Mix Data Error in v. 1.6

[Stephen Baca]

Greetings,

I have been trying to run a mixed-data analysis in v. 1.6. 

The data consists of two subalignments, DNA and morphology, saved as separate NEXUS files. I have the partitions set as instructed in the Manual, though I omit the Charpartitions command (see below). 

I use the following options to run the analyses:

 -sp partitionfile.nex -NT AUTO -M TEST -BB 1000

The analysis seems to load the partitions\alignments fine, but then I get the following: 

NOTE: Restoring information from model checkpoint file Partition-CHRY-IQtree-01.nex.model.gz

CHECKPOINT: Initial tree restored

NOTE: ModelFinder requires 59 MB RAM!

NUMBER OF THREADS FOR PARTITION FINDING: 8

ERROR: Cannot concatenate sub-alignments of different type

And this is my abbreviated partition file text:

#NEXUS

BEGIN SETS;

CHARSET 1st  = CHRYcomb-IQ-tree_local01_mole.nex:DNA, 1-657;

CHARSET 2nd  = CHRYcomb-IQ-tree_local01_mole.nex:DNA, 658-771;

CHARSET 3rd  = CHRYcomb-IQ-tree_local01_mole.nex:DNA, 772-2304;

.... 

CHARSET 21st = CHRYcomb-IQ-tree_local01_mole.nex:DNA, 16353-18452;

CHARSET 22nd = CHRYcomb-IQ-tree_local01_morph.nex:MORPH, 1-87;

END;

Any insight as to what the problem might be? I will note that for some taxa, I have only morphological data. These are included in the DNA matrix, but only with missing data "?". I did run both aligments individually on the web server as a quick test. The analyses did not much like that the DNA alignment had taxa with only missing data, but once I added a dummy site at the beginning of the alignment, there were no problems.

Thank you much for your time,

Stephen

  

[Minh Bui]

Hi Stephen,

I confirm that v1.6 does not support mixed data types, unfortunately. This will be fixed in the next release. However, I’ve seen that you do edge-unlinked ModelFinder. Therefore, you can use the latest v1.5 version, which indeed supports such analysis.

Cheers,

Minh

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[Stephen Baca]

Hi Minh,

Ahh ok, I apologize for the misunderstanding. Thank you for clarifying!

Kind regards,

Stephen

[Minh Bui]

Hi Stephen, No need to apologise, this is indeed an issue that we need to fix.

Cheers

Minh