IQTree crashes with Signal Aborted

[Marc Hömberger]

Hi, 

I wanted to do a topology evaluation for a set of trees I have from a Phylobayes run. I have as input file the consensus tree that I hand over as -te parameter. Then the list of trees generated during Phylobayes run (for trouble shooting purposes I just choose to use the last 100sampled trees) is handed over as -z. 

The command used is: 

iqtree-omp-latest -nt 4  -s alignment_final.fas -st AA  -te tree.newick -z all.trees -zb 50000  -au.

I attached the files as well as the error log file. 

The exact error I get when IQtree crashes: 

155 ERROR:
156 ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
157 ERROR: *** For bug report please send to developers:
158 ERROR: ***    Log file: alignment_final.fas.log
159 ERROR: ***    Alignment files (if possible)

[James Bickerstaff]

Hi Marc, 

I also get a similar error when running IQ Tree. I was running the beginner's tutorial when I ran into the problem. I've tried on two various windows machines (both running intel core i5 processors), but both seem to fail. I didn't get any error log files, but attached is a screenshot and the alignment file from the tutorial.

Cheers, 

James Bickerstaff

[Marc Hömberger]

That is interesting. 

I should add that I tried it both with the latest version from the github as well as the stable release. I get the error reproducible for both compilations. Also I tested both linux (blade server) architecture as well as my local macbook. I do get the same error on both architectures. 

-Marc 

[James Bickerstaff]

And I just tested the latest release on a MacBook too (also intel i5), and still the same issue

- James

[Dominik Schrempf]

Dear James and Marc,

I am not the main developer of IQ-TREE who is not in office this week.
However, I have some comments, that may help you.

I believe that your problems are unrelated.

James, it looks like IQ-TREE is unable to read the example data file
`example.phy`. I tried to reproduce your error but the analysis
succeeded. Can you check that `example.phy` is available in your folder
of analysis and complete (maybe do an md5sum check)? However, it may be
a problem of having different operating systems (I run Linux here).

Marc, I am afraid that the error might be a consequence of a weak
multisequence alignment. I can redproduce your error. It basically says,
that during parameter estimation, it does not know what to do, because
any change in the parameters leads to a big difference in the likelihood
(Minh, please correct me if this is wrong). When I check your alignment,
I notice that there are shifts in the sequences.

Lets compare the second and third sequences
sp_A0A1U8DSZ3_JAK3_Alligator_sinensis and
sp_H0VSL1_JAK3_Cavia_porcellus. The first three measured amino acids are
MAP, but they are shifted by two. Is there a way to improve your
alignment before further analysis?

I hope that I could help.

Best wishes,
Dominik

--
Dominik Schrempf PhD Student

Vienna Graduate School of Population Genetics
Vetmeduni Vienna
Austria

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[Marc Hömberger]

Hi Dominik, 

thanks for the reply, I will see what I can do about the alignment. I will let you know how it goes. 

-Marc

[Bui Quang Minh]

Dear All,

Dominik had good points - thanks for that. I confirm that the problem James had is because there is no alignment (example.phy) in the current folder (C:\Users\James). But I admit that error message is not informative, it should have been like failure reading alignment. We will fix that.

Marc reported a different problem, which seems like a bug - I will have a look.

Cheers, Minh

--

Bui Quang Minh

Center for Integrative Bioinformatics Vienna (CIBIV)

Campus Vienna Biocenter 5, VBC5, Ebene 1

A-1030 Vienna, Austria

Phone: ++43 1 4277 74326

Email: minh.bui (AT) univie.ac.at

[Bui Quang Minh]

Dear Marc,

I can’t reproduce this behavior with the stable release 1.5.5. I noticed that you used beta version 1.6.beta5. Did you compile the code from GitHub? There is an issue with with beta version which I fixed recently. Thus, this crash may have been fixed as well. 

Cheers, Minh

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