ddarriba / jmodeltest2 Goto Github PK

jModelTest is not able to find the configuration file when the path contains a 
bracket character (e.g., C:\{Programs\...).

This problem affects at least Windows 7 users.

What steps will reproduce the problem?

1. Start JModelTest and load the primate-mtDNA.nex data file from the 
"example-data" folder.
2. Compute likelihood scores using BioNJ-JC tree and "3" substitution schemes.
3. Do BIC calculations.

What is the expected output? What do you see instead?

The -lnL of the JC model computed by PAUP* is 6424.202.  The value reported by 
JModelTest is "6442.6510".  Similarly, PAUP* obtains 6284.996 for the F81 
model, whereas JModelTest reports "6305.0338".  JC+I, JC+G, etc. have similar 
discrepancies.  However, for models other than JC and F81 the two programs 
report identical likelihood scores.

What version of the product are you using? On what operating system?

JModelTest 2.1.4, Mac OSX 10.8.5

Please provide any additional information below.

I noticed the problem because there were slight discrepancies in the BIC (or 
AIC) weights reported by JModelTest and a new feature being added to PAUP*.  
Although the JC and F81 models typically fit poorly compared to other models, 
for some data sets the error in calculating BIC (or AIC) scores was large 
enough to produce a slight, but noticeable, difference in the resulting weights.

It is interesting that when PhyML is run standalone, it obtains the same lnL 
values as PAUP* for the JC and F81 models (see attached file).  So the problem 
is likely either in the command-line arguments passed to PhyML by JModelTest, 
or in the parsing of the output.

From the command console interface, users can optimize the model set without 
selecting any information criterion (i.e., without setting -AIC, -BIC, -AICc 
and -DT arguments).

In this situation, if a phylogenetic averaging is selected (i.e., -a or -z 
arguments), jModelTest will throw an exception.

What steps will reproduce the problem?
1. Loading fasta alignment of 58 sequences (2488 sites)
2. Reading file ok
3. Launch Computation of likelihood values (same error with all parameters)

What is the expected output? What do you see instead?
---------------------------------------------------------------
*                                                             *
*        COMPUTATION OF LIKELIHOOD SCORES WITH PHYML          *
*                                                             *
---------------------------------------------------------------

::Settings::

 Phyml version = 3.0
 Phyml binary = PhyML_3.0_win32.exe
 Candidate models = 88
  number of substitution schemes = 11
  including models with equal/unequal base frequencies (+F)
  including models with/without a proportion of invariable sites (+I)
  including models with/without rate variation among sites (+G) (nCat = 4)
 Optimized free parameters (K) = substitution parameters + 113 branch lengths + topology 
 Base tree for likelihood calculations = ML tree
 Tree topology search operation = BEST

::Progress::

Model        Exec. Time      Total Time      -lnL
-------------------------------------------------------------------------
ML tree for HKY+I+G is invalid.ML tree for F81+I+G is invalid. 

Computation of likelihood scores interrupted. It took 00h:00:00:01.

ML tree for TrN+I+G is invalid.F81+I+G      00h:00:02:01    00h:00:02:01    0.0000
TrN+I+G     00h:00:02:09    00h:00:03:00    0.0000
HKY+I+G     00h:00:03:05    00h:00:03:05    0.0000


What version of the product are you using? On what operating system?
jModelTest2 with Windows and Linux

thanks 
It is quite strange, every time  i try to open jmodeltest2 under 
java1.6.0_26_b03_384 and load sequences, after that i try to analysis, it is 
quickly closed! what's the problem?
there is what i got from terminal

Tue Aug 21 12:18:39 CEST 2012
Mac OS X 10.5.8, arch: x86_64, bits: 64, numcores: 8 

--------------------------------------------------------------------------------
Citation: Darriba D, Taboada GL, Doallo R and Posada D. 2012.
          "jModelTest 2: more models, new heuristics and parallel computing".
          Nature Methods 9, 772.
--------------------------------------------------------------------------------

jModelTest 2.1.1
Copyright (C) 2011 D. Darriba, G.L. Taboada, R. Doallo and D. Posada
This program comes with ABSOLUTELY NO WARRANTY
This is free software, and you are welcome to redistribute it under certain 
conditions

Notice: This program may contain errors. Please inspect results carefully.


Arguments = -d example-data/aP6.fas -g 4 -i -f -AIC -BIC -a

Reading data file "aP6.fas"... OK.
  number of sequences: 6
  number of sites: 631
  ambiguity : false

Settings::

 Phyml version = 3.0
 Phyml binary = PhyML_3.0_macOS_i386
 Candidate models = 24
   number of substitution schemes = 3
   including models with equal/unequal base frequencies (+F)
   including models with/without a proportion of invariable sites (+I)
   including models with/without rate variation among sites (+G) (nCat = 4)
 Optimized free parameters (K) = substitution parameters + 9 branch lengths + topology 
 Base tree for likelihood calculations = ML tree
 Tree topology search operation = BEST



::Progress::

Model        Exec. Time      Total Time      -lnL
-------------------------------------------------------------------------
ERROR>dyld: unknown required load command 0x80000022
ERROR>dyld: unknown required load command 0x80000022
ERROR>dyld: unknown required load command 0x80000022


Computation of likelihood scores discontinued ...
Optimization results file does not exist: 
/var/folders/BR/BRdwq5SNGVywJiLK2kAHV++++TM/-Tmp-/jmodeltest9044392534325094443.
phy_phyml_stats_HKY+G.txt

Computation of likelihood scores discontinued ...

Computation of likelihood scores discontinued ...
Optimization results file does not exist: 
/var/folders/BR/BRdwq5SNGVywJiLK2kAHV++++TM/-Tmp-/jmodeltest9044392534325094443.
phy_phyml_stats_F81+G.txt

Computation of likelihood scores discontinued ...
Optimization results file does not exist: 
/var/folders/BR/BRdwq5SNGVywJiLK2kAHV++++TM/-Tmp-/jmodeltest9044392534325094443.
phy_phyml_stats_GTR+I+G.txt

Computation of likelihood scores discontinued ...

What steps will reproduce the problem?
1. Any jModelTest 2.0.2 execution with a fixed BIONJ-JC starting topology

Before the model optimizations, the JC model should be optimized. However, the 
F81+I+G model is optimized instead. Therefore, the starting topology for each 
model is the BIONJ-F81+I+G instead the BIONJ-JC.

The default tree search strategy for the ML starting topology should be changed 
from NNI to "Best" (best of SPR and NNI, after testing both of them).

It's not possible to select the criterion used in the clustering search from 
the Graphic Interface.

That possibility exists from the command line using -H argument.

If required, PAUP block should appear in the log files.

Whenever I search for a model, and the choosen model is GTR, the values for the 
rate matrix of instantaneous substitution rates [R a,b,c...f] are too high, 
reaching hundrends of thousands (excepto for one or two that will obviousy be 
one).

This values seem to be too high, according to MrBayes, which will only take 
values up to 1000.


This happened both on Mac and Windows with jModeltest 2.1.4

What steps will reproduce the problem?
1. load the data file
2. specify 11 patterns, exclude +I, increase +G to 8
3. specify AICc, BIC, and DT, after likelihood scores calculated

What is the expected output? What do you see instead?

Program freezes on local machine. Running online, AICc has negative values. BIC 
and DT not computed. K differs across models

What version of the product are you using? On what operating system?

OSX 10.6.8, jmodeltest 2.1.1.

Please provide any additional information below.

Here is the example output:

---------------------------------------------------------------
*                                                             *
*        CORRECTED AKAIKE INFORMATION CRITERION (AICc)        *
*                                                             *
---------------------------------------------------------------

 Model selected: 
   Model = TVM+G
   partition = 012314
   -lnL = 2974.5260
   K = 375
   freqA = 0.1869 
   freqC = 0.3538 
   freqG = 0.2607 
   freqT = 0.1987 
   R(a) [AC] =  1.1003
   R(b) [AG] =  3.8034
   R(c) [AT] =  0.9051
   R(d) [CG] =  0.9751
   R(e) [CT] =  3.8034
   R(f) [GT] =  1.0000
   gamma shape = 0.1270 


* AICc MODEL SELECTION : Selection uncertainty

Model             -lnL    K        AICc      delta      weight cumWeight
------------------------------------------------------------------------ 
TVM+G        2974.5260   375  -275300.9481     0.0000      1.0000    1.0000 
GTR          3517.3863   375  -274215.2274  1085.7207   0.00e+000    1.0000 
GTR+G        2960.7373   376  -135078.5255  140222.4226   0.00e+000    1.0000 
JC           3655.7368   367  46632.9021  321933.8501   0.00e+000    1.0000 
JC+G         3077.3968   368  52154.7937  327455.7417   0.00e+000    1.0000 
K80          3578.3957   368  53156.7913  328457.7394   0.00e+000    1.0000 
K80+G        2994.5908   369  61339.1817  336640.1297   0.00e+000    1.0000 
TrNef        3536.0330   369  62422.0661  337723.0141   0.00e+000    1.0000 
TPM3         3575.8030   369  62501.6061  337802.5541   0.00e+000    1.0000 
TPM2         3577.6094   369  62505.2188  337806.1668   0.00e+000    1.0000 
TPM1         3578.3616   369  62506.7232  337807.6713   0.00e+000    1.0000 
TrNef+G      2980.1488   370  75335.2975  350636.2456   0.00e+000    1.0000 
TPM3+G       2992.1638   370  75359.3276  350660.2757   0.00e+000    1.0000 
TPM2+G       2993.5295   370  75362.0591  350663.0071   0.00e+000    1.0000 
TPM1+G       2994.5600   370  75364.1199  350665.0680   0.00e+000    1.0000 
TIM3ef       3533.3276   370  76441.6551  351742.6032   0.00e+000    1.0000 
TIM2ef       3535.2259   370  76445.4518  351746.3998   0.00e+000    1.0000 
TIM1ef       3536.0039   370  76447.0077  351747.9558   0.00e+000    1.0000 
F81          3645.2379   370  76665.4758  351966.4238   0.00e+000    1.0000 
TIM3ef+G     2977.3015   371  98704.6031  374005.5511   0.00e+000    1.0000 
TIM2ef+G     2978.7527   371  98707.5053  374008.4534   0.00e+000    1.0000 
TIM1ef+G     2980.1399   371  98710.2797  374011.2278   0.00e+000    1.0000 
F81+G        3054.3464   371  98858.6928  374159.6409   0.00e+000    1.0000 
HKY          3561.0965   371  99872.1930  375173.1411   0.00e+000    1.0000 
TVMef        3574.9119   371  99899.8238  375200.7718   0.00e+000    1.0000 
HKY+G        2974.7730   372  145449.5459  420750.4940   0.00e+000    1.0000 
TVMef+G      2990.9115   372  145481.8230  420782.7711   0.00e+000    1.0000 
TrN          3517.7249   372  146535.4498  421836.3978   0.00e+000    1.0000 
SYM          3532.3952   372  146564.7903  421865.7384   0.00e+000    1.0000 
TPM3uf       3560.7858   372  146621.5715  421922.5196   0.00e+000    1.0000 
TPM2uf       3561.0500   372  146622.1001  421923.0482   0.00e+000    1.0000 
TPM1uf       3561.0688   372  146622.1376  421923.0856   0.00e+000    1.0000 
TrN+G        2961.0899   373  285672.1798  560973.1278   0.00e+000    1.0000 
TPM1uf+G     2974.6176   373  285699.2352  561000.1832   0.00e+000    1.0000 
TPM3uf+G     2974.7166   373  285699.4332  561000.3813   0.00e+000    1.0000 
TPM2uf+G     2974.7471   373  285699.4942  561000.4422   0.00e+000    1.0000 
SYM+G        2975.6656   373  285701.3313  561002.2793   0.00e+000    1.0000 
TIM2         3517.5914   373  286785.1828  562086.1309   0.00e+000    1.0000 
TIM3         3517.6407   373  286785.2814  562086.2294   0.00e+000    1.0000 
TIM1         3517.6916   373  286785.3832  562086.3313   0.00e+000    1.0000 
TIM1+G       2961.0297   374

The specified file "test.fasta" cannot be read as an alignment 
failed.
Alignment parse exception: Copy character (.) in first sequence not allowed (pos. 4)

>stu|PGSC0003DMP400006353
...
>araAT4G36090.3
...

\providecommand{\versionnumber}{0.1.10}

I know was reported before, but there is no solution of it after they requested 
the log.

What steps will reproduce the problem?
1.Check the format using alter
2.Upload the file
3.Run the program

What is the expected output? What do you see instead?
The Calculations instead I have an error

______________
::Settings::

 Phyml version = 3.0
 Phyml binary = PhyML_3.0_macOS_i386
 Candidate models = 88
   number of substitution schemes = 11
   including models with equal/unequal base frequencies (+F)
   including models with/without a proportion of invariable sites (+I)
   including models with/without rate variation among sites (+G) (nCat = 4)
 Optimized free parameters (K) = substitution parameters + 185 branch lengths + topology 
 Base tree for likelihood calculations = ML tree
 Tree topology search operation = NNI


::Progress::

Model        Exec. Time      Total Time      -lnL
-------------------------------------------------------------------------


Computation of likelihood scores interrupted. It took 00h:00:40:09.
_________________________

What version of the product are you using? On what operating system?
jmodeltest 2.1.4

Please provide any additional information below.

This is created without the closing parenthesis in the RMAT option parameter.

e.g.
BEGIN PAUP;
Lset base=(0.2822 0.2892 0.1525 ) nst=6  rmat=(1.0000 55.1750 1.0000 1.0000 
21.4512  rates=equal pinvar=0.6670;
END;

This, of course, creates problems when used in Paup*.

Further than the plain text logging for each execution, an HTML report brings a 
more user-friendly and prettier results output.

jModelTest crashes if input branch lengths don't have decimal places.

Users should be able to select the number of simultaneous processes (i.e, the 
number of cores) jModelTest will use in the execution from the GUI.

What steps will reproduce the problem?
1.Check the format using alter
2.Upload the file
3.Run the program

What is the expected output? What do you see instead?
The Calculations instead I have an error

Phyml version = 3.0
 Phyml binary = PhyML_3.0_win32.exe
 Phyml path = C:\Program Files\jmodeltest-2.1.6\exe\phyml\
 Candidate models = 88
   number of substitution schemes = 11
   including models with equal/unequal base frequencies (+F)
   including models with/without a proportion of invariable sites (+I)
   including models with/without rate variation among sites (+G) (nCat = 4)
 Optimized free parameters (K) = substitution parameters + 55 branch lengths + topology 
 Base tree for likelihood calculations = ML tree
 Tree topology search operation = NNI


::Progress::

Model        Exec. Time      Total Time      -lnL
-------------------------------------------------------------------------


Computation of likelihood scores interrupted. It took 00h:00:14:08.

What version of the product are you using? On what operating system?
jmodeltest 2.1.6 with window 7

Please provide any additional information below.
I run this file few days ago. But today suddenly it doesn,t work.
When i run with example files there is no error, that means the program is OK.
My data file is composed only numbers and nucleotide sequences.
I don't know why it has error
would you help me?

What steps will reproduce the problem?
1. run java -jar jModelTest.jar
2. load DNA alignment example-data/example.nex
3. compute likelihood scores

What is the expected output? What do you see instead?
If any thread is idle, it is labeled as 'iddle'

What version of the product are you using? On what operating system?
I am using 2.1.3, downloaded from 
https://code.google.com/p/jmodeltest2/downloads/detail?name=jmodeltest-2.1.3-201
30306.tar.gz&can=2&q=

Please provide any additional information below.
This isn't really a bug, just a heads up to help improve your program.

JModeltest will not run properly on Windows 7 which is a pity.
I used an older version 0.1.1 which computes likelihoods but only if set to "ML 
optimized", otherwise the programm hangs up. 
Version 2.1.1 does not even start with this setting but simply closes the 
window. So Windows users are stuck with an old version. Maybe this can be fixed 
as it is a great program!
Greetings! Axel

What steps will reproduce the problem?
1. Don't set checkpointing configuration option in conf/jmodeltest.conf
2. run jmodeltest in a way that isCkpEnabled() is run

What is the expected output? What do you see instead?

Exception is raised because isCkpEnabled calls getProperty(CKP_LOG).
Since there is not a checkpointing option set in the config file, getProperty 
returns null which in turn ends up in a null pointer exception.

What version of the product are you using? On what operating system?
Effects all OS
Latest source as well as 2.1.4

Please provide any additional information below.

You can either implement a configuration check or you can make a custom 
exception that is raised when null is returned from trying to gather a property 
value from the config file

[deleted issue]

What steps will reproduce the problem?

1. java -jar jModelTest.jar -d example-data/aP6.fas -f
2. or any other parameters, input files or argument order 


What is the expected output? What do you see instead?

With -d argument only, i get:
[MPI] Testing MPI environment...
[MPI] Proceed without MPI
(Then the normal computation of likelihood scores)

With 2 arguments i get:
[MPI] Testing MPI environment... 
[MPI] Unknown exception!
For input string: "-d"

What version of the product are you using? On what operating system?

jmodeltest-2.0.1-20111123.tar.gz on mac os x 10.7.2 with java 1.6.0_29 (same 
problem on ubuntu) 

In old versions of phyml, the application asks for confirmation when using 
large datasets with high memory requirements. This problem induces jModelTest 
to stall waiting for user input. 

The latest versions of phyml include the "--no_memory_check" argument, 
performing a full batch processing.

What steps will reproduce the problem?
1. Start JModelTest and load the primate-mtDNA.nex data file from the 
"example-data" folder.
2. Compute likelihood scores using "BioNJ" base tree, "11" substitution 
schemes, and uncheck "+I" and "+G".
(the bug does not depend on these settings; I just wanted to reduce the model 
set to simplify comparisons).
3. Do DT calculations.

What is the expected output? What do you see instead?

I believe that the correct values are shown in this table (computed using the 
"automodel" command in a forthcoming version of PAUP*):

                                                                   delta
         #  Model               -lnL       K            DT            DT
    --------------------------------------------------------------------
        22  GTR           5934.14686      29      0.000729      0.000000
        20  TVM           5938.56165      28      0.002006      0.001276
        16  TIM2          5948.70508      27      0.007330      0.006600
        18  TIM3          5964.67497      27      0.008686      0.007956
        14  TIM           5970.48937      27      0.009140      0.008410
        12  TPM3uf        5967.29493      26      0.009318      0.008588
        10  TPM2uf        5953.37500      26      0.009349      0.008620
         8  K81uf         5973.23914      26      0.010403      0.009673
         6  TrN           5978.85492      26      0.014152      0.013423
         4  HKY           5981.72023      25      0.015449      0.014720
         7  K81           6132.14429      23      0.015855      0.015126
        11  TPM3          6130.17784      23      0.016391      0.015661
        13  TIMef         6075.94240      24      0.018402      0.017673
         3  K80           6142.42908      22      0.019825      0.019095
        17  TIM3ef        6073.43494      24      0.019870      0.019141
         5  TrNef         6086.21799      23      0.022145      0.021416
         2  F81           6284.99563      24      0.033963      0.033233
        19  TVMef         6045.36435      25      0.035274      0.034544
         1  JC            6424.20245      21      0.035506      0.034777
        21  SYM           5989.38158      26      0.036224      0.035494
         9  TPM2          6058.50316      23      0.037819      0.037090
        15  TIM2ef        6003.14926      24      0.038347      0.037618

Here is what is output by JModelTest:

    * DT MODEL SELECTION : Selection uncertainty

    Model             -lnL    K          DT      delta      weight cumWeight
    ------------------------------------------------------------------------ 
    GTR          5934.1469   29      0.0004     0.0000      0.6515    0.6515 
    TVM          5938.5617   28      0.0027     0.0024      0.0856    0.7371 
    TIM2         5948.7051   27      0.0085     0.0082      0.0272    0.7643 
    TIM3         5964.6750   27      0.0099     0.0095      0.0235    0.7878 
    TIM1         5970.4894   27      0.0106     0.0102      0.0220    0.8098 
    TPM3uf       5967.2950   26      0.0107     0.0103      0.0217    0.8315 
    TPM2uf       5953.3750   26      0.0109     0.0106      0.0212    0.8527 
    TPM1uf       5973.2392   26      0.0120     0.0117      0.0192    0.8720 
    TrN          5978.8549   26      0.0162     0.0159      0.0143    0.8862 
    HKY          5981.7202   25      0.0177     0.0174      0.0131    0.8993 
    TPM1         6132.1443   23      0.0180     0.0176      0.0129    0.9122 
    TPM3         6130.1779   23      0.0185     0.0182      0.0125    0.9247 
    TIM1ef       6075.9424   24      0.0206     0.0203      0.0112    0.9360 
    TIM3ef       6073.4349   24      0.0223     0.0219      0.0104    0.9464 
    K80          6142.4291   22      0.0225     0.0222      0.0103    0.9567 
    TrNef        6086.2180   23      0.0250     0.0246      0.0093    0.9660 
    F81          6284.9956   24      0.0385     0.0382      0.0060    0.9720 
    TVMef        6045.3644   25      0.0399     0.0395      0.0058    0.9778 
    JC           6424.2025   21      0.0403     0.0399      0.0058    0.9836 
    SYM          5989.3816   26      0.0409     0.0405      0.0057    0.9892 
    TPM2         6058.5032   23      0.0427     0.0424      0.0054    0.9946 
    TIM2ef       6003.1493   24      0.0433     0.0430      0.0054    1.0000
    ------------------------------------------------------------------------


What version of the product are you using? On what operating system?

JModelTest 2.1.4, Mac OSX 10.8.5

Please provide any additional information below.

I have done a thorough analysis of why I think the results from PAUP* are the 
correct ones in the attached document.  Also note that for the example above, I 
can get my program to match ModelTest by simulating the coding mistakes 
described in this document.

What steps will reproduce the problem?
1.Loading NEXUS alignment of 13 sequences (1521 sites)
2.Read perfectly the alignment
3.Launch Computation of likelihood values (same error with all parameters). It 
doesn't launch the error with BioNJ.

What is the expected output? What do you see instead?
---------------------------------------------------------------
*                                                             *
*        COMPUTATION OF LIKELIHOOD SCORES WITH PHYML          *
*                                                             *
---------------------------------------------------------------

::Settings::

 Phyml version = 3.0
 Phyml binary = PhyML_3.0_macOS_i386
 Candidate models = 40
   number of substitution schemes = 5
   including models with equal/unequal base frequencies (+F)
   including models with/without a proportion of invariable sites (+I)
   including models with/without rate variation among sites (+G) (nCat = 4)
 Optimized free parameters (K) = substitution parameters + 23 branch lengths + topology 
 Base tree for likelihood calculations = ML tree
 Tree topology search operation = SPR


::Progress::

Model        Exec. Time      Total Time      -lnL
-------------------------------------------------------------------------


Computation of likelihood scores interrupted. It took 00h:00:16:07.

ML tree for TrN+I+G is invalid.TrN+I+G      00h:00:16:07    00h:00:16:08    0.0000


What version of the product are you using? On what operating system?
jModelTest-2.1.4 on MacOSX 10.8.5

Please provide any additional information below.

HTML logging is calling swing methods even in console mode, what raises 
exceptions if X11 is not available:

Exception in thread "main" java.lang.InternalError: Can't connect to X11 window 
server using 'localhost:10.0' as the value of the DISPLAY variable.
        at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method)
        at sun.awt.X11GraphicsEnvironment.access$200(X11GraphicsEnvironment.java:65)
        at sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:110)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.awt.X11GraphicsEnvironment.<clinit>(X11GraphicsEnvironment.java:74)
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Class.java:186)
        at java.awt.GraphicsEnvironment.createGE(GraphicsEnvironment.java:102)
        at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:81)
        at sun.swing.SwingUtilities2.isLocalDisplay(SwingUtilities2.java:1457)
        at javax.swing.plaf.metal.MetalLookAndFeel.initComponentDefaults(MetalLookAndFeel.java:1556)
        at javax.swing.plaf.basic.BasicLookAndFeel.getDefaults(BasicLookAndFeel.java:148)
        at javax.swing.plaf.metal.MetalLookAndFeel.getDefaults(MetalLookAndFeel.java:1592)
        at javax.swing.UIManager.setLookAndFeel(UIManager.java:536)
        at javax.swing.UIManager.setLookAndFeel(UIManager.java:576)
        at javax.swing.UIManager.initializeDefaultLAF(UIManager.java:1345)
        at javax.swing.UIManager.initialize(UIManager.java:1455)
        at javax.swing.UIManager.maybeInitialize(UIManager.java:1422)
        at javax.swing.UIManager.getDefaults(UIManager.java:656)
        at javax.swing.UIManager.getColor(UIManager.java:698)
        at org.jfree.chart.JFreeChart.<clinit>(JFreeChart.java:263)
        at org.jfree.chart.ChartFactory.createHistogram(ChartFactory.java:2120)
        at es.uvigo.darwin.jmodeltest.io.RFHistogram.buildHistogram(Unknown Source)
        at es.uvigo.darwin.jmodeltest.io.RFHistogram.buildDistancesHistogram(Unknown Source)
        at es.uvigo.darwin.jmodeltest.io.RFHistogram.buildRFHistogram(Unknown Source)
        at es.uvigo.darwin.jmodeltest.io.HtmlReporter.buildChart(Unknown Source)
        at es.uvigo.darwin.jmodeltest.io.HtmlReporter.buildReport(Unknown Source)
        at es.uvigo.darwin.jmodeltest.ModelTest.runCommandLine(Unknown Source)
        at es.uvigo.darwin.jmodeltest.ModelTest.<init>(Unknown Source)
        at es.uvigo.darwin.jmodeltest.ModelTest.main(Unknown Source)

What steps will reproduce the problem?
1. running jMT2 with the parameters:  -g 4 -i -f -AIC -BIC -AICc
2. example of the problematic phy inputs attached. I tried to change the taxa's 
names- didn't help.
3.

What is the expected output? What do you see instead?
I get an output suddenly interrupted with no error (Just halts in the middle of 
the printing- with the -o option, or the output on the screen). The outputs are 
attached as well.
*****This problem occurs in many alignment inputs, over 100 alignments I tried 
to work with.******
The running just stops printing- but it looks as if it's still running.

What version of the product are you using? On what operating system?
I tried two versions of unix, windows, both jMT2 2.1.6 and 2.1.4

Please provide any additional information below.

Third party developers might need parsing jModelTest output instead of directly 
calling API.

The current activity log is intended for final users, and this makes difficult 
parsing from an external tool, and also the logging format might change in 
future versions.

Parsing the html output is a more elegant solution, but it could be also quite 
complex. So giving an XML, or any formatted output will make things easier.

Hi,

It is said in the README file of the distribution 
(jmodeltest-2.1.2-20130103.tar.gz file):
        4.1. Required conditions
-----------------------------------------------------------------------------

In order to run jModelTest there will be some general constraints you have to
satisfy:

- You should run it from the jModelTest root directory (i.e. the directory where
you have unpackaged the distribution).
-----------------------------------------------------------------------------

Can you add and option/argument to change the output path. This way, we will be 
able to install once for many different users. Users usually don't have write 
permission into root/admin installation directories. 

This is the error I got when I tried to run jmodeltest2 as a normal user:
There was a problem building the html log files: 
/home/apps/jmodeltest2/jmodeltest-2.1.2/log/aP6.fas.jmodeltest.1360685129357.htm
l (Permission denied)

Thanks,
François 

What steps will reproduce the problem?
1. Loading alignment file (~550 sequences)
2.Starting "Compute likelyhood scores"
3.Running modeltest with any (5,7 or 11 models)

What is the expected output? What do you see instead?
The "running window" appears. Even after 24 hours no progress is visible. the 
counter stays on 0% and it is still running on the first model.

What version of the product are you using? On what operating system?
Jmodeltest 2.1.1 running on Winodws 7 and the latest Java (including recent 
updates)