SEQCROW: self.start_time is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.8.0-45-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed 'SEQCROW==1.8.12'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Collecting SEQCROW==1.8.12  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/seqcrow/releases/1.8.12/SEQCROW-1.8.12-py3-none-
any.whl (3.3 MB)  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 2.2 MB/s eta 0:00:00  
Requirement already satisfied: ChimeraX-Core<=1.9,>=1.3 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from SEQCROW==1.8.12) (1.6.1)  
Requirement already satisfied: jinja2 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from SEQCROW==1.8.12) (3.1.2)  
Requirement already satisfied: scipy in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from SEQCROW==1.8.12) (1.9.3)  
Requirement already satisfied: psutil in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from SEQCROW==1.8.12) (5.9.4)  
Requirement already satisfied: Send2Trash in ./.local/share/ChimeraX/1.6/site-
packages (from SEQCROW==1.8.12) (1.8.2)  
Requirement already satisfied: MarkupSafe>=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from jinja2->SEQCROW==1.8.12) (2.1.2)  
Requirement already satisfied: numpy<1.26.0,>=1.18.5 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from scipy->SEQCROW==1.8.12) (1.23.5)  
Installing collected packages: SEQCROW  
Attempting uninstall: SEQCROW  
Found existing installation: SEQCROW 1.7.3  
Uninstalling SEQCROW-1.7.3:  
Successfully uninstalled SEQCROW-1.7.3  
Successfully installed SEQCROW-1.8.12  
  

  
[notice] A new release of pip is available: 23.0 -> 24.2  
[notice] To update, run: chimerax -m pip install --upgrade pip  
  

> open /home/mateus/Documents/GitHub/bolsa_astroesul/ORCA/TD-
> DFT/inputs_outputs/C6H6/16T_10P/C6H6.cis

Unrecognized file suffix '.cis'  

> open /home/mateus/Documents/GitHub/bolsa_astroesul/ORCA/TD-
> DFT/inputs_outputs/C6H6/16T_10P/C6H6.out

Summary of feedback from opening
/home/mateus/Documents/GitHub/bolsa_astroesul/ORCA/TD-
DFT/inputs_outputs/C6H6/16T_10P/C6H6.out  
---  
note | C6H6.out has 0 imaginary harmonic vibrational modes  
  
Opened C6H6.out as an ORCA output file  

> ui tool show "IR Spectrum"

anharmonic frequencies requested on the 'plot settings' tab, but anharmonic
data was not parsed from C6H6.out  

> ui tool show Thermochemistry

> ui tool show "Orbital Viewer"

Opened MO alpha 21 as #1.1, grid size 55,54,31, pixel 0.201,0.202,0.2, shown
at level -0.026,0.026, step 1, values float64  

> hide #1.1

Opened MO alpha 20 as #1.2, grid size 55,54,31, pixel 0.201,0.202,0.2, shown
at level -0.026,0.026, step 1, values float64  

> hide #1.2

Opened MO alpha 16 as #1.3, grid size 55,54,31, pixel 0.201,0.202,0.2, shown
at level -0.026,0.026, step 1, values float64  

> ui tool show "Transition State Structures"

settings migrated from version 2  

synchornous transit-guided quasi-Newton is not available for ORCA; change
algorithms before applying this preset  

invalid job name: ''  
must be alphanumeric  
job started: local ORCA QST job "seila"  
Traceback (most recent call last):  
File "/home/mateus/.local/share/ChimeraX/1.6/site-packages/SEQCROW/jobs.py",
line 1449, in run  
"%s %s" % (self.name, self.start_time.replace(':', '.')), \  
AttributeError: 'NoneType' object has no attribute 'replace'  
  
AttributeError: 'NoneType' object has no attribute 'replace'  
  
File "/home/mateus/.local/share/ChimeraX/1.6/site-packages/SEQCROW/jobs.py",
line 1449, in run  
"%s %s" % (self.name, self.start_time.replace(':', '.')), \  
  
See log for complete Python traceback.  
  
job finished: local ORCA QST job "seila"  
job started: local ORCA QST job "seila"  
Traceback (most recent call last):  
File "/home/mateus/.local/share/ChimeraX/1.6/site-packages/SEQCROW/jobs.py",
line 1449, in run  
"%s %s" % (self.name, self.start_time.replace(':', '.')), \  
AttributeError: 'NoneType' object has no attribute 'replace'  
  
AttributeError: 'NoneType' object has no attribute 'replace'  
  
File "/home/mateus/.local/share/ChimeraX/1.6/site-packages/SEQCROW/jobs.py",
line 1449, in run  
"%s %s" % (self.name, self.start_time.replace(':', '.')), \  
  
See log for complete Python traceback.  
  
job finished: local ORCA QST job "seila"  




OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CML GT2)
OpenGL vendor: Intel

Python: 3.9.11
Locale: pt_BR.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu-xorg
XDG_SESSION_DESKTOP=ubuntu-xorg
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:0
Manufacturer: PCWARE
Model: IPMH510G
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i3-10100 CPU @ 3.60GHz
Cache Size: 6144 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi       3.3Gi       7.2Gi       752Mi       4.9Gi        11Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation CometLake-S GT2 [UHD Graphics 630] [8086:9bc8] (rev 03)	
	DeviceName: Onboard - Video	
	Subsystem: Gigabyte Technology Co., Ltd CometLake-S GT2 [UHD Graphics 630] [1458:d000]

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    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: 1.1.1
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    Send2Trash: 1.8.2
    SEQCROW: 1.8.12
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0