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genetics-statistics / GEMMA

Genome-wide Efficient Mixed Model Association
https://github.com/genetics-statistics/GEMMA
GNU General Public License v3.0
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Got a nan in the p-value results #273

Open voichek opened 1 year ago

voichek commented 1 year ago

Describe the bug When I run a GWAS I got one SNP that have a nan value in the three columns logl_H1, l_mle, and p_lrt

chr     rs      ps      n_miss  allele1 allele0 af      logl_H1 l_mle   p_lrt
1       1_5861128       5861128 62      C       T       0.161   nan     nan     nan

Gemma version - 0.98.5 (2021-08-25) Command line run: gemma-0.98.5-linux-static-AMD64 -bfile table -lmm 2 -k table.kinship -snps snps.txt -maf 0.05 -miss 0.5

To Reproduce I have made a small example to reproduce the error, it has all the files needed to run it (attached). The exact run command can be found in the log file of running the gemma, as well as all other exact parameters. 20230411_gemma_bug_report.zip

I couldn't find a previous issue like this in the GitHub issues page

Best wishes, Yoav

yefanglee commented 1 year ago

Hi, did you address it? I met with same problem