cannot parse region

[VSowmya Venkat]

Hello,

I am currently getting this error when I am running single variant analysis in EPACTS

Successfully written phenotypes and 0 covariates across 7586 individuals

Processing chromosome 21...

Loading required package: epactsR

^GWARNING -

Cannot parse region 21:1-10000000.. Returning empty

Loading required package: epactsR

^GWARNING -

Cannot parse region 21:10000001-20000000.. Returning empty

Loading required package: epactsR

^GWARNING -

Cannot parse region 21:20000001-30000000.. Returning empty

Loading required package: epactsR

^GWARNING -

Cannot parse region 21:30000001-40000000.. Returning empty

Loading required package: epactsR

^GWARNING -

Cannot parse region 21:40000001-48129895.. Returning empty

nsnps = 0

The code that I am using is:

/users/svenkata/WGS_fructosamine_glyalbumin/software/EPACTS/bin/epacts single \

 --vcf path/ARIC_8.chr21.hg38.vcf.gz \

 --ped (path)/tidy_data/phenotype_ped_files/temp_fruc_ped_file.ped \

 --chr 21 --pheno v2fruc --test q.linear \

 --out (path)/tidy_data/SV_test_0318/chr21_test_run --run 4

Can you let me know where I am going wrong?

[Matt]

Were you able to find a solution? I am getting pretty much the same error:

WARNING -

Cannot parse region 21:20000001-30000000.. Returning empty

 /home/data.phe /home/data.cov /home/data.ind /home/data/rm_chr_mergeSnpIndel.vcf.gz 21:40000001-48129895 /home/data.21.40000001.48129895.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score

Loading required package: epactsR

Any help would be greatly appreciated!!

[VSowmya Venkat]

Actually, the issue is my build GRCh38 is not compatible with EPACTS

--
You received this message because you are subscribed to a topic in the Google Groups "EPACTS" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/epacts/bVGckeu-P9s/unsubscribe.
To unsubscribe from this group and all its topics, send an email to epacts+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/epacts/f8fc93db-2982-4975-ad0b-998426518ea2n%40googlegroups.com.