calculateDiffMeth timing out on Mox - do I need to run R Studio server?

[yaaminiv]

I can finally run R scripts on mox!...but the calculateDiffMeth command within methylKit is timing out. I first called this R script from this SLURM script. This is the calculateDiffMeth code:

differentialMethylationStatsTreatmentFem <- methylKit::calculateDiffMeth(methylationInformationFilteredCov5Fem, covariates = covariateMetadataFem, overdispersion = "MN", test = "Chisq")

My script ran, but it timed out in ~5 hours with the following error when it hit the calculateDiffMeth code:

I couldn't see the warnings since I wasn't running the script interactively, so I thought I should try an interactive build node. I then opened a build node for 4 hours, loaded the R data I saved, and ran the the same calculateDiffMeth code. The job was force terminated and I didn't see any warnings.

@kubu4 @sr320 Do you think it's worth trying this command on the R Studio server, at least to investigate the warnings?

edited to include links

[kubu4]

Do you think it's worth trying this command on the R Studio server,

Sure!

[yaaminiv]

The job was force terminated and I didn't see any warnings.

The job was likely force terminated since I only requested a build node for 4 hours

My script ran, but it timed out in ~5 hours with the following error when it hit the calculateDiffMeth code

...turns out it was a typo in my code the entire time, and not a function of running R SLURM script, since I got the same error with R Studio server 😬 😑 😅

At least I can fix the code as I go with R Studio Server!

edited to properly quote previous error message descriptions