id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8138 Fatal error: maxassem 1 has no models in it kristen.browne@… Eric Pettersen "{{{ Below is an output from a run we did recently on NIH 3D. This is a QS for 5TEP. It looked into the pdbe_bio database and found no assemblies, and that seems to have errored it out. According to Phil, the behaviour should be that if it doesn't find anything there, it should just use the open:5TEP command and try there. This should be successful by our testing in ChimeraX. Thanks! K NIH 3D Job (chimerax_flow -- 4f771bd8-f0a6-45a9-9c52-ab06d42fa0f8) Workflows version: 0.5.1 Run ID: a74fee15-2391-49e2-85a5-3fc3c3b5b394 Submission ID: 6870 File ID: None Input file URL: None Status URL: https://api-app-testing.threed.niaiddev.net/submissions/6870/runs/status Output file URL: https://api-app-testing.threed.niaiddev.net/submissions/6870/output-files Output files list URL: https://api-app-testing.threed.niaiddev.net/submissions/6870/runs/a74fee15-2391-49e2-85a5-3fc3c3b5b394/output-files File metadata URL: https://api-app-testing.threed.niaiddev.net/files/{file_id}/metadata Job directory: /tmp/nih3d_job_v44rk70d Input file: None treatment: None level: None accession code: 5TEP external database: ExternalDatabase.PDB is quick-submit: True Task 'init_job': Finished task run for task with final state: 'Success' Task 'get_file_local': Starting task run... Task 'get_file_local': Finished task run for task with final state: 'Success' Task 'check_file_extension': Starting task run... Task 'check_file_extension': Finished task run for task with final state: 'Success' Task 'get_chimerax_command': Starting task run... Using: ExternalDatabase.PDB 5TEP ChimeraX command: /usr/bin/chimerax --offscreen --exit --script '/usr/local/lib/python3.9/site-packages/nih_3d_workflows/flows/chimerax_flow/chimera_x_scripts/cx_unified.py --outdir /tmp/nih3d_job_v44rk70d --voxel_size_file /tmp/nih3d_job_v44rk70d/voxel_size.json --pixel_spacing_file /tmp/nih3d_job_v44rk70d/pixel_spacing.json --molecule_size_file /tmp/nih3d_job_v44rk70d/molecule_size.json --messages_file /tmp/nih3d_job_v44rk70d/messages.json --pdb 5TEP' Task 'get_chimerax_command': Finished task run for task with final state: 'Success' Task 'ShellTask': Starting task run... QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-nih3duser' INFO: available bundle cache has not been initialized yet Qt WebEngine seems to be initialized from a plugin. Please set Qt::AA_ShareOpenGLContexts using QCoreApplication::setAttribute and QSGRendererInterface::OpenGLRhi using QQuickWindow::setGraphicsApi before constructing QGuiApplication. INFO: Executing: runscript /usr/local/lib/python3.9/site-packages/nih_3d_workflows/flows/chimerax_flow/chimera_x_scripts/cx_unified.py --outdir /tmp/nih3d_job_v44rk70d --voxel_size_file /tmp/nih3d_job_v44rk70d/voxel_size.json --pixel_spacing_file /tmp/nih3d_job_v44rk70d/pixel_spacing.json --molecule_size_file /tmp/nih3d_job_v44rk70d/molecule_size.json --messages_file /tmp/nih3d_job_v44rk70d/messages.json --pdb 5TEP INFO: Executing: open pdbe_bio:5TEP maxAssemblies 1 autoStyle false STATUS: No biogical assemblies available for 5TEP INFO: No biogical assemblies available for 5TEP STATUS: No biogical assemblies available for 5TEP NIH3D FATAL ERROR: pdbe_bio:5TEP maxassem 1 has no models in it Command failed with exit code 1 Kristen Browne, MSc, MscBMC Contractor - MSC, Inc. | A Guidehouse Company 3D Modeling and Biovisualization Specialist Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 5601 Fishers Lane, Room 4A60 Rockville, MD 20852 Office 202-253-5228 }}} " defect closed normal Input/Output limitation Tom Goddard all ChimeraX