AlphaFold: no space left on device

[gideanemendes.o@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here) 

I am trying to predict an oligomer of about 1500 amino acids but it does not work. I have receiving this mensage error. Could you help me?

2023-07-30 05:58:53,791 Running on GPU
2023-07-30 05:58:53,879 Found 4 citations for tools or databases
2023-07-30 05:58:53,879 Query 1/1: af1508 (length 1508)
2023-07-30 05:58:54,251 Server didn't reply with json: mkdir /nvme2/colabfold_2022/jobs/rcu5mzGkEOWaTJUkCoHdqPWr8bW-LGOcFhYi6w: no space left on device

2023-07-30 05:58:54,259 Could not get MSA/templates for af1508: MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.
Traceback (most recent call last):
  File "/usr/local/lib/python3.10/dist-packages/colabfold/batch.py", line 1360, in run
    = get_msa_and_templates(jobname, query_sequence, result_dir, msa_mode, use_templates,
  File "/usr/local/lib/python3.10/dist-packages/colabfold/batch.py", line 803, in get_msa_and_templates
    a3m_lines = run_mmseqs2(
  File "/usr/local/lib/python3.10/dist-packages/colabfold/colabfold.py", line 197, in run_mmseqs2
    raise Exception(f'MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.')
Exception: MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.
2023-07-30 05:58:54,261 Done

Log:
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  

> ui tool show AlphaFold

> alphafold predict
> MAPVALEQENHLRDAEFNRAMHGKSAQFRGGFAALRGKDSAAQKAAVDEYFKHWDNKPAEDETEETRAARRAEYATLTRHYYNLATDLYEYGWGTSFHFCRFAQGEPFYQAIARHEHYLAHQMGIKEGMKVLDVGCGVGGPAREIVKFTDANVVGLNNNDYQIERATRYAEREGLSHKLSFVKGDFMQMKFPDNSFDAVYAIEATVHAPDLEGVYKEIFRVLKPGGVFGVYEWLMTDAYDNDNPEHRRIRLGIELGDGISNMVKVSEGLTAFKNAGFELLHNEDLADRPDAIPWYYPLAGSFKHMTSPWDFFTIARMTWWGRGIAHRFCGAMETIGLFPKGTQKTADSLAIAGDCLVAGGEKKLFTPMYLMVGRKPE,MAPVALEQENHLRDAEFNRAMHGKSAQFRGGFAALRGKDSAAQKAAVDEYFKHWDNKPAEDETEETRAARRAEYATLTRHYYNLATDLYEYGWGTSFHFCRFAQGEPFYQAIARHEHYLAHQMGIKEGMKVLDVGCGVGGPAREIVKFTDANVVGLNNNDYQIERATRYAEREGLSHKLSFVKGDFMQMKFPDNSFDAVYAIEATVHAPDLEGVYKEIFRVLKPGGVFGVYEWLMTDAYDNDNPEHRRIRLGIELGDGISNMVKVSEGLTAFKNAGFELLHNEDLADRPDAIPWYYPLAGSFKHMTSPWDFFTIARMTWWGRGIAHRFCGAMETIGLFPKGTQKTADSLAIAGDCLVAGGEKKLFTPMYLMVGRKPE,MAPVALEQENHLRDAEFNRAMHGKSAQFRGGFAALRGKDSAAQKAAVDEYFKHWDNKPAEDETEETRAARRAEYATLTRHYYNLATDLYEYGWGTSFHFCRFAQGEPFYQAIARHEHYLAHQMGIKEGMKVLDVGCGVGGPAREIVKFTDANVVGLNNNDYQIERATRYAEREGLSHKLSFVKGDFMQMKFPDNSFDAVYAIEATVHAPDLEGVYKEIFRVLKPGGVFGVYEWLMTDAYDNDNPEHRRIRLGIELGDGISNMVKVSEGLTAFKNAGFELLHNEDLADRPDAIPWYYPLAGSFKHMTSPWDFFTIARMTWWGRGIAHRFCGAMETIGLFPKGTQKTADSLAIAGDCLVAGGEKKLFTPMYLMVGRKPE,MAPVALEQENHLRDAEFNRAMHGKSAQFRGGFAALRGKDSAAQKAAVDEYFKHWDNKPAEDETEETRAARRAEYATLTRHYYNLATDLYEYGWGTSFHFCRFAQGEPFYQAIARHEHYLAHQMGIKEGMKVLDVGCGVGGPAREIVKFTDANVVGLNNNDYQIERATRYAEREGLSHKLSFVKGDFMQMKFPDNSFDAVYAIEATVHAPDLEGVYKEIFRVLKPGGVFGVYEWLMTDAYDNDNPEHRRIRLGIELGDGISNMVKVSEGLTAFKNAGFELLHNEDLADRPDAIPWYYPLAGSFKHMTSPWDFFTIARMTWWGRGIAHRFCGAMETIGLFPKGTQKTADSLAIAGDCLVAGGEKKLFTPMYLMVGRKPE

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  
AlphaFold prediction finished  
Results in C:\Users\gideanemendes/Downloads/ChimeraX/AlphaFold/prediction_8  

Downloaded prediction file not found:
C:\Users\gideanemendes/Downloads/ChimeraX/AlphaFold/prediction_8\best_model.pdb  

> alphafold predict
> MAPVALEQENHLRDAEFNRAMHGKSAQFRGGFAALRGKDSAAQKAAVDEYFKHWDNKPAEDETEETRAARRAEYATLTRHYYNLATDLYEYGWGTSFHFCRFAQGEPFYQAIARHEHYLAHQMGIKEGMKVLDVGCGVGGPAREIVKFTDANVVGLNNNDYQIERATRYAEREGLSHKLSFVKGDFMQMKFPDNSFDAVYAIEATVHAPDLEGVYKEIFRVLKPGGVFGVYEWLMTDAYDNDNPEHRRIRLGIELGDGISNMVKVSEGLTAFKNAGFELLHNEDLADRPDAIPWYYPLAGSFKHMTSPWDFFTIARMTWWGRGIAHRFCGAMETIGLFPKGTQKTADSLAIAGDCLVAGGEKKLFTPMYLMVGRKPE

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in C:\Users\gideanemendes/Downloads/ChimeraX/AlphaFold/prediction_9  

Downloaded prediction file not found:
C:\Users\gideanemendes/Downloads/ChimeraX/AlphaFold/prediction_9\best_model.pdb  

> alphafold predict
> MSSTVPLAEKDHARDQEFAKALHGNSYKKTGLGALMSKSKDAADVANNGYFKHWDGGVTEEDEKKRLGDYSQLTSHYYNLVTDFYEYGWGSSFHFSRYYRGEAFRQATARHEHYLAYKMGLTEDMKVLDVGCGVGGPGREICRFTDCTIVGLNNNDYQIERANHYAKKYHLDDKLSYVKGDFMQMDFEPESFDAVYAIEATVHAPVLEGVYSEIYRVLKPGGVFGVYEWVMTDKYDESNEEHRKIAYGIEVGDGIPKMYKRDVAEQALKNVGFEIEYQKDLAAADDEIPWYYPLSGQFKYVQTLGDYFTVFRTSRIGRTVTTELVGLMEKIGLAPKGSKQVTGALEDAAVNLVKGGEQKLFTPMMLYVVRKPKNA

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in C:\Users\gideanemendes/Downloads/ChimeraX/AlphaFold/prediction_10  

Downloaded prediction file not found:
C:\Users\gideanemendes/Downloads/ChimeraX/AlphaFold/prediction_10\best_model.pdb  




OpenGL version: 3.3.0 - Build 25.20.100.6577
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel

Python: 3.9.11
Locale: pt_BR.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LG Electronics                  
Model: 14Z980-G.BH51P1
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 8,415,170,560
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
OSLanguage: pt-BR

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-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
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    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
    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
    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
    pywin32: 305
    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
    WMI: 1.5.1
    zipp: 3.15.0
File attachment: log.txt

log.txt​

[gideanemendes.o@…]

Added by email2trac

[pett]

Reported by Gideane Oliveira

[Tom Goddard]

A ChimeraX AlphaFold prediction runs on Google Colab, and the sequence alignment step happens on a massive sequence search server, I believe in Korea, and the error appears to come from that sequence search server and says "mkdir ... no space left on device". So it sounds like the ColabFold sequence server ran out of disk space. We have have nothing to do with that server. As the message says you should try again later. If it persist and you want to pursue it, track down who maintains the ColabFold sequence server and contact them.

2023-07-30 05:58:54,251 Server didn't reply with json: mkdir /nvme2/colabfold_2022/jobs/rcu5mzGkEOWaTJUkCoHdqPWr8bW-LGOcFhYi6w: no space left on device

2023-07-30 05:58:54,259 Could not get MSA/templates for af1508: MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.