example_concat failure

[josephwb]

[I am obviously working through the examples. I hope this is not too annoying.]

How do I run the concatenation example? A blind running of the script delivers the error:

$ python3 example_concat.py 
Building concat config object
Traceback (most recent call last):
  File "example_concat.py", line 14, in <module>
    config = concat_config.ConcatConfigObj(configfi, workdir_comb)
  File "/home/josephwb/Downloads/PhylUp/src/concat/Concat/concat_config.py", line 47, in __init__
    self.run_modeltest = config['concat']['run_modeltest']
  File "/usr/lib/python3.6/configparser.py", line 1233, in __getitem__
    raise KeyError(key)
KeyError: 'run_modeltest'

which suggests modeltest is the issue. But I looked at the code and it is looking for modeltest-ng which I have installed and on my PATH.

However, in looking at example_config.py itself it looks like the raw data are missing? For example, the directories workdir_its ('Senecioneae_its') and workdir_ets ('Senecioneae_ets') are not present, and the workdir_comb ("remote/concat_nr") is completely empty. Is there a step I am missing to populate these data?

Thanks again.

[mkandziora]

[Thanks for going through them, this is very helpful - I know the program to well to spot inconsistencies and unclear documentation]

The example_concat.py should probably be removed from this repository. I added it as an example of how you could concatenate independent PhylUp runs. For this the independent PhylUp runs first would need to be run. This file basically calls the small package "phylogenetic_concatenation" I wrote to concatenate single gene alignments (either using the PhylUp setup or just alignments files). The example workdirs are really just examples - you would need to replace them with your output folders.

Nevertheless, your run_modeltest error is unrelated to that - I forgot to update the concat.config file in the data folder to include the run_modeltest configuration setting. Fixed.

[josephwb]

Ok, thanks.

I thought that was what was missing from the config file, but no config file in the repository includes run_modeltest at all (either True or False). In fact, the wiki does not mention the run_modeltest config argument either. The settings page mentions modeltest_criteria, but not turning on model testing itself (unless specifying a criterion indirectly sets run_modeltest = True)?

[mkandziora]

Yes, this is currently not optional for PhylUp. When you are running example_config.py you are basically not running PhylUp code, but the phylogenetic_concatentation. I will remove it from the examples and link to the phylogenetic_concatenation page instead to make this less confusing.