Opened 3 years ago
Closed 3 years ago
#6836 closed defect (can't reproduce)
Crash running AlphaFold prediction
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19044
ChimeraX Version: 1.4rc202205060510 (2022-05-06 05:10:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation
Thread 0x000033a4 (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00000544 (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002ec8 (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002590 (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003b2c (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000039cc (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000012e0 (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000026b4 (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002388 (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003abc (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003224 (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000015a4 (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003b38 (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001d50 (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000036a4 (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000008e0 (most recent call first):
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\runpy.py", line 87 in _run_code
File "C:\Program Files\ChimeraX 1.4rc202205060510\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.4rc202205060510 (2022-05-06)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
> alphafold predict
> MDLDGGDSPWGDVPSQSTNNLAASQSETEGTAQDQSTQQETPRSTVRRGPRGRGKIAAQVTKLEAVDDTIDPLGPLGDKPAENSPTGLEQAPVPPQKEAFASRNVRPASTTSQTSSGAGMMDSVNLEEDGTGFRNPPPVQPPSDVEASKRQQQPSVSVEKAAHPTFEISVGDPHKVGDLTSSHIVYQVRTKTTSKAYRQPEFTVSRRYRDFLWLYNSLHSNNPGVVVPPPPEKQAVGRFDTNFVESRRAALERMLNKIAAHPILQHDGDLKIFLESEAFNVDIKNKENREPDLGQSKGMFSSFGISVGGGGKFIEHDDWFHDRKIYLDALENQLKSLMKAIDTVVAQRKGLSEAAGEFSTSIQSLAAVELSPLLSGPLYGLSDLQLRIKELYDRQAQQDVLTLGITIDEYLRLIGSVKTAFSQRQKAYHSWHAAESELQKRKHSQEKLLRQGKSQQDRLNQANADVADAERRVHQARLLFEDMGRLMRNELQRFEKEKVEDFKSGVETFLESAVEAQKELIELWETFLLQLDAGEDGNPFYPPAGEHNASAESAPGAPSESTVSTAEAA,MDYSSIQQDPAGASPWASPRATEATYPPSSTSDIPPSPLPPHHESPYEAAGDSQPAEAAEHKTPGEGDVGSPSLSERVQNTHLNEAGYAAEQQPRSQVPARYQTGARQNARQPAPVYKIQAKITGLERTGKKDPILRFDVHTNIPKFRTTQYRDVRRTHSEFGKLADHLMSANPEALVPAVPAPLTPAGAGTDEDEFRVKASMQRWLNTVLNNEVLIQDDEIVLFVESDFGYSPVVRMKQPATGVRRKVLKQFAPPPDDTPELQNARPVVKMFYLGTMDASHKVDRVVKARRGLGLAESDFGVKVGQMHVQETHPGLSNAYRKLGKVIQAVGDYHAVQATAEATTLGDPLSYHSSDAFIVKETLTNRHILLRELLQAQQATRSKRAAADRLKVSSSVRPEKVDEAISALDEAQSQEDYLTKKTQRVTSNLLNEKRRWFERTSNDVWLALREYTLRQIEAERRTLATLESVRPDIRSIDASGGLSRLGRESHPTGRRPNLASSQGPKGDAWSGIPRRSDSLGRSLSGSFAAPAPEEDEETNGRLRSPSGVSSIVEDDDDRLDARNAASRLAGSTF
Running AlphaFold prediction
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4rc202205060510 (2022-05-06)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0
OpenGL renderer: GeForce 8600 GT/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: es_ES.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows
Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 10 Pro for Workstations (Build 19044)
Memory: 17,005,506,560
MaxProcessMemory: 137,438,953,344
CPU: 12 11th Gen Intel(R) Core(TM) i5-11400F @ 2.60GHz
OSLanguage: es-ES
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4rc202205060510
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.2
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.8
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pywin32: 303
pyzmq: 22.3.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash running AlphaFold prediction |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
Third report in 2 days by same user, running AlphaFold prediction on Windows and crashing in event loop.