Library translate tsv: IndexError: index 4 is out of bounds for axis 1 with size 4

[J-Burgess]

Hi, hope you are well!

Describe the bug I get an error that index is out of bounds when using the library command with mostly default settings apart from new Phospho modifications added. The spectral library generation works up to the HDF but on translating to TSV errors and hangs with no progress being made yet the process not being killed.

To Reproduce Steps to reproduce the behavior:

1. Install developer mode alphapeptdeep.
2. conda activate peptdeep
3. peptdeep export-settings /home/james.burgess/projects/JB240206_AlphaPeptDeep/AlphaPeptDeep/configs/default-settings.yaml
4. Make some changes to the default-settings.yaml to add Phospho modifications and adjust file paths. default-settings.txt
5. peptdeep library /home/james.burgess/projects/JB240206_AlphaPeptDeep/AlphaPeptDeep/configs/default-settings.yaml

Expected behavior A tsv spectral library should also be produced that can be used in DIA-NN or Spectronaut.

Logs Provided error message from terminal which was same as log file. See context below.

Version (please complete the following information):

• Installation Type: Developer 2024-02-06 15:59:24> [PeptDeep] Running library task ... 2024-02-06 15:59:24> Input files (fasta): ['/ibm/hpcfs1/tmp/JB230123_DATA/DATA/MaxDIA/fasta/JB230123_quantms_database.fasta']
  2024-02-06 15:59:24> Platform information: 2024-02-06 15:59:24> system - Linux 2024-02-06 15:59:24> release - 4.18.0-513.5.1.el8_9.x86_64 2024-02-06 15:59:24> version - #1 SMP Fri Nov 17 03:31:10 UTC 2023 2024-02-06 15:59:24> machine - x86_64 2024-02-06 15:59:24> processor - x86_64 2024-02-06 15:59:24> cpu count - 128 2024-02-06 15:59:24> ram - 325.7/503.0 Gb (available/total) 2024-02-06 15:59:24> 2024-02-06 15:59:24> Python information: 2024-02-06 15:59:24> alphabase - 1.2.1 2024-02-06 15:59:24> alphabase> - 2024-02-06 15:59:24> alpharaw - 0.4.2 2024-02-06 15:59:24> alpharaw> - 2024-02-06 15:59:24> biopython - 1.83 2024-02-06 15:59:24> click - 8.1.7 2024-02-06 15:59:24> lxml - 5.1.0 2024-02-06 15:59:24> numba - 0.59.0 2024-02-06 15:59:24> numpy - 1.26.3 2024-02-06 15:59:24> pandas - 2.2.0 2024-02-06 15:59:24> peptdeep - 1.1.5 2024-02-06 15:59:24> psutil - 5.9.8 2024-02-06 15:59:24> pyteomics - 4.6.3 2024-02-06 15:59:24> python - 3.9.18 2024-02-06 15:59:24> scikit-learn - 1.4.0 2024-02-06 15:59:24> streamlit - 1.30.0 2024-02-06 15:59:24> streamlit-aggrid - 0.3.4.post3 2024-02-06 15:59:24> streamlit> - 2024-02-06 15:59:24> torch - 2.2.0 2024-02-06 15:59:24> tqdm - 4.66.1 2024-02-06 15:59:24> transformers - 4.37.2

Additional context error_message.txt

[jalew188]

Thank you for your report, i will investigate this soon.