"ERROR: Cannot concatenate sub-alignments of different #states"

[Morgan Jackson]

Hi,

I'm trying to run a partitioned analysis of DNA and CODON data. My partition file is as such: 

#nexus
begin sets;
charset rDNA1 =  dna.phy: 1-1022;
charset rDNA2 =  dna.phy: 1023-5239;
charset cDNA3 =  codon1.phy: CODON, 1-822;
charset mitoDNA4 =  codon2.phy: CODON5, 1-1533;
charset cDNA5 =  codon3.phy: CODON, 1-3753;
end;

IQTree seems to recognize the partitions and data correctly, but then I get the following error message and it quits:

Subset	Type	Seqs	Sites	Infor	Invar	Model	Name
1		42	1022	228	593	TESTNEWMERGE	rDNA1
2		42	4217	776	2865	TESTNEWMERGE	rDNA2
3	CODON	42	274	175	33	TESTNEWMERGE	cDNA3
4	CODON5	42	511	475	16	TESTNEWMERGE	mitoDNA4
5	CODON	42	1251	1146	60	TESTNEWMERGE	cDNA5
Degree of missing data: 0.000
Info: multi-threading strategy over partitions

NOTE: Mixed codon and other data, branch lengths of codon partitions are rescaled by 3!
Computing Juke-Cantor distances...

Computing BIONJ tree...
0.013 seconds
NOTE: ModelFinder requires 476 MB RAM!
NUMBER OF THREADS FOR PARTITION FINDING: 11
ERROR: Cannot concatenate sub-alignments of different #states

The same error occurs using both the CIPRES build (v1.6.6) and the cibiv build, and if I input a single .phy datafile partitioned as above but without the alignment file modifiers.

Thanks in advance.

Morgan

[Minh Bui]

Hi Morgan,

Many thanks for the report. I confirm this is a problem in IQ-Tree. I overlooked that a species can have two different genetic codes. But of course the mitochondria may have a different code than the nuclear genome. This ERROR happened when IQ-Tree tries to concatenate the CODON with CODON5 partitions, which have different number of non-stop codons. But it shouldn’t do so. I created a github issue to fix for the next release 1.6.9.

Minh

--
You received this message because you are subscribed to the Google Groups "IQ-TREE" group.
To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com.
To post to this group, send email to iqt...@googlegroups.com.
Visit this group at https://groups.google.com/group/iqtree.
For more options, visit https://groups.google.com/d/optout.