Opened 4 years ago

Closed 4 years ago

#5220 closed defect (fixed)

Blastprotein: List index out of range while parsing NR results

Reported by: Elaine Meng Owned by: Zach Pearson
Priority: critical Milestone: 1.3
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202109130037 (2021-09-13 00:37:33 UTC)
Description
tried to search blast nr with query 3p5b chain P

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html

executed startup.cxc  
UCSF ChimeraX version: 1.3.dev202109130037 (2021-09-13)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Blast Protein"

> open 3p5b format mmcif fromDatabase pdb

3p5b title:  
The structure of the LDLR/PCSK9 complex reveals the receptor in an extended
conformation [more info...]  
  
Chain information for 3p5b #1  
---  
Chain | Description | UniProt  
A | Proprotein convertase subtilisin/kexin type 9 | PCSK9_HUMAN  
L | Low density lipoprotein receptor variant | Q59FQ1_HUMAN  
P | Proprotein convertase subtilisin/kexin type 9 | PCSK9_HUMAN  
  
Non-standard residues in 3p5b #1  
---  
CA — calcium ion  
  

> blastprotein /P database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name bp1

ChimeraX REST job id: job_gu83iluc  

> open PCSK9_HUMAN fromDatabase uniprot

Summary of feedback from opening PCSK9_HUMAN fetched from uniprot  
---  
notes | UniProt identifier PCSK9_HUMAN maps to entry Q8NBP7  
Alignment identifier is PCSK9_HUMAN  
Associated 3p5b chain A to PCSK9_HUMAN with 1 mismatch  
Associated 3p5b chain P to PCSK9_HUMAN with 0 mismatches  
  
Opened UniProt PCSK9_HUMAN  

> ui tool show "Blast Protein"

[Repeated 1 time(s)]Cannot run BLAST without a chain.  

> blastprotein /P database nr cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name bp2

ChimeraX REST job id: job_mjr1i9ki  

> ui tool show "Blast Protein"

[Repeated 1 time(s)]BlastProtein finished.  
Parsing BLAST results.  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/results.py", line 287, in _get_results  
self.job._database.parse("query", self.job.seq, results)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/databases.py", line 46, in parse  
self.parser = self.parser_factory(query, sequence, results)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/dbparsers.py", line 241, in __init__  
super().__init__(query_title, query_seq, output, self._extract_hit)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/dbparsers.py", line 27, in __init__  
self._parse(extract_hit)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/dbparsers.py", line 71, in _parse  
extract_hit(hit)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/dbparsers.py", line 260, in _extract_hit  
name = pdb = id_list[0][0] + '_' + id_list[0][1]  
IndexError: list index out of range  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/results.py", line 268, in run  
self._get_results()  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/results.py", line 290, in _get_results  
self.job_failed.emit(err + str(e))  
TypeError: BlastResultsWorker.job_failed[] signal has 0 argument(s) but 1
provided  
  
TypeError: BlastResultsWorker.job_failed[] signal has 0 argument(s) but 1
provided  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/results.py", line 290, in _get_results  
self.job_failed.emit(err + str(e))  
  
See log for complete Python traceback.  
  
BlastProtein finished.  
Parsing BLAST results.  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/results.py", line 287, in _get_results  
self.job._database.parse("query", self.job.seq, results)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/databases.py", line 46, in parse  
self.parser = self.parser_factory(query, sequence, results)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/dbparsers.py", line 241, in __init__  
super().__init__(query_title, query_seq, output, self._extract_hit)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/dbparsers.py", line 27, in __init__  
self._parse(extract_hit)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/dbparsers.py", line 71, in _parse  
extract_hit(hit)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/dbparsers.py", line 260, in _extract_hit  
name = pdb = id_list[0][0] + '_' + id_list[0][1]  
IndexError: list index out of range  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/results.py", line 268, in run  
self._get_results()  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/results.py", line 290, in _get_results  
self.job_failed.emit(err + str(e))  
TypeError: BlastResultsWorker.job_failed[] signal has 0 argument(s) but 1
provided  
  
TypeError: BlastResultsWorker.job_failed[] signal has 0 argument(s) but 1
provided  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/results.py", line 290, in _get_results  
self.job_failed.emit(err + str(e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.18
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,4
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 427.140.8.0.0
      SMC Version (system): 2.29f24

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1323)
      Kernel Version: Darwin 19.6.0
      Time since boot: 2:29

Graphics/Displays:

    Intel Iris Pro:

      Chipset Model: Intel Iris Pro
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0d26
      Revision ID: 0x0008
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.29.1
    ChimeraX-AtomicLibrary: 4.1.4
    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: 2.5.3
    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: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.4.1
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202109130037
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    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: 2.1.1
    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-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: 2.0.1
    ChimeraX-MDcrds: 2.5
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.1.2
    ChimeraX-ModelPanel: 1.1.1
    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: 2.6.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    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
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    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: 2.4.3
    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
    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: 1.12
    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: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    distlib: 0.3.2
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    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: 4.7.1
    kiwisolver: 1.3.2
    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: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.20
    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: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.2.1
    qtconsole: 5.1.1
    QtPy: 1.11.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.7.1
    setuptools: 58.0.4
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    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
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (9)

comment:1 by Zach Pearson, 4 years ago

Component: Unassigned → Sequence
Milestone: → 1.3
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned

comment:2 by Zach Pearson, 4 years ago

Summary: ChimeraX bug report submission → Blastprotein: List index out of range while parsing NR results

comment:3 by Elaine Meng, 4 years ago

Priority: normal → critical

comment:4 by Elaine Meng, 4 years ago

need to be able to search sequence databases (not just AlphaFold and PDB)

comment:5 by Eric Pettersen, 4 years ago

testing Trac email notifications

comment:6 by Eric Pettersen, 4 years ago

another notification test

comment:7 by Zach Pearson, 4 years ago

Downloaded results.json from the job's folder on Plato; will see why it is not being parsed correctly today and push a change in time for tomorrow's daily build.

comment:8 by Zach Pearson, 4 years ago

Curiously, I couldn't even get a job I ran today (47ghpgmq) to return -- I thought at first this was because because the time exceeded ~5 minutes, the limit for checking job completion in core/tasks.py, but I'm not certain. About the job, or the time limit, since another job took 30 but returned. 

➜  cxservices git:(blast_qt_gui) ✗ curl http://webservices.rbvi.ucsf.edu/cxservices/api/v1/chimerax/files/job_47ghpgmq/_start_time
2021-09-23T00:23:15.368727%
➜  cxservices git:(blast_qt_gui) ✗ curl http://webservices.rbvi.ucsf.edu/cxservices/api/v1/chimerax/files/job_47ghpgmq/_end_time
2021-09-23T00:57:43.588670%
➜  cxservices git:(blast_qt_gui) ✗ curl http://webservices.rbvi.ucsf.edu/cxservices/api/v1/chimerax/files/job_gu83iluc/_start_time
2021-09-13T15:09:08.871013%
➜  cxservices git:(blast_qt_gui) ✗ curl http://webservices.rbvi.ucsf.edu/cxservices/api/v1/chimerax/files/job_gu83iluc/_end_time
2021-09-13T15:24:10.215290%
➜  cxservices git:(blast_qt_gui) ✗ curl http://webservices.rbvi.ucsf.edu/cxservices/api/v1/chimerax/files/job_mjr1i9ki/_start_time
2021-09-13T15:10:29.752294%
➜  cxservices git:(blast_qt_gui) ✗ curl http://webservices.rbvi.ucsf.edu/cxservices/api/v1/chimerax/files/job_mjr1i9ki/_end_time
2021-09-13T15:25:33.781648%
Last edited 4 years ago by Zach Pearson (previous) (diff)

comment:9 by Zach Pearson, 4 years ago

Resolution: → fixed
Status: assigned → closed

​This should do it. I'll open a separate ticket for the long-running job not coming back.

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