Molecular Clock Tutorial Error

[MartGro]

Hi,
I was trying to get the Tutorial No1 to run, but it exits with an error:
python3 Zombi.py T ./Tutorials/Tutorial1/SpeciesTreeParameters.tsv MC_test

returns the following error:

...
Time: 99.85704549536541 ; Number of lineages alive: 174
Time: 99.93861005352342 ; Number of lineages alive: 175
Time: 99.95671755007255 ; Number of lineages alive: 174
Traceback (most recent call last):
File "Zombi.py", line 427, in
Z.T(parameters_file, experiment_folder, advanced_mode)
File "Zombi.py", line 112, in T
if parameters["SCALE_TREE"] != 0:
KeyError: 'SCALE_TREE'

[Theo Tricou]

Hi MartGo,

The SpeciesTree Parameters file was not updated.
It should work know.
Just clone the current version of Zombi repo.

Theo

[MartGro]

Thanks for the quick reply, it works now.

When running python RateCustomizer.py S SequenceParameters.tsv MC_test, I got another error:

Traceback (most recent call last):
File "RateCustomizer.py", line 204, in
parameters = af.prepare_genome_parameters(af.read_parameters(parameters_file))
File "home/user_ab/ZOMBI/AuxiliarFunctions.py", line 55, in read_parameters
with open(parameters_file) as f:
FileNotFoundError: [Errno 2] No such file or directory: 'SequenceParameters.tsv'

I could solve it by using:
python RateCustomizer.py S "Tutorials/Tutorial1/SequenceParameters.tsv" MC_test

Where is the SequenceParameters.tsv file supposed to be?

[Theo Tricou]

either in the directory "Tutorials/Tutorial1/".
or simply in the directory "Parameters".

I would recommend only using files from the directory "Parameters", as I'm not sure how up to date files are in the "Tutorials" directory.

T

[MartGro]

Perfect, thanks a lot 👍
Maybe it would be good to also describe that in the Wiki of the Tutorial.
Best,
Martin