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wheaton5 / souporcell

Clustering scRNAseq by genotypes
MIT License
165 stars 46 forks source link

Unable to run via Singularity - any issues with Singularity image? #129

Open learning-MD opened 2 years ago

learning-MD commented 2 years ago

Hi, thanks for a great tool! I installed Singularity and confirmed it's working fine. However, whenever I run anything related to the following code:

singularity exec souporcell_latest.sif souporcell_pipeline.py

I just get an error. So, I can't run typical commands or even get look at the souporcell options by adding -h at the end of the above code. Wanted to make sure there were no issues with the Singularity image (obtained by using the code singularity pull shub://wheaton5/souporcell).

Thanks!

wheaton5 commented 2 years ago

I have not seen anyone with this problem. Can you tell me the error?

learning-MD commented 2 years ago

Sorry for the delay - this is what pops up:

WARNING: failed to set O_CLOEXEC flags on image
WARNING: failed to set O_CLOEXEC flags on image
ERROR  : Failed to set securebits: Invalid argument

I couldn't find as much help when I searched around about that warning. There are some threads on other githubs, StackOverflow, etc, related to this warning but they all seem to be discussing WSL. I'm using Ubuntu for all of this. I apologize in advance if this is a rookie mistake, but still early in the process of learning bioinformatics. Thanks!