t= 50:00 h CANCELLED AT DUE TO TIME LIMIT ***

[AnnaAP]

Dear all, 

I have faced difficulties running the step 4 "Combine the summary statistics and LDSC output and run the common factor GWAS". I have already read the previous comments and following the suggestions, I increased the number of tasks and extended the time limit. Despite making these adjustments, the task did not finish within 24 or even 48 hours, as limited by the time, even when running for just one chromosome. Could you please provide guidance on how to proceed? 

#!/bin/bash
#SBATCH --job-name=GenomicSEM
#SBATCH --nodes=1
#SBATCH --mem=110GB
#SBATCH --cpus-per-task=22
#SBATCH --output=log4_genomicSEM_ch1.txt
#SBATCH --error=log4_genomicSEM_ch1.err
#SBATCH -t 50:00:00

load("2traits_LDSC.Rdata")
load("2traits_sumstats.Rdata")
nrow(BP_sumstats)
BP_sumstats<-subset(BP_sumstats,BP_sumstats$CHR==1)
BP_factor <- commonfactorGWAS(covstruc = LDSCoutput,
           SNPs = BP_sumstats,
           toler = 1e-30)          
save(BP_factor,file="2traits_DWLS_1chr.Rdata")
q()

I appreciate your guidance, 

Kind regards,

Anna