Title: RecombinationProcessor.bf crash
Post by tlefebure on Dec 21st, 2006 at 2:23pm
Hello, On some dataset (~10%), I obtain a crash of the GARD post-processing with RecombinationProcessor.bf. Here is the command and the output: Code (][tristan@babylon GARD): /home/tristan/bin/HYPHY_Source/HYPHYMP RecombinationProcessor.bf < 1850-answers
(/home/tristan/Documents/w/Scanis/comp_genomic/GARD/) Please load a nucleotide data file:
(/home/tristan/Documents/w/Scanis/comp_genomic/GARD/) Please load a GA partition analysis result file:
Loaded 3 partitions
Sequences :5
Sites :990
Variable :303
f(A) = 0.293081
f(C) = 0.16702
f(G) = 0.246818
f(T) = 0.293081
c-AIC = 5370.69
Log Likelihood = -2670.09960166085;
Shared Parameters:
GT=0.105971=0.105971
CT=3.07402=3.07402
CG=0.376865=0.376865
AT=0.484845=0.484845
AC=0.741006=0.741006
alpha=0.2493=0.2493
betaQ=1.61188=1.61188
betaP=0.695935=0.695935
Tree givenTree=(((aga2603:0.630534,canis:0.0720785)Node2:0.0608297,pyo10394:0.00198773)Node1:0.00621686,pyo10750:0.00616671,pyo8232:0.00622424);
Mean divergence : 32.7024%
Fitting a single-tree, multiple partition model
Log Likelihood = -2666.6700419052;
Shared Parameters:
S_1=0.630241
S_2=1.02979
betaP=0.695935=0.695935
betaQ=1.61188=1.61188
alpha=0.2493=0.2493
AC=0.741006=0.741006
AT=0.484845=0.484845
CG=0.376865=0.376865
CT=3.07402=3.07402
GT=0.105971=0.105971
Tree tree_0=(((aga2603:0.747052,canis:0.088941)Node2:0.0670713,pyo10394:0.00220889)Node1:0.00740498,pyo10750:0.00726891,pyo8232:0.0073344);
Tree tree_1=(((aga2603:0.470823,canis:0.0560543)Node2:0.0422711,pyo10394:0.00139213)Node1:0.00466692,pyo10750:0.00458117,pyo8232:0.00462244);
Tree tree_2=(((aga2603:0.769311,canis:0.091591)Node2:0.0690697,pyo10394:0.0022747)Node1:0.00762561,pyo10750:0.00748549,pyo8232:0.00755293);
Fitting a mutilple tree, multiple partition model
Log Likelihood = -2650.75677803647;
Shared Parameters:
betaP=0.695935=0.695935
betaQ=1.61188=1.61188
alpha=0.2493=0.2493
AC=0.741006=0.741006
AT=0.484845=0.484845
CG=0.376865=0.376865
CT=3.07402=3.07402
GT=0.105971=0.105971
Tree tree_0=((pyo10394:0,pyo10750:0)Node1:0.00703031,pyo8232:0.017498,(aga2603:0.703347,canis:0.130926)Node5:0.0243752);
Tree tree_1=((pyo10750:0.00910772,pyo8232:0)Node1:0.0121614,pyo10394:0.00148369,(aga2603:0.38862,canis:0.0723504)Node5:0.0364327);
Tree tree_2=((pyo10750:0.00600447,pyo8232:0.00307609)Node1:0.0036795,pyo10394:0.00235061,(aga2603:1.08916,canis:0)Node5:0.143441);
Versus the single partition model: c-AIC = 5361.33
Delta AIC = 9.36596
Versus the single tree/multiple partition model: Delta AIC = 6.64366
Partition 1 : 219 sites
Partition 2 : 447 sites
Partition 3 : 324 sites
Fitting tree 1 to partition 1
Log Likelihood = -607.771985999151;
Shared Parameters:
betaP=0.695935=0.695935
betaQ=1.61188=1.61188
alpha=0.2493=0.2493
AC=0.741006=0.741006
AT=0.484845=0.484845
CG=0.376865=0.376865
CT=3.07402=3.07402
GT=0.105971=0.105971
Tree aTree=((pyo10394:0,pyo10750:0)Node1:0.00693603,pyo8232:0.0175644,(aga2603:0.707631,canis:0.135304)Node5:0.0209077);
Fitting tree 2 to partition 1
Log Likelihood = -608.43731122233;
Shared Parameters:
betaP=0.695935=0.695935
betaQ=1.61188=1.61188
alpha=0.2493=0.2493
AC=0.741006=0.741006
AT=0.484845=0.484845
CG=0.376865=0.376865
CT=3.07402=3.07402
GT=0.105971=0.105971
Tree aTree=((pyo10750:0,pyo8232:0.0246961)Node1:0,pyo10394:0,(aga2603:0.718025,canis:0.147579)Node5:0.0195866);
KH Testing partition 1
Tree 2 base LRT = 1.33065. p-value = 0.3242
Fitting tree 1 to partition 2
Log Likelihood = -1137.21140254908;
Shared Parameters:
betaP=0.695935=0.695935
betaQ=1.61188=1.61188
alpha=0.2493=0.2493
AC=0.741006=0.741006
AT=0.484845=0.484845
CG=0.376865=0.376865
CT=3.07402=3.07402
GT=0.105971=0.105971
Tree aTree=((pyo10394:0.0137574,pyo10750:0.00916878)Node1:0,pyo8232:0,(aga2603:0.406959,canis:0.0735457)Node5:0.044728);
Fitting tree 2 to partition 2
Log Likelihood = -1133.47964697387;
Shared Parameters:
betaP=0.695935=0.695935
betaQ=1.61188=1.61188
alpha=0.2493=0.2493
AC=0.741006=0.741006
AT=0.484845=0.484845
CG=0.376865=0.376865
CT=3.07402=3.07402
GT=0.105971=0.105971
Tree aTree=((pyo10750:0.0090949,pyo8232:0)Node1:0.0122124,pyo10394:0.00143842,(aga2603:0.388757,canis:0.0725362)Node5:0.0363287);
Fitting tree 3 to partition 2
Log Likelihood = -1133.48081826306;
Shared Parameters:
betaP=0.695935=0.695935
betaQ=1.61188=1.61188
alpha=0.2493=0.2493
AC=0.741006=0.741006
AT=0.484845=0.484845
CG=0.376865=0.376865
CT=3.07402=3.07402
GT=0.105971=0.105971
Tree aTree=((pyo10750:0.00909512,pyo8232:0)Node1:0.0123836,pyo10394:0.001245,(aga2603:0.388864,canis:0.0730605)Node5:0.0360738);
KH Testing partition 2
Tree 1 base LRT = 7.46351. p-value = 0.4973
Tree 3 base LRT = 0.00234258. p-value = Error:
Operation MAccess is not defined for 0
Current BL Command:jvec[1][k]=vec2[k]
Check errors.log for details on execution errors.
Check messages.log details of this run.
Segmentation fault
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here is the file 1850-answers: Code (]1850.phy
1850-results_splits[/code):
here is the file 1850-results_splits:
[code]
0-218
((pyo10394:0,pyo10750:0):0.171555,pyo8232:0.982269,(aga2603:25.4786,canis:6.39188):4.39343)
219-665
((pyo10750:0.0262135,pyo8232:0):0.0389569,pyo10394:0,(aga2603:16.1661,canis:2.28447):3.17527)
666-989
((pyo10750:0.0145416,pyo8232:0.00698474):0.0148641,pyo10394:0.000373128,(aga2603:32.79,canis:2.1698):5.68653) |
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I can send you the data file if you want. I registered to the bugzilla server, but I didn't receive my password by email ??? Thank you -Tristan
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