Why is IQ-Tree ignoring terminals with only morphological data in my total evidence analysis?

[Denis Jacob Machado]

Hello!

GENERAL OBJECTIVES

I want to access topological sensitivity to the addition of morphological characters under a total evidence analysis.

OVERVIEW OF MY DATASET

Morphological (185 characters) and nucleotide (13,686 characters) data for 338 terminals. Both matrices contain the exact same terminals. The partition scheme, including the models I selected, is attached here (partitions.nex).

HOW I EXECUTED IQ-TREE

I ran 10 replicates on IQ-Tree, folowwed by a final replicate in which I read all the tree files produced before.

iqtree \
        -spp partitions.nex \
        -nt AUTO \
        -t totev_10reps.treefile \
        -pre totev_final \
        -cptime 30 \
        -pers 0.2 \
        -nstop 500

VERSION OF IQ-TREE

IQ-TREE multicore version 1.6.1 for Linux 64-bit built Dec 26 2017.

OS

#36~14.04.1-Ubuntu SMP Fri Feb 26 18:49:23 UTC 2016.

PROBLEM

Output trees for all replicates have all but two terminals, named t119 and t40. Those are the only two terminals for which I have morphological data but no DNA data (i.e., they are included in the molecular dataset but their alignment contain only missing data). Standart error and standart output make no mentions to theses terminals except in the table of Gap/ Ambiguity (100% for both), Composition (both passed) and p-value (-nan% for both). See totev_final.log attached here.

FINAL REMARKS

• Does anyone know why is IQ-Tree ignoring the terminals which have only morphological data?
• Is there any way to make IQ-Tree do not ignore these terminals?

Thank you very much for your time and attention.

Best regards,

Denis Jacob Machado

[Minh Bui]

Hi Denis,

Thanks for the detailed description. The quick answer is because of semi-colon (instead of comma) in charpartition command:

        TRN+I:   ncx1_1c;

        K81+G:   Rag_1b;

Semi-colon means the end of charpartition and IQ-Tree stops loading partitions there. You can see from this part of the log file:

Subset  Type    Seqs    Sites   Infor   Invar   Model   Name

1       DNA     21      850     76      705     GTR+I+G 28S_1

2       DNA     336     3308    2013    922     GTR+I+G h1_1

…

15              5       425     4       417     TRN+I   ncx1_1c

Since this same issue was reported a few weeks ago, we’ll change the code to do better error-checking. 

Also please update the latest version 1.6.8. It fixes a number of issues (incl. crash when mixing data like this).

Thanks,

Minh

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<partitions.nex><totev_final.log>

[Denis Jacob Machado]

Dear Dr. Minh Bui,

Thank you for the explanation, I was having difficulties finding this error by myself.

Best wishes,

Denis Jacob Machado