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
 

here is the file 1850-answers:
Code:

1850.phy
1850-results_splits 

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) 

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

Dear Tristan,

I fixed the indexing problem you have reported. You can find the updated version of the .bf at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

Thanks!
Sergei