AlphaFold: I/O operation on closed file

[blemire@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
I'm using Alphafold to predict complexes between 2 proteins. It has worked many times, but the last few times give an error message (see screenshot attached) 'I/O operation on closed file'. I'd appreciate any advice you can give me.

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> MSSDKSNLLKKYKIVFLGDQSVGKTSLITRFMYDTFDETYAATIGIDFLSKTMYLEEGKTIRLQLWDTAGQERFRSLIPSYIRDSHVAVICYDITNKKSFDNLDKWIKDVKLERGDDVIIVLVGNKSDLASDKRQVSLDDVENLQIKIGAKFFIETSTKANHNVKLLFKKIAQSLPDFNQDSNDKSNDNNNNNNNNQSETIDITIDNTAPNPQGTSTCC,MKSDLKTYRSKVLFECKDGASLYSIPCTDNLSTIKFTERNKIWQGSLLFIEEEQLSNSYMEGFEQTKNDKFIIHPFLKMKSKLEFRNGRYLWGETWYCPVVEDLNLSTTTATNVDVQKVTKISHDGTNTIEQISSNKFKVIVQLPNSGYKPYYRNHSPDDLPQVALGLEFENPDMAAQFEYMLAVYDARFKYESQSYYYDRMVYAVNIINFKTIMQEQEEEEEEDIHELTEEFKNQNITDEFSYYEKTSKELEEFEKENANKFDHDTNDDDDGNDDEDDDFGDFIAC

Running AlphaFold prediction  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 64 GB
      System Firmware Version: 1916.40.6.0.0
      OS Loader Version: 540.120.3~22
      SMC Version (system): 2.46f12

Software:

    System Software Overview:

      System Version: macOS 12.6.1 (21G217)
      Kernel Version: Darwin 21.6.0
      Time since boot: 6 days 18:12

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      EFI Driver Version: 01.B1.042
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        Thunderbolt Display:
          Display Type: LCD
          Resolution: 2048 x 1152
          UI Looks like: 2048 x 1152
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: C02MC33KF2GC
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    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
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    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: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
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    ChimeraX-DataFormats: 1.2.2
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    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
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    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
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    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
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    ChimeraX-LookingGlass: 1.1
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    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
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    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
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    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
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    ChimeraX-RestServer: 1.1
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    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
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    ChimeraX-Shape: 1.0.1
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    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: 1.18.3
    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
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    colorama: 0.4.4
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    cycler: 0.11.0
    Cython: 0.29.26
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    entrypoints: 0.4
    filelock: 3.4.2
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    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
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    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
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    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: 21.0
    ParmEd: 3.4.3
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File attachment: Screen Shot 2022-11-19 at 11.00.32 AM.png

Screen Shot 2022-11-19 at 11.00.32 AM.png​

[blemire@…]

Added by email2trac

[Eric Pettersen]

Reported by Bernard Lemire

[Tom Goddard]

That is an error in AlphaFold code, not in ChimeraX. It says it is routine overwrite_b_factors() in line 69 of

alphafold/relax/utils.py

and reports

ValueError: I/O operation on closed file

Looking at that code it is adding b-factor to PDB. It is odd because that code just writes the PDB to a in memory string buffer and returns the value. The input to the function is a string and the output is a string, and I don't see any files being used in that routine. Maybe the error is just misleading. Searching online does suggest that the in memory StringIO will produce this error if it has been closed and then you try to read from it. That doesn't look like it could happen in the AlphaFold code. The preceding line saved the PDB file to this string buffer using BioPython code and that save routine does not close the stream.

Searching for this error and the word alphafold didn't produce anything.

I am suspicious that this is an error produced by Google Colab. Maybe Google Colab is shutting down your virtual machine and it results in this error.

It might be a bit helpful to press on that "4 frames" up/down arrow in the middle of the stack trace to reveal the routines that were being called before overwrite_b_factors().

[blemire@…]

Thank you for looking into this.

I re-started a job this morning and got what appears to be a different
error. I took screenshots of the "29 frames" in the middle of the stack
trace and attached them.
The original error had "4 frames". I hope this gets us closer to figuring
out the problem.

Bernard
[image: Screen Shot 2022-11-21 at 1.09.12 PM.png][image: Screen Shot
2022-11-21 at 1.09.29 PM.png][image: Screen Shot 2022-11-21 at 1.09.43
PM.png][image: Screen Shot 2022-11-21 at 1.10.04 PM.png][image: Screen Shot
2022-11-21 at 1.10.18 PM.png][image: Screen Shot 2022-11-21 at 1.10.33
PM.png]

On Mon, Nov 21, 2022 at 11:23 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[blemire@…]

Added by email2trac

[blemire@…]

Added by email2trac

[blemire@…]

Added by email2trac

[blemire@…]

Added by email2trac

[blemire@…]

Added by email2trac

[blemire@…]

Added by email2trac

[Tom Goddard]

This error is apparently caused by an update to a library JAX that AlphaFold uses

​https://github.com/deepmind/dm-haiku/issues/565

I also get this error when running AlphaFold in ChimeraX. I will see if ColabFold, which is the AlphaFold package ChimeraX uses has fixed it.

[Tom Goddard]

The ColabFold prediction web server

​https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb

is also failing with the same error. And my test with the latest ColabFold failed with the same error. So apparently they have not yet fixed the problem from the updated jax. So I will try to make a fix forcing ChimeraX ColabFold to use an older JAX.

[Tom Goddard]

The bug has been reported to ColabFold just a minute ago

​https://github.com/sokrypton/ColabFold/issues/332

[Tom Goddard]

Fixed.

The release of jax 0.3.25 broke ColabFold. Unfortunately ColabFold asks for jax version >= 0.3.8 and < 4 so whenever jax updates to 0.3.x ColabFold automatically uses it. This has caused ColabFold to break multiple times in the past. So to fix it this time I pinned the jax and jaxlib versions to 0.3.24.