Work with another dataset: ValueError("No objects to concatenate")
I am trying to work with dnadna
with another dataset:
Here are the steps I did:
Command: dnadna simulation init cattle
=> Then, modified cattle/cattle_simulation_config.yml (find in attached file)
Command: dnadna init --simulation-config=cattle/cattle_simulation_config.yml
=> Then, modified cattle/cattle_training_config.yml (find in attached file)
Command: dnadna --debug preprocess cattle/cattle_training_config.yml
and got log_error:
dnadna --debug preprocess cattle/cattle_training_config.yml
an unexpected error occurred: No objects to concatenate; run again with --debug to view the full traceback
an unexpected error occurred: No objects to concatenate; run again with --debug to view the full traceback
Traceback (most recent call last):
File "/home/pjobic/anaconda3/envs/dnadna/bin/dnadna", line 11, in <module>
load_entry_point('dnadna', 'console_scripts', 'dnadna')()
File "/home/pjobic/Work/DNADNA/master/dnadna/utils/__init__.py", line 821, in main
raise exc
File "/home/pjobic/Work/DNADNA/master/dnadna/utils/__init__.py", line 813, in main
ret2 = cls.run_subcommand(args)
File "/home/pjobic/Work/DNADNA/master/dnadna/utils/__init__.py", line 782, in run_subcommand
return command_cls.main(command[1:], namespace=args)
File "/home/pjobic/Work/DNADNA/master/dnadna/utils/__init__.py", line 821, in main
raise exc
File "/home/pjobic/Work/DNADNA/master/dnadna/utils/__init__.py", line 805, in main
ret = cls.run(args)
File "/home/pjobic/Work/DNADNA/master/dnadna/data_preprocessing.py", line 676, in run
progress_bar=True)
File "/home/pjobic/Work/DNADNA/master/dnadna/data_preprocessing.py", line 454, in prepare_training_run
progress_bar=progress_bar)
File "/home/pjobic/Work/DNADNA/master/dnadna/data_preprocessing.py", line 302, in preprocess_scenario_params
training_params = self.learned_params.training_params
File "/home/pjobic/Work/DNADNA/master/dnadna/utils/decorators.py", line 70, in __get__
val = self.fget(obj)
File "/home/pjobic/Work/DNADNA/master/dnadna/params.py", line 360, in training_params
training_params = training_params.astype(convert_dtypes)
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/pandas/core/generic.py", line 5887, in astype
result = pd.concat(results, axis=1, copy=False)
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 255, in concat
sort=sort,
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/pandas/core/reshape/concat.py", line 304, in __init__
raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate
my guess is that dnadna
didn't find the dataset
Or the learned_parameters
in training_config.yml
are not corresponding to those of the parameters.csv
file
data_root: /home/pjobic/Work/DNADNA/notebooks/data/cattle
Format: data_root/scenario_XXX
dataset_path_on_titanic: titanic:/home/tau/thsanche/data/cattle/scenario_{0_to_99}
working directory: /home/pjobic/Work/DNADNA/master (named master but i created a git branch)