DSS-2.40.0 running out of time

[MithilG]

Hello Developers and the Users of DSS,
I am working with several differentially methylated region (DMR) callers, including DSS. I am using the DSS v2.40 in order to maintain the consistency across on-going projects in the lab.

Presently I am calling the DMRs in non-CG context which cannot be collapsed and thus the loci (or sites) are high in number from both strands.

From couple of weeks, I am facing a problem while using the DSS v2.40 as follows:

DSS runs out of time even when I try to run the program in the HPC cluster with its highest resources (shown below) for the following code:

HPC resources used were:

#! /bin/bash
#SBATCH --time=96:00:00
#SBATCH --mem=255536
#SBATCH --cpus-per-task=20
#SBATCH --job-name=DSS_DMRcalling

Code for DMR-calling using the DSS:

mParam = MulticoreParam(workers=madetectCores() - 3, 1), progressbar=TRUE) # which are 29 cores
dmlTest.sm <- DMLtest(bs.filtered,
                             group1=1:6,
                             group2=7:12,
                             smoothing=TRUE,
                 BPPARAM=mParam) # computes parallely
dmrs0<- callDMR(dmlTest.sm, p.threshold=0.05)

The 96hrs (maximum time period) at HPC cluster is less for DSS to finish the DMRcalling step by DSS. Further, I extracted the samples into fractions such as chromosomes 1-6. But still my program cannot complete the "computing test statistic" function. It gives the following text as an output:

Smoothing ...
Estimating dispersion for each CpG site, this will take a while ...
  |======================================================================| 100%

  |======================================================================| 100%

Computing test statistics ...
slurmstepd: error: *** JOB 17623606 ON hpc-n547 CANCELLED AT 2024-11-20T13:40:35 DUE TO TIME LIMIT ***

Previously even when I used chromosomes 1-2 or 1-3 (without using the BPPARAM argument in the DMLTest), I faced the same issue.

Is this expected or there is some crucial parameter that I am missing out?
Did anyone faced this issue earlier?
I will be really grateful if anyone of you provide me your feedback over this issue.

Looking forward to hearing from you.

Have a nice day.