SKATO hangs after going through several genes
Entering edit mode
8 days ago
@anna • 0

Hi there

I'm doing skato analysis with rvtest/2.1.0. My script:

rvtest --inVcf file.vcf.gz --pheno phenofile --out newfile --geneFile refFlat_hg19.txt --kernel skato

it runs for a while, but them skato seems to hang after a few genes

Retrieve remote version failed, use '--noweb' to skip.
[INFO]  Program version: 20190205
[INFO]  Analysis started at: Tue Nov 23 17:40:31 2021
[INFO]  Loaded [ 198 ] samples from genotype files
[INFO]  Loaded [ 101 ] sample phenotypes
[INFO]  Discard [ 5 ] samples as they do not have genotypes
[INFO]  Loaded 47 male, 32 female and 17 sex-unknown samples from /executable/
[INFO]  Loaded 45 cases, 51 controls, and 0 missing phenotypes
[WARN]  -- Enabling binary phenotype mode --
[INFO]  Analysis begins with [ 96 ] samples...
[INFO]  SKAT-O test significance will be evaluated using weight = Beta[beta1 = 1.00, beta2 = 25.00]
[INFO]  Loaded [ 22480 ] genes.
[INFO]  Impute missing genotype to mean (by default)
[INFO]  Analysis started
[INFO]  Gene FAM138A has 0 variants, skipping
[INFO]  Gene MIR194-1 has 0 variants, skipping
[INFO]  Gene AURKAPS1 has 0 variants, skipping

Does anyone knows what is happening and how I can solve it? thank you

rvtest skato • 87 views

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