Have to pass index?

[hmf0103]

Hi I was trying to use the module to run the 2nd step: processing_experiment.py after the 1st step is finished. The counts file were from the 1st step. I also tried to config the experiment setup by carefully modifying the strings so that all formats and indentations are the same. But I still encounter a problem that requires me to pass an index. Do you know how to solve this problem?

(ScreenProcessing) [hmf0103@c4-dev1 ScreenProcessing]$ python process_experiments.py "/c4/home/hmf0103/software/ScreenProcessing/Demo/Step2/MH_config_file_MH.txt" library_tables/

Accessing library information
Loading counts data
Merging experiment counts split across lanes/indexes
-generating sgRNA read count histograms
findfont: Font family ['sans-serif'] not found. Falling back to DejaVu Sans.
findfont: Generic family 'sans-serif' not found because none of the following families were found: Helvetica, Arial, Verdana, Bitstream Vera Sans
findfont: Font family ['sans-serif'] not found. Falling back to DejaVu Sans.
findfont: Generic family 'sans-serif' not found because none of the following families were found: Helvetica, Arial, Verdana, Bitstream Vera Sans
findfont: Font family ['sans-serif'] not found. Falling back to DejaVu Sans.
findfont: Generic family 'sans-serif' not found because none of the following families were found: Helvetica, Arial, Verdana, Bitstream Vera Sans
/c4/home/hmf0103/Work/Opool_Amplicon/30-934503947/output/process_exp_output/opool_sb28_plots/009_fig_counts_hist.png
/c4/home/hmf0103/Work/Opool_Amplicon/30-934503947/output/process_exp_output/opool_sb28_plots/010_fig_counts_hist.png
/c4/home/hmf0103/Work/Opool_Amplicon/30-934503947/output/process_exp_output/opool_sb28_plots/011_fig_counts_hist.png
Computing sgRNA phenotype scores
/c4/home/hmf0103/software/ScreenProcessing/process_experiments.py:501: RuntimeWarning: invalid value encountered in double_scalars
  countsRatio = float(totalCounts[0])/totalCounts[1]
Traceback (most recent call last):
  File "/c4/home/hmf0103/software/ScreenProcessing/process_experiments.py", line 635, in <module>
    processExperimentsFromConfig(
  File "/c4/home/hmf0103/software/ScreenProcessing/process_experiments.py", line 154, in processExperimentsFromConfig
    'phenotypes': pd.DataFrame(phenotypeScoreDict)}
  File "/c4/home/hmf0103/.local/lib/python3.9/site-packages/pandas/core/frame.py", line 529, in __init__
    mgr = init_dict(data, index, columns, dtype=dtype)
  File "/c4/home/hmf0103/.local/lib/python3.9/site-packages/pandas/core/internals/construction.py", line 287, in init_dict
    return arrays_to_mgr(arrays, data_names, index, columns, dtype=dtype)
  File "/c4/home/hmf0103/.local/lib/python3.9/site-packages/pandas/core/internals/construction.py", line 80, in arrays_to_mgr
    index = extract_index(arrays)
  File "/c4/home/hmf0103/.local/lib/python3.9/site-packages/pandas/core/internals/construction.py", line 391, in extract_index
    raise ValueError("If using all scalar values, you must pass an index")
ValueError: If using all scalar values, you must pass an index
/