dockered vardict issue about somaticseq HOT 11 CLOSED

Try it again. There wasn't 3.5.1 in docker hub. I just added it.

from somaticseq.

Hi,

it starts now, but eventually fails. I am attaching the output in a file. The error message is
FATAL: Failed to initialize runtime engine: engine "" is not found

Any ideas ?
error.log

Thanks

from somaticseq.

Hi,

I have an update. I processed three samples. The "FATAL: Failed to initialize runtime engine: engine "" is not found" error is only for the first sample. The other two samples are ok. Can you think of any reason for this ?
The other callers, with the exception of vardict2 (I opened another issue for it), work.
Thanks

from somaticseq.

What was the command you've used?

from somaticseq.

Hi,

this error is probably caused by causes external to your code. Possibly, the fact that Singularity defaults to the HOME dir for cache and this may cause issues because of limited quota. After setting the SINGULARITY_CACHEDIR var to a different path it seems ok. If this is indeed the case, I will close this issue.

Thanks for looking into it!

Best

from somaticseq.

Hi,

I am still having an issue. It seems that as soon as one is solved, a new issue comes up....

I am attaching the output from one of the tools. It is the same as for the others. This seem to be happening for Mutect2, Strelka, VarDict, SomaticSniper and JointSNVMix2.
out.log

Can you please look into it and tell me what you think ?

Thanks

from somaticseq.

Did the singularity tasks run despite the warning, or did it stop running?
I'm no expert in singularities. It seems to be complaining about mounting /home/user in your local environment to /home/user in singularities, because somehow the container already has /home/user/project, either because it was mounted already or reasons that I don't know.

from somaticseq.

Thanks for the prompt reply!!
The ones I pointed out stop running. The warning you are referring to is present also in the ones that complete, and I do not think it is a major issue.
In the file I sent you there is a "panic" line after "copying blob". What do you think ?

from somaticseq.

It looks similar to this issue: apptainer/singularity#5329, that may be fixed with this answer apptainer/singularity#5329 (comment).

from somaticseq.

thanks!!
I am testing vardict and, so far, it is not stopping. I am really grateful for your help.

from somaticseq.

It seems ok now.
Thanks!

from somaticseq.