rare variant analysis hangs/stops midway

[ruthchia]

Hi, There seem to be a problem with running the following script below when I apply a --freqUpper filter of 0.01 or 0.05. The script would run without a problem when the --freqUpper is set to 1 (equivalent to not having an upper maf), but would fail to continue running when it reaches a certain gene - please see snippet below. I do not think my input .vcf.gz or refgene files are the problem given that it would complete successfully when no upper filter is applied. I've reran twice with the same problem at the same gene.

This SAMD13 gene is on chr1 and the input .vcf.gz file is on chr11. It should have skipped it like the other genes before.

I have made sure to pass the variables to the code. I am so confused as to what might cause the code hang midway only when --freqUpper was applied. Any ideas?

thanks Ruth

rvtest \
--noweb \
--hide-covar \
--out $OUTPUT/BURDEN_LOF_001MAF.11 \
--kernel skat,skato --burden cmc  \
--inVcf $WORKING_DIR/BURDEN/DEMENTIASEQ_WGS_LBD_LOF_only.11.vcf.gz \
--pheno $COVARIATE_FILE \
--pheno-name AFFECTION_STATUS \
--covar $COVARIATE_FILE \
--freqUpper 0.01 \
--covar-name $COVARIATES \
--geneFile $REFFLAT_FILE

[INFO]  Gene HECTD2 has 0 variants, skipping
[INFO]  Gene CASP10 has 0 variants, skipping
[INFO]  Gene TAB2 has 0 variants, skipping
[INFO]  Gene PXK has 0 variants, skipping
[INFO]  Gene EVC has 0 variants, skipping
[INFO]  Gene EHMT2 has 0 variants, skipping
[INFO]  Gene LINC01362 has 0 variants, skipping
[INFO]  Gene LINC01361 has 0 variants, skipping
[INFO]  Gene LINC01712 has 0 variants, skipping
[INFO]  Gene LINC01725 has 0 variants, skipping
[INFO]  Gene LOC101927560 has 0 variants, skipping
[INFO]  Gene TTLL7 has 0 variants, skipping
[INFO]  Gene KRTAP22-1 has 0 variants, skipping
[INFO]  Gene SAMD13 has 0 variants, skipping

[m-makarious]

I'm running into a similar issue - wondering what some next troubleshooting steps might be (other than possibly removing genes that RVtests are getting hung up on?)

[anna-321]

Hi there, I'm having the same problem. Did you find out what's happening and how to solve it?

[ChakrabortyShreya]

I'm running into a similar issue - wondering what some next troubleshooting steps might be (other than possibly removing genes that RVtests are getting hung up on?)

Did this work after removal of the genes which have 0 variants?

[Vibha-Acharya]

Did anyone find a solution to this? I am having same issue!