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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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Integration failed with a error [ exceeded max number of iterations ] #65

Closed zx8754 closed 5 years ago

zx8754 commented 5 years ago

I am running below command:

rvtest --inVcf ... \
--noweb \
--pheno ... --pheno-name ... \
--covar ... --covar-name ... \
--siteFile ... \
--geneFile $fileRefUCSC \
--kernel skato \
--out ...

What is the meaning of this error?

...
[INFO]  Gene LILRA1 has 0 variants, skipping
[INFO]  Gene RAB35 has 0 variants, skipping
Integration failed with a error [ exceeded max number of iterations ]
Integration failed with a error [ exceeded max number of iterations ]
[INFO]  Gene MIR609 has 0 variants, skipping
[INFO]  Gene NAGK has 0 variants, skipping
...
zhanxw commented 5 years ago

SKAT-O test will internally perform numeric integration. The errors about integration means this algorithm failed.

Sorry about these error message although I have tried to avoid them.

Would you mind send example inputs so that I can reproduce/fix this error? You can use --outputRaw option combined with the problematic gene --gene RAB35. Then you will get some extra files with covariate, genotypes, and phenotypes. These will be helpful for debug.