HDF5: file signature not found

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.18.0-553.16.1.el8_10.x86_64-x86_64-with-glibc2.28
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  

> open x

'x' has no suffix  

> open /data/processed/zhao/ift/ZO-
> RP2_2-1_vpp_33k_120e_ef_df-1_tomo-14/tomograms/ZO-
> RP2_2-1_vpp_33k_120e_ef_df-1_tomo-14__bin4_preproc.hdf

Opened ZO-RP2_2-1_vpp_33k_120e_ef_df-1_tomo-14__bin4_preproc.hdf as #1, grid
size 1024,1024,400, pixel 14.4, shown at step 1, values float32  

> open /data/processed/zhao/ift/ZO-
> RP2_2-1_vpp_33k_120e_ef_df-1_tomo-14/segmentations/ZO-
> RP2_2-1_vpp_33k_120e_ef_df-1_tomo-14__bin4_preproc_ift1tz_good_seg.hdf

Opened ZO-
RP2_2-1_vpp_33k_120e_ef_df-1_tomo-14__bin4_preproc_ift1tz_good_seg.hdf as #2,
grid size 1024,1024,400, pixel 14.4, shown at step 1, values float32  

> open /data/processed/zhao/ift/ZO-
> RP2_2-1_vpp_33k_120e_ef_df-1_tomo-14/segmentations/ZO-
> RP2_2-1_vpp_33k_120e_ef_df-1_tomo-14__bin4_preproc_mt_mask.hdf

Traceback (most recent call last):  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 176, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 464, in collated_open  
return remember_data_format()  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/map/__init__.py", line 169, in open  
return open_map(session, path, format=_name, **kw)  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/map/volume.py", line 3577, in open_map  
grids = open_file(path, file_type = format, log = session.logger, **kw)  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/map_data/fileformats.py", line 163, in open_file  
data.extend(open_func(p, **okw))  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path, array_name = array_name)  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/map_data/emanhdf/eman_hdf_format.py", line 58, in __init__  
f = tables.open_file(path)  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-packages/tables/file.py",
line 300, in open_file  
return File(filename, mode, title, root_uep, filters, **kwargs)  
File "/opt/cryoem/chimerax-1.6.1/lib/python3.9/site-packages/tables/file.py",
line 750, in __init__  
self._g_new(filename, mode, **params)  
File "tables/hdf5extension.pyx", line 486, in tables.hdf5extension.File._g_new  
tables.exceptions.HDF5ExtError: HDF5 error back trace  
  
File "H5F.c", line 620, in H5Fopen  
unable to open file  
File "H5VLcallback.c", line 3501, in H5VL_file_open  
failed to iterate over available VOL connector plugins  
File "H5PLpath.c", line 578, in H5PL__path_table_iterate  
can't iterate over plugins in plugin path '(null)'  
File "H5PLpath.c", line 620, in H5PL__path_table_iterate_process_path  
can't open directory: /usr/local/hdf5/lib/plugin  
File "H5VLcallback.c", line 3351, in H5VL__file_open  
open failed  
File "H5VLnative_file.c", line 97, in H5VL__native_file_open  
unable to open file  
File "H5Fint.c", line 1990, in H5F_open  
unable to read superblock  
File "H5Fsuper.c", line 405, in H5F__super_read  
file signature not found  
  
End of HDF5 error back trace  
  
Unable to open/create file '/data/processed/zhao/ift/ZO-
RP2_2-1_vpp_33k_120e_ef_df-1_tomo-14/segmentations/ZO-
RP2_2-1_vpp_33k_120e_ef_df-1_tomo-14__bin4_preproc_mt_mask.hdf'  
  
tables.exceptions.HDF5ExtError: HDF5 error back trace  
  
File "H5F.c", line 620, in H5Fopen  
unable to open file  
File "H5VLcallback.c", line 3501, in H5VL_file_open  
failed to iterate over available VOL connector plugins  
File "H5PLpath.c", line 578, in H5PL__path_table_iterate  
can't iterate over plugins in plugin path '(null)'  
File "H5PLpath.c", line 620, in H5PL__path_table_iterate_process_path  
can't open directory: /usr/local/hdf5/lib/plugin  
File "H5VLcallback.c", line 3351, in H5VL__file_open  
open failed  
File "H5VLnative_file.c", line 97, in H5VL__native_file_open  
unable to open file  
File "H5Fint.c", line 1990, in H5F_open  
unable to read superblock  
File "H5Fsuper.c", line 405, in H5F__super_read  
file signature not found  
  
End of HDF5 error back trace  
  
Unable to open/create file '/data/processed/zhao/ift/ZO-
RP2_2-1_vpp_33k_120e_ef_df-1_tomo-14/segmentations/ZO-
RP2_2-1_vpp_33k_120e_ef_df-1_tomo-14__bin4_preproc_mt_mask.hdf'  
  
File "tables/hdf5extension.pyx", line 486, in tables.hdf5extension.File._g_new  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 550.107.02
OpenGL renderer: NVIDIA T1000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.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=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: ASUSTeK COMPUTER INC.
Model: Z9PE-D8 WS
OS: Rocky Linux 8.10 Green Obsidian
Architecture: 64bit ELF
Virtual Machine: none
CPU: 40 Intel(R) Xeon(R) CPU E5-2660 v2 @ 2.20GHz
Cache Size: 25600 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          109Gi       7.3Gi       6.3Gi       146Mi        95Gi       101Gi
	Swap:          15Gi       163Mi        15Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU117GLM [Quadro T1000 Mobile] [10de:1fb0] (rev a1)	
	Subsystem: Hewlett-Packard Company Device [103c:12db]	
	Kernel driver in use: nvidia

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
    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

[Tom Goddard]

This is the 5th report of HDF "file signature not found". Four of the reports were with ChimeraX 1.6.1 on Mac and one with ChimeraX 1.8 on Linux. It seems likely to be a PyTables issue and probably resolved in current ChimeraX.