Opened 2 years ago
Last modified 2 years ago
#9522 assigned defect
Interfaces/NetworkX: libbz2.so.1.0: cannot open shared object file: No such file or directory
Reported by: | Owned by: | Greg Couch | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Platform | Version: | |
Keywords: | Cc: | Tom Goddard | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-3.10.0-1160.92.1.el7.x86_64-x86_64-with-glibc2.17 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /nfs/home/pksingh/DATA/Other_PilB_Str/PilBgm_Bio_unit_5tsg.pdb PilBgm_Bio_unit_5tsg.pdb title: Pilb from geobacter metallireducens bound to adp [more info...] Chain information for PilBgm_Bio_unit_5tsg.pdb --- Chain | Description 1.1/B 1.2/B | No description available 1.1/C 1.2/C | No description available 1.1/D 1.2/D | No description available > open > /nfs/home/pksingh/DATA/PilB_PA/volumes/MapFile_Csparc_P12_J184/PilBpk2_chainD_corrected/RealSpaceRefine_22/PilBpk2_RSR5_real_space_refined_022.pdb Chain information for PilBpk2_RSR5_real_space_refined_022.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available > ui tool show Matchmaker > matchmaker #2 to #1.1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PilBgm_Bio_unit_5tsg.pdb, chain B (#1.1) with PilBpk2_RSR5_real_space_refined_022.pdb, chain B (#2), sequence alignment score = 1041.2 RMSD between 299 pruned atom pairs is 1.103 angstroms; (across all 381 pairs: 1.942) > matchmaker #2 to #1.1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PilBgm_Bio_unit_5tsg.pdb, chain B (#1.1) with PilBpk2_RSR5_real_space_refined_022.pdb, chain B (#2), sequence alignment score = 1041.2 RMSD between 299 pruned atom pairs is 1.103 angstroms; (across all 381 pairs: 1.942) > hide #2 models > select Zn 6 atoms, 6 residues, 2 models selected > select Mg 4 atoms, 4 residues, 2 models selected > select nucleic-acid Nothing selected > select ::name="ADP" 108 atoms, 116 bonds, 4 residues, 2 models selected > select #1/A Nothing selected > blastprotein Missing or invalid "atoms" argument: Expected an atom specifier or [alignment- id:]sequence-name-or-number > select #1/A-b 5556 atoms, 5640 bonds, 6 pseudobonds, 774 residues, 5 models selected > hide sel cartoons > show sel cartoons > ui mousemode right select > select clear > hide #!1.1-2 cartoons > select #1/A-b 5556 atoms, 5640 bonds, 6 pseudobonds, 774 residues, 5 models selected > show sel cartoons > hide #!1.2 models > select clear > ui tool show Contacts > interfaces #!1.1 & ~solvent 2 buried areas: C D 1361, C B 1308 Traceback (most recent call last): File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/toolbar/tool.py", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 381, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider return cls._get_func(api, "run_provider")(session, name, mgr, **kw) File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/shortcuts/__init__.py", line 52, in run_provider shortcuts.run_provider(session, name) File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py", line 1334, in run_provider keyboard_shortcuts(session).try_shortcut(name) File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py", line 390, in try_shortcut self.run_shortcut(keys) File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py", line 408, in run_shortcut sc.run(self.session, status = self._enabled) File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py", line 327, in run f(s) File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py", line 569, in run_expanded_command run(session, cmd) File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/shortcuts/shortcuts.py", line 512, in run run_command(session, command, **kw) File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/core/commands/run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/core/commands/cli.py", line 2856, in run result = ci.function(session, **kw_args) File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/interfaces/cmd.py", line 49, in interfaces tool.ContactPlot(session, sg, ba, interface_residue_area_cutoff) File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/interfaces/tool.py", line 25, in __init__ Graph.__init__(self, session, groups, contacts, File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/interfaces/graph.py", line 139, in __init__ self.graph = self._make_graph() File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/interfaces/graph.py", line 160, in _make_graph import networkx as nx File "/opt/chimerax-1.3/lib/python3.9/site-packages/networkx/__init__.py", line 57, in <module> from networkx import utils File "/opt/chimerax-1.3/lib/python3.9/site- packages/networkx/utils/__init__.py", line 2, in <module> from networkx.utils.decorators import * File "/opt/chimerax-1.3/lib/python3.9/site- packages/networkx/utils/decorators.py", line 12, in <module> import re, gzip, bz2 File "/opt/chimerax-1.3/lib/python3.9/bz2.py", line 18, in <module> from _bz2 import BZ2Compressor, BZ2Decompressor ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory ImportError: libbz2.so.1.0: cannot open shared object file: No such file or directory File "/opt/chimerax-1.3/lib/python3.9/bz2.py", line 18, in from _bz2 import BZ2Compressor, BZ2Decompressor See log for complete Python traceback. > select #1 16712 atoms, 16958 bonds, 21 pseudobonds, 2316 residues, 6 models selected > interfaces select & #!1.1 & ~solvent Missing or invalid "atoms" argument: invalid atoms specifier Traceback (most recent call last): File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2251, in <lambda> dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e) File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/ui/gui.py", line 654, in close_request tool_instance.delete() File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/interfaces/tool.py", line 47, in delete atomic.get_triggers(self._session()).remove_handler(self._handler) AttributeError: 'ContactPlot' object has no attribute '_handler' AttributeError: 'ContactPlot' object has no attribute '_handler' File "/opt/chimerax-1.3/lib/python3.9/site- packages/chimerax/interfaces/tool.py", line 47, in delete atomic.get_triggers(self._session()).remove_handler(self._handler) See log for complete Python traceback. > ~select #1 Nothing selected > hide #!1 models > hide #!1.1 models > show #!1 models > show #!1.1 models Drag select of 128 atoms, 5 pseudobonds, 119 bonds Drag select of 132 atoms, 5 pseudobonds, 121 bonds > hide sel atoms Drag select of 58 atoms, 4 pseudobonds, 51 bonds > hide sel atoms > show #2 models > hide #2 models > select #1/A-b 5556 atoms, 5640 bonds, 6 pseudobonds, 774 residues, 5 models selected > hide #!1 models > show #!1 models > hide #1.1.1 models > show #1.1.1 models > hide #1.1.2 models > show #1.1.2 models > hide #1.2.1 models > show #1.2.1 models > hide #1.2.1 models > show #1.2.1 models > hide #1.2.1 models > undo [Repeated 3 time(s)] > show #2 models > select clear > select #2/c #2/a 3886 atoms, 3946 bonds, 496 residues, 1 model selected > hide sel cartoons > select #2/d\ Nothing selected > select #2/d 2095 atoms, 2123 bonds, 273 residues, 1 model selected > hide sel cartoons > select #2/B:454 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/B:293 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/B:334 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #2/B:293 13 atoms, 11 bonds, 2 residues, 1 model selected > select add #2/B:454 21 atoms, 18 bonds, 3 residues, 1 model selected > label sel text "/{0.chain_id} {0.label_one_letter_code} > {0.number}{0.insertion_code}" Traceback (most recent call last): File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/ui/gui.py", line 629, in changeEvent self.hide_floating_tools = self.isMinimized() File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/ui/gui.py", line 725, in hide_floating_tools if not tw.floating: File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1994, in _get_floating return self.__toolkit.dock_widget.isFloating() RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1994, in _get_floating return self.__toolkit.dock_widget.isFloating() See log for complete Python traceback. Traceback (most recent call last): File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/ui/gui.py", line 629, in changeEvent self.hide_floating_tools = self.isMinimized() File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/ui/gui.py", line 725, in hide_floating_tools if not tw.floating: File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1994, in _get_floating return self.__toolkit.dock_widget.isFloating() RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted File "/opt/chimerax-1.3/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1994, in _get_floating return self.__toolkit.dock_widget.isFloating() See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 418.56 OpenGL renderer: Quadro P5000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Supermicro Model: X10SRA OS: CentOS Linux 7 Core Architecture: 64bit ELF Virutal Machine: none CPU: 12 Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz Cache Size: 15360 KB Memory: total used free shared buff/cache available Mem: 15G 5.2G 3.4G 192M 6.9G 9.7G Swap: 7.5G 2.8M 7.4G Graphics: 02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P5000] [10de:1bb0] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11b2] Kernel driver in use: nvidia Locale: ('en_US', 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 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: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 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: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 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 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 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: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 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: 2.4.6 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: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 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: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 distro: 1.6.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 line-profiler: 3.3.0 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0
Change History (1)
comment:1 by , 2 years ago
Cc: | added |
---|---|
Component: | Unassigned → Platform |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Interfaces/NetworkX: libbz2.so.1.0: cannot open shared object file: No such file or directory |
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