'Values are either not list nor dict' error from var2value function in model.py

[stevemussmann]

Good afternoon,

I have been trying to run the gadma-run_ls_on_boot_data script and keep receiving the following error:

Traceback (most recent call last):
  File "/home/mussmann/miniconda3/envs/gadma/bin/gadma-run_ls_on_boot_data", line 10, in <module>
    sys.exit(main())
  File "/home/mussmann/miniconda3/envs/gadma/lib/python3.8/site-packages/gadma/run_ls_on_boot_data.py", line 247, in main
    res = run_job((fs_filename, fs, p0, settings))
  File "/home/mussmann/miniconda3/envs/gadma/lib/python3.8/site-packages/gadma/run_ls_on_boot_data.py", line 50, in run_job
    theta = engine.get_theta(popt, *grid_size)
  File "/home/mussmann/miniconda3/envs/gadma/lib/python3.8/site-packages/gadma/engines/dadi_engine.py", line 170, in get_theta
    return super(DadiEngine, self).get_theta(values, pts)
  File "/home/mussmann/miniconda3/envs/gadma/lib/python3.8/site-packages/gadma/engines/dadi_moments_common.py", line 136, in get_theta
    key = self._get_key(values, grid_sizes)
  File "/home/mussmann/miniconda3/envs/gadma/lib/python3.8/site-packages/gadma/engines/dadi_moments_common.py", line 71, in _get_key
    var2value = self.model.var2value(x)
  File "/home/mussmann/miniconda3/envs/gadma/lib/python3.8/site-packages/gadma/models/model.py", line 127, in var2value
    raise TypeError(f"Values are either not list nor dict: {values}")
TypeError: Values are either not list nor dict: None

The command I have been using is gadma-run_ls_on_boot_data -b sfs/ -d "gadma/3pop/efh_slow/models/m1/best_logLL_model_dadi_code.py" -o step1/ --opt log

When trying to troubleshoot the issue I noticed that I was running gadma v2.0.0, so I tried updating to v2.0.3 and still received the same error. I also get basically the same error in v2.0.0 if I try running the best_logLL_model_moments_code.py file.

Do you have any ideas of what may be causing the issue, or any recommendations for troubleshooting?

[stevemussmann]

I have also attached my .sfs and .py files here (renamed to .txt since it won't let me upload .py or .sfs files)

CVWS-IND-EFH_2026.txt
best_logLL_model_dadi_code.txt
best_logLL_model_moments_code.txt

[noscode]

Hi @stevemussmann ,

Thank you for your feedback, that is very interesting. I think the issue is in the first element of lower_bound and upper_bound. Can you remove 1.0 from lower_bound and 100000000.0 from upper_bound and check if that helps?

Is it true that you have not modified code files generated my GADMA and that these two values were originally there? If so, then this confirms that there is a bug in GADMA that I need to fix. Thank you.

Best,
Ekaterina

[stevemussmann]

Hi Ekaterina,

Thank you for your quick response. I will remove those and report back what happens later today.

That is correct, I did not modify the code files in any way.

Thank you,

-Steve

[stevemussmann]

Hi @noscode ,

I followed your suggestion and although gadma-run_ls_on_boot_data has not yet finished running, it has run far past the point where it crashed yesterday. It seems it will probably complete sometime after I go home for the day, but I will update again once it finishes.

-Steve

[stevemussmann]

Hi @noscode ,

This completed successfully over the weekend. If you need any information from me to help troubleshoot the bug that caused this, just let me know.

Thanks for your help,

-Steve

[noscode]

Thank you very much for your feedback and help, I hope this bug can be easily resolved.