Member Site › Forums › PyRosetta › PyRosetta – Scripts › D100 Docking script error test.output
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Anonymous.
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April 26, 2019 at 3:29 pm #3128
Anonymous
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
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April 26, 2019 at 4:26 pm #14683
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
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April 26, 2019 at 4:47 pm #14684
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’
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April 26, 2019 at 8:25 pm #14687
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.
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April 26, 2019 at 8:39 pm #14688
thank you! will look into this.
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April 30, 2019 at 3:39 pm #14691
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.
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