Issue with GEMMA-Wrapper

[vinod1981]

I am running GEMMA_Wrapper. It is running without any problem but not producing the final results with significant and suggestive P-values.

Commands I am running:

To generate K.json env GEMMA_COMMAND=/prj/pflaphy-robot/software/gemma-0.98.5-linux-static-AMD64 /homes/vkumar/.gem/ruby/2.7.0/bin/gemma-wrapper --json -- -g /prj/pflaphy-robot/software/fcgene-1.0.7/src/impute_thinned_test_bimbam_file_final.txt -p /prj/pflaphy-robot/genotypeGVCF_allsamples_updated/linkimpute/vcf2gwas/soil_pH/output/lmm/files/files_soil_pH_GWAS_updated_output_all_imputed_final_chr7Mod_js_GT/mod_sub_soil_pH_GWAS_updated_output_all_imputed_final_chr7Mod_js_GT_bimbam_recode_pheno.txt -a /prj/pflaphy-robot/software/fcgene-1.0.7/src/impute_thinned_test_bimbam_file_final_bimbam_rearranged.pos.txt -gk -debug > K.json

K.json as input env GEMMA_COMMAND=/prj/pflaphy-robot/software/gemma-0.98.5-linux-static-AMD64 /homes/vkumar/.gem/ruby/2.7.0/bin/gemma-wrapper --json --loco --input K.json --permutate 10 --permute-phenotype /prj/pflaphy-robot/genotypeGVCF_allsamples_updated/linkimpute/vcf2gwas/soil_pH/output/lmm/files/files_soil_pH_GWAS_updated_output_all_imputed_final_chr7Mod_js_GT/mod_sub_soil_pH_GWAS_updated_output_all_imputed_final_chr7Mod_js_GT_bimbam_recode_pheno.txt -- -g /prj/pflaphy-robot/software/fcgene-1.0.7/src/impute_thinned_test_bimbam_file_final.txt -a /prj/pflaphy-robot/software/fcgene-1.0.7/src/impute_thinned_test_bimbam_file_final_bimbam_rearranged.pos.txt -lmm 1 -maf 0.01 -debug > gwas.json

The programming is running beautifully but not generating the final p-values after permutation:

 env GEMMA_COMMAND=/prj/pflaphy-robot/software/gemma-0.98.5-linux-static-AMD64 /homes/vkumar/.gem/ruby/2.7.0/bin/gemma-wrapper --json --loco --force --input K.json --permutate 10 --permute-phenotype /prj/pflaphy-robot/genotypeGVCF_allsamples_updated/linkimpute/vcf2gwas/soil_pH/output/lmm/files/files_soil_pH_GWAS_updated_output_all_imputed_final_chr7Mod_js_GT/mod_sub_soil_pH_GWAS_updated_output_all_imputed_final_chr7Mod_js_GT_bimbam_recode_pheno.txt --no-parallel  -- -g /prj/pflaphy-robot/software/fcgene-1.0.7/src/impute_thinned_test_bimbam_file_final.txt -a /prj/pflaphy-robot/software/fcgene-1.0.7/src/impute_thinned_test_bimbam_file_final_bimbam_rearranged.pos.txt -lmm 1 -maf 0.01 -debug > gwas.json
gemma-wrapper 0.99.5 (Ruby 2.7.0) by Pjotr Prins 2017-2021

NOTE: gemma-wrapper is soon to be replaced by gemma2/lib
Using GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021

Found 0.98.5, comparing against expected v0.98.4
GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021
Executing: /prj/pflaphy-robot/software/gemma-0.98.5-linux-static-AMD64 -g /prj/pflaphy-robot/software/fcgene-1.0.7/src/impute_thinned_test_bimbam_file_final.txt -a /prj/pflaphy-robot/software/fcgene-1.0.7/src/impute_thinned_test_bimbam_file_final_bimbam_rearranged.pos.txt -lmm 1 -maf 0.01 -debug -outdir /tmp/16490003.1.interactive/d20211223-3683321-1139frb -k /tmp/16490003.1.interactive/da39a3ee5e6b4b0d3255bfef95601890afd80709.cXX.txt -o 74f9e75c197d25d710f93e3328d11e2f5fbb5f1d -p /prj/pflaphy-robot/genotypeGVCF_allsamples_updated/linkimpute/vcf2gwas/soil_pH/output/lmm/files/files_soil_pH_GWAS_updated_output_all_imputed_final_chr7Mod_js_GT/mod_sub_soil_pH_GWAS_updated_output_all_imputed_final_chr7Mod_js_GT_bimbam_recode_pheno.txt
GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021
GSL random generator type: mt19937; seed = 45976 (option -1); first value = 3488764641
Reading Files ... 
## number of total individuals = 835
## number of analyzed individuals = 835
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var        =    10000
## number of analyzed SNPs         =    10000
Start Eigen-Decomposition...
pve estimate =0.167393
se(pve) =0.128413
================================================== 100%
**** INFO: Done.
Iteration 1
Executing: /prj/pflaphy-robot/software/gemma-0.98.5-linux-static-AMD64 -g /prj/pflaphy-robot/software/fcgene-1.0.7/src/impute_thinned_test_bimbam_file_final.txt -a /prj/pflaphy-robot/software/fcgene-1.0.7/src/impute_thinned_test_bimbam_file_final_bimbam_rearranged.pos.txt -lmm 1 -maf 0.01 -debug -outdir /tmp/16490003.1.interactive/d20211223-3683321-1139frb -k /tmp/16490003.1.interactive/da39a3ee5e6b4b0d3255bfef95601890afd80709.cXX.txt -o abbcb830314d0ad6c5c35b2fdd304a723cc645ee -p phenotypes-1
GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021
GSL random generator type: mt19937; seed = 45985 (option -1); first value = 717344232
Reading Files ... 
## number of total individuals = 835
## number of analyzed individuals = 835
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var        =    10000
## number of analyzed SNPs         =    10000
Start Eigen-Decomposition...
pve estimate =0.0105545
se(pve) =0.0145437
================================================== 100%
**** INFO: Done.
Iteration 2
.
.
.
.
.
Iteration 10
Executing: /prj/pflaphy-robot/software/gemma-0.98.5-linux-static-AMD64 -g /prj/pflaphy-robot/software/fcgene-1.0.7/src/impute_thinned_test_bimbam_file_final.txt -a /prj/pflaphy-robot/software/fcgene-1.0.7/src/impute_thinned_test_bimbam_file_final_bimbam_rearranged.pos.txt -lmm 1 -maf 0.01 -debug -outdir /tmp/16490003.1.interactive/d20211223-3683321-1139frb -k /tmp/16490003.1.interactive/da39a3ee5e6b4b0d3255bfef95601890afd80709.cXX.txt -o a0700e6b419a0a82957225e0e262271f244802bb -p phenotypes-10
GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021
GSL random generator type: mt19937; seed = 46060 (option -1); first value = 1062464796
Reading Files ... 
## number of total individuals = 835
## number of analyzed individuals = 835
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var        =    10000
## number of analyzed SNPs         =    10000
Start Eigen-Decomposition...
pve estimate =0.111323
se(pve) =0.0618144
================================================== 100%
**** INFO: Done.

But the GWAS.json is not showing the final p-values: "phenotypes-1" "phenotypes-2" "phenotypes-3" "phenotypes-4" "phenotypes-5" "phenotypes-6" "phenotypes-7" "phenotypes-8" "phenotypes-9" "phenotypes-10" [1000.0, 1000.0, 1000.0, 1000.0, 1000.0, 1000.0, 1000.0, 1000.0, 1000.0, 1000.0] ["95 percentile (significant) ", 1000.0, -3.0] ["67 percentile (suggestive) ", 1000.0, -3.0]

I feel there is an issue with gemma-wrapper. I have also requested in gemma-google group. Thanks,

Vinod,

[github-wow]

I also faced the same issue and have the same in GWA.json as @vinod1981. Any help is very welcome