runHawk Error line 30: 32451 Aborted

[cesarayala13]

Hello! I am currently getting this error message while excecuting runHawk (complete log adjacent file ).

(base) user@DESKTOP-NOLVR42:/mnt/e/TestHAWK/Test2MG/Gwas2$ ./runHawk fatalx: (putgtypes) ./runHawk: line 30: 32451 Aborted (core dumped) $eigenstratDir/bin/smartpca -p $hawkDir/parfile.txt > log_eigen.txt Error while null model optimizing at kmer 0 to 0 singularity error : 0 nan error : 1 Null model optimization has exited early due to singularity error Achived error 0.0625 , Exited at iteration 0 Error while alt model optimizing at kmer 0 to 416 singularity error : 0 nan error : 1 Alt model optimization has exited early due to singularity error Achived error Error while alt model optimizing at kmer 0 to 416 singularity error : 0 nan error : 1 Alt model optimization has exited early due to singularity error Achived error Error while alt model optimizing at kmer 0 to 416 singularity error : 0 nan error : 1 Alt model optimization has exited early due to singularity error Achived error Error while alt model optimizing at kmer 0 to 416 singularity error : 0 nan error : 1 Alt model optimization has exited early due to singularity error Achived error Error while alt model optimizing at kmer 0 to 416 singularity error : 0 nan error : 1 Alt model optimization has exited early due to singularity error Achived error Error while alt model optimizing at kmer 0 to 416 singularity error : 0 nan error : 1 Alt model optimization has exited early due to singularity error Achived error 0.0625 , Exited at iteration 0 0.0625 , Exited at iteration 0 0.0625 , Exited at iteration 0 0.0625 , Exited at iteration 0 0.0625 , Exited at iteration 0 0.0625 , Exited at iteration 0 Nan error happend or log_likelihood_ratio is <0 while estimating log_liklelihood_ratio at kmer no. 0 at thread 0 alt model : Nan error happend or log_likelihood_ratio is <0 while estimating log_liklelihood_ratio at kmer no. 1 at thread 1 alt model : Nan error happend or log_likelihood_ratio is <0 while estimating log_liklelihood_ratio at kmer no. 5 at thread 5 alt model : Nan error happend or log_likelihood_ratio is <0 while estimating log_liklelihood_ratio at kmer no. 4 at thread 4 alt model : Nan error happend or log_likelihood_ratio is <0 while estimating log_liklelihood_ratio at kmer no. 2 at thread 2 alt model : 1 1 1 1

This is happening always while "log_reg_case" is being executed

I am using jelly-fish version present in supplemets folder with 4 samples, two cases and two controls

I will appreciate some help

runHawk_Error.txt

[atifrahman]

Hi, it looks like the error is from Eigenstrat which is possibly due to too few samples. With only four samples, even if it runs properly, it's unlikely that k-mers significantly associated with the phenotypes will be obtained.