I am interested in running Clomial R package for a fairly large dataset (23 regional samples with 247 SNVs) and, while reading the documentation, I’ve found that one can run this tool in parallel in a Unix SGE cluster.
Since we have one available at our lab, I am trying to implement Clomial to work in parallel but I keep getting error messages such as:
Unable to run job: denied: host is no submit host.
I was therefore wondering whether you have any example on how to use Clomial with SGE.
Here's the Clomial command line that I'm using:
1. sh script
module load R/3.2.2_1
R CMD BATCH /home/jmf.alves/Clomial.c3.R
2. R script (Clomial.c3.R)
data.Dc <- as.matrix(read.table("Dc.txt", head=T, sep="\t", row.names=1, as.is=T))
data.Dt <- as.matrix(read.table("Dt.txt", head=T, sep="\t", row.names=1, as.is=T))
Clomial.c3 <- Clomial(Dc=data.Dc, Dt=data.Dt, maxIt=20, C=3, doParal=T, binomTryNum=100, outPrefix="/home/jmf.alves/", jobNamePrefix="C3", fitBinomJobFile="/home/jmf.alves/Clomial.C3", doTalk=T)
I managed to fix it by modifying the Rsub function and the fitBinomJobFile template
Now everything seems to be working properly.
Thank you again for your help,