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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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[ERROR] Error loading gene file or gene list is empty! #90

Open MDiezFairen opened 4 years ago

MDiezFairen commented 4 years ago

Hi! I usually run rvtests for rare variant testing with no problems at all. However, only for some genes, I've been getting the following error message: 

[INFO]  Analysis begins with [ 15301 ] samples...
[INFO]  MadsonBrowning test significance will be evaluated using 10000 permutations at alpha = 0.05
[INFO]  SKAT test significance will be evaluated using 10000 permutations at alpha = 0.05 weight = Beta[beta1 = 1.00, beta2 = 25.00]
[INFO]  SKAT-O test significance will be evaluated using weight = Beta[beta1 = 1.00, beta2 = 25.00]
[ERROR] Error loading gene file or gene list is empty!

I have checked and the vcf that I use as an input for the rvtests has 1,087 variants for this particular gene... Have you ever seen an error message like this?

Thank you!!!

zhanxw commented 4 years ago

Your VCF file does not seem to have problem, but the the gene file have some problem. Can you check it again?