Dear All,
I have already run successfully on my mac os x. I am trying to run the same job on Ubuntu linux machine. However, I receive the following error:
Starting HADDOCK on: 2021-02-01 02:14:42
HADDOCK version: 2.4 - January 2021 release
Python version: 2.7.18 (default, Aug 4 2020, 11:16:42)
[GCC 9.3.0]
parsing run.cns file
parsing run.param in /home/alireza_antiverse_io/haddock2.4-2021-01/project/run1/data
reading parameters from the file /home/alireza_antiverse_io/haddock2.4-2021-01/project/run1/data/run.param
setting some variables:
N_COMP set to: 2
RUN_NUMBER set to: 1
HADDOCK_DIR set to: /home/alireza_antiverse_io/haddock2.4-2021-01
UNAMBIG_TBL set to: antibody-antigen-unambig.tbl
PROT_SEGID_2 set to: B
PROT_SEGID_1 set to: A
PDB_FILE1 set to: 4g6k_clean.pdb
AMBIG_TBL set to: antibody-antigen-ambig.tbl
PROJECT_DIR set to: /home/alireza_antiverse_io/haddock2.4-2021-01/project
PDB_FILE2 set to: 4i1b.pdb
N_COMP 2
RUN_NUMBER 1
HADDOCK_DIR /home/alireza_antiverse_io/haddock2.4-2021-01
UNAMBIG_TBL antibody-antigen-unambig.tbl
PROT_SEGID_2 B
PROT_SEGID_1 A
PDB_FILE1 4g6k_clean.pdb
AMBIG_TBL antibody-antigen-ambig.tbl
PROJECT_DIR /home/alireza_antiverse_io/haddock2.4-2021-01/project
PDB_FILE2 4i1b.pdb
looking for existing files
waterdock false
waiting for the psf files…
looking for iteration 0
working on iteration 0
increased number of structures requested for it0
==> regenerating file.nam file.list and file.cns in begin directory
starting DOCKING protocol
FIX: Modifying random seed for it 0 structure 2
Waiting to restart job…
Structure 1: running
Structure 2: crashed
Structure 3: crashed
Structure 4: crashed
Structure 5: crashed
Structure 6: crashed
Structure 7: crashed
Structure 8: crashed
Structure 9: crashed
Structure 10: crashed
calculating structure 2
queue command:
/bin/csh project_run1_it0_refine_2.job
Structure 1: running
Structure 2: running
Structure 3: failed
Structure 4: failed
Structure 5: failed
Structure 6: failed
Structure 7: failed
Structure 8: failed
Structure 9: failed
Structure 10: failed
python: Command not found.
Structure 1: running
Structure 2: failed
Structure 3: failed
Structure 4: failed
Structure 5: failed
Structure 6: failed
Structure 7: failed
Structure 8: failed
Structure 9: failed
Structure 10: failed
Timeout - deleting: /home/alireza_antiverse_io/haddock2.4-2021-01/project/run1/project_run1_it0_refine_1.out
Time-out of structure 1
Restarting failed structures…
calculating structure 1
queue command:
/bin/csh project_run1_it0_refine_1.job
Structure 1: running
Structure 2: failed
Structure 3: failed
Structure 4: failed
Structure 5: failed
Structure 6: failed
Structure 7: failed
Structure 8: failed
Structure 9: failed
Structure 10: failed
python: Command not found.
HADDOCK cannot continue due to too many (>20%) failed structures in it0
The following structures could not be docked:
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
##############################################################################
Finishing HADDOCK on: 2021-02-01 02:20:12
Au revoir.
Tot ziens.
Bye bye.
For some reason, HADDOCK fails to run the jobs. I could not figure out what “Python: command not found” meant. I use python2.7. I also see the PDB files in it0 directory.
Could you advise me why I get this error?
Thank you,
Alireza