partitioned matrix: dna + morphology

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max maronna

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May 15, 2015, 10:26:29 PM5/15/15
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Hi Derrick and Garli users,
I´m trying to run a partitioned analysis, considering several partitions (dna data) combined with a morphological matrix.

I read the garli´s wiki
https://www.nescent.org/wg_garli/Using_partitioned_models#Dividing_up_the_data
and I define my taxa block and dataset (3 molecular markers and a morphological dataset with 32 characters) as 7 different characters blocks.
Defining the characters sets and partitions (partitions for dna were defined in partition finder), I tried

begin sets;
    charset 16s = 1-404;
    charset coi_1 = 405-1037\3;
    charset coi_2 = 406-1037\3;
    charset coi_3 = 407-1037\3;
    charset coii_1 = 1038-1403\3;
    charset coii_2 = 1039-1403\3;
    charset coii_3 = 1040-1403\3;
    charset morfo = 1004-1435;

charpartition pfinder = chunk1:16s, chunk2:coi_1, chunk3:coi_2, chunk4:coi_3 coii_3, chunk5:coii_1, chunk6:coii_2, chunk7:morfo;
END;

It didn´t work: Garli log file said:

----------------------------------
READING OF DATA
Attempting to read data file in Nexus format (using NCL):
    16s_coi_coii_pfinder_morfo.nex ...
Reading TAXA block... successful
Reading CHARACTERS block... found dna data... successful
Reading CHARACTERS block... found dna data... successful
Reading CHARACTERS block... found dna data... successful
Reading CHARACTERS block... found standard data... successful
Reading SETS block...
Error in the Character descriptor of a CharSet command.
Expecting a character name or a number corresponding to a character's number (a number from 1 to 32). Found 404
Line:   102
Column: 25

ERROR: NCL encountered a problem reading the dataset.
----------------------------------

Line 102 is "charset 16s = 1-404;" in the original nexus file...
I don´t know what I´m doing wrong...any idea?

Thanks in advance, best
max
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