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Nick's example log files
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@MatthewMah
MatthewMah committed Apr 3, 2023
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1 change: 0 additions & 1 deletion .gitignore
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Expand Up @@ -27,4 +27,3 @@ examples.qpGraph/*:log
examples.qpGraph/*.ggg
examples.qpGraph/*.dot
examples.qpGraph/*.ps
examples/*.log
22 changes: 22 additions & 0 deletions examples/qp3Pop.log
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parameter file: parqp3Pop
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
DIR: ../data/
SSS: allmap
indivname: ../data//allmap.ind
snpname: ../data//allmap.snp
genotypename: ../data//allmap.geno
popfilename: list_qp3Pop
## qp3Pop version: 300
packed geno read OK
nplist: 6
number of blocks for block jackknife: 711
snps: 621038
Source 1 Source 2 Target f_3 std. err Z SNPs
result: French Japanese Uygur -0.025170 0.000379 -66.384 428873
result: French Han Uygur -0.025172 0.000375 -67.090 429972
result: Russian Japanese Uygur -0.021377 0.000357 -59.897 428523
result: Russian Han Uygur -0.021403 0.000363 -58.920 429573
result: Italian Japanese Uygur -0.025345 0.000391 -64.880 424716
result: Italian Han Uygur -0.025102 0.000400 -62.757 425595
##end of qp3Pop
23 changes: 23 additions & 0 deletions examples/qp4diff.log
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parameter file: parqp4diff
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
DIR: ../data/
SSS: allmap
indivname: ../data//allmap.ind
snpname: ../data//allmap.snp
genotypename: ../data//allmap.geno
popfilename: list_qp4diff
## qp4diff version: 340
packed geno read OK
end of inpack
nplist: 1
0 Yoruba 21
1 French 26
2 Han 32
3 Uygur 9
4 Japanese 28
jackknife block size: 0.050
snps: 621037 indivs: 116
number of blocks for moving block jackknife: 711
result: Yoruba French Han Uygur : Yoruba French Japanese Uygur 0.000088 0.000059 1.488
##end of qp4diff: 17.700 seconds cpu 447.402 Mbytes in use
133 changes: 133 additions & 0 deletions examples/qpAdm.log
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### lines added as comments by Nick
qpAdm: parameter file: parqpAdm
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
DIR: ../data
S1: qpdata
indivname: ../data/qpdata.ind
snpname: ../data/qpdata.snp
genotypename: ../data/qpdata.geno
popleft: left1
popright: right1
details: YES
## qpAdm version: 352
packed geno read OK
end of inpack

left pops:
Corded_Ware_LN
WHG
LBK_EN
Yamnaya

right pops:
Han
Eskimo
Mbuti
Karitiana
Ulchi

0 Corded_Ware_LN 4
1 WHG 2
2 LBK_EN 12
3 Yamnaya 9
4 Han 33
5 Eskimo 22
6 Mbuti 10
7 Karitiana 12
8 Ulchi 25
jackknife block size: 0.050
snps: 354212 indivs: 129
number of blocks for block jackknife: 710
dof (jackknife): 606.426
numsnps used: 351683
codimension 1
f4info:
f4rank: 2 dof: 2 chisq: 0.536 tail: 0.764859564 dofdiff: 4 chisqdiff: -0.536 taildiff: 1
### this is line for
B:
scale 1.000 1.000
Eskimo 1.021 0.540
Mbuti -0.990 1.738
Karitiana 1.387 0.831
Ulchi 0.233 0.001
A:
scale 1205.754 3115.503
WHG -0.476 -1.556
LBK_EN -1.581 0.634
Yamnaya 0.523 0.421


full rank
f4info:
f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 2 chisqdiff: 0.536 taildiff: 0.764859564
### taildiff: is p-value for corank 1 against full rank (LRT). If very small qpAdm model is likely incorrect.
B:
scale 1.000 1.000 1.000
Eskimo 0.988 0.490 1.642
Mbuti -0.992 1.730 0.100
Karitiana 1.409 0.875 -1.116
Ulchi 0.231 -0.005 0.218
A:
scale 1196.552 3119.151 29992.158
WHG -0.492 -1.570 0.542
LBK_EN -1.584 0.614 0.339
Yamnaya 0.499 0.399 1.610


best coefficients: 0.228 0.140 0.632

### CW = .228 WHG + .140 LBK_EN + .632 Yamnaya is best model
ssres:
0.000046129 0.000008872 -0.000072290 0.000004983
1.068348230 0.205472447 -1.674245198 0.115395622

Jackknife mean: 0.224241123 0.142160839 0.633598038
std. errors: 0.156 0.089 0.098

### std. errors are NOT independent

error covariance (* 1000000)
24258 -11342 -12916
-11342 7951 3391
-12916 3391 9526


fixed pat wt dof chisq tail prob
000 0 2 0.536 0.76486 0.228 0.140 0.632
001 1 3 14.811 0 1.291 -0.291 0.000 infeasible
010 1 3 2.767 0.428944 0.436 0.000 0.564
100 1 3 2.710 0.438595 0.000 0.246 0.754
011 2 4 19.817 0.000542598 1.000 -0.000 0.000
101 2 4 168.302 0 0.000 1.000 0.000
110 2 4 22.430 0.000164556 0.000 -0.000 1.000
best pat: 000 0.76486 - -
best pat: 100 0.438595 chi(nested): 2.173 p-value for nested model: 0.140407
best pat: 011 0.000542598 chi(nested): 17.108 p-value for nested model: 3.53172e-05

## 100 (WHG dropped is fine model, but no model dropping 2 sources is much use.

coeffs: 0.228 0.140 0.632
details: WHG Eskimo -0.000623 -3.409522
details: LBK_EN Eskimo -0.001193 -8.378403
details: Yamnaya Eskimo 0.000563 4.139291
dscore: Eskimo f4: 0.000046 Z: 0.364543

### Look at f4(CW, X; Han, Eskimo) where X is from leftpops. dscore is Z score for weighted sum (fitted model)

details: WHG Mbuti -0.000461 -1.503609
details: LBK_EN Mbuti 0.001655 7.167962
details: Yamnaya Mbuti -0.000187 -0.814624
dscore: Mbuti f4: 0.000009 Z: 0.042347

details: WHG Karitiana -0.001040 -3.869928
details: LBK_EN Karitiana -0.001706 -8.173287
details: Yamnaya Karitiana 0.000640 3.215214
dscore: Karitiana f4: -0.000072 Z: -0.399554

details: WHG Ulchi -0.000088 -0.749233
details: LBK_EN Ulchi -0.000304 -3.623063
details: Yamnaya Ulchi 0.000107 1.230690
dscore: Ulchi f4: 0.000005 Z: 0.064000

## end of run
20 changes: 20 additions & 0 deletions examples/qpBound.log
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parameter file: parqpBound
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
DIR: ../data/
SSS: allmap
indivname: ../data//allmap.ind
snpname: ../data//allmap.snp
genotypename: ../data//allmap.geno
popfilename: list_qpBound
outpop: Yoruba
## qpBound version: 120
packed geno read OK
nplist: 6
French Japanese Uygur -0.025170 -66.384 0.447 0.531
French Han Uygur -0.025172 -67.090 0.437 0.527
Russian Japanese Uygur -0.021377 -59.897 0.544 0.587
Russian Han Uygur -0.021403 -58.920 0.533 0.583
Italian Japanese Uygur -0.025345 -64.880 0.422 0.521
Italian Han Uygur -0.025102 -62.757 0.411 0.520
##end of qpBound
26 changes: 26 additions & 0 deletions examples/qpDstat.log
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parameter file: parqpDstat
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
DIR: ../data/
SSS: allmap
indivname: ../data//allmap.ind
snpname: ../data//allmap.snp
genotypename: ../data//allmap.geno
poplistname: list_qpDstat
## qpDstat version: 662
packed geno read OK
0 Yoruba 21
1 French 26
2 Han 32
3 Uygur 9
jackknife block size: 0.050
nodata: Affx-50079445
nodata: Affx-36048139
nodata: Affx-50056055
snps: 621035 indivs: 88
number of blocks for jackknife: 711
nrows, ncols: 88 621035
result: Yoruba French Han Uygur 0.0410 32.300 - 30753 28328 621026
result: Yoruba Han French Uygur 0.0865 51.447 - 33690 28328 621026
result: Yoruba Uygur French Han 0.0456 22.403 best 33690 30753 621026
## end of run
25 changes: 25 additions & 0 deletions examples/qpDstat1.log
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parameter file: parqpDstat1
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
DIR: ../data/
SSS: allmap
indivname: ../data//allmap.ind
snpname: ../data//allmap.snp
genotypename: ../data//allmap.geno
popfilename: list_qpDstat1
## qpDstat version: 662
packed geno read OK
number of quadruples 2
0 Yoruba 21
1 French 26
2 Han 32
3 Japanese 28
4 Uygur 9
jackknife block size: 0.050
nodata: Affx-50079445
snps: 621037 indivs: 116
number of blocks for jackknife: 711
nrows, ncols: 116 621037
result: Yoruba French Han Uygur 0.0410 32.300 30753 28328 621026
result: Yoruba French Japanese Uygur 0.0402 31.016 30690 28320 621026
## end of run
25 changes: 25 additions & 0 deletions examples/qpF4ratio.log
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parameter file: parqpF4ratio
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
DIR: ../data/
SSS: allmap
indivname: ../data//allmap.ind
snpname: ../data//allmap.snp
genotypename: ../data//allmap.geno
popfilename: list_qpF4ratio
## qpF4ratio version: 300
packed geno read OK
nplist: 2
0 Yoruba 21
1 Papuan 12
2 Uygur 9
3 Han 32
4 French 26
5 Adygei 15
jackknife block size: 0.050
snps: 621038 indivs: 115
number of blocks for block jackknife: 711
alpha std. err Z (null=0)
result: Yoruba Papuan Uygur Han : Yoruba Papuan French Han 0.467437 0.015800 29.585
result: Yoruba Adygei Uygur Han : Yoruba Adygei French Han 0.474091 0.011546 41.060
## end of run
84 changes: 84 additions & 0 deletions examples/qpWave.log
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parameter file: parqpWave
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
DIR: ../data
S1: qpdata
indivname: ../data/qpdata.ind
snpname: ../data/qpdata.snp
genotypename: ../data/qpdata.geno
popleft: left1
popright: right1
## qpWave version: 201

left pops:
Corded_Ware_LN
WHG
LBK_EN
Yamnaya

right pops:
Han
Eskimo
Mbuti
Karitiana
Ulchi
0 Corded_Ware_LN 4
1 WHG 2
2 LBK_EN 12
3 Yamnaya 9
4 Han 33
5 Eskimo 22
6 Mbuti 10
7 Karitiana 12
8 Ulchi 25
jackknife block size: 0.050
snps: 354212 indivs: 129
number of blocks for block jackknife: 710
dof (jackknife): 606.426
numsnps used: 351683
f4info:
f4rank: 0 dof: 12 chisq: 460.444 tail: 5.71351953e-91 dofdiff: 0 chisqdiff: 0.000 taildiff: 1

f4info:
f4rank: 1 dof: 6 chisq: 24.489 tail: 0.00042443713 dofdiff: 6 chisqdiff: 435.955 taildiff: 5.16806732e-91
B:
scale 1.000
Eskimo 0.966
Mbuti -1.099
Karitiana 1.342
Ulchi 0.246
A:
scale 1211.444
WHG -0.427
LBK_EN -1.594
Yamnaya 0.525

f4info:
f4rank: 2 dof: 2 chisq: 0.536 tail: 0.764859692 dofdiff: 4 chisqdiff: 23.953 taildiff: 8.16355044e-05
B:
scale 1.000 1.000
Eskimo 1.021 0.540
Mbuti -0.990 1.738
Karitiana 1.387 0.830
Ulchi 0.233 0.001
A:
scale 1202.997 3105.760
WHG -0.477 -1.556
LBK_EN -1.581 0.634
Yamnaya 0.522 0.420

f4info:
f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 2 chisqdiff: 0.536 taildiff: 0.764859692
B:
scale 1.000 1.000 1.000
Eskimo 0.988 0.490 1.642
Mbuti -0.992 1.730 0.101
Karitiana 1.409 0.875 -1.116
Ulchi 0.231 -0.005 0.218
A:
scale 1193.784 3109.317 29979.194
WHG -0.493 -1.570 0.541
LBK_EN -1.584 0.614 0.338
Yamnaya 0.498 0.398 1.610

## end of run

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