ERROR too large ID using DNA and CODON5

[gusta10]

Hi all,

I have a problem with my partition file:

The error in iqtree v1.6.7 says: 

ERROR: Too large site ID

Cannot figure out why. Here is my partition.nex

#nexus

begin sets;

    charset part1 = codon.aln:CODON5, 1-11367;

    charset part2 = mitomarker2.aln: 11368-12502;

    charset part3 = mitomarker3: 12503-13319;

    charset part4 = mitomarker4: 13320-14655;

    charset part5 = nuclearmarker5: 14656-15063;

    charset part6 = nuclearmarker6.aln: 15064-17243;

    charset part7 = nuclearmarker7.aln: 17244-20848;

    charpartition mine = GY+F+R6:part1, GTR+F+I+G4:part2, TIM3+F+I+G4:part3, GTR+F+I+G4:part4, K2P+G4:part5, TN+F+I+G4:part6, TIM3+F+I+G4:part7;

end;

Also, since I am using mito genes (codon), mitorRNA, and nuclear genes .. I believe I should call my work as -sp partition.nex, right?

Any suggestion?

[Minh Bui]

Hi there,

On 9 Jan 2019, at 3:49 pm, gusta10 <gus.san...@gmail.com> wrote:

Hi all,

I have a problem with my partition file:

The error in iqtree v1.6.7 says: 

ERROR: Too large site ID

Cannot figure out why. Here is my partition.nex

#nexus

begin sets;

    charset part1 = codon.aln:CODON5, 1-11367;

    charset part2 = mitomarker2.aln: 11368-12502;

    charset part3 = mitomarker3: 12503-13319;

    charset part4 = mitomarker4: 13320-14655;

    charset part5 = nuclearmarker5: 14656-15063;

    charset part6 = nuclearmarker6.aln: 15064-17243;

    charset part7 = nuclearmarker7.aln: 17244-20848;

    charpartition mine = GY+F+R6:part1, GTR+F+I+G4:part2, TIM3+F+I+G4:part3, GTR+F+I+G4:part4, K2P+G4:part5, TN+F+I+G4:part6, TIM3+F+I+G4:part7;

end;

This error means that the position range exceeds the number of sites in the alignment. Quick look at your partition file: part2 should start from 1 instead of 11368, because this is a different alignment file (mitomarker2.aln) compared with part1 (codon.aln). The same for all other partitions.

Also, since I am using mito genes (codon), mitorRNA, and nuclear genes .. I believe I should call my work as -sp partition.nex, right?

I would perform both edge-unlinked (-sp) and edge-linked (-spp) analysis, and then look at the BIC/AICc score of the resulting trees printed in .iqtree file. The one with lower BIC/AICc scores will be preferred.

Cheers

Minh

Any suggestion?

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