You are here

D100 Docking script error test.output

6 posts / 0 new
Last post
D100 Docking script error test.output
#1

Hi:  I have researched this error I am getting, but don't see any reference to it.   Thanks in advance for any help.

When I run

 

python D100_Docking.py --pdb_filename /81q1D100_Dock/ferudock81q1cds.clean.pdb --jobs 400 --job_output 81q1_docking_output --translation 3 --rotation 8 --PyMOLMover_ip off
 

I can't get past this error with the constant seed:

In [1]: import optparse

In [2]: from pyrosetta import *

In [3]: from rosetta import *
/usr/bin/ipython3:1: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.
  #! /bin/sh

 

In [5]: from rosetta.protocols.rigid import *

In [6]: init(extra_options = "-constant_seed")
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: PyRosetta4.Release.python36.ubuntu r213 2019.10+release.fd1bdffb01b fd1bdffb01b7866da84942b9bf1b06e96270656e http://www.pyrosetta.org 2019-03-05T15:28:05
core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/database
core.init: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111
core.init.random: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937

In [7]: import os; os.chdir('.test.output')
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-7-b5b59622dcff> in <module>()
----> 1 import os; os.chdir('.test.output')

FileNotFoundError: [Errno 2] No such file or directory: '.test.output'

 

thank you much for all your kind assistance, I have been making progress!  - Amy

 

 

Category: 
Post Situation: 
Fri, 2019-04-26 08:29
Amy F

ok in the script I commented out   #import os; os.chdir('.test.output')#   and I got further, but new errors

RuntimeError                              Traceback (most recent call last)
/opt/PyRosetta4.Release.python36.ubuntu.release-213/D100_Docking.py in <module>()
   359  
   360 sample_docking(pdb_filename, partners, translation, rotation,
--> 361     jobs, job_output)
   362                                                                                                                     
   363 ################################################################################

/opt/PyRosetta4.Release.python36.ubuntu.release-213/D100_Docking.py in sample_docking(pdb_filename, partners, translation,
rotation, jobs, job_output)                                                                                                 
   125     # 1. creates a pose from the desired PDB file
   126     pose = Pose()
--> 127     pose_from_file(pose, pdb_filename)
   128  
   129     # 2. setup the docking FoldTree

RuntimeError:  

File: /scratch/benchmark/W.glass/rosetta.Glass/_commits_/main/source/src/core/import_pose/import_pose.cc:350
[ ERROR ] UtilityExitException
ERROR: Cannot open file "/81q1D100_Dock/ferudock81q1cds.clean.pdb"

so something is bad in my pdb?  I ran the rosetta clean script on it prior to D100 ie

 

./score_jd2.opencl.linuxgccrelease -ignore_unrecognized_res -ignore_zero_occupancy false -out:pdb -s ferudock81q1cds.pdb
 

 

thanks!  Amy

 

Fri, 2019-04-26 09:26
Amy F

got a bit further, now new error is

 

AttributeError                            Traceback (most recent call last)
/opt/PyRosetta4.Release.python36.ubuntu.release-213/D100_Docking.py in <module>()
   359  
   360 sample_docking(pdb_filename, partners, translation, rotation,
--> 361     jobs, job_output)
   362                                                                                                                     
   363 ################################################################################

/opt/PyRosetta4.Release.python36.ubuntu.release-213/D100_Docking.py in sample_docking(pdb_filename, partners, translation,
rotation, jobs, job_output)                                                                                                 
   144     #    docking...but Rosetta doesn't currently)
   145     # the FoldTrees setup by this method are for TWO BODY docking ONLY!
--> 146     protocols.docking.setup_foldtree(pose, partners, Vector1([dock_jump]))
   147  
   148     # 3. create centroid <--> fullatom conversion Movers

AttributeError: module 'pyrosetta.protocols' has no attribute 'docking'

 

Fri, 2019-04-26 09:47
Amy F

Amy, from your early logs it looks like you trying to run this from iPython, is this correct? If so, then my guess that some of early imports might have failed and Python was not restarted after that. So i would recommend to try to re-run this from command line instead.

Also, if all you want is to run docking protocol then using Rosetta docking applicatio itself will probably be a better choice.

Fri, 2019-04-26 13:25
Sergey

thank you!  will look into this. ;-)

Fri, 2019-04-26 13:39
Amy F

still getting the same error, outside of the ipython env


root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213# python3 D100_Dock
ing.py --pdb_filename full81q1.clean.pdb  --jobs 700 --job_output full81q1__docking_outp
ut --translation 3 --rotation 8
D100_Docking.py:90: UserWarning: Import of 'rosetta' as a top-level module is deprecated
and may be removed in 2018, import via 'pyrosetta.rosetta'.
 from rosetta import *
core.init: Checking for fconfig files in pwd and ./rosetta/flags  
core.init: Rosetta version: PyRosetta4.Release.python36.ubuntu r213 2019.10+release.fd1b
dffb01b fd1bdffb01b7866da84942b9bf1b06e96270656e http://www.pyrosetta.org 2019-03-05T15:
28:05
core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /opt/PyRosetta4.Rele
ase.python36.ubuntu.release-213/pyrosetta/database
core.init: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111
core.init.random: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.
Created 696 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.628563 seconds.
core.import_pose.import_pose: File 'full81q1.clean.pdb' automatically determined to be o
f type PDB
Traceback (most recent call last):
 File "D100_Docking.py", line 361, in <module>
   jobs, job_output)
 File "D100_Docking.py", line 146, in sample_docking
   protocols.docking.setup_foldtree(pose, partners, Vector1([dock_jump]))
AttributeError: module 'pyrosetta.protocols' has no attribute 'docking'
root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213#

 

seem to have fewer problems loading the script in ipython3

 

root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213# ipython3
Python 3.6.7 (default, Oct 22 2018, 11:32:17)  
Type "copyright", "credits" or "license" for more information.

IPython 5.5.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: run D100_Docking.py
/opt/PyRosetta4.Release.python36.ubuntu.release-213/D100_Docking.py:90: UserWarning: Imp
ort of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import
via 'pyrosetta.rosetta'.
 from rosetta import *
core.init: Checking for fconfig files in pwd and ./rosetta/flags  
core.init: Rosetta version: PyRosetta4.Release.python36.ubuntu r213 2019.10+release.fd1b
dffb01b fd1bdffb01b7866da84942b9bf1b06e96270656e http://www.pyrosetta.org 2019-03-05T15:
28:05
core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /opt/PyRosetta4.Rele
ase.python36.ubuntu.release-213/pyrosetta/database
core.init: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111
core.init.random: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
/opt/PyRosetta4.Release.python36.ubuntu.release-213/D100_Docking.py in <module>()
   105 # WARNING: option '-constant_seed' is for testing only! MAKE SURE TO REMOVE IT I
N PRODUCTION RUNS!!!!!                                                                   
   106  
--> 107 import os; os.chdir('.test.output')
   108  
   109  

FileNotFoundError: [Errno 2] No such file or directory: '.test.output'

 

changed 107 to test/output  and now new interesting errors

 

RuntimeError                              Traceback (most recent call last)
/opt/PyRosetta4.Release.python36.ubuntu.release-213/D100_Docking.py in <module>()
   359  
   360 sample_docking(pdb_filename, partners, translation, rotation,
--> 361     jobs, job_output)
   362                                                                                  
   363 ################################################################################

/opt/PyRosetta4.Release.python36.ubuntu.release-213/D100_Docking.py in sample_docking(pd
b_filename, partners, translation, rotation, jobs, job_output)                           
   125     # 1. creates a pose from the desired PDB file
   126     pose = Pose()
--> 127     pose_from_file(pose, pdb_filename)
   128  
   129     # 2. setup the docking FoldTree

RuntimeError:  

File: /scratch/benchmark/W.glass/rosetta.Glass/_commits_/main/source/src/core/import_pos
e/import_pose.cc:350
[ ERROR ] UtilityExitException
ERROR: Cannot open file "../test/data/test_dock.pdb"

 

NOW I have got this - the script won't read my clean pdb or my original pdb

File: /scratch/benchmark/W.glass/rosetta.Glass/_commits_/main/source/src/core/import_pos
e/import_pose.cc:350
[ ERROR ] UtilityExitException
ERROR: Cannot open file "full81q1.pdb"

 

RuntimeError                              Traceback (most recent call last)
/opt/PyRosetta4.Release.python36.ubuntu.release-213/D100_Docking.py in <module>()
   359  
   360 sample_docking(pdb_filename, partners, translation, rotation,
--> 361     jobs, job_output)
   362                                                                                  
   363 ################################################################################

/opt/PyRosetta4.Release.python36.ubuntu.release-213/D100_Docking.py in sample_docking(pd
b_filename, partners, translation, rotation, jobs, job_output)                           
   125     # 1. creates a pose from the desired PDB file
   126     pose = Pose()
--> 127     pose_from_file(pose, pdb_filename)
   128  
   129     # 2. setup the docking FoldTree

RuntimeError:  

File: /scratch/benchmark/W.glass/rosetta.Glass/_commits_/main/source/src/core/import_pos
e/import_pose.cc:350
[ ERROR ] UtilityExitException
ERROR: Cannot open file "full81q1.pdb"

 

Further...

 

In [1]: run D100_Docking.py --pdb_filename full81q1.clean.pdb --jobs=1000 --job_output 8
  ...: 1q1_docking_output --translation 3 --rotation 8
/opt/PyRosetta4.Release.python36.ubuntu.release-213/D100_Docking.py:90: UserWarning: Imp
ort of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import
via 'pyrosetta.rosetta'.
 from rosetta import *
core.init: Checking for fconfig files in pwd and ./rosetta/flags  
core.init: Rosetta version: PyRosetta4.Release.python36.ubuntu r213 2019.10+release.fd1b
dffb01b fd1bdffb01b7866da84942b9bf1b06e96270656e http://www.pyrosetta.org 2019-03-05T15:
28:05
core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /opt/PyRosetta4.Rele
ase.python36.ubuntu.release-213/pyrosetta/database
core.init: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111
core.init.random: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.
Created 696 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.633868 seconds.
core.import_pose.import_pose: [ ERROR ] File: full81q1.clean.pdb not found!

ERROR: Cannot open file "full81q1.clean.pdb"                                             
ERROR:: Exit from: /scratch/benchmark/W.glass/rosetta.Glass/_commits_/main/source/src/co
re/import_pose/import_pose.cc line: 350                                                  
BACKTRACE:                                                                               
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x4882b73) [0x
7f0c9cbf2b73]                                                                            
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x618295b) [0x
7f0c9e4f295b]                                                                            
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x4857c9e) [0x
7f0c9cbc7c9e]                                                                            
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x4856177) [0x
7f0c9cbc6177]                                                                            
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x48548aa) [0x
7f0c9cbc48aa]                                                                            
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x8e59d44) [0x
7f0ca11c9d44]                                                                            
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x65d62f1) [0x
7f0c9e9462f1]                                                                            
python3() [0x5030d5]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3() [0x502540]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3() [0x511d78]                                                                     
python3() [0x502d6f]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3() [0x502540]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3() [0x502540]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x1231) [0x507641]                                      
python3() [0x504c28]                                                                     
python3() [0x502540]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3() [0x58650d]                                                                     
python3(PyObject_Call+0x3e) [0x59ebbe]                                                   
python3(_PyEval_EvalFrameDefault+0x1807) [0x507c17]                                      
python3() [0x504c28]                                                                     
python3() [0x502540]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3(_PyFunction_FastCallDict+0x2de) [0x501b2e]                                       
python3() [0x591461]                                                                     
python3(PyObject_Call+0x3e) [0x59ebbe]                                                   
python3(_PyEval_EvalFrameDefault+0x1807) [0x507c17]                                      
python3() [0x502209]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x502209]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3() [0x511eca]                                                                     
python3() [0x502d6f]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3() [0x502540]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3() [0x502540]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x1231) [0x507641]                                      
python3() [0x504c28]                                                                     
python3() [0x502540]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x1231) [0x507641]                                      
python3() [0x504c28]                                                                     
python3() [0x502540]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3() [0x502540]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x502209]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3() [0x502540]                                                                     
python3() [0x502f3d]                                                                     
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]                                       
python3() [0x504c28]                                                                     
python3(PyRun_StringFlags+0xaf) [0x634f9f]                                               
python3(PyRun_SimpleStringFlags+0x3d) [0x63840d]                                         
python3(Py_Main+0x33c) [0x638f1c]                                                        
python3(main+0xe0) [0x4a6f10]                                                            
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f0cc7c2cb97]                 
python3(_start+0x2a) [0x5afa0a]                                                          
---------------------------------------------------------------------------              
RuntimeError                              Traceback (most recent call last)
/opt/PyRosetta4.Release.python36.ubuntu.release-213/D100_Docking.py in <module>()
   359  
   360 sample_docking(pdb_filename, partners, translation, rotation,
--> 361     jobs, job_output)
   362                                                                                  
   363 ################################################################################

/opt/PyRosetta4.Release.python36.ubuntu.release-213/D100_Docking.py in sample_docking(pd
b_filename, partners, translation, rotation, jobs, job_output)                           
   125     # 1. creates a pose from the desired PDB file
   126     pose = Pose()
--> 127     pose_from_file(pose, pdb_filename)
   128  
   129     # 2. setup the docking FoldTree

RuntimeError:  

File: /scratch/benchmark/W.glass/rosetta.Glass/_commits_/main/source/src/core/import_pos
e/import_pose.cc:350
[ ERROR ] UtilityExitException
ERROR: Cannot open file "full81q1.clean.pdb"



In [2]: run D100_Docking.py --pdb_filename full81q1.clean.pdb --jobs=1000 --job_output 8
  ...: 1q1_docking_output --translation 3 --rotation 8
ERROR:root:File `'D100_Docking.py'` not found.

 







 

Tue, 2019-04-30 08:39
Amy F