IndexError: positional indexers are out-of-bounds

[laurenfields]

Hello,

I am trying to use the transfer_learn function via the PeptDeep GUI to refine a model based on results from DIA-NN. I have done this successfully using just one output file from DIA-NN and the corresponding .mzML file that was processed in DIA-NN.
successful_1results_1mzML.txt

However, if I try to include multiple results.tsv files from DIA-NN with their corresponding .mzML files, I get an IndexError: positional indexers are out-of-bounds.
failing_2results_2mzML.txt

I also tried reprocessing all my files in DIA-NN simultaneously to give one report, but this still gives an issue.

failing_1results_ManyMzML.txt

I have included all the .yaml files. When it fails, the error is always the same:

2025-03-19 17:08:48> Loaded 58252 PSMs for fragment extraction.
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 33/33 [20:11<00:00, 36.71s/it]
2025-03-19 17:29:00> Extracted 174756 PSMs.
2025-03-19 17:29:00> Traceback (most recent call last):
  File "peptdeep\pipeline_api.py", line 323, in transfer_learn
    psm_df, frag_mz_df, frag_df = match_psms()
  File "peptdeep\pipeline_api.py", line 230, in match_psms
    psm_df["median_pcc"] = get_median_pccs_for_dia_psms(
  File "peptdeep\pipeline_api.py", line 99, in get_median_pccs_for_dia_psms
    _df, metrics_df = calc_ms2_similarity(
  File "peptdeep\model\ms2.py", line 825, in calc_ms2_similarity
    get_sliced_fragment_dataframe(
  File "alphabase\peptide\fragment.py", line 331, in get_sliced_fragment_dataframe
    return fragment_df.iloc[frag_slices, charged_frag_idxes]
  File "pandas\core\indexing.py", line 1184, in __getitem__
  File "pandas\core\indexing.py", line 1690, in _getitem_tuple
  File "pandas\core\indexing.py", line 966, in _validate_tuple_indexer
  File "pandas\core\indexing.py", line 1612, in _validate_key
IndexError: positional indexers are out-of-bounds

positional indexers are out-of-bounds

Additionally, here are all of my version information:

2025-03-19 17:08:41> Platform information:
2025-03-19 17:08:41> system        - Windows
2025-03-19 17:08:41> release       - 10
2025-03-19 17:08:41> version       - 10.0.19045
2025-03-19 17:08:41> machine       - AMD64
2025-03-19 17:08:41> processor     - Intel64 Family 6 Model 63 Stepping 2, GenuineIntel
2025-03-19 17:08:41> cpu count     - 4
2025-03-19 17:08:41> ram           - 75.3/127.9 Gb (available/total)
2025-03-19 17:08:41>
2025-03-19 17:08:41> Python information:
2025-03-19 17:08:41> alphabase>       -
2025-03-19 17:08:41> alpharaw>        -
2025-03-19 17:08:41> biopython        -
2025-03-19 17:08:41> click            -
2025-03-19 17:08:41> lxml             -
2025-03-19 17:08:41> numba            -
2025-03-19 17:08:41> numpy<2          -
2025-03-19 17:08:41> pandas           -
2025-03-19 17:08:41> peptdeep         - 1.3.1
2025-03-19 17:08:41> psutil           - 6.1.0
2025-03-19 17:08:41> pydivsufsort     -
2025-03-19 17:08:41> pyteomics        -
2025-03-19 17:08:41> python           - 3.9.20
2025-03-19 17:08:41> scikit-learn     - 1.6.0
2025-03-19 17:08:41> streamlit-aggrid -
2025-03-19 17:08:41> streamlit>       -
2025-03-19 17:08:41> torch            - 2.5.1
2025-03-19 17:08:41> tqdm             - 4.67.1
2025-03-19 17:08:41> transformers     -
2025-03-19 17:08:41>

Do you have any suggestions or guidance on how to navigate around this? Thanks!