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Opened 19 months ago
Last modified 19 months ago
#14928 assigned defect
Problem handling SEQCROW job error(?)
| Reported by: | Owned by: | Tony Schaefer | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\Users\TillStensitzki\Downloads\orca_files\2-N3-a-Glc\2-N3-a-Glc.xyz
> format xyz
Install the SEQCROW bundle to open "XYZ file" format files.
Opener for format 'XYZ file' is not installed; see log for more info
> toolshed show
Downloading bundle MolecularDynamicsViewer-1.4-py3-none-any.whl
Installed MolecularDynamicsViewer (1.4)
Downloading bundle SEQCROW-1.8.7-py3-none-any.whl
[Repeated 1 time(s)]Installed SEQCROW (1.8.7)
> open C:\Users\TillStensitzki\Downloads\orca_files\2-N3-a-Glc\2-N3-a-Glc-
> scan_trj.xyz format xyz
opened 2-N3-a-Glc-scan_trj.xyz as an XYZ coordinate file movie
> close session
> open C:\Users\TillStensitzki\Downloads\orca_files\2-N3-a-Glc\2-N3-a-Glc-
> scan.allxyz format allxyz
opened 2-N3-a-Glc-scan.allxyz as an XYZ coordinate file
> ui tool show "AaronTools Fragment Library"
> ui mousemode right "bond rotation"
> torsion /a:1@N2,N1,C2,C1 -81.50
[Repeated 1 time(s)]
> torsion /a:1@N3,N2,N1,C2 -178.45
> torsion /a:1@N2,N1,C2,C1 85.70
> ui tool show "Job Queue"
paused SEQCROW queue
> open "C:/Users/TillStensitzki/SEQCROW_SCRATCH/gd Thu Oct 26 11.32.23
> 2023/seqcrow_log.txt"
Unrecognized file suffix '.txt'
> ui tool show "IR Spectrum"
> ui tool show "Build QM Input"
invalid job name: ''
must be alphanumeric
resumed SEQCROW queue
job started: local xTB job "opt"
job finished: local xTB job "opt"
> open "C:\Users\TillStensitzki\SEQCROW_SCRATCH\opt Mon Apr 8 11.37.21
> 2024\opt.xyz" format xyz
opened opt.xyz as an XYZ coordinate file
> open "C:\Users\TillStensitzki\SEQCROW_SCRATCH\opt Mon Apr 8 11.37.21
> 2024\xtbopt.xyz" format xyz
opened xtbopt.xyz as an XYZ coordinate file
> open "C:\Users\TillStensitzki\SEQCROW_SCRATCH\opt Mon Apr 8 11.37.21
> 2024\xtbtopo.mol" format sdf
Traceback (most recent call last):
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\tools\job_manager_tool.py", line 216, in <lambda>
error.clicked.connect(lambda *args, job=job: self.show_error(job))
^^^^^^^^^^^^^^^^^^^^
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\tools\job_manager_tool.py", line 292, in show_error
errors, error_msgs, filereaders = job.get_errors()
^^^^^^^^^^^^^^^^
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\jobs.py", line 276, in get_errors
fr = FileReader(file, just_geom=False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 1510, in __init__
self.read_file(
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 1629, in read_file
if os.path.isfile(self.name):
^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen genericpath>", line 30, in isfile
TypeError: stat: path should be string, bytes, os.PathLike or integer, not
list
TypeError: stat: path should be string, bytes, os.PathLike or integer, not
list
File "", line 30, in isfile
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\tools\job_manager_tool.py", line 216, in <lambda>
error.clicked.connect(lambda *args, job=job: self.show_error(job))
^^^^^^^^^^^^^^^^^^^^
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\tools\job_manager_tool.py", line 292, in show_error
errors, error_msgs, filereaders = job.get_errors()
^^^^^^^^^^^^^^^^
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\jobs.py", line 276, in get_errors
fr = FileReader(file, just_geom=False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 1510, in __init__
self.read_file(
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 1629, in read_file
if os.path.isfile(self.name):
^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen genericpath>", line 30, in isfile
TypeError: stat: path should be string, bytes, os.PathLike or integer, not
list
TypeError: stat: path should be string, bytes, os.PathLike or integer, not
list
File "", line 30, in isfile
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\tools\job_manager_tool.py", line 216, in <lambda>
error.clicked.connect(lambda *args, job=job: self.show_error(job))
^^^^^^^^^^^^^^^^^^^^
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\tools\job_manager_tool.py", line 292, in show_error
errors, error_msgs, filereaders = job.get_errors()
^^^^^^^^^^^^^^^^
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\jobs.py", line 276, in get_errors
fr = FileReader(file, just_geom=False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 1510, in __init__
self.read_file(
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 1629, in read_file
if os.path.isfile(self.name):
^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen genericpath>", line 30, in isfile
TypeError: stat: path should be string, bytes, os.PathLike or integer, not
list
TypeError: stat: path should be string, bytes, os.PathLike or integer, not
list
File "", line 30, in isfile
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\tools\job_manager_tool.py", line 216, in <lambda>
error.clicked.connect(lambda *args, job=job: self.show_error(job))
^^^^^^^^^^^^^^^^^^^^
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\tools\job_manager_tool.py", line 292, in show_error
errors, error_msgs, filereaders = job.get_errors()
^^^^^^^^^^^^^^^^
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\SEQCROW\jobs.py", line 276, in get_errors
fr = FileReader(file, just_geom=False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 1510, in __init__
self.read_file(
File "C:\Users\TillStensitzki\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\AaronTools\fileIO.py", line 1629, in read_file
if os.path.isfile(self.name):
^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen genericpath>", line 30, in isfile
TypeError: stat: path should be string, bytes, os.PathLike or integer, not
list
TypeError: stat: path should be string, bytes, os.PathLike or integer, not
list
File "", line 30, in isfile
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 30.0.101.1692
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Python: 3.11.2
Locale: en_DE.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex 5090
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 16,898,920,448
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i5-10505 CPU @ 3.20GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
comtypes: 1.1.14
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.4
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pywin32: 305
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
Send2Trash: 1.8.3
SEQCROW: 1.8.7
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
WMI: 1.5.1
Change History (2)
comment:1 by , 19 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem handling SEQCROW job error(?) |
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