TypeError: bad operand type for abs(): 'str'

[KhanhLPBao]

sample.zip
I'm running NIPT samples then suddenly I found this error occurred in some samples

[INFO - 2021-04-29 10:19:51]: Starting CNA prediction
[INFO - 2021-04-29 10:19:51]: Importing data ...
[INFO - 2021-04-29 10:19:51]: Normalizing autosomes ...
[INFO - 2021-04-29 10:19:59]: Normalizing gonosomes ...
[INFO - 2021-04-29 10:20:02]: Applying blacklist ...
[INFO - 2021-04-29 10:20:02]: Executing circular binary segmentation ...
[INFO - 2021-04-29 10:20:07]: Writing tables ...
Traceback (most recent call last):
File "/home/tgd/.local/bin/WisecondorX", line 8, in
sys.exit(main())
File "/home/tgd/.local/lib/python3.8/site-packages/wisecondorX/main.py", line 404, in main
args.func(args)
File "/home/tgd/.local/lib/python3.8/site-packages/wisecondorX/main.py", line 244, in tool_test
generate_output_tables(rem_input, results)
File "/home/tgd/.local/lib/python3.8/site-packages/wisecondorX/predict_output.py", line 43, in generate_output_tables
_generate_chr_statistics_file(rem_input, results)
File "/home/tgd/.local/lib/python3.8/site-packages/wisecondorX/predict_output.py", line 130, in _generate_chr_statistics_file
cpa = round(get_cpa(results['results_c'], rem_input['binsize']), 5)
File "/home/tgd/.local/lib/python3.8/site-packages/wisecondorX/overall_tools.py", line 133, in get_cpa
x += (segment[2] - segment[1] + 1) * binsize * abs(segment[3])
TypeError: bad operand type for abs(): 'str'

Its appeared in some files, not all samples. I don't know what's wrong with those file. I have attached 1 .npz file that be bugged out.

[leraman]

Hard to say what's going on, I'm not getting the error when using your file with one of our references.

• How much samples are in your reference?
• What is your reference bin size?
  If possible, could you provide a reference for me to reproduce the error?

Best, Lennart

[KhanhLPBao]

Hi @leraman
My sample size is more than 1000 samples, when making reference I use default args. Sorry for not reply you for a long time due to some emergency works but I cannot give you the reference file. Also I found that the error comes from the calculation of CPA. I have modified the script of get_cpa function to:

def get_cpa(results_c, binsize):
    x = 0
    for segment in results_c:
        try:
            x += (segment[2] - segment[1] + 1) * binsize * abs(segment[3])
            CPA = x / len(results_c) * (10 ** -8)
        except:
             pass
    return(CPA)

And after that I'm not encountered the error again. Does I do right? Because what I need mostly is zscore