emmax-CMC issue

[smhaider]

HI,

I am actually running "EMMAX-CMC" on gene panel sequencing data from 61000 individuals. Although I am running 40 jobs in parallel but still its been almost 16 days the job is running on the cluster but no results so far. So after having a look into the job I noticed that --run 40 only works till "MAKE Files" but unfortunately p.emmax is not able to do parallelization. I am just curious if this is the limitation of the tool or I did something wrong? I would really appreciate if someone can help me in fixing this issue since its taking so long to get the gene burden results.

epacts-group --vcf $SCRATCH/input.vcf.gz --ped $SCRATCH/input.ped --kin $SCRATCH/kinship/phenotype.kinf --test emmaxCMC --pheno PHENO --groupf $SCRATCH/lof.grp --out $SCRATCH/result/rareLOF --max-maf 0.01 --min-callrate 0.95 --cov Sex --cov PC1 --cov PC2 --cov PC3 --cov PC4 --cov PC5 --cov PC6 --cov PC7 --cov PC8 --cov PC9 --cov PC10 --run 40

Looking forward to hearing from you.

Kind Regards,
Haider