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sriramlab / SCORE

SCalable genetic CORrelation Estimator
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Getting Nans when running example script #4

Open hrushikeshloya opened 2 years ago

hrushikeshloya commented 2 years ago

Hi, I have been trying to run SCORE for some of my analysis and was wondering if there is a fix for getting nan estimates when you run the example script ./build/SCORE -g ./example/all -p pheno_1.pheno.plink -mpheno 1,2 -b 10 ? Also pasting the output log below, is there something wrong with the way I am using it ?

perform GWAS: 0 Binary phenotype: 0 Filling phenotype with mean: 0 Compute heritability: 1 Analysing phenotype 1, 2 Read in 2 phenotypes There are 0 0 individuals with no missing phenotypes read in bim file reading functional annotation... Total number of annotation groups: 1 num of random vectors: 100 inverse of exist_ind: inf inf No Covariate File Specified genotype size: 8430 X 14821 Total number of blocks: 22initialized Xzb_total.. initialized resid_total.... initialized zb .. 1.17844 -0.365868 -0.0782989 0.446422BLOCK_SIZE: 0 Start reading genotype... Reading chromosome 0 Reading chromosome 1 Reading chromosome 2 Reading chromosome 3 Reading chromosome 4 Reading chromosome 5 Reading chromosome 6 Reading chromosome 7 Reading chromosome 8 Reading chromosome 9 Reading chromosome 10 Reading chromosome 11 Reading chromosome 12 Reading chromosome 13 Reading chromosome 14 Reading chromosome 15 Reading chromosome 16 Reading chromosome 17 Reading chromosome 18 Reading chromosome 19 Reading chromosome 20 Reading chromosome 21 A: -nan -nan -nan 0 b: -nan -nan V(e): -nan Vp -nan V(G)(0): -nan A: -nan -nan -nan 0 b: -nan -nan V(e): -nan Vp -nan V(G)(0): -nan total comman samples: 0 A: -nan -nan -nan 0 b: -nan -nan rho_g(0): -nan rho_e: -nan gamma_g(0): -nan Start reading genotype... reading chromosome 0 reading chromosome 1 reading chromosome 2 reading chromosome 3 reading chromosome 4 reading chromosome 5 reading chromosome 6 reading chromosome 7 reading chromosome 8 reading chromosome 9 reading chromosome 10 reading chromosome 11 reading chromosome 12 reading chromosome 13 reading chromosome 14 reading chromosome 15 reading chromosome 16 reading chromosome 17 reading chromosome 18 reading chromosome 19 reading chromosome 20 reading chromosome 21 SE(h2g_0(0)): nan SE(h2g_1(0)): nan SE(rg_(0,1)(0)): nan

ariel-wu commented 2 years ago

Hi! Thanks for reaching out to us! By looking at the output, "There are 0 0 individuals..", there are no phenotypes passed to the software. It could be helpful to check the place you run your code. If you run from the "[path to repo]/SCORE"directory, please use "./build/SCORE", if you're running from the build directory, please use "./SCORE ... ". We also updated the README. Please check. Also please note we update with an output option, with "-o [output name]", which you could use within a loop. If this option is not given, all output will be written to a file called "output" to your running directory.

Let me know if there is any other issues coming up!

khramts commented 2 years ago

Hello, I ran into the same issue. To fix this you also need to add a path before the phenotype file.

Change from ./SCORE -g ../example/all -p pheno_1.pheno.plink -mpheno 1,2 -b 10 -o [OUTPUT DESTINATION DEFINED]

to this: ./SCORE -g ../example/all -p ../example/pheno_1.pheno.plink -mpheno 1,2 -b 10 -o [OUTPUT DESTINATION DEFINED]