jMT2 stops printing in the middle of the output

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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.

Original issue reported on code.google.com by shira...@gmail.com on 17 Nov 2014 at 7:14

Attachments:

• aln1.phy
• output1.txt
• aln2.phy
• output2.txt

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Original comment by DiegoDL84 on 17 Nov 2014 at 4:43

• Changed state: Accepted

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There is a bug in jModelTest that seems to make it stop when the criteria 
produces a negative score. Actually the data does not contain information 
enough for making a reliable selection. In the first case, there are only 60 
sites for 30 taxa (i.e., k = 58 branch length parameters + 0 to 10 model 
parameters). AICc expects (n - k + 1) to be a positive number, where n is the 
sample size (i.e., the sequence length). That means that you should not use 
AICc for that datasets.

However, jModelTest should not get stuck in any case, so this is a bug I must 
fix.

Thank you for your report!

Original comment by DiegoDL84 on 17 Nov 2014 at 5:00

• Changed state: Started

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Hi, thanks!
First of all, please note that it happens not only in the AICc table (e.g. 
example2). I would be able to generate more instances if you need it.
Second, can you please indicate in which cases this may occur? I also have 
alignments (e.g. 194 taxa, 246 length - attached) whose penalty should be 
negative (-140 for 0 additional parameters in this case), but the running 
completed without a problem.
I want to get the AICc score for most of my data-sets. What exactly should I 
check to predict that jModelTest is going to get stuck?
Thank you!

Original comment by shira...@gmail.com on 18 Nov 2014 at 11:27

Attachments:

• example3.phy

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I fixed the problem with AICc (only in the repository so far). The correction 
part of the AICc is 2*k*(k+1)/(s - k - 1), where s is the sample size and k the 
number of parameters. The problem in those alignments was that for some models, 
(s = k - 1), producing a division by zero. I fixed it such that in that case 
the AICc score will be zero. However, I will also add a WARNING, because the 
results will not be accurate when s is close to k.

Moreover, AICc produces negative values when s <= k and the correction part is 
larger than the AIC score.

What I could not see so far is the problem with example3.phy. Could you please 
attach the output for this file?

Original comment by DiegoDL84 on 19 Nov 2014 at 4:39

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Could you try the new 2.1.7 version?

Original comment by DiegoDL84 on 20 Nov 2014 at 3:18

• Changed state: Fixed
• Added labels: Milestone-Release2.1.7

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Hi,
Thank you! It ends as expected for inputs it got stuck on before.
I'll try it on many inputs in the next two days, and let you know if it 
finished safely.

Tell me, is there supposed to be any difference in computation between v.2.1.7 
and v.2.1.5? Is it possible that I get different scores if I use the same PhyML 
version?

Thanks,
Shiran

Original comment by shira...@gmail.com on 21 Nov 2014 at 8:22

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No. The results will be the same. 

Original comment by DiegoDL84 on 21 Nov 2014 at 8:27