[INFO]	Program version: 20170307
[INFO]	Git Version: Unknown
[INFO]	Parameters BEGIN
# ParameterList created by 698711 on gena.erasmusmc.nl at Mon Jun 19 06:44:52 2017
--inVcf "/home/698711/GIANTGLC/RS2/chrX.imputed.poly.vcf.gz" --out "/home/698711/GIANTGLC/RS2/TC_INV/RS2_CEU_1000G_imputation_TC_INV_MALE_chrX" --pheno "/home/698711/GIANTGLC/RS2/RS2TC_INV_male.txt" --dosage "DS" --xLabel "X" --meta "score" --xHemiKinship "/home/698711/GIANTGLC/RS2/RS2_kinship_matrix.xHemi.kinship"
[INFO]	Parameters END
[INFO]	Analysis started at: Mon Jun 19 06:44:52 2017
[INFO]	Loaded [ 2150 ] samples from VCF files
[WARN]	Skip: Missing or invalid phenotype type, skipping line 2 [ 1 1 0 0 NA NA ] ... 
[WARN]	Skip: Missing or invalid phenotype type, skipping line 3 [ 1000 1000 0 0 NA NA ] ... 
[WARN]	Skip: Missing or invalid phenotype type, skipping line 4 [ 1001002 1001002 0 0 NA NA ] ... 
[WARN]	Skip: Missing or invalid phenotype type, skipping line 5 [ 1002 1002 0 0 NA NA ] ... 
[WARN]	Skip: Missing or invalid phenotype type, skipping line 6 [ 1003 1003 0 0 NA NA ] ... 
[WARN]	Skip: Missing or invalid phenotype type, skipping line 10 [ 1015002 1015002 0 0 NA NA ] ... 
[WARN]	Skip: Missing or invalid phenotype type, skipping line 12 [ 1019 1019 0 0 NA NA ] ... 
[WARN]	Skip: Missing or invalid phenotype type, skipping line 13 [ 1020 1020 0 0 NA NA ] ... 
[WARN]	Skip: Missing or invalid phenotype type, skipping line 15 [ 1024 1024 0 0 NA NA ] ... 
[WARN]	Skip: Missing or invalid phenotype type, skipping line 16 [ 1025 1025 0 0 NA NA ] ... 
[WARN]	Skip: Additional [ 1254 ] lines have missing or invalid phenotype type
[INFO]	Loaded [ 886 ] sample pheontypes
[WARN]	Total [ 1264 ] samples are dropped from VCF file due to missing phenotype.
[WARN]	Drop sample [ 1 ] from VCF file due to missing phenotype
[WARN]	Drop sample [ 1000 ] from VCF file due to missing phenotype
[WARN]	Drop sample [ 1001002 ] from VCF file due to missing phenotype
[WARN]	Drop sample [ 1002 ] from VCF file due to missing phenotype
[WARN]	Drop sample [ 1003 ] from VCF file due to missing phenotype
[WARN]	Drop sample [ 1015002 ] from VCF file due to missing phenotype
[WARN]	Drop sample [ 1019 ] from VCF file due to missing phenotype
[WARN]	Drop sample [ 1020 ] from VCF file due to missing phenotype
[WARN]	Drop sample [ 1024 ] from VCF file due to missing phenotype
[WARN]	Drop sample [ 1025 ] from VCF file due to missing phenotype
[WARN]	Skip outputting additional [ 1254 ] samples due to missing phenotype.
[INFO]	Loaded 886 male, 0 female and 0 sex-unknonw samples from /home/698711/GIANTGLC/RS2/RS2TC_INV_male.txt
[INFO]	Analysis begins with [ 886 ] samples...
[INFO]	Impute missing genotype to mean (by default)
[INFO]	Use dosage genotype from VCF flag DS.
[INFO]	Analysis started
[INFO]	Analyzed [ 503525 ] variants
[INFO]	Analysis ends at: Mon Jun 19 06:50:57 2017
[INFO]	Analysis took 365 seconds