EMMAX error : MAGIC number for kinship matrix does not match

[Manav Kapoor]

HI,

I am trying to run single SNP analysis using EMMAX. I have exome chip data. I have converted ped file to vcf file using plink1.9 and annotated vcf file using epacts. I used 

epacts make-kin --vcf annotated_plink.vcf.gz --ped plink_fam_pheno.ped --min-maf 0.01 --min-CallRate 0.9 --out test_make_kinship.kinf

to make kinship file. This process created EPACTS Makefile. I provided this makefile to the EMMAX and its is giving me error 

FATAL ERROR - 

MAGIC number for kinship matrix does not match

terminate called after throwing an instance of 'pException'

  what():  Exception was thrown

make: *** [test_emax.reml] Aborted

Please let me know what this error might be. 

Thanks,

Manav

[Hyun Min Kang]

Hi Manav,

You need to run make -f test_make_kinship.kinf.Makefile -j [# of parallel jobs to create the kinship file, or put "--run [# of parellel jobs]" in your command line argument of epacts make-kin

Thanks,

Hyun.

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