| 1 | 27 October 2022,02:18:01 prefect.ShellTask INFO color name nih_blue 12.5,33.3,54.1
|
|---|
| 2 | 27 October 2022,02:18:01 prefect.ShellTask INFO color name jmol_carbon 56.5,56.5,56.5
|
|---|
| 3 | 27 October 2022,02:18:01 prefect.ShellTask INFO color name bond_purple 57.6,43.9,85.9
|
|---|
| 4 | 27 October 2022,02:18:01 prefect.ShellTask INFO color name struts_grey 48,48,48
|
|---|
| 5 | 27 October 2022,02:18:01 prefect.ShellTask INFO color name carbon_grey 22.2,22.2,22.2
|
|---|
| 6 | 27 October 2022,02:18:01 prefect.ShellTask INFO surface close
|
|---|
| 7 | 27 October 2022,02:18:01 prefect.ShellTask INFO preset 'initial styles' 'original look'
|
|---|
| 8 | 27 October 2022,02:18:01 prefect.ShellTask INFO delete solvent
|
|---|
| 9 | 27 October 2022,02:18:01 prefect.ShellTask INFO hide H|ligand|~(protein|nucleic-acid)
|
|---|
| 10 | 27 October 2022,02:18:01 prefect.ShellTask INFO ~nuc
|
|---|
| 11 | 27 October 2022,02:18:01 prefect.ShellTask INFO ~ribbon
|
|---|
| 12 | 27 October 2022,02:18:01 prefect.ShellTask INFO ~display
|
|---|
| 13 | 27 October 2022,02:18:01 prefect.ShellTask INFO surface #1 enclose #1 grid 2.5 sharp true
|
|---|
| 14 | 27 October 2022,02:18:01 prefect.ShellTask INFO color magenta
|
|---|
| 15 | 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
|
|---|
| 16 | 27 October 2022,02:18:01 prefect.ShellTask INFO
|
|---|
| 17 | 27 October 2022,02:18:01 prefect.ShellTask INFO
|
|---|
| 18 | 27 October 2022,02:18:01 prefect.ShellTask INFO
|
|---|
| 19 | 27 October 2022,02:18:05 prefect.ShellTask INFO INFO:
|
|---|
| 20 | 27 October 2022,02:18:05 prefect.ShellTask INFO Executing: view
|
|---|
| 21 | 27 October 2022,02:18:08 prefect.ShellTask INFO INFO:
|
|---|
| 22 | 27 October 2022,02:18:08 prefect.ShellTask INFO Executing: save 6B1T-surf-hydropathy_thumb_NIH3D.png width 512 height 512 supersample 3
|
|---|
| 23 | 27 October 2022,02:21:26 prefect.ShellTask INFO INFO:
|
|---|
| 24 | 27 October 2022,02:21:26 prefect.ShellTask INFO Executing: save 6B1T-surf-hydropathy_NIH3D.glb
|
|---|
| 25 | 27 October 2022,02:21:33 prefect.ShellTask INFO INFO:
|
|---|
| 26 | 27 October 2022,02:21:33 prefect.ShellTask INFO Executing: preset NIH3D "surface by chain"
|
|---|
| 27 | 27 October 2022,02:21:33 prefect.ShellTask INFO INFO:
|
|---|
| 28 | 27 October 2022,02:21:33 prefect.ShellTask INFO Using preset: NIH3D / Surface by Chain
|
|---|
| 29 | 27 October 2022,02:21:38 prefect.ShellTask INFO STATUS:
|
|---|
| 30 | 27 October 2022,02:21:38 prefect.ShellTask INFO Changed 6008040 atom radii, 6164400 bond radii, 3420 pseudobond radii
|
|---|
| 31 | 27 October 2022,02:21:38 prefect.ShellTask INFO INFO:
|
|---|
| 32 | 27 October 2022,02:21:38 prefect.ShellTask INFO Changed 6008040 atom radii, 6164400 bond radii, 3420 pseudobond radii
|
|---|
| 33 | 27 October 2022,02:21:38 prefect.ShellTask INFO STATUS:
|
|---|
| 34 | 27 October 2022,02:21:38 prefect.ShellTask INFO Changed 1 pseudobond dash
|
|---|
| 35 | 27 October 2022,02:21:38 prefect.ShellTask INFO INFO:
|
|---|
| 36 | 27 October 2022,02:21:38 prefect.ShellTask INFO Changed 1 pseudobond dash
|
|---|
| 37 | 27 October 2022,02:21:38 prefect.ShellTask INFO INFO:
|
|---|
| 38 | 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff
|
|---|
| 39 | 27 October 2022,02:21:38 prefect.ShellTask INFO INFO:
|
|---|
| 40 | 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22
|
|---|
| 41 | 27 October 2022,02:21:38 prefect.ShellTask INFO INFO:
|
|---|
| 42 | 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400
|
|---|
| 43 | 27 October 2022,02:21:38 prefect.ShellTask INFO INFO:
|
|---|
| 44 | 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd
|
|---|
| 45 | 27 October 2022,02:21:38 prefect.ShellTask INFO INFO:
|
|---|
| 46 | 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a
|
|---|
| 47 | 27 October 2022,02:21:38 prefect.ShellTask INFO INFO:
|
|---|
| 48 | 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090
|
|---|
| 49 | 27 October 2022,02:21:38 prefect.ShellTask INFO INFO:
|
|---|
| 50 | 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db
|
|---|
| 51 | 27 October 2022,02:21:38 prefect.ShellTask INFO INFO:
|
|---|
| 52 | 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a
|
|---|
| 53 | 27 October 2022,02:21:38 prefect.ShellTask INFO INFO:
|
|---|
| 54 | 27 October 2022,02:21:38 prefect.ShellTask INFO Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939
|
|---|
| 55 | 27 October 2022,02:21:38 prefect.ShellTask INFO INFO:
|
|---|
| 56 | 27 October 2022,02:21:38 prefect.ShellTask INFO Using preset: Initial Styles / Original Look
|
|---|
| 57 | 27 October 2022,02:21:52 prefect.ShellTask INFO INFO:
|
|---|
| 58 | 27 October 2022,02:21:52 prefect.ShellTask INFO Preset implemented in Python; no expansion to individual ChimeraX commands available.
|
|---|
| 59 | 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'
|
|---|
| 60 | 27 October 2022,04:11:50 prefect.ShellTask ERROR Command failed with exit code 137
|
|---|
| 61 | 27 October 2022,04:11:50 prefect.CloudTaskRunner INFO FAIL signal raised: FAIL('Command failed with exit code 137')
|
|---|
| 62 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'ShellTask': Finished task run for task with final state: 'Failed'
|
|---|
| 63 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'collect_expected_output_suffixes': Starting task run...
|
|---|
| 64 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'collect_expected_output_suffixes': Finished task run for task with final state: 'TriggerFailed'
|
|---|
| 65 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'get_glb_fps': Starting task run...
|
|---|
| 66 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'get_glb_fps': Finished task run for task with final state: 'TriggerFailed'
|
|---|
| 67 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'gen_trimesh': Starting task run...
|
|---|
| 68 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'gen_trimesh': Finished task run for task with final state: 'Failed'
|
|---|
| 69 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Starting task run...
|
|---|
| 70 | 27 October 2022,04:11:51 prefect.CloudTaskRunner ERROR Task 'FilterTask': Exception encountered during task execution!
|
|---|
| 71 | Traceback (most recent call last):
|
|---|
| 72 | File "/usr/local/lib/python3.9/site-packages/prefect/engine/task_runner.py", line 880, in get_task_run_state
|
|---|
| 73 | value = prefect.utilities.executors.run_task_with_timeout(
|
|---|
| 74 | File "/usr/local/lib/python3.9/site-packages/prefect/utilities/executors.py", line 468, in run_task_with_timeout
|
|---|
| 75 | return task.run(*args, **kwargs) # type: ignore
|
|---|
| 76 | File "/usr/local/lib/python3.9/site-packages/prefect/tasks/control_flow/filter.py", line 81, in run
|
|---|
| 77 | filtered = [r for r in task_results if self.filter_func(r)]
|
|---|
| 78 | TypeError: 'NoneType' object is not iterable
|
|---|
| 79 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Finished task run for task with final state: 'Failed'
|
|---|
| 80 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'gen_wrl': Starting task run...
|
|---|
| 81 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'gen_wrl': Finished task run for task with final state: 'Failed'
|
|---|
| 82 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Starting task run...
|
|---|
| 83 | 27 October 2022,04:11:51 prefect.CloudTaskRunner ERROR Task 'FilterTask': Exception encountered during task execution!
|
|---|
| 84 | Traceback (most recent call last):
|
|---|
| 85 | File "/usr/local/lib/python3.9/site-packages/prefect/engine/task_runner.py", line 880, in get_task_run_state
|
|---|
| 86 | value = prefect.utilities.executors.run_task_with_timeout(
|
|---|
| 87 | File "/usr/local/lib/python3.9/site-packages/prefect/utilities/executors.py", line 468, in run_task_with_timeout
|
|---|
| 88 | return task.run(*args, **kwargs) # type: ignore
|
|---|
| 89 | File "/usr/local/lib/python3.9/site-packages/prefect/tasks/control_flow/filter.py", line 81, in run
|
|---|
| 90 | filtered = [r for r in task_results if self.filter_func(r)]
|
|---|
| 91 | TypeError: 'NoneType' object is not iterable
|
|---|
| 92 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Finished task run for task with final state: 'Failed'
|
|---|
| 93 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'gen_x3d': Starting task run...
|
|---|
| 94 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'gen_x3d': Finished task run for task with final state: 'Failed'
|
|---|
| 95 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Starting task run...
|
|---|
| 96 | 27 October 2022,04:11:51 prefect.CloudTaskRunner ERROR Task 'FilterTask': Exception encountered during task execution!
|
|---|
| 97 | Traceback (most recent call last):
|
|---|
| 98 | File "/usr/local/lib/python3.9/site-packages/prefect/engine/task_runner.py", line 880, in get_task_run_state
|
|---|
| 99 | value = prefect.utilities.executors.run_task_with_timeout(
|
|---|
| 100 | File "/usr/local/lib/python3.9/site-packages/prefect/utilities/executors.py", line 468, in run_task_with_timeout
|
|---|
| 101 | return task.run(*args, **kwargs) # type: ignore
|
|---|
| 102 | File "/usr/local/lib/python3.9/site-packages/prefect/tasks/control_flow/filter.py", line 81, in run
|
|---|
| 103 | filtered = [r for r in task_results if self.filter_func(r)]
|
|---|
| 104 | TypeError: 'NoneType' object is not iterable
|
|---|
| 105 | 27 October 2022,04:11:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Finished task run for task with final state: 'Failed'
|
|---|
| 106 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'gen_stl': Starting task run...
|
|---|
| 107 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'gen_stl': Finished task run for task with final state: 'Failed'
|
|---|
| 108 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'is_quicksubmit': Starting task run...
|
|---|
| 109 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'process_thumbnail': Starting task run...
|
|---|
| 110 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'process_thumbnail': Finished task run for task with final state: 'TriggerFailed'
|
|---|
| 111 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'validate_outputs': Starting task run...
|
|---|
| 112 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'is_quicksubmit': Finished task run for task with final state: 'Success'
|
|---|
| 113 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'validate_outputs': Finished task run for task with final state: 'TriggerFailed'
|
|---|
| 114 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'case(False)': Starting task run...
|
|---|
| 115 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'clean_up': Starting task run...
|
|---|
| 116 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'clean_up': Finished task run for task with final state: 'TriggerFailed'
|
|---|
| 117 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO SKIP signal raised: SKIP('Provided value "True" did not match "False"')
|
|---|
| 118 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'case(False)': Finished task run for task with final state: 'Skipped'
|
|---|
| 119 | 27 October 2022,04:11:52 prefect.CloudTaskRunner INFO Task 'post_pixel_spacing_and_voxel_size': Starting task run...
|
|---|
| 120 | 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'
|
|---|
| 121 | 27 October 2022,04:11:52 prefect.CloudFlowRunner INFO Flow run FAILED: some reference tasks failed.
|
|---|
| 122 | 27 October 2022,04:11:52 prefect INFO Notifying NIH 3D API of status: Status.FAIL
|
|---|
| 123 | 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'}
|
|---|
| 124 | 27 October 2022,04:11:52 prefect INFO POST successful: status_code=200
|
|---|
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
