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= Troubleshooting Common Issues =
= Troubleshooting Common Issues =
== ERROR: No overlapping IDs between VCF and PED file. Cannot proceed. ==
== EPACTS installation errors ==
== Errors when running EPACTS ==
=== Rscript execution error: No such file or directory ===
/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 &<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
'''Rscript execution error: No such file or directory'''The issue seem to be the absence with Rscript, which is usually installed with R.
<br>
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).
=== ERROR: No overlapping IDs between VCF and PED file. Cannot proceed. ===
Check that your individual ID's in your PED file are the same as those in your VCF file.
For example, if your VCF individual ID's include the family ID's (i.e. ABCD->ABCD001), the individual ID's in the PED file must match it exactly.
<br>
=== Estimated allele frequencies and analysis results do not exactly match results from my existing association software ===
Check that you have included the same set of covariates (with categorical variables encoded as dummy variables).
Check that you have the same number of cases and controls analyzed.
FInally, check that you used dosages by adding the appropriate "-field" option. For example, suppose your VCF is:
<br>
<pre>#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A001 B001 C001
<pre>#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A001 B001 C001
11 180567 11:180567 C G 0 PASS . GT:EC 1/1:2.0000 1/1:2.0000 1/1:2.0000
11 180567 11:180567 C G 0 PASS . GT:EC 1/1:2.0000 1/1:2.0000 1/1:2.0000
11 193146 11:193146 G A 0 PASS . GT:EC 1/1:1.8550 1/1:1.8460 1/1:1.7940
11 193146 11:193146 G A 0 PASS . GT:EC 1/1:1.8550 1/1:1.8460 1/1:1.7940
</pre>
</pre>
<br> The genotype information has FORMAT "GT:EC". For the first SNP (chr11:180567) and individual A001, the genotype is 1/1 and dosage is 2.0000. To access the dosages, you must specify the option "-field EC"
The genotype information has FORMAT "GT:EC". For the first SNP (chr11:180567) and individual A001, the genotype is 1/1 and dosage is 2.0000. To access the dosages, you must specify the option "-field EC"
