume it has to do with the tmp directory not being present. I have seen this after the jobs have been in the queue for a week (and other jobs ran fine). Maybe the /tmp directory is automatically deleted from time to time which causes this error.
$ git clone [email protected]:reslp/annocomba.git
$ ./annocomba --setup