Hi, I ran a impute2 command and get the following summary and the running stopped. no output file.
impute2 -known_haps_g chr10.haps -h 1000GP_Phase3_chr10.hap -l 1000GP_Phase3_chr10.legend -m genetic_map_chr10_combined_b37.txt -int 1 5e6 -o chr10_imputed.gen
The following is from the summary file.
-reading genetic map from -m file
--filename=[genetic_map_chr10_combined_b37.txt]
--read 9196 SNPs in the analysis interval+buffer region
-reading Panel 2 haplotypes from -known_haps_g file
--filename=[chr10.haps]
--detected 418 individuals
--read 1491 SNPs in the analysis interval+buffer region
--added 1491 new SNPs based on known haplotypes
-reading Panel 0 haplotypes from -h and -l files
--filename=[1000GP_Phase3_chr10.hap]
--filename=[1000GP_Phase3_chr10.legend]
--detected 5008 haplotypes
Killed
What is the problem? Any comments? Thanks everyone.
impute2 -known_haps_g chr10.haps -h 1000GP_Phase3_chr10.hap -l 1000GP_Phase3_chr10.legend -m genetic_map_chr10_combined_b37.txt -int 1 5e6 -o chr10_imputed.gen
The following is from the summary file.
-reading genetic map from -m file
--filename=[genetic_map_chr10_combined_b37.txt]
--read 9196 SNPs in the analysis interval+buffer region
-reading Panel 2 haplotypes from -known_haps_g file
--filename=[chr10.haps]
--detected 418 individuals
--read 1491 SNPs in the analysis interval+buffer region
--added 1491 new SNPs based on known haplotypes
-reading Panel 0 haplotypes from -h and -l files
--filename=[1000GP_Phase3_chr10.hap]
--filename=[1000GP_Phase3_chr10.legend]
--detected 5008 haplotypes
Killed
What is the problem? Any comments? Thanks everyone.