OverflowError: value too large to convert to int

[xiekunwhy]

Hi,

I got following errors when using mikado. Do you know why and how to resolve?

2025-06-14 11:25:19,616 - prepare - prepare.py:204 - INFO - _analyse_chrom - MainProcess - Excluding strT_str.Chr01:1898329069-2372911336.2522.1 as redundant with gemT_gem.Chr01_1898329069_23729113361246.1
2025-06-14 11:25:19,616 - prepare - prepare.py:204 - INFO - _analyse_chrom - MainProcess - Excluding strT_str.Chr01:1898329069-2372911336.2522.2 as redundant with gemT_gem.Chr01_1898329069_23729113361246.2
2025-06-14 11:25:19,636 - prepare - prepare.py:686 - ERROR - prepare - MainProcess - value too large to convert to int
Traceback (most recent call last):
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/mikado/lib/python3.9/site-packages/Mikado/preparation/prepare.py", line 684, in prepare
    perform_check(divide_by_chrom(), shelve_names, mikado_config, logger)
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/mikado/lib/python3.9/site-packages/Mikado/preparation/prepare.py", line 293, in perform_check
    batches = list(enumerate(keys, 1))
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/mikado/lib/python3.9/site-packages/Mikado/preparation/prepare.py", line 681, in divide_by_chrom
    yield from _analyse_chrom(chrom, rows.loc[transcripts.groups[chrom], columns],
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/mikado/lib/python3.9/site-packages/Mikado/preparation/prepare.py", line 182, in _analyse_chrom
    data, caught = _retrieve_data(shelf, shelf_name, tid, chrom, (start, end), strand, score,
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/mikado/lib/python3.9/site-packages/Mikado/preparation/prepare.py", line 82, in _retrieve_data
    for i in chains[data["introns"]].find(data["start"], data["end"], contained_check=True,
  File "Mikado/utilities/intervaltree.pyx", line 234, in Mikado.utilities.intervaltree.IntervalTree.find
OverflowError: value too large to convert to int
2025-06-14 11:25:19,673 - prepare - prepare.py:689 - ERROR - prepare - MainProcess - Mikado has encountered an error, exiting
2025-06-14 11:25:19,693 - prepare - prepare.py:706 - ERROR - prepare - MainProcess - Mikado prepare has encountered a fatal error. Please check the logs and, if there is a bug,report it to https://github.com/EI-CoreBioinformatics/mikado/issues

prepare.log

Best,
Kun

[xiekunwhy]

Mikado/utilities/intervaltree.pyx can not deal with chromosome size >2.1G, many bioinformatic software have 2.1G limits.