libutil Error - List index out of range #1459
Description
Module/Workflow/Library affected
Possibly part of the topoaa module, it's hard to tell.
Expected behavior
Run protein-protein docking
Actual behavior
Run crashed after ~10 seconds
Steps to reproduce the behavior
Haddock3 was freshly installed using pip into a conda virtual environment. No modifications were made.
Suggestions on how to fix it
Based on the error output, I changed line 111 in the file haddock/libs/libhpc.py from
self.job_id = int(p.stdout.decode("utf-8").split()[-1])
to
self.job_id = p.stdout.decode("utf-8")
which permitted the code to run.
Version
HADDOCK3 v2025.11.0
Additional context
Below is the output I received when I encountered the error.
##############################################
# #
# HADDOCK3 #
# #
##############################################
!! Some of the HADDOCK3 components use CNS (Crystallographic and NMR System) which is free of use for non-profit applications. !!
!! For commercial use it is your own responsibility to have a proper license. !!
!! For details refer to the DISCLAIMER file in the HADDOCK3 repository. !!
Starting HADDOCK3 v2025.11.0 on 2025-12-03 13:07:00
Python 3.11.14 (main, Oct 21 2025, 18:31:21) [GCC 11.2.0]
[2025-12-03 13:07:10,018 libworkflow INFO] Reading instructions step 0_topoaa
[2025-12-03 13:07:10,018 libworkflow INFO] Reading instructions step 1_rigidbody
[2025-12-03 13:07:10,019 libworkflow INFO] Reading instructions step 2_seletop
[2025-12-03 13:07:10,019 libworkflow INFO] Reading instructions step 3_flexref
[2025-12-03 13:07:10,019 libworkflow INFO] Reading instructions step 4_emref
[2025-12-03 13:07:10,019 libworkflow INFO] Reading instructions step 5_clustfcc
[2025-12-03 13:07:10,019 libworkflow INFO] Reading instructions step 6_seletopclusts
[2025-12-03 13:07:10,039 base_cns_module INFO] Running [topoaa] module
[2025-12-03 13:07:10,039 __init__ INFO] [topoaa] Molecule 1: VEGFR_A_conf_renum.pdb
[2025-12-03 13:07:10,050 __init__ INFO] [topoaa] Termini of molecule 1:
N-ter: uncharged C-ter: uncharged 5'phosphate: no
[2025-12-03 13:07:10,050 __init__ INFO] [topoaa] Sanitizing molecule VEGFR_A_conf_renum_1.pdb
[2025-12-03 13:07:10,065 __init__ INFO] [topoaa] Topology CNS input created
[2025-12-03 13:07:10,066 __init__ INFO] [topoaa] Sanitizing molecule VEGFR_A_conf_renum_2.pdb
[2025-12-03 13:07:10,081 __init__ INFO] [topoaa] Topology CNS input created
[2025-12-03 13:07:10,081 __init__ INFO] [topoaa] Molecule 2: Doppel_1lg4.pdb
[2025-12-03 13:07:10,082 __init__ INFO] [topoaa] Termini of molecule 2:
N-ter: uncharged C-ter: uncharged 5'phosphate: no
[2025-12-03 13:07:10,083 __init__ INFO] [topoaa] Sanitizing molecule Doppel_1lg4.pdb
[2025-12-03 13:07:10,088 __init__ INFO] [topoaa] Topology CNS input created
[2025-12-03 13:07:10,088 __init__ INFO] [topoaa] Running CNS Jobs n=3
[2025-12-03 13:07:10,088 libhpc INFO] > Running batch 1/1
[2025-12-03 13:07:10,113 libutil ERROR] list index out of range
Traceback (most recent call last):
File "/uufs/chpc.utah.edu/common/home/u0907234/.conda/envs/doppel/lib/python3.11/site-packages/haddock/libs/libutil.py", line 382, in log_error_and_exit
yield
File "/uufs/chpc.utah.edu/common/home/u0907234/.conda/envs/doppel/lib/python3.11/site-packages/haddock/clis/cli.py", line 193, in main
workflow.run()
File "/uufs/chpc.utah.edu/common/home/u0907234/.conda/envs/doppel/lib/python3.11/site-packages/haddock/libs/libworkflow.py", line 43, in run
step.execute()
File "/uufs/chpc.utah.edu/common/home/u0907234/.conda/envs/doppel/lib/python3.11/site-packages/haddock/libs/libworkflow.py", line 173, in execute
self.module.run() # type: ignore
^^^^^^^^^^^^^^^^^
File "/uufs/chpc.utah.edu/common/home/u0907234/.conda/envs/doppel/lib/python3.11/site-packages/haddock/modules/base_cns_module.py", line 61, in run
self._run()
File "/uufs/chpc.utah.edu/common/home/u0907234/.conda/envs/doppel/lib/python3.11/site-packages/haddock/modules/topology/topoaa/__init__.py", line 301, in _run
engine.run()
File "/uufs/chpc.utah.edu/common/home/u0907234/.conda/envs/doppel/lib/python3.11/site-packages/haddock/libs/libhpc.py", line 180, in run
worker.run()
File "/uufs/chpc.utah.edu/common/home/u0907234/.conda/envs/doppel/lib/python3.11/site-packages/haddock/libs/libhpc.py", line 111, in run
self.job_id = int(p.stdout.decode("utf-8").split()[-1])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^
IndexError: list index out of range
[2025-12-03 13:07:10,117 libutil ERROR] list index out of range
[2025-12-03 13:07:10,117 libutil ERROR] An error has occurred, see log file. And contact the developers if needed.
[2025-12-03 13:07:10,117 libutil INFO] Finished at 03/12/2025 13:07:10. For any help contact us at https://github.com/haddocking/haddock3/issues. Do pobachennya! Adiós! >再见!.