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sample_output.log
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sample_output.log
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***************************************************************************************************
* GAT (Generic Genome-Wide Association Tool)
* Description: Generic module for associating bialleic/multialleic phased/unphased markers
* version 1.0
* (C) 2020-, Seoul National University
* Please report bugs to: Chanwoo Kim <[email protected]>
* https://github.com/ch6845/GAT
***************************************************************************************************
Start time: Sat Mar 14 19:57:58 2020
Working directory: /data/ch6845/MHC_phewas_testbench
Hostname: h5
Parameters
--assoc linear
--out data/out_assoc/height/step_01.GAT
--bgl_phased data/genotype/4_merge/HLA_AA_SNP.bgl.phased
--bfile data/genotype/4_merge/1000G
--multialleic "(?P<name>HLA_[0-9A-Z]*)\*(?P<allele>[0-9:]*)"
--multialleic_always "(?P<name>AA_[A-Z0-9]*_[\-0-9]*_[0-9]*_exon[0-9]*)_*(?P<allele>[A-Z]*)"
--skip "(?P<name>6:[0-9]*_[A-Z]*/[\<\>A-Z\:0-9]*),(?P<name>AX\-[0-9]*),(?P<name>SNPS_.*),(?P<name>INS_SNPS_.*)"
--pheno data/out_pheno/height.phe
--covar data/out_assoc/height/covar
--condition_list data/out_assoc/height/step_01.cond
********************************************Data Loading********************************************
125673 samples (0 males, 0 females) loaded from data/genotype/4_merge/1000G
56598 unphased variants loaded from data/genotype/4_merge/1000G
Loading bgl phased
14391 phsaed variants loaded from data/genotype/4_merge/HLA_AA_SNP.bgl.phased
125673 samples (45647 males, 80026 females) loaded from data/genotype/4_merge/HLA_AA_SNP.bgl.phased
125673 pheotype loaded from data/out_pheno/height.phe
Among them, valid: 125264, missing: 409
mean=160.255 std=8.192 median=159.400 min=135.600 max=185.000
***********************************Multialleic expression parsing***********************************
plink, multialleic:
plink, multialleic always:
phased, multialleic: HLA_A,HLA_C,HLA_B,HLA_DRB1,HLA_DQA1,HLA_DQB1,HLA_DPA1,HLA_DPB1
phased, multialleic always: AA_A_-15_29910359_exon1,AA_A_-11_29910371_exon1,AA_A_9_29910558_exon2,AA_A_17_29910582_exon2,AA_A_44_29910663_exon2,AA_A_56_29910699_exon2,AA_A_62_29910717_exon2,AA_A_63_29910720_exon2,AA_A_65_29910726_exon2,AA_A_66_29910729_exon2,AA_A_67_29910732_exon2,AA_A_70_29910741_exon2,AA_A_73_29910750_exon2,AA_A_74_29910753_exon2,AA_A_76_29910759_exon2,AA_A_77_29910762_exon2,AA_A_79_29910768_exon2,AA_A_80_29910771_exon2,AA_A_81_29910774_exon2,AA_A_82_29910777_exon2,AA_A_83_29910780_exon2,AA_A_90_29910801_exon2,AA_A_95_29911057_exon3,AA_A_97_29911063_exon3,AA_A_99_29911069_exon3,AA_A_105_29911087_exon3,AA_A_107_29911093_exon3,AA_A_114_29911114_exon3,AA_A_116_29911120_exon3,AA_A_127_29911153_exon3,AA_A_142_29911198_exon3,AA_A_144_29911204_exon3,AA_A_145_29911207_exon3,AA_A_149_29911219_exon3,AA_A_150_29911222_exon3,AA_A_151_29911225_exon3,AA_A_152_29911228_exon3,AA_A_156_29911240_exon3,AA_A_158_29911246_exon3,AA_A_161_29911255_exon3,AA_A_163_29911261_exon3,AA_A_166_29911270_exon3,AA_A_167_29911273_exon3,AA_A_184_29911903_exon4,AA_A_193_29911930_exon4,AA_A_194_29911933_exon4,AA_A_207_29911972_exon4,AA_A_246_29912089_exon4,AA_A_253_29912110_exon4,AA_A_276_29912281_exon5,AA_A_282_29912299_exon5,AA_A_294_29912335_exon5,AA_A_298_29912347_exon5,AA_A_299_29912350_exon5,AA_A_307_29912374_exon5,AA_A_311_29912386_exon5,AA_A_321_29912858_exon6,AA_A_334_29913039_exon7,AA_C_339_31237131_exon7,AA_C_326_31237170_exon7,AA_C_324_31237283_exon6,AA_C_321_31237292_exon6,AA_C_307_31237773_exon5,AA_C_306_31237776_exon5,AA_C_305_31237779_exon5,AA_C_304_31237782_exon5,AA_C_303_31237785_exon5,AA_C_295_31237809_exon5,AA_C_285_31237839_exon5,AA_C_275_31237869_exon5,AA_C_273_31237996_exon4,AA_C_267_31238014_exon4,AA_C_261_31238032_exon4,AA_C_253_31238056_exon4,AA_C_248_31238071_exon4,AA_C_219_31238158_exon4,AA_C_194_31238233_exon4,AA_C_184_31238263_exon4,AA_C_177_31238871_exon3,AA_C_173_31238883_exon3,AA_C_163_31238913_exon3,AA_C_156_31238934_exon3,AA_C_152_31238946_exon3,AA_C_147_31238961_exon3,AA_C_138_31238988_exon3,AA_C_116_31239054_exon3,AA_C_114_31239060_exon3,AA_C_113_31239063_exon3,AA_C_103_31239093_exon3,AA_C_99_31239105_exon3,AA_C_97_31239111_exon3,AA_C_95_31239117_exon3,AA_C_94_31239120_exon3,AA_C_91_31239129_exon3,AA_C_90_31239378_exon2,AA_C_80_31239408_exon2,AA_C_77_31239417_exon2,AA_C_73_31239429_exon2,AA_C_66_31239450_exon2,AA_C_49_31239501_exon2,AA_C_35_31239543_exon2,AA_C_24_31239576_exon2,AA_C_21_31239585_exon2,AA_C_14_31239606_exon2,AA_C_11_31239615_exon2,AA_C_9_31239621_exon2,AA_C_6_31239630_exon2,AA_C_1_31239645_exon2,AA_C_-9_31239802_exon1,AA_C_-15_31239820_exon1,AA_C_-17_31239826_exon1,AA_B_325_31322303_exon7,AA_B_305_31322910_exon5,AA_B_282_31322979_exon5,AA_B_245_31323183_exon4,AA_B_199_31323321_exon4,AA_B_194_31323336_exon4,AA_B_180_31323952_exon3,AA_B_178_31323958_exon3,AA_B_177_31323961_exon3,AA_B_171_31323979_exon3,AA_B_167_31323991_exon3,AA_B_163_31324003_exon3,AA_B_158_31324018_exon3,AA_B_156_31324024_exon3,AA_B_152_31324036_exon3,AA_B_147_31324051_exon3,AA_B_145_31324057_exon3,AA_B_143_31324063_exon3,AA_B_131_31324099_exon3,AA_B_116_31324144_exon3,AA_B_114_31324150_exon3,AA_B_113_31324153_exon3,AA_B_103_31324183_exon3,AA_B_99_31324195_exon3,AA_B_97_31324201_exon3,AA_B_95_31324207_exon3,AA_B_94_31324210_exon3,AA_B_83_31324488_exon2,AA_B_82_31324491_exon2,AA_B_81_31324494_exon2,AA_B_80_31324497_exon2,AA_B_77_31324506_exon2,AA_B_76_31324509_exon2,AA_B_74_31324515_exon2,AA_B_71_31324524_exon2,AA_B_70_31324527_exon2,AA_B_69_31324530_exon2,AA_B_67_31324536_exon2,AA_B_66_31324539_exon2,AA_B_65_31324542_exon2,AA_B_63_31324548_exon2,AA_B_62_31324551_exon2,AA_B_52_31324581_exon2,AA_B_46_31324599_exon2,AA_B_45_31324602_exon2,AA_B_41_31324614_exon2,AA_B_32_31324641_exon2,AA_B_24_31324665_exon2,AA_B_12_31324701_exon2,AA_B_11_31324704_exon2,AA_B_9_31324710_exon2,AA_B_-8_31324886_exon1,AA_B_-10_31324892_exon1,AA_B_-11_31324895_exon1,AA_B_-16_31324910_exon1,AA_B_-21_31324925_exon1,AA_B_-23_31324931_exon1,AA_DRB1_233_32548048_exon5,AA_DRB1_231_32548054_exon5,AA_DRB1_189_32548667_exon4,AA_DRB1_181_32549392_exon3,AA_DRB1_180_32549395_exon3,AA_DRB1_166_32549437_exon3,AA_DRB1_149_32549488_exon3,AA_DRB1_142_32549509_exon3,AA_DRB1_140_32549515_exon3,AA_DRB1_133_32549536_exon3,AA_DRB1_120_32549575_exon3,AA_DRB1_104_32549623_exon3,AA_DRB1_98_32549641_exon3,AA_DRB1_96_32549647_exon3,AA_DRB1_86_32551904_exon2,AA_DRB1_85_32551907_exon2,AA_DRB1_78_32551928_exon2,AA_DRB1_77_32551931_exon2,AA_DRB1_74_32551940_exon2,AA_DRB1_73_32551943_exon2,AA_DRB1_71_32551949_exon2,AA_DRB1_70_32551952_exon2,AA_DRB1_67_32551961_exon2,AA_DRB1_60_32551982_exon2,AA_DRB1_58_32551988_exon2,AA_DRB1_57_32551991_exon2,AA_DRB1_47_32552021_exon2,AA_DRB1_40_32552042_exon2,AA_DRB1_38_32552048_exon2,AA_DRB1_37_32552051_exon2,AA_DRB1_33_32552063_exon2,AA_DRB1_32_32552066_exon2,AA_DRB1_31_32552069_exon2,AA_DRB1_30_32552072_exon2,AA_DRB1_28_32552078_exon2,AA_DRB1_26_32552084_exon2,AA_DRB1_25_32552087_exon2,AA_DRB1_16_32552114_exon2,AA_DRB1_14_32552120_exon2,AA_DRB1_13_32552123_exon2,AA_DRB1_12_32552126_exon2,AA_DRB1_11_32552129_exon2,AA_DRB1_10_32552132_exon2,AA_DRB1_9_32552135_exon2,AA_DRB1_4_32557422_exon1,AA_DRB1_-1_32557434_exon1,AA_DRB1_-16_32557479_exon1,AA_DRB1_-17_32557482_exon1,AA_DRB1_-24_32557503_exon1,AA_DRB1_-25_32557506_exon1,AA_DQA1_-16_32605258_exon1,AA_DQA1_-13_32605267_exon1,AA_DQA1_-7_32605285_exon1,AA_DQA1_-6_32605288_exon1,AA_DQA1_2_32605309_exon1,AA_DQA1_11_32609111_exon2,AA_DQA1_18_32609132_exon2,AA_DQA1_25_32609153_exon2,AA_DQA1_26_32609156_exon2,AA_DQA1_34_32609180_exon2,AA_DQA1_40_32609198_exon2,AA_DQA1_41_32609201_exon2,AA_DQA1_45_32609213_exon2,AA_DQA1_47_32609219_exon2,AA_DQA1_48_32609222_exon2,AA_DQA1_50_32609228_exon2,AA_DQA1_51_32609231_exon2,AA_DQA1_52_32609234_exon2,AA_DQA1_53_32609237_exon2,AA_DQA1_54_32609240_exon2,AA_DQA1_55_32609243_exon2,AA_DQA1_56_32609246_exon2,AA_DQA1_61_32609261_exon2,AA_DQA1_64_32609270_exon2,AA_DQA1_66_32609276_exon2,AA_DQA1_69_32609285_exon2,AA_DQA1_75_32609303_exon2,AA_DQA1_76_32609306_exon2,AA_DQA1_80_32609318_exon2,AA_DQA1_107_32609812_exon3,AA_DQA1_129_32609878_exon3,AA_DQA1_130_32609881_exon3,AA_DQA1_156_32609959_exon3,AA_DQA1_160_32609971_exon3,AA_DQA1_161_32609974_exon3,AA_DQA1_163_32609980_exon3,AA_DQA1_175_32610016_exon3,AA_DQA1_187_32610410_exon4,AA_DQA1_199_32610446_exon4,AA_DQA1_207_32610470_exon4,AA_DQA1_215_32610494_exon4,AA_DQA1_218_32610503_exon4,AA_DQB1_234_32627649_exon6,AA_DQB1_233_32628263_exon5,AA_DQB1_232_32628266_exon5,AA_DQB1_231_32628269_exon5,AA_DQB1_230_32628272_exon5,AA_DQB1_229_32628275_exon5,AA_DQB1_228_32628278_exon5,AA_DQB1_227_32628281_exon5,AA_DQB1_224_32628775_exon4,AA_DQB1_221_32628784_exon4,AA_DQB1_220_32628787_exon4,AA_DQB1_203_32628838_exon4,AA_DQB1_197_32628856_exon4,AA_DQB1_185_32629408_exon3,AA_DQB1_182_32629417_exon3,AA_DQB1_167_32629462_exon3,AA_DQB1_140_32629543_exon3,AA_DQB1_135_32629558_exon3,AA_DQB1_130_32629573_exon3,AA_DQB1_126_32629585_exon3,AA_DQB1_125_32629588_exon3,AA_DQB1_116_32629615_exon3,AA_DQB1_90_32632582_exon2,AA_DQB1_89_32632585_exon2,AA_DQB1_87_32632591_exon2,AA_DQB1_86_32632594_exon2,AA_DQB1_85_32632597_exon2,AA_DQB1_84_32632600_exon2,AA_DQB1_77_32632621_exon2,AA_DQB1_75_32632627_exon2,AA_DQB1_74_32632630_exon2,AA_DQB1_71_32632639_exon2,AA_DQB1_70_32632642_exon2,AA_DQB1_67_32632651_exon2,AA_DQB1_66_32632654_exon2,AA_DQB1_57_32632681_exon2,AA_DQB1_56_32632684_exon2,AA_DQB1_55_32632687_exon2,AA_DQB1_53_32632693_exon2,AA_DQB1_52_32632696_exon2,AA_DQB1_47_32632711_exon2,AA_DQB1_46_32632714_exon2,AA_DQB1_45_32632717_exon2,AA_DQB1_38_32632738_exon2,AA_DQB1_37_32632741_exon2,AA_DQB1_30_32632762_exon2,AA_DQB1_28_32632768_exon2,AA_DQB1_26_32632774_exon2,AA_DQB1_23_32632783_exon2,AA_DQB1_14_32632810_exon2,AA_DQB1_13_32632813_exon2,AA_DQB1_9_32632825_exon2,AA_DQB1_3_32634281_exon1,AA_DQB1_-4_32634299_exon1,AA_DQB1_-5_32634302_exon1,AA_DQB1_-6_32634305_exon1,AA_DQB1_-9_32634314_exon1,AA_DQB1_-10_32634317_exon1,AA_DQB1_-17_32634338_exon1,AA_DQB1_-18_32634341_exon1,AA_DQB1_-21_32634350_exon1,AA_DQB1_-27_32634368_exon1,AA_DPA1_228_33036434_exon4,AA_DPA1_160_33036852_exon3,AA_DPA1_127_33036951_exon3,AA_DPA1_111_33036999_exon3,AA_DPA1_83_33037423_exon2,AA_DPA1_50_33037522_exon2,AA_DPA1_31_33037579_exon2,AA_DPA1_11_33037639_exon2,AA_DPB1_8_33048463_exon2,AA_DPB1_9_33048466_exon2,AA_DPB1_11_33048472_exon2,AA_DPB1_35_33048544_exon2,AA_DPB1_36_33048547_exon2,AA_DPB1_55_33048604_exon2,AA_DPB1_56_33048607_exon2,AA_DPB1_57_33048610_exon2,AA_DPB1_65_33048634_exon2,AA_DPB1_69_33048646_exon2,AA_DPB1_76_33048667_exon2,AA_DPB1_84_33048691_exon2,AA_DPB1_85_33048694_exon2,AA_DPB1_86_33048697_exon2,AA_DPB1_87_33048700_exon2,AA_DPB1_96_33052678_exon3,AA_DPB1_170_33052900_exon3,AA_DPB1_178_33052924_exon3,AA_DPB1_205_33053552_exon4
**************************************Skip expression parsing**************************************
(?P<name>6:[0-9]*_[A-Z]*/[\<\>A-Z\:0-9]*)
(?P<name>AX\-[0-9]*)
(?P<name>SNPS_.*)
(?P<name>INS_SNPS_.*)
70425 markers were identified from --skip
8 covariates loaded from data/out_assoc/height/covar
Empty --condition-list data/out_assoc/height/step_01.cond
***************************************Input integrity check***************************************
Passed individual integrity check (Individuals from --bfile is the same as individuals from --bgl-phased)
However, sex is not matching
Passed individual integrity check (Individuals from --bfile or --bgl-phased is the same as individuals from --covar)
Passed condition integrity check (All variants in --condition-list are identified from loaded variants)
**********************************Converting condtion to covariate**********************************
covariate of this analysis was saved to data/out_assoc/height/step_01.GAT.covar.tsv , data/out_assoc/height/step_01.GAT.covar_unphased.tsv
*********************************************Regression*********************************************
Start time: Sat Mar 14 20:04:18 2020
70425 markers were identified from --skip
And 70295 markers were skipped
Total markers to test : 240
Time: Sat Mar 14 20:04:19 2020 - 0.000 %
Time: Sat Mar 14 20:04:35 2020 - 5.000 %
Time: Sat Mar 14 20:04:50 2020 - 10.000 %
Time: Sat Mar 14 20:05:03 2020 - 15.000 %
Time: Sat Mar 14 20:05:16 2020 - 20.000 %
Time: Sat Mar 14 20:05:29 2020 - 25.000 %
Time: Sat Mar 14 20:05:44 2020 - 30.000 %
Time: Sat Mar 14 20:05:57 2020 - 35.000 %
Time: Sat Mar 14 20:06:09 2020 - 40.000 %
Time: Sat Mar 14 20:06:25 2020 - 45.000 %
Time: Sat Mar 14 20:06:35 2020 - 50.000 %
Time: Sat Mar 14 20:06:46 2020 - 55.000 %
Time: Sat Mar 14 20:06:52 2020 - 60.000 %
Time: Sat Mar 14 20:07:00 2020 - 65.000 %
Time: Sat Mar 14 20:07:06 2020 - 70.000 %
Time: Sat Mar 14 20:07:14 2020 - 75.000 %
Time: Sat Mar 14 20:07:22 2020 - 80.000 %
Time: Sat Mar 14 20:07:31 2020 - 85.000 %
Time: Sat Mar 14 20:07:36 2020 - 90.000 %
Time: Sat Mar 14 20:07:45 2020 - 95.000 %
End time: Sat Mar 14 20:07:51 2020