Problem running MBASED

[readmanchiu]

Hello,

I am having trouble in getting the mbased step in the pipeline to work. I'm not familiar with R but I got the following error message no matter how many threads I asked it to use:

Calls: runMBASED ... runMBASED1s -> bplapply -> bplapply -> bploop -> bploop.lapply
In addition: Warning message:
In parallel::mccollect(wait = FALSE, timeout = 1) :
  1 parallel job did not deliver a result
Execution halted

Needless to say it's using a lot of memory, upward of 300GB.
The above message is not captured in any of the snakemake log, I only spotted it when I ran the individual step:

singularity exec --bind /projects/nanopore_pog ase_rcontainer_2.0.sif Rscript src/mbased.snpEff.R --phase=/projects/nanopore_pog/workflow/FNN031/POG1694-OCT-1_F138890/clair_3_0_1/clair_3_0_1_F138890/phased_merge_output.vcf.gz  --rna=output/POG1694-OCT-1_F138890/1_variant/rna.isec.filterSnps.tsv --outdir=output/POG1694-OCT-1_F138890/2_mBASED/ --threads=6