Error log |
One of Aggrescan3D modules (CABS) encountered an error.
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[INFO] Logger: Verbosity set to: 4 - [DEBUG] (00:14:47)
[WARNING] JOB: /STORAGE/DATA/lcbio/aggreskan/adaba832e54dd5b/CABS_sim already exists.
Output data will be overwritten. (00:14:47)
[DEBUG] Protein: Preparing the complex (00:14:47)
[DEBUG] PDB: Creating Pdb object from input.pdb (00:14:47)
[DEBUG] PDB: Processing input.pdb (00:14:47)
[DEBUG] PDB: Removing alternative locations from input.pdb (00:14:47)
[DEBUG] PDB: Removing water molecules from input.pdb (00:14:47)
[DEBUG] PDB: Scanning input.pdb for non-standard amino acids (00:14:47)
[DEBUG] PDB: Removing heteroatoms from input.pdb (00:14:48)
[DEBUG] PDB: Selecting [name CA] from input.pdb (00:14:48)
[INFO] Protein: Loading input.pdb as input protein (00:14:48)
[DEBUG] PDB: Running DSSP (00:14:48)
[DEBUG] PDB: DSSP successful (00:14:48)
[OUT FILES] Logger: Saving DSSP output to /STORAGE/DATA/lcbio/aggreskan/adaba832e54dd5b/CABS_si
m/output_data/DSSP_output_input.txt (00:14:48)
[WARNING] Protein: Could not read weights file: gauss (00:14:49)
[WARNING] Protein: Using default weights(1.0) for all atoms. (00:14:49)
[DEBUG] Protein: Complex successfully created (00:14:49)
[INFO] CABS: Setting up CABS simulation. (00:14:49)
[DEBUG] CABS: Loading structures... (00:14:49)
[DEBUG] CABS: Loading restraints... (00:14:52)
[DEBUG] CABS: Building exe... (00:14:52)
[WARNING] CABS: Program received signal SIGSEGV: Segmentation fault - invalid memory
reference. Backtrace for this error: #0 0x2B02E853F6F7 #1 0x2B02E853FD3E
#2 0x2B02E8FD22EF #3 0x40A266 in MAIN__ at -:? (00:14:55)
[DEBUG] JOB: Loading trajectories from the CABS run (00:14:55)
[CRITICAL] CABSflex: 'NoneType' object has no attribute 'replica' 'NoneType' object has no
attribute 'replica': 'NoneType' object has no attribute 'replica' (00:14:55)
Traceback (most recent call last):
File "/home/users/lcbio/anaconda2/envs/exec/lib/python2.7/site-packages/CABS/__main__.py", line 55, in run
job.run()
File "/home/users/lcbio/anaconda2/envs/exec/lib/python2.7/site-packages/CABS/job.py", line 180, in run
self.load_output(file_traf, file_seq)
File "/home/users/lcbio/anaconda2/envs/exec/lib/python2.7/site-packages/CABS/job.py", line 726, in load_output
ret = super(FlexTask, self).load_output(*args, **kwargs)
File "/home/users/lcbio/anaconda2/envs/exec/lib/python2.7/site-packages/CABS/job.py", line 406, in load_output
self.trajectory = self.cabsrun.get_trajectory()
File "/home/users/lcbio/anaconda2/envs/exec/lib/python2.7/site-packages/CABS/cabs.py", line 302, in get_trajectory
return Trajectory.read_trajectory(traf, seq)
File "/home/users/lcbio/anaconda2/envs/exec/lib/python2.7/site-packages/CABS/trajectory.py", line 158, in read_trajectory
headers, coordinates = Trajectory.read_traf(traf)
File "/home/users/lcbio/anaconda2/envs/exec/lib/python2.7/site-packages/CABS/trajectory.py", line 147, in read_traf
save_coord(current_coord, current_header.replica)
AttributeError: 'NoneType' object has no attribute 'replica'
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