Blink result output is making 0 sense
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Rômulo Carleial
Dec 11, 2024, 7:17:59 AM12/11/24
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Hi, I am running GWAS in BLINK and as far as I am aware, I did everything correctly. The log file seems to show everything went fine, but the results.txt file is nonsensical: i mostly have p values of exactly 0 or 1, and the rest are huge values of -log10 > 200. My qqplots are horrible as well, just a line shooting upwards, i cannot even seem to plot the manhattan plots. Can someone explain to me what is going on? Also, why doesn't BLINK report effect sizes???
LOG FILE:
one cycle include 1000 SNPs inside!
The number of traits = 1
--------
In PLINK files
number of markers is 5931605
number of individuals is 2042
--------
plink_mode is 1
The number of traits = 19
The number of marker = 5931605
--------
The number of individual = 1861
The number of marker = 5931605
--------
The number of covariates = 7
=====================================
na_length=78
number of missing phenotype in HTCM08 = 78
===HTCM08===
Get yy!
Get yw and ww!
Get wwi!
Time consumption of first get pvalue = 462.400000 seconds
length_bin_min=2336342
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=0, q0=15
iteration 1 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127,
cutoff_pvalue is 1.685884e-07
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 2 = 1032.780000 seconds
length_bin_min=2086292
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=30
iteration 2 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 3 = 2103.800000 seconds
length_bin_min=1023212
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=45
iteration 3 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 4 = 2657.870000 seconds
length_bin_min=1108512
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=60
iteration 4 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 5 = 2582.450000 seconds
length_bin_min=2807325
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=75
iteration 5 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894, 2471797, 2471813, 2471806, 2471716, 2471695, 2471773, 2471757, 2471841, 2471943, 2471926, 2472008, 2471973, 2471896, 2471893, 2471922,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 6 = 4421.460000 seconds
length_bin_min=398712
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=90
iteration 6 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894, 2471797, 2471813, 2471806, 2471716, 2471695, 2471773, 2471757, 2471841, 2471943, 2471926, 2472008, 2471973, 2471896, 2471893, 2471922, 1834859, 1834874, 1834901, 3463272, 5211646, 4556675, 1834831, 5211549, 5211615, 5211434, 3463171, 1835086, 1835129, 3463156, 5211523,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 7 = 4531.870000 seconds
length_bin_min=3289406
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=105
iteration 7 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894, 2471797, 2471813, 2471806, 2471716, 2471695, 2471773, 2471757, 2471841, 2471943, 2471926, 2472008, 2471973, 2471896, 2471893, 2471922, 1834859, 1834874, 1834901, 3463272, 5211646, 4556675, 1834831, 5211549, 5211615, 5211434, 3463171, 1835086, 1835129, 3463156, 5211523, 1730938, 2977108, 2977109, 4363511, 1730954, 1730956, 4363506, 4363509, 1730943, 1730913, 1730918, 1730912, 1730907, 4363515, 1730926,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 8 = 7420.500000 seconds
length_bin_min=741996
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=120
iteration 8 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894, 2471797, 2471813, 2471806, 2471716, 2471695, 2471773, 2471757, 2471841, 2471943, 2471926, 2472008, 2471973, 2471896, 2471893, 2471922, 1834859, 1834874, 1834901, 3463272, 5211646, 4556675, 1834831, 5211549, 5211615, 5211434, 3463171, 1835086, 1835129, 3463156, 5211523, 1730938, 2977108, 2977109, 4363511, 1730954, 1730956, 4363506, 4363509, 1730943, 1730913, 1730918, 1730912, 1730907, 4363515, 1730926, 2707992, 2707986, 2708055, 2708160, 2708117, 2708084, 2707818, 2707795, 2707786, 2707861, 2707970, 2707947, 2707937, 2708475, 2708455,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 9 = 5490.450000 seconds
length_bin_min=373943
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=135
iteration 9 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894, 2471797, 2471813, 2471806, 2471716, 2471695, 2471773, 2471757, 2471841, 2471943, 2471926, 2472008, 2471973, 2471896, 2471893, 2471922, 1834859, 1834874, 1834901, 3463272, 5211646, 4556675, 1834831, 5211549, 5211615, 5211434, 3463171, 1835086, 1835129, 3463156, 5211523, 1730938, 2977108, 2977109, 4363511, 1730954, 1730956, 4363506, 4363509, 1730943, 1730913, 1730918, 1730912, 1730907, 4363515, 1730926, 2707992, 2707986, 2708055, 2708160, 2708117, 2708084, 2707818, 2707795, 2707786, 2707861, 2707970, 2707947, 2707937, 2708475, 2708455, 2924671, 5585116, 2924773, 2924722, 2924710, 2924585, 2924573, 5585140, 2924788, 2924894, 2924881, 2924871, 2924998, 2924904, 2924900,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 10 = 8399.770000 seconds
length_bin_min=836515
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=150
iteration 10 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894, 2471797, 2471813, 2471806, 2471716, 2471695, 2471773, 2471757, 2471841, 2471943, 2471926, 2472008, 2471973, 2471896, 2471893, 2471922, 1834859, 1834874, 1834901, 3463272, 5211646, 4556675, 1834831, 5211549, 5211615, 5211434, 3463171, 1835086, 1835129, 3463156, 5211523, 1730938, 2977108, 2977109, 4363511, 1730954, 1730956, 4363506, 4363509, 1730943, 1730913, 1730918, 1730912, 1730907, 4363515, 1730926, 2707992, 2707986, 2708055, 2708160, 2708117, 2708084, 2707818, 2707795, 2707786, 2707861, 2707970, 2707947, 2707937, 2708475, 2708455, 2924671, 5585116, 2924773, 2924722, 2924710, 2924585, 2924573, 5585140, 2924788, 2924894, 2924881, 2924871, 2924998, 2924904, 2924900, 3175952, 3175955, 3175941, 3175885, 3175939, 3175940, 3175970, 3176062, 3176082, 3176159, 3176013, 3175976, 3175991, 3176001, 3175689,
===BLINK successfully accomplished her GWAS mission!===
All the time consumption = 43482 seconds
The head of the results file:
taxa chr pos maf p_value
lcl_Bpe_Chr1:6090 1 6090 7.319125e-02 1.000000e+00
lcl_Bpe_Chr1:6310 1 6310 2.058329e-01 1.000000e+00
lcl_Bpe_Chr1:6356 1 6356 9.674706e-02 1.000000e+00
lcl_Bpe_Chr1:6386 1 6386 8.076276e-02 1.000000e+00
lcl_Bpe_Chr1:6597 1 6597 1.828379e-01 1.000000e+00
lcl_Bpe_Chr1:6692 1 6692 1.121705e-01 1.000000e+00
lcl_Bpe_Chr1:6885 1 6885 7.908020e-02 1.000000e+00
lcl_Bpe_Chr1:7614 1 7614 9.085810e-02 1.599350e-47
lcl_Bpe_Chr1:7714 1 7714 1.601234e-01 1.000000e+00
LOG FILE:
one cycle include 1000 SNPs inside!
The number of traits = 1
--------
In PLINK files
number of markers is 5931605
number of individuals is 2042
--------
plink_mode is 1
The number of traits = 19
The number of marker = 5931605
--------
The number of individual = 1861
The number of marker = 5931605
--------
The number of covariates = 7
=====================================
na_length=78
number of missing phenotype in HTCM08 = 78
===HTCM08===
Get yy!
Get yw and ww!
Get wwi!
Time consumption of first get pvalue = 462.400000 seconds
length_bin_min=2336342
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=0, q0=15
iteration 1 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127,
cutoff_pvalue is 1.685884e-07
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 2 = 1032.780000 seconds
length_bin_min=2086292
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=30
iteration 2 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 3 = 2103.800000 seconds
length_bin_min=1023212
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=45
iteration 3 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 4 = 2657.870000 seconds
length_bin_min=1108512
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=60
iteration 4 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 5 = 2582.450000 seconds
length_bin_min=2807325
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=75
iteration 5 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894, 2471797, 2471813, 2471806, 2471716, 2471695, 2471773, 2471757, 2471841, 2471943, 2471926, 2472008, 2471973, 2471896, 2471893, 2471922,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 6 = 4421.460000 seconds
length_bin_min=398712
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=90
iteration 6 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894, 2471797, 2471813, 2471806, 2471716, 2471695, 2471773, 2471757, 2471841, 2471943, 2471926, 2472008, 2471973, 2471896, 2471893, 2471922, 1834859, 1834874, 1834901, 3463272, 5211646, 4556675, 1834831, 5211549, 5211615, 5211434, 3463171, 1835086, 1835129, 3463156, 5211523,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 7 = 4531.870000 seconds
length_bin_min=3289406
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=105
iteration 7 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894, 2471797, 2471813, 2471806, 2471716, 2471695, 2471773, 2471757, 2471841, 2471943, 2471926, 2472008, 2471973, 2471896, 2471893, 2471922, 1834859, 1834874, 1834901, 3463272, 5211646, 4556675, 1834831, 5211549, 5211615, 5211434, 3463171, 1835086, 1835129, 3463156, 5211523, 1730938, 2977108, 2977109, 4363511, 1730954, 1730956, 4363506, 4363509, 1730943, 1730913, 1730918, 1730912, 1730907, 4363515, 1730926,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 8 = 7420.500000 seconds
length_bin_min=741996
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=120
iteration 8 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894, 2471797, 2471813, 2471806, 2471716, 2471695, 2471773, 2471757, 2471841, 2471943, 2471926, 2472008, 2471973, 2471896, 2471893, 2471922, 1834859, 1834874, 1834901, 3463272, 5211646, 4556675, 1834831, 5211549, 5211615, 5211434, 3463171, 1835086, 1835129, 3463156, 5211523, 1730938, 2977108, 2977109, 4363511, 1730954, 1730956, 4363506, 4363509, 1730943, 1730913, 1730918, 1730912, 1730907, 4363515, 1730926, 2707992, 2707986, 2708055, 2708160, 2708117, 2708084, 2707818, 2707795, 2707786, 2707861, 2707970, 2707947, 2707937, 2708475, 2708455,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 9 = 5490.450000 seconds
length_bin_min=373943
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=135
iteration 9 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894, 2471797, 2471813, 2471806, 2471716, 2471695, 2471773, 2471757, 2471841, 2471943, 2471926, 2472008, 2471973, 2471896, 2471893, 2471922, 1834859, 1834874, 1834901, 3463272, 5211646, 4556675, 1834831, 5211549, 5211615, 5211434, 3463171, 1835086, 1835129, 3463156, 5211523, 1730938, 2977108, 2977109, 4363511, 1730954, 1730956, 4363506, 4363509, 1730943, 1730913, 1730918, 1730912, 1730907, 4363515, 1730926, 2707992, 2707986, 2708055, 2708160, 2708117, 2708084, 2707818, 2707795, 2707786, 2707861, 2707970, 2707947, 2707937, 2708475, 2708455, 2924671, 5585116, 2924773, 2924722, 2924710, 2924585, 2924573, 5585140, 2924788, 2924894, 2924881, 2924871, 2924998, 2924904, 2924900,
Get yw and ww!
Get wwi!
Time consumption of get pvalue in iteration 10 = 8399.770000 seconds
length_bin_min=836515
LD_cutoff is 0.700000
Number of all the candidate QTNs is 237
indicator=15, q0=150
iteration 10 successful!
3592378, 3592384, 4914699, 1749093, 1749088, 5433045, 1749049, 1749047, 1749046, 1749050, 3592397, 3592407, 1749055, 1749129, 1749127, 2235802, 4675208, 2235814, 4675207, 2235818, 2235817, 4675223, 2235767, 2235760, 2235749, 2235775, 2235783, 4675239, 4675206, 4675188, 3098849, 3098902, 3098877, 3098742, 3098732, 3098831, 3098780, 3098907, 3098957, 3098949, 3098981, 3098971, 3098921, 3098916, 3098929, 2167968, 4647104, 4647106, 4647122, 2167906, 2167925, 4647091, 4647069, 2168060, 2168062, 2168023, 2167994, 2168001, 4647072, 2167894, 2471797, 2471813, 2471806, 2471716, 2471695, 2471773, 2471757, 2471841, 2471943, 2471926, 2472008, 2471973, 2471896, 2471893, 2471922, 1834859, 1834874, 1834901, 3463272, 5211646, 4556675, 1834831, 5211549, 5211615, 5211434, 3463171, 1835086, 1835129, 3463156, 5211523, 1730938, 2977108, 2977109, 4363511, 1730954, 1730956, 4363506, 4363509, 1730943, 1730913, 1730918, 1730912, 1730907, 4363515, 1730926, 2707992, 2707986, 2708055, 2708160, 2708117, 2708084, 2707818, 2707795, 2707786, 2707861, 2707970, 2707947, 2707937, 2708475, 2708455, 2924671, 5585116, 2924773, 2924722, 2924710, 2924585, 2924573, 5585140, 2924788, 2924894, 2924881, 2924871, 2924998, 2924904, 2924900, 3175952, 3175955, 3175941, 3175885, 3175939, 3175940, 3175970, 3176062, 3176082, 3176159, 3176013, 3175976, 3175991, 3176001, 3175689,
===BLINK successfully accomplished her GWAS mission!===
All the time consumption = 43482 seconds
The head of the results file:
taxa chr pos maf p_value
lcl_Bpe_Chr1:6090 1 6090 7.319125e-02 1.000000e+00
lcl_Bpe_Chr1:6310 1 6310 2.058329e-01 1.000000e+00
lcl_Bpe_Chr1:6356 1 6356 9.674706e-02 1.000000e+00
lcl_Bpe_Chr1:6386 1 6386 8.076276e-02 1.000000e+00
lcl_Bpe_Chr1:6597 1 6597 1.828379e-01 1.000000e+00
lcl_Bpe_Chr1:6692 1 6692 1.121705e-01 1.000000e+00
lcl_Bpe_Chr1:6885 1 6885 7.908020e-02 1.000000e+00
lcl_Bpe_Chr1:7614 1 7614 9.085810e-02 1.599350e-47
lcl_Bpe_Chr1:7714 1 7714 1.601234e-01 1.000000e+00
Meng Huang
Dec 11, 2024, 10:05:47 AM12/11/24
to Rômulo Carleial, BLINK Forum
It is inflation. I assume you have added PCA as covariates. So please filter snps with maf<0.05 for each trait.
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Meng Huang
Dec 11, 2024, 10:12:54 AM12/11/24
to Rômulo Carleial, BLINK Forum
Also, it seems like your cutoff of pvalue for each iteration is too low. Please make sure it is 0.01/markerNumber
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