Association analysis running but remains at 0% for hours

[marionamujal]

Hello, Kindly requesting for your help, I am trying to do an association analysis, both for rare and common variants, however as I try to do some variant level summaries using the code below, it runs for over two hours but however remains at 0%. /home/bpeng/VariantTools$ vtools update variant --from_stat 'total=#(GT)' 'num=#(alt)' 'het=#(het)' 'hom=#(hom)' 'other=#(other)' 'minDP=min(DP_geno)' 'maxDP=max(DP_geno)' 'meanDP=avg(DP_geno)' 'maf=maf()' INFO: 29304 variants in pseudo-autosomal regions on chromosome X are treated as autosomal variants. INFO: 241 males and 279 females are identified Counting variants: 0.0% [> ] in 00:00:00

Additionally am running a common variant association analysis (different dataset) that also remains at 0% for over 3 hours. @cd246ea27c11:~$ vtools associate common_variants Phenotype --covariates Gender --discard_variants "%(NA)>0.1" --method "LogitRegBurden --name SNV_permute --alternative 2 -p 100000000 --adaptive 5e-5" --to_db Round1_SNV -j6 > SNV.asso.res INFO: 314 samples are found INFO: Grouping variants by 'variant.chr:variant.pos', please be patient ... INFO: 106461 groups are found WARNING: Temp files are not regenerated! Testing for association: 0.0% [> ] in 00:00:00

Note; I run the same association analysis yesterday and it successfully completed in about 10 minutes however all the tests failed, with it producing errors related to Field sample_size_SNV_permute has all missing values No valid integer values has been found for field sample_size_SNV_permute Field num_variants_SNV_permute has all missing values No valid integer values has been found for field num_variants_SNV_permute Field total_mac_SNV_permute has all missing values No valid integer values has been found for field total_mac_SNV_permute Field beta_x_SNV_permute has all missing values No valid float values has been found for field beta_x_SNV_permute Field pvalue_SNV_permute has all missing values No valid float values has been found for field pvalue_SNV_permute Field std_error_SNV_permute has all missing values No valid float values has been found for field std_error_SNV_permute Field num_permutations_SNV_permute has all missing values No valid integer values has been found for field num_permutations_SNV_permute

I am running variant tools in docker. Your assistance is very much appreciated.

[BoPeng]

So it is the vtools update variant command that has stalled for 3 hours?

[marionamujal]

No, both commands.

[BoPeng]

I cannot really debug here. What if you run the update command with fewer fields, or just vtools output variant chr pos ref al -l 100 just to see if the database is not locked or something?

[BoPeng]

AFAIR, maf() can handle sex chromosomes correctly.