Example of gebvtest.log
2024-Aug-12 15:13:43 gebvtest_2024A.py: start Options: -v -m hol abc ../sample_data gebvtest_2024A.py version=2022.12.20 absolute DATADIR: /home/interbull/valpal/GEBVtest_2024/gtest_2024A_data/sample_data Processing brd=HOL pop=ABC cou=ABC datadir=../sample_data stored 1014 records from file file736_ABCHOL opening output file /home/interbull/valpal/GEBVtest_2024/gtest_2024A_data/sample_data/file735_ABCHOL ... opening output file /home/interbull/valpal/GEBVtest_2024/gtest_2024A_data/sample_data/file735adj_ABCHOL ... reading file300Cr_ABCHOL ... stored 991 records for trait mil from file file300Cr_ABCHOL reading file300Gr_ABCHOL ... stored 785 records for trait mil from file file300Gr_ABCHOL reading file300Cf_ABCHOL ... stored 967 records for trait mil from file file300Cf_ABCHOL reading file300Df_ABCHOL ... stored 726 records for trait mil from file file300Df_ABCHOL reading file300Gf_ABCHOL ... stored 742 records for trait mil from file file300Gf_ABCHOL ------------------------------------------------------------------------------- processing trt=mil h2=0.4000 evdate=20120801 depvar=GM byear=2004 type2x=N ------------------------------------------------------------------------------- derived 401 records for trait mil for a DGEBV file300 equivalent Summary statistics on candidate bulls (CB) and test bulls (TB) -------------------------------------------------------------- Trait Variable N Mean Std Min Max -------------------------------------------------------------- mil CB EBV 177 573.367 813.411 -1908.00 2962.00 mil TB EBV 164 544.957 804.675 -1908.00 2962.00 mil TB VAL(y) 164 1064.972 903.443 -1436.40 4147.10 Base=Current mil TB GEBV(x1) 164 1047.909 599.771 -726.00 2624.00 Base=Old mil TB EBVr(x2) 164 1244.341 548.582 -564.00 2616.00 Base=Old mil TB GEBV(x1) 164 707.550 624.813 -1140.42 2349.45 Base=Current mil TB EBVr(x2) 164 912.185 571.487 -971.66 2341.11 Base=Current mil BB EBVf(y) 570 -97.361 780.743 -2580.00 1884.00 mil BB EBVr(x) 570 310.270 745.217 -1984.00 2318.00 mil BB EBV(wt) 570 48.554 42.090 0.00 97.00 -------------------------------------------------------------- mil : DGEBV : Base 0.25: Full = -384.11 + 1.042 * Red b1 0.940 ~> 0.902 b2 1.101 ~> 1.057 Details of GEBVtest calculations mil i_est = (544.957 - 573.367) / 813.411 = -0.035 After Base adjustments: mil p=0.987 x=-2.213 i=0.035 k=0.079 R2b=0.414 E(b1)=0.952 b1=0.902 mil b1-E(b1) = -0.050 t = -0.53 bootstrap P(b=Eb) = 57.6 b1_test = Pass mil R2_1 = 39.4 R2_2 = 45.0 bootstrap P(R2_gain) = 15.4 R2_test = NS- mil stat_test=Y pract_test=Y bio_test=Y R2_test=- overall = PASS 2024-Aug-12 15:13:43 gebvtest_2024A.py: finished mil reading file300Cr_ABCHOL ... stored 991 records for trait fat from file file300Cr_ABCHOL reading file300Gr_ABCHOL ... stored 785 records for trait fat from file file300Gr_ABCHOL reading file300Cf_ABCHOL ... stored 967 records for trait fat from file file300Cf_ABCHOL reading file300Df_ABCHOL ... stored 726 records for trait fat from file file300Df_ABCHOL reading file300Gf_ABCHOL ... stored 742 records for trait fat from file file300Gf_ABCHOL ------------------------------------------------------------------------------- processing trt=fat h2=0.4000 evdate=20120801 depvar=GM byear=2004 type2x=N ------------------------------------------------------------------------------- derived 401 records for trait fat for a DGEBV file300 equivalent Summary statistics on candidate bulls (CB) and test bulls (TB) -------------------------------------------------------------- Trait Variable N Mean Std Min Max -------------------------------------------------------------- fat CB EBV 176 24.284 29.839 -65.00 95.00 fat TB EBV 164 22.939 28.980 -65.00 95.00 fat TB VAL(y) 164 34.659 31.137 -35.31 108.31 Base=Current fat TB GEBV(x1) 164 37.720 20.138 -19.00 86.00 Base=Old fat TB EBVr(x2) 164 44.335 20.490 -4.00 88.00 Base=Old fat TB GEBV(x1) 164 29.060 21.330 -31.02 80.20 Base=Current fat TB EBVr(x2) 164 36.068 21.703 -15.13 82.32 Base=Current fat BB EBVf(y) 570 -12.807 32.849 -109.00 65.00 fat BB EBVr(x) 570 -0.105 30.713 -83.00 81.00 fat BB EBV(wt) 570 48.554 42.090 0.00 97.00 -------------------------------------------------------------- fat : DGEBV : Base 0.25: Full = -10.89 + 1.059 * Red b1 0.774 ~> 0.730 b2 0.721 ~> 0.680 Details of GEBVtest calculations fat i_est = (22.939 - 24.284) / 29.839 = -0.045 After Base adjustments: fat p=0.982 x=-2.097 i=0.045 k=0.097 R2b=0.270 E(b1)=0.928 b1=0.730 fat b1-E(b1) = -0.197 t = -2.06 bootstrap P(b=Eb) = 3.0 b1_test = Fail fat R2_1 = 25.1 R2_2 = 22.5 bootstrap P(R2_gain) = 73.5 R2_test = NS+ fat stat_test=N pract_test=N bio_test=N R2_test=- overall = FAIL 2024-Aug-12 15:13:44 gebvtest_2024A.py: finished fat reading file300Cr_ABCHOL ... stored 991 records for trait pro from file file300Cr_ABCHOL reading file300Gr_ABCHOL ... stored 785 records for trait pro from file file300Gr_ABCHOL reading file300Cf_ABCHOL ... stored 967 records for trait pro from file file300Cf_ABCHOL reading file300Df_ABCHOL ... stored 726 records for trait pro from file file300Df_ABCHOL reading file300Gf_ABCHOL ... stored 742 records for trait pro from file file300Gf_ABCHOL ------------------------------------------------------------------------------- processing trt=pro h2=0.4000 evdate=20120801 depvar=GM byear=2004 type2x=N ------------------------------------------------------------------------------- derived 457 records for trait pro for a DGEBV file300 equivalent Summary statistics on candidate bulls (CB) and test bulls (TB) -------------------------------------------------------------- Trait Variable N Mean Std Min Max -------------------------------------------------------------- pro CB EBV 176 20.926 22.004 -50.00 89.00 pro TB EBV 164 20.335 21.066 -50.00 89.00 pro TB VAL(y) 164 36.017 23.991 -29.35 102.68 Base=Current pro TB GEBV(x1) 164 35.177 15.715 -12.00 72.00 Base=Old pro TB EBVr(x2) 164 40.768 15.368 -8.00 76.00 Base=Old pro TB GEBV(x1) 164 24.941 16.351 -24.15 63.26 Base=Current pro TB EBVr(x2) 164 30.759 15.990 -19.98 67.42 Base=Current pro BB EBVf(y) 620 -4.660 23.030 -72.00 61.00 pro BB EBVr(x) 620 7.800 22.285 -56.00 64.00 pro BB EBV(wt) 620 35.936 38.719 0.00 97.00 -------------------------------------------------------------- pro : DGEBV : Base 0.25: Full = -11.66 + 1.040 * Red b1 0.873 ~> 0.839 b2 0.823 ~> 0.791 Details of GEBVtest calculations pro i_est = (20.335 - 20.926) / 22.004 = -0.027 After Base adjustments: pro p=0.990 x=-2.327 i=0.027 k=0.063 R2b=0.338 E(b1)=0.957 b1=0.839 pro b1-E(b1) = -0.118 t = -1.20 bootstrap P(b=Eb) = 19.4 b1_test = Pass pro R2_1 = 32.3 R2_2 = 27.4 bootstrap P(R2_gain) = 79.7 R2_test = NS+ pro stat_test=Y pract_test=Y bio_test=N R2_test=- overall = PASS 2024-Aug-12 15:13:44 gebvtest_2024A.py: finished pro reading file300Cr_ABCHOL ... stored 966 records for trait scs from file file300Cr_ABCHOL reading file300Gr_ABCHOL ... stored 762 records for trait scs from file file300Gr_ABCHOL reading file300Cf_ABCHOL ... stored 966 records for trait scs from file file300Cf_ABCHOL reading file300Df_ABCHOL ... stored 726 records for trait scs from file file300Df_ABCHOL reading file300Gf_ABCHOL ... stored 762 records for trait scs from file file300Gf_ABCHOL ------------------------------------------------------------------------------- processing trt=scs h2=0.2500 evdate=20120801 depvar=GM byear=2004 type2x=N ------------------------------------------------------------------------------- derived 530 records for trait scs for a DGEBV file300 equivalent Summary statistics on candidate bulls (CB) and test bulls (TB) -------------------------------------------------------------- Trait Variable N Mean Std Min Max -------------------------------------------------------------- scs CB EBV 172 2.946 0.212 2.44 3.72 scs TB EBV 161 2.944 0.212 2.44 3.72 scs TB VAL(y) 161 2.815 1.931 -3.14 9.85 Base=Current scs TB GEBV(x1) 161 2.918 0.168 2.38 3.28 Base=Old scs TB EBVr(x2) 161 2.938 0.141 2.61 3.20 Base=Old scs TB GEBV(x1) 161 2.931 0.165 2.40 3.29 Base=Current scs TB EBVr(x2) 161 2.951 0.138 2.63 3.21 Base=Current scs BB EBVf(y) 710 3.157 0.250 2.48 3.85 scs BB EBVr(x) 710 3.134 0.224 2.50 3.73 scs BB EBV(wt) 710 9.288 21.446 0.00 95.00 -------------------------------------------------------------- scs : DGEBV : Base 0.25: Full = 0.06 + 0.984 * Red b1 1.093 ~> 1.111 b2 0.364 ~> 0.370 Details of GEBVtest calculations scs i_est = (2.944 - 2.946) / 0.212 = -0.006 After Base adjustments: scs p=0.998 x=-2.890 i=0.006 k=0.018 R2b=0.010 E(b1)=0.982 b1=1.111 scs b1-E(b1) = 0.129 t = 0.16 bootstrap P(b=Eb) = 90.2 b1_test = Pass scs R2_1 = 1.0 R2_2 = 0.1 bootstrap P(R2_gain) = 81.4 R2_test = NS+ scs stat_test=Y pract_test=Y bio_test=Y R2_test=- overall = PASS 2024-Aug-12 15:13:44 gebvtest_2024A.py: finished scs 2024-Aug-12 15:13:44 gebvtest_2024A.py: end
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