amjjbonvin
commented
1 day ago You should change the running mode. It looks like the sbatch command (part of slurm) is not found.
Open bestz123 opened 1 day ago
amjjbonvin
commented
1 day ago You should change the running mode. It looks like the sbatch command (part of slurm) is not found.
Question
When I run this script haddock3 docking-protein-peptide-full.cfg, the code has the following error
Code snippet
[2024-12-01 18:57:46,976 cli INFO] ##############################################
HADDOCK3
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!! 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 v2024.10.0b7 on 2024-12-01 18:57:00
Python 3.11.10 | packaged by conda-forge | (main, Oct 16 2024, 01:27:36) [GCC 13.3.0]
[2024-12-01 18:57:51,095 libworkflow INFO] Reading instructions step 0_topoaa [2024-12-01 18:57:51,096 libworkflow INFO] Reading instructions step 1_rigidbody [2024-12-01 18:57:51,096 libworkflow INFO] Reading instructions step 2_caprieval [2024-12-01 18:57:51,096 libworkflow INFO] Reading instructions step 3_seletop [2024-12-01 18:57:51,096 libworkflow INFO] Reading instructions step 4_flexref [2024-12-01 18:57:51,096 libworkflow INFO] Reading instructions step 5_caprieval [2024-12-01 18:57:51,096 libworkflow INFO] Reading instructions step 6_emref [2024-12-01 18:57:51,096 libworkflow INFO] Reading instructions step 7_caprieval [2024-12-01 18:57:51,096 libworkflow INFO] Reading instructions step 8_clustfcc [2024-12-01 18:57:51,097 libworkflow INFO] Reading instructions step 9_seletopclusts [2024-12-01 18:57:51,097 libworkflow INFO] Reading instructions step 10_caprieval [2024-12-01 18:57:51,097 libworkflow INFO] Reading instructions step 11_caprieval [2024-12-01 18:57:51,111 base_cns_module INFO] Running [topoaa] module [2024-12-01 18:57:51,111 init INFO] [topoaa] Molecule 1: 1NX1_protein.pdb [2024-12-01 18:57:51,112 init INFO] [topoaa] Sanitizing molecule 1NX1_protein.pdb [2024-12-01 18:57:51,117 init INFO] [topoaa] Topology CNS input created [2024-12-01 18:57:51,117 init INFO] [topoaa] Molecule 2: DAIDALSSDFT_3conformations.pdb [2024-12-01 18:57:51,117 init INFO] [topoaa] Sanitizing molecule DAIDALSSDFT_3conformations_1.pdb [2024-12-01 18:57:51,118 init INFO] [topoaa] Topology CNS input created [2024-12-01 18:57:51,118 init INFO] [topoaa] Sanitizing molecule DAIDALSSDFT_3conformations_2.pdb [2024-12-01 18:57:51,119 init INFO] [topoaa] Topology CNS input created [2024-12-01 18:57:51,119 init INFO] [topoaa] Sanitizing molecule DAIDALSSDFT_3conformations_3.pdb [2024-12-01 18:57:51,120 init INFO] [topoaa] Topology CNS input created [2024-12-01 18:57:51,120 init INFO] [topoaa] Running CNS Jobs n=4 [2024-12-01 18:57:51,120 libhpc INFO] Concatenating, each .job will produce 5 (or less) models [2024-12-01 18:57:51,120 libhpc INFO] > Running batch 1/1 [2024-12-01 18:57:51,122 libutil ERROR] [Errno 2] No such file or directory: 'sbatch' Traceback (most recent call last): File "/mnt/zyz/work/github/hdock3/src/haddock/libs/libutil.py", line 335, in log_error_and_exit yield File "/mnt/zyz/work/github/hdock3/src/haddock/clis/cli.py", line 195, in main workflow.run() File "/mnt/zyz/work/github/hdock3/src/haddock/libs/libworkflow.py", line 43, in run step.execute() File "/mnt/zyz/work/github/hdock3/src/haddock/libs/libworkflow.py", line 162, in execute self.module.run() # type: ignore ^^^^^^^^^^^^^^^^^ File "/mnt/zyz/work/github/hdock3/src/haddock/modules/base_cns_module.py", line 61, in run self._run() File "/mnt/zyz/work/github/hdock3/src/haddock/modules/topology/topoaa/init.py", line 279, in _run engine.run() File "/mnt/zyz/work/github/hdock3/src/haddock/libs/libhpc.py", line 180, in run worker.run() File "/mnt/zyz/work/github/hdock3/src/haddock/libs/libhpc.py", line 110, in run p = subprocess.run(shlex.split(cmd), capture_output=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/mnt/zyz/anaconda3/envs/haddock/lib/python3.11/subprocess.py", line 548, in run with Popen(*popenargs, **kwargs) as process: ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/mnt/zyz/anaconda3/envs/haddock/lib/python3.11/subprocess.py", line 1026, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/mnt/zyz/anaconda3/envs/haddock/lib/python3.11/subprocess.py", line 1955, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'sbatch' [2024-12-01 18:57:51,123 libutil ERROR] [Errno 2] No such file or directory: 'sbatch' [2024-12-01 18:57:51,123 libutil ERROR] An error has occurred, see log file. And contact the developers if needed. [2024-12-01 18:57:51,123 libutil INFO] Finished at 01/12/2024 18:57:51. For any help contact us at https://github.com/haddocking/haddock3/issues. Adiós! Agur! Tot ziens!.