Hi: working with the D100_Docking.py script, have got past several errors but now stuck on this
root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213# ls
D100_Docking.py demo rosetta version.json
PyMOL-RosettaServer.py full81q1.clean.pdb self-test.py
PyMOL-RosettaServer.python3.py full81q1.pdb setup
apps pyrosetta test
root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213# python3 ./D100_Do
cking.py --pdb_filename 1TOH.pdb --jobs=1000 --job_output 1TOH_docking_output --translat
ion 3 --rotation 8
./D100_Docking.py:90: UserWarning: Import of 'rosetta' as a top-level module is deprecat
ed 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 0.630071 seconds.
core.import_pose.import_pose: [ ERROR ] File: 1TOH.pdb not found!
ERROR: Cannot open file "1TOH.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
7f492a798b73]
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x618295b) [0x
7f492c09895b]
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x4857c9e) [0x
7f492a76dc9e]
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x4856177) [0x
7f492a76c177]
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x48548aa) [0x
7f492a76a8aa]
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x8e59d44) [0x
7f492ed6fd44]
/opt/PyRosetta4.Release.python36.ubuntu.release-213/pyrosetta/rosetta.so(+0x65d62f1) [0x
7f492c4ec2f1]
python3() [0x5030d5]
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]
python3() [0x504c28]
python3() [0x502540]
python3() [0x502f3d]
python3(_PyEval_EvalFrameDefault+0x449) [0x506859]
python3() [0x504c28]
python3(PyEval_EvalCode+0x23) [0x506393]
python3() [0x634d52]
python3(PyRun_FileExFlags+0x9a) [0x634e0a]
python3(PyRun_SimpleFileExFlags+0x188) [0x6385c8]
python3(Py_Main+0x57a) [0x63915a]
python3(main+0xe0) [0x4a6f10]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f4942b23b97]
python3(_start+0x2a) [0x5afa0a]
Traceback (most recent call last):
File "./D100_Docking.py", line 361, in <module>
jobs, job_output)
File "./D100_Docking.py", line 127, in sample_docking
pose_from_file(pose, pdb_filename)
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 "1TOH.pdb"
root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213#
I have tried a variety of pdb files, and pdb files I ran a clean script on also. Thanks in advance for any input! - Amy
root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213# ls
1TOH.pdb apps pyrosetta test
D100_Docking.py demo rosetta version.json
PyMOL-RosettaServer.py full81q1.clean.pdb self-test.py
PyMOL-RosettaServer.python3.py full81q1.pdb setup
root@ebe6d1a96d89:/opt/PyRosetta4.Release.python36.ubuntu.release-213#
Could you provide another set of logs from the second time you run the command:
The error you originally had was that the file 1TOH.pdb wasn't in the directory that you were working in.
but then later you posted
where the file was there so I'm slightly confused :/
the file was there (should have been there anyway!) all along, ls showed it when I rechecked it ; I have tried this on a number of pdb files. thanks! - Amy
Actually... looking deeper...
Try supplying the full name of the pdb file in your commandline (make sure you use an O or a 0 (zero), correctly -- I can't tell what it is on this forums font)
ie
For some reason the script moves you to a new directory on the line
not really sure why. once you're in .test.output the script wont be able to 'see' your files. (they will now be '../1TOH.pdb'
you can also remove the os.chdir bit if you like and are feeling adventurous . (I'm not sure of the consequences of that)
you can also try 'ls -la' to see if the folder .test.output even exists.
I'm looking at https://graylab.jhu.edu/pyrosetta/downloads/scripts/demo/D100_Docking.py
Hopefully that matches the python script you are using.