ERROR Line 2: More supplies than defined in the header

[Juan Diego Ariza López]

Hi guys i have a problem, i hope you can help. thank u 

C:\Users\home\Anaconda>python "C:\Users\home\Desktop\Sis molecular\partition\partitionfinder-2.1.1\PartitionFinder.py" "C:\Users\home\Desktop\Sis molecular\partition\partitionfinder-2.1.1\examples\nucleotide - alouatta"

INFO     | 2021-02-27 20:51:00,094 | ------------- PartitionFinder 2.1.1 -----------------

INFO     | 2021-02-27 20:51:00,094 | You have Python version 2.7

INFO     | 2021-02-27 20:51:00,094 | Command-line arguments used: C:\Users\home\Desktop\Sis molecular\partition\partitionfinder-2.1.1\PartitionFinder.py C:\Users\home\Desktop\Sis molecular\partition\partitionfinder-2.1.1\examples\nucleotide - alouatta

INFO     | 2021-02-27 20:51:00,095 | ------------- Configuring Parameters -------------

INFO     | 2021-02-27 20:51:00,095 | Setting datatype to 'DNA'

INFO     | 2021-02-27 20:51:00,095 | Setting phylogeny program to 'phyml'

INFO     | 2021-02-27 20:51:00,095 | Program path is here C:\Users\home\Desktop\Sis molecular\partition\partitionfinder-2.1.1\programs

INFO     | 2021-02-27 20:51:00,098 | Setting working folder to: 'C:\Users\home\Desktop\Sis molecular\partition\partitionfinder-2.1.1\examples\nucleotide - alouatta'

INFO     | 2021-02-27 20:51:00,099 | Loading configuration at '.\partition_finder.cfg'

INFO     | 2021-02-27 20:51:00,105 | Setting 'alignment' to 'falouatta.phy'

INFO     | 2021-02-27 20:51:00,107 | Setting 'branchlengths' to 'linked'

INFO     | 2021-02-27 20:51:00,108 | You set 'models' to: GTR, GTR+G, GTR+I+G

C:\Users\home\Anaconda\lib\site-packages\pandas\computation\ops.py:62: DeprecationWarning: object() takes no parameters

  return supr_new(klass, name, env, side=side, encoding=encoding)

C:\Users\home\Anaconda\lib\site-packages\pandas\computation\ops.py:62: DeprecationWarning: object() takes no parameters

  return supr_new(klass, name, env, side=side, encoding=encoding)

C:\Users\home\Anaconda\lib\site-packages\pandas\computation\ops.py:62: DeprecationWarning: object() takes no parameters

  return supr_new(klass, name, env, side=side, encoding=encoding)

C:\Users\home\Anaconda\lib\site-packages\pandas\computation\ops.py:62: DeprecationWarning: object() takes no parameters

  return supr_new(klass, name, env, side=side, encoding=encoding)

INFO     | 2021-02-27 20:51:00,125 | This analysis will use the following 3 models of molecular evolution

INFO     | 2021-02-27 20:51:00,125 | GTR, GTR+G, GTR+I+G

INFO     | 2021-02-27 20:51:00,127 | Setting 'model_selection' to 'aicc'

INFO     | 2021-02-27 20:51:00,134 | Setting 'search' to 'greedy'

INFO     | 2021-02-27 20:51:00,137 | ------------------------ BEGINNING NEW RUN -------------------------------

INFO     | 2021-02-27 20:51:00,138 | Looking for alignment file '.\falouatta.phy'...

INFO     | 2021-02-27 20:51:00,138 | Using 4 cpus

INFO     | 2021-02-27 20:51:00,141 | Beginning Analysis

INFO     | 2021-02-27 20:51:00,177 | Reading alignment file '.\falouatta.phy'

ERROR    | 2021-02-27 20:51:00,178 | Line 2: More supplied than defined in the header

ERROR    | 2021-02-27 20:51:00,183 | Failed to run. See previous errors.

i dont know what is the problem, i tried everything :(

[Rob Lanfear]

Hi there,

Can you post a copy of your alignment? It looks to me like the number of sites or species you define in the alignment header doesn't match what's actually in the alignment itself.

Rob

[Juan Diego Ariza López]

of course bro, this is my alignment,

thank u so much

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