Changes

== Errors when running EPACTS ==

== Errors when running EPACTS ==

=== Rscript execution error: No such file or directory ===

=== Rscript execution error: No such file or directory ===

/epacts2.1/epacts single \

epacts2.1/epacts single \  

--vcf /ep10/disks/SANA4/dorothee/logiciels/epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \<br>--ped /ep10/disks/SANA4/dorothee/logiciels/epacts2.1/example/1000G_dummy_pheno.ped \<br>--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno \<br>--out /ep10/disks/SANA4/dorothee/logiciels/out/test --run 1 &amp;<br>[4] 13569<br>

--vcf epacts2.1/example/1000G_exome_chr20_example_softFiltered.calls.vcf.gz \<br>--ped epacts2.1/example/1000G_dummy_pheno.ped \<br>--min-maf 0.001 --chr 20 --pheno DISEASE --cov AGE --cov SEX --test b.score --anno \<br>--out out/test --run 1 &amp;<br>[4] 13569<br>  

$ Detected phenotypes with 2 unique values - 1 and 2 - considering them as binary phenotypes... re-encoding them into 1 and 2<br>Successfully written phenotypes and 2 covariates across 266 individuals<br>Processing chromosome 20...<br>Finished generating EPACTS Makefile<br>Running 1 parallel jobs of EPACTS<br>/ep10/disks/SANA4/dorothee/logiciels/epacts2.1/bin/..//bin/make -f /ep10/disks/SANA4/dorothee/logiciels/out/test.Makefile -j 1

$ Detected phenotypes with 2 unique values - 1 and 2 - considering them as binary phenotypes... re-encoding them into 1 and 2<br>Successfully written phenotypes and 2 covariates across 266 individuals<br>Processing chromosome 20...<br>Finished generating EPACTS Makefile<br>Running 1 parallel jobs of EPACTS<br>epacts2.1/bin/..//bin/make -f out/test.Makefile -j 1  

'''Rscript execution error: No such file or directory'''The issue seem to be the absence with Rscript, which is usually installed with R.

'''Rscript execution error: No such file or directory'''

The issue seems to be the absence with Rscript, which is usually installed with R.  

If you can find Rscript (e.g. /usr/bin/Rscript, /usr/local/bin/Rscript), or if you can re-install the full Rscript, you can simply avoid the problem by setting your environment variable.

If you can find Rscript (e.g. /usr/bin/Rscript, /usr/local/bin/Rscript), or if you can re-install the full Rscript, you can simply avoid the problem by setting your environment variable.  

Otherwise, Hyun will modify EPACTS to not requiring this (I can run R CMD BATCH instead of Rscript).

Otherwise, Hyun will modify EPACTS to not requiring this (I can run R CMD BATCH instead of Rscript).

=== ERROR: No overlapping IDs between VCF and PED file. Cannot proceed.  ===

=== ERROR: No overlapping IDs between VCF and PED file. Cannot proceed.  ===