ValueError a few seconds after run starts on example

[batelz]

Hi,
When running the example you provided:
python READ2.py -i Srubnaya.subset_bed

I get an error:

  ===Thank you for using Relationship Estimation from Ancient DNA version 2 (R                                                                                                              EADv2)===

Window size: 5000000
Calculating one genome-wide P0 value and using a block-jackknife to estimate the standard error.
Traceback (most recent call last):
 File "READ2.py", line 366, in <module>
   s=6, rot=90, figsize=((8+0.1*(len(df_P0.index)), 8)), fontsize=8)
 File "/usr/lib/python3/dist-packages/pandas/plotting/_core.py", line 2941, in __call__
   sort_columns=sort_columns, **kwds)
 File "/usr/lib/python3/dist-packages/pandas/plotting/_core.py", line 1977, in plot_frame
   **kwds)
 File "/usr/lib/python3/dist-packages/pandas/plotting/_core.py", line 1743, in _plot
   kind=kind, **kwds)
 File "/usr/lib/python3/dist-packages/pandas/plotting/_core.py", line 845, in __init__
   super(ScatterPlot, self).__init__(data, x, y, s=s, **kwargs)
 File "/usr/lib/python3/dist-packages/pandas/plotting/_core.py", line 820, in __init__
   raise ValueError(self._kind + ' requires x column to be numeric')
ValueError: scatter requires x column to be numeric

What could be the issue?

Thank you,

[SonofLastPanda]

Hi @batelz,

Thank you for reporting the issue. Could you check:

• the versions of the uploaded libraries in conda

• which version of READ you have clonned from Github

So I can try to replicate the issue myself.

[batelz]

Hi, and thank you for the fast reply @SonofLastPanda

I was not using conda for the libraries, but pip:

(READ_V2) :~$ pip show pandas numpy pip matplotlib plinkio
Name: pandas
Version: 1.3.5
---
Name: numpy
Version: 1.21.6
---
Name: pip
Version: 24.0
---
Name: matplotlib
Version: 3.5.3
---
Name: plinkio
Version: 0.9.8

I've cloned the READv2 yesterday, so it's the most up to date version, I guess...

[SonofLastPanda]

Thank you for the extra information @batelz!

Interestingly, I could run the script with those versions as well. I guess that there is something going on with the dependencies. I would suggest setting up the conda environment so the dependencies are managed better.