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← Revision 6 as of 2024-08-13 10:39:05 ⇥
Size: 10048
Comment:
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| Deletions are marked like this. | Additions are marked like this. |
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| 2013-Jan-25 09:15:24 gebvtest.py: start gebvtest.py version=2013.01.24 absolute DATADIR: /fs6c/service/jette/GTEST/sample_data |
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 |
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| stored 426 records from file file732 stored 426 records from file bdate_ABCHOL |
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 |
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| stored 379 records for trait mil from file file300Cf_ABCHOL stored 290 records for trait mil from file file300Df_ABCHOL stored 403 records for trait mil from file file300Cr_ABCHOL stored 349 records for trait mil from file file300Gr_ABCHOL |
derived 401 records for trait mil for a DGEBV file300 equivalent |
| Line 23: | Line 35: |
| mil TB DPGM(y) 164 513.530 778.346 -1874.00 2608.00 mil TB GEBV(x1) 164 1047.909 599.771 -726.00 2624.00 mil TB EBVr(x2) 164 1244.341 548.582 -564.00 2616.00 |
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 |
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| mil : DGEBV : Base 0.25: Full = -384.11 + 1.042 * Red b1 0.940 ~> 0.902 b2 1.101 ~> 1.057 |
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| mil p=0.987 x=-2.213 i=0.035 k=0.079 R2b=0.642 E(b1)=0.970 mil b1=1.022 se=0.063 E(b1)=0.970 t=0.83 R2_1=62.3 R2_2=28.8 mil passes t-test=Y bio-test=Y R2-test=Y |
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 |
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| stored 379 records for trait fat from file file300Cf_ABCHOL stored 290 records for trait fat from file file300Df_ABCHOL stored 403 records for trait fat from file file300Cr_ABCHOL stored 349 records for trait fat from file file300Gr_ABCHOL |
derived 401 records for trait fat for a DGEBV file300 equivalent |
| Line 45: | Line 79: |
| fat TB DPGM(y) 164 21.799 29.369 -68.00 98.00 fat TB GEBV(x1) 164 37.720 20.138 -19.00 86.00 fat TB EBVr(x2) 164 44.335 20.490 -4.00 88.00 |
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 |
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| fat : DGEBV : Base 0.25: Full = -10.89 + 1.059 * Red b1 0.774 ~> 0.730 b2 0.721 ~> 0.680 |
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| fat p=0.982 x=-2.097 i=0.045 k=0.097 R2b=0.543 E(b1)=0.953 fat b1=1.047 se=0.079 E(b1)=0.953 t=1.18 R2_1=51.8 R2_2=24.2 fat passes t-test=Y bio-test=Y R2-test=Y |
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 |
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| stored 379 records for trait pro from file file300Cf_ABCHOL stored 290 records for trait pro from file file300Df_ABCHOL stored 403 records for trait pro from file file300Cr_ABCHOL stored 349 records for trait pro from file file300Gr_ABCHOL |
derived 457 records for trait pro for a DGEBV file300 equivalent |
| Line 67: | Line 123: |
| pro TB DPGM(y) 164 19.110 20.544 -51.00 81.00 pro TB GEBV(x1) 164 35.177 15.715 -12.00 72.00 pro TB EBVr(x2) 164 40.768 15.368 -8.00 76.00 |
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 |
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| pro : DGEBV : Base 0.25: Full = -11.66 + 1.040 * Red b1 0.873 ~> 0.839 b2 0.823 ~> 0.791 |
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| pro p=0.990 x=-2.327 i=0.027 k=0.063 R2b=0.604 E(b1)=0.974 pro b1=1.000 se=0.066 E(b1)=0.974 t=0.40 R2_1=58.8 R2_2=25.4 pro passes t-test=Y bio-test=Y R2-test=Y |
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 |
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| stored 378 records for trait scs from file file300Cf_ABCHOL stored 290 records for trait scs from file file300Df_ABCHOL stored 378 records for trait scs from file file300Cr_ABCHOL stored 326 records for trait scs from file file300Gr_ABCHOL |
derived 530 records for trait scs for a DGEBV file300 equivalent |
| Line 88: | Line 166: |
| scs TB EBV 163 2.944 0.212 2.44 3.72 scs TB DPGM(y) 163 2.947 0.253 2.33 3.83 scs TB GEBV(x1) 163 2.919 0.167 2.38 3.28 scs TB EBVr(x2) 163 2.938 0.140 2.61 3.20 |
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 |
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| scs : DGEBV : Base 0.25: Full = 0.06 + 0.984 * Red b1 1.093 ~> 1.111 b2 0.364 ~> 0.370 |
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| scs i_est = (2.944 - 2.946) / 0.212 = -0.005 scs p=0.998 x=-2.945 i=0.005 k=0.015 R2b=0.399 E(b1)=0.991 scs b1=0.950 se=0.093 E(b1)=0.991 t=-0.44 R2_1=39.6 R2_2=19.4 scs passes t-test=Y bio-test=Y R2-test=Y 2013-Jan-25 09:15:24 gebvtest.py: end |
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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| }}} |
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
}}}