27 October 2022,02:18:01 prefect.ShellTask INFO color name nih_blue 12.5,33.3,54.1 27 October 2022,02:18:01 prefect.ShellTask INFO color name jmol_carbon 56.5,56.5,56.5 27 October 2022,02:18:01 prefect.ShellTask INFO color name bond_purple 57.6,43.9,85.9 27 October 2022,02:18:01 prefect.ShellTask INFO color name struts_grey 48,48,48 27 October 2022,02:18:01 prefect.ShellTask INFO color name carbon_grey 22.2,22.2,22.2 27 October 2022,02:18:01 prefect.ShellTask INFO surface close 27 October 2022,02:18:01 prefect.ShellTask INFO preset 'initial styles' 'original look' 27 October 2022,02:18:01 prefect.ShellTask INFO delete solvent 27 October 2022,02:18:01 prefect.ShellTask INFO hide H|ligand|~(protein|nucleic-acid) 27 October 2022,02:18:01 prefect.ShellTask INFO ~nuc 27 October 2022,02:18:01 prefect.ShellTask INFO ~ribbon 27 October 2022,02:18:01 prefect.ShellTask INFO ~display 27 October 2022,02:18:01 prefect.ShellTask INFO surface #1 enclose #1 grid 2.5 sharp true 27 October 2022,02:18:01 prefect.ShellTask INFO color magenta 27 October 2022,02:18:01 prefect.ShellTask INFO color byattribute kd_hydrophobicity protein target rs palette 16,67,87:white:100,45,0 novalue magenta 27 October 2022,02:18:01 prefect.ShellTask INFO 27 October 2022,02:18:01 prefect.ShellTask INFO 27 October 2022,02:18:01 prefect.ShellTask INFO 27 October 2022,02:18:05 prefect.ShellTask INFO INFO: 27 October 2022,02:18:05 prefect.ShellTask INFO Executing: view 27 October 2022,02:18:08 prefect.ShellTask INFO INFO: 27 October 2022,02:18:08 prefect.ShellTask INFO Executing: save 6B1T-surf-hydropathy_thumb_NIH3D.png width 512 height 512 supersample 3 27 October 2022,02:21:26 prefect.ShellTask INFO INFO: 27 October 2022,02:21:26 prefect.ShellTask INFO Executing: save 6B1T-surf-hydropathy_NIH3D.glb 27 October 2022,02:21:33 prefect.ShellTask INFO INFO: 27 October 2022,02:21:33 prefect.ShellTask INFO Executing: preset NIH3D "surface by chain" 27 October 2022,02:21:33 prefect.ShellTask INFO INFO: 27 October 2022,02:21:33 prefect.ShellTask INFO Using preset: NIH3D / Surface by Chain 27 October 2022,02:21:38 prefect.ShellTask INFO STATUS: 27 October 2022,02:21:38 prefect.ShellTask INFO Changed 6008040 atom radii, 6164400 bond radii, 3420 pseudobond radii 27 October 2022,02:21:38 prefect.ShellTask INFO INFO: 27 October 2022,02:21:38 prefect.ShellTask INFO Changed 6008040 atom radii, 6164400 bond radii, 3420 pseudobond radii 27 October 2022,02:21:38 prefect.ShellTask INFO STATUS: 27 October 2022,02:21:38 prefect.ShellTask INFO Changed 1 pseudobond dash 27 October 2022,02:21:38 prefect.ShellTask INFO INFO: 27 October 2022,02:21:38 prefect.ShellTask INFO Changed 1 pseudobond dash 27 October 2022,02:21:38 prefect.ShellTask INFO INFO: 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff 27 October 2022,02:21:38 prefect.ShellTask INFO INFO: 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 27 October 2022,02:21:38 prefect.ShellTask INFO INFO: 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400 27 October 2022,02:21:38 prefect.ShellTask INFO INFO: 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd 27 October 2022,02:21:38 prefect.ShellTask INFO INFO: 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a 27 October 2022,02:21:38 prefect.ShellTask INFO INFO: 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090 27 October 2022,02:21:38 prefect.ShellTask INFO INFO: 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db 27 October 2022,02:21:38 prefect.ShellTask INFO INFO: 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a 27 October 2022,02:21:38 prefect.ShellTask INFO INFO: 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939 27 October 2022,02:21:38 prefect.ShellTask INFO INFO: 27 October 2022,02:21:38 prefect.ShellTask INFO Using preset: Initial Styles / Original Look 27 October 2022,02:21:52 prefect.ShellTask INFO INFO: 27 October 2022,02:21:52 prefect.ShellTask INFO Preset implemented in Python; no expansion to individual ChimeraX commands available. 27 October 2022,04:11:50 prefect.ShellTask INFO /tmp/prefect-otxftk23: line 1: 52 Killed /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_py_un945 --voxel_size_file /tmp/nih3d_job_py_un945/voxel_size.json --pixel_spacing_file /tmp/nih3d_job_py_un945/pixel_spacing.json --molecule_size_file /tmp/nih3d_job_py_un945/molecule_size.json --pdb 6B1T' 27 October 2022,04:11:50 prefect.ShellTask ERROR Command failed with exit code 137 27 October 2022,04:11:50 prefect.CloudTaskRunner INFO FAIL signal raised: FAIL('Command failed with exit code 137') 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'ShellTask': Finished task run for task with final state: 'Failed' 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'collect_expected_output_suffixes': Starting task run... 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'collect_expected_output_suffixes': Finished task run for task with final state: 'TriggerFailed' 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'get_glb_fps': Starting task run... 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'get_glb_fps': Finished task run for task with final state: 'TriggerFailed' 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'gen_trimesh': Starting task run... 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'gen_trimesh': Finished task run for task with final state: 'Failed' 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Starting task run... 27 October 2022,04:11:51 prefect.CloudTaskRunner ERROR Task 'FilterTask': Exception encountered during task execution! Traceback (most recent call last): File "/usr/local/lib/python3.9/site-packages/prefect/engine/task_runner.py", line 880, in get_task_run_state value = prefect.utilities.executors.run_task_with_timeout( File "/usr/local/lib/python3.9/site-packages/prefect/utilities/executors.py", line 468, in run_task_with_timeout return task.run(*args, **kwargs) # type: ignore File "/usr/local/lib/python3.9/site-packages/prefect/tasks/control_flow/filter.py", line 81, in run filtered = [r for r in task_results if self.filter_func(r)] TypeError: 'NoneType' object is not iterable 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Finished task run for task with final state: 'Failed' 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'gen_wrl': Starting task run... 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'gen_wrl': Finished task run for task with final state: 'Failed' 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Starting task run... 27 October 2022,04:11:51 prefect.CloudTaskRunner ERROR Task 'FilterTask': Exception encountered during task execution! Traceback (most recent call last): File "/usr/local/lib/python3.9/site-packages/prefect/engine/task_runner.py", line 880, in get_task_run_state value = prefect.utilities.executors.run_task_with_timeout( File "/usr/local/lib/python3.9/site-packages/prefect/utilities/executors.py", line 468, in run_task_with_timeout return task.run(*args, **kwargs) # type: ignore File "/usr/local/lib/python3.9/site-packages/prefect/tasks/control_flow/filter.py", line 81, in run filtered = [r for r in task_results if self.filter_func(r)] TypeError: 'NoneType' object is not iterable 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Finished task run for task with final state: 'Failed' 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'gen_x3d': Starting task run... 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'gen_x3d': Finished task run for task with final state: 'Failed' 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Starting task run... 27 October 2022,04:11:51 prefect.CloudTaskRunner ERROR Task 'FilterTask': Exception encountered during task execution! Traceback (most recent call last): File "/usr/local/lib/python3.9/site-packages/prefect/engine/task_runner.py", line 880, in get_task_run_state value = prefect.utilities.executors.run_task_with_timeout( File "/usr/local/lib/python3.9/site-packages/prefect/utilities/executors.py", line 468, in run_task_with_timeout return task.run(*args, **kwargs) # type: ignore File "/usr/local/lib/python3.9/site-packages/prefect/tasks/control_flow/filter.py", line 81, in run filtered = [r for r in task_results if self.filter_func(r)] TypeError: 'NoneType' object is not iterable 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Finished task run for task with final state: 'Failed' 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'gen_stl': Starting task run... 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'gen_stl': Finished task run for task with final state: 'Failed' 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'is_quicksubmit': Starting task run... 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'process_thumbnail': Starting task run... 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'process_thumbnail': Finished task run for task with final state: 'TriggerFailed' 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'validate_outputs': Starting task run... 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'is_quicksubmit': Finished task run for task with final state: 'Success' 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'validate_outputs': Finished task run for task with final state: 'TriggerFailed' 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'case(False)': Starting task run... 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'clean_up': Starting task run... 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'clean_up': Finished task run for task with final state: 'TriggerFailed' 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO SKIP signal raised: SKIP('Provided value "True" did not match "False"') 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'case(False)': Finished task run for task with final state: 'Skipped' 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'post_pixel_spacing_and_voxel_size': Starting task run... 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'post_pixel_spacing_and_voxel_size': Finished task run for task with final state: 'Skipped' 27 October 2022,04:11:52 prefect.CloudFlowRunner INFO Flow run FAILED: some reference tasks failed. 27 October 2022,04:11:52 prefect INFO Notifying NIH 3D API of status: Status.FAIL 27 October 2022,04:11:52 prefect INFO POST (https://api-app-testing.threed.niaiddev.net/submissions/11307/runs/status): json={'message': 'placeholder', 'prefectRunId': '97810889-f020-4b43-ad6e-58e436b71949', 'status': 'fail'} 27 October 2022,04:11:52 prefect INFO POST successful: status_code=200