Rscript execution error: No such file or directory

[SN]

Hi,

I am trying to run q.linear using epacts-single  (shown below). I am able to generate the .cov, makefie, ind and phe file. However, I get an Rscript execution error. I saw in the wiki, it says to install Rscript. Since I am working on my university's cluster, I am not sure how to install R script in /usr/bin. I have loaded the R module, and it works fine. Please help me resolve this issue. The error is shown below: -

/EPACTS/bin/epacts single --ped /gpfs/X/EPACTS/new3.ped --pheno SCORE --cov AGE --cov GENDER --cov PC1 --cov PC2 --cov PC3 --cov PC4 --min-maf 0.01 --vcf /gpfs/pace1/X/EPACTS/VCF_CAUC.vcf.gz --test q.linear --run 1 --out /gpfs/X/EPACTS/EPACT_QLINEAR_RESULTS/PEACE_GWAS_EPACTS

Detected phenotypes with more than 3 unique values -- considering as quantitative phenotypes.
Successfully written phenotypes and 6 covariates across 311 individuals
Processing chromosome 1...
Processing chromosome 2...
Processing chromosome 3...
Processing chromosome 4...
Processing chromosome 5...
Processing chromosome 6...
Processing chromosome 7...
Processing chromosome 8...
Processing chromosome 9...
Processing chromosome 10...
Processing chromosome 11...
Processing chromosome 12...
Processing chromosome 13...
Processing chromosome 14...
Processing chromosome 15...
Processing chromosome 16...
Processing chromosome 17...
Processing chromosome 18...
Processing chromosome 19...
Processing chromosome 20...
Processing chromosome 21...
Processing chromosome 22...
Processing chromosome X...
Processing chromosome Y...
Processing chromosome MT...
Finished generating EPACTS Makefile
Running 1 parallel jobs of EPACTS
forkExecWait(): make -f /gpfs/X/EPACTS/EPACT_QLINEAR_RESULTS/PEACE_GWAS_EPACTS.Makefile -j 1
Rscript /gpfs/X/EPACTS/share/EPACTS/epactsSingle.R --vanilla /gpfs/X/EPACTS /gpfs/X/EPACTS/EPACT_QLINEAR_RESULTS/PEACE_GWAS_EPACTS.phe /gpfs/X/EPACT_QLINEAR_RESULTS/PEACE_GWAS_EPACTS.cov /gpfs/X/EPACT_QLINEAR_RESULTS/PEACE_GWAS_EPACTS.ind /gpfs/X/EPACTS/CHDWB_VCF_CAUC.vcf.gz 1:1-10000000 /gpfs/X/EPACTS/EPACT_QLINEAR_RESULTS/PEACE_GWAS_EPACTS.1.1.10000000.epacts GT 0.01 1 3 1000000000 0.5 0 FALSE single.q.linear
Rscript execution error: No such file or directory
make: *** [/gpfs/X/EPACTS/EPACT_QLINEAR_RESULTS/PEACE_GWAS_EPACTS.1.1.10000000.epacts] Error 255

Error in running make -f /gpfs/X/EPACTS/EPACT_QLINEAR_RESULTS/PEACE_GWAS_EPACTS.Makefile -j 1. Exit code is 2

Thanks!

[Hyun Min Kang]

This is an error in your Rscript setting. Reinstall R or reconfigure Rscript

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