Segmentation fault (core dumped) with user tree as input in PhyML

[Chitra Narayanan]

Hi Stephane,

I'm posting this issue here as the solutions suggested in the forum for other segmentation fault issues are not applicable in this case.

I am try to run PhyML to optimize the branch length and rate while using a user input for the tree. I get the following message:

Command line: /home/chtra/Dropbox/phyml-master/src/phyml -i input.phy -d aa -m JTT -u user_tree.nwk -o lr

                        ⁜        SETTINGS       ⁜

        ‣ Sequence filename:                             input.phy

        ‣ Data type:                                     aa

        ‣ Alphabet size:                                 20

        ‣ Sequence format:                               interleaved

        ‣ Number of data sets:                           1

        ‣ Nb of bootstrapped data sets:                  0

        ‣ Compute approximate likelihood ratio test:     yes (aBayes branch supports)

        ‣ Model name:                                    JTT

        ‣ Proportion of invariable sites:                0.000000

        ‣ Number of subst. rate catgs:                   4

        ‣ Gamma distribution parameter:                  estimated

        ‣ 'Middle' of each rate class:                   mean

        ‣ Amino acid equilibrium frequencies:            model

        ‣ Optimise tree topology:                        no

        ‣ Evaluated tree:                                "user tree (user_tree.nwk)"

        ‣ Optimise branch lengths:                       yes

        ‣ Optimise substitution model parameters:        yes

        ‣ Run ID:                                        none

        ‣ Random seed:                                   1505925579

        ‣ Subtree patterns aliasing:                     no

        ‣ Version:                                       3.3.20170530

        ‣ Byte alignment:                                16

        ‣ AVX enabled:                                   no

        ‣ SSE enabled:                                   yes

                         ⁜ ⁜ ⁜ ⁜ ⁜ ⁜ ⁜ ⁜ ⁜ ⁜ ⁜ ⁜

• 218 patterns found (out of a total of 220 sites).

• 36 sites without polymorphism (16.36%).

• Reading tree...Segmentation fault (core dumped)

Do you have suggestions on what could fix this issue?

Thanks!

Chitra

[Stephane Guindon]

I couldn't reproduce this issue on my side. Any chance you could send me the sequence and tree files you've used here?

Regards,

-Stephane-

--
You received this message because you are subscribed to the Google Groups "PhyML forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to phyml-forum+unsubscribe@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Chitra Narayanan]

Hi Stephane,

I sent the files in an email to your institute lirmm.fr email. I hope you can help resolve this.

Chitra

To unsubscribe from this group and stop receiving emails from it, send an email to phyml-forum...@googlegroups.com.

[Stephane Guindon]

Hi Chitra,

Thanks for the files. It looks like there is an issue with the tree file. More specifically,

the following part of the Newick string is problematic:

((RN6_Hedgeh:0.31152396,RN6_Shrew_:0.119382655):0.139625219)

There an extra set of parentheses here as if a taxon was missing... 

The sequence file looks fine.

Regards,

-Stephane-

To unsubscribe from this group and stop receiving emails from it, send an email to phyml-forum+unsubscribe@googlegroups.com.

[Chitra Narayanan]

Hi Stephane,

Thanks for pinpointing the problem! I'm going to check work towards rectifying this. 

Just curious - when I ran the code, I only got the 'segmentation fault'. Is there some option to use in PhyML to pinpoint what the origin for the error is (such as the newick string being a problem)?

Chitra

[Stephane Guindon]

Hi Chitra,

Yes, I've just added a proper error message for this particular case. That should help users identify what the problem is.

Cheers,

Stéphane

To unsubscribe from this group and stop receiving emails from it, send an email to phyml-forum+unsubscribe@googlegroups.com.

[Chitra Narayanan]

That's great! Thank you very much for the quick responses and for helping pinpoint the problem, Stephane!

Best regards,

Chitra

--
You received this message because you are subscribed to a topic in the Google Groups "PhyML forum" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/phyml-forum/fTojHfKoZEA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to phyml-forum+unsubscribe@googlegroups.com.