| 1 | 27 October 2022,09:44:56 prefect.ShellTask INFO color name nih_blue 12.5,33.3,54.1
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| 2 | 27 October 2022,09:44:56 prefect.ShellTask INFO color name jmol_carbon 56.5,56.5,56.5
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| 3 | 27 October 2022,09:44:56 prefect.ShellTask INFO color name bond_purple 57.6,43.9,85.9
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| 4 | 27 October 2022,09:44:56 prefect.ShellTask INFO color name struts_grey 48,48,48
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| 5 | 27 October 2022,09:44:56 prefect.ShellTask INFO color name carbon_grey 22.2,22.2,22.2
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| 6 | 27 October 2022,09:44:56 prefect.ShellTask INFO surface close
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| 7 | 27 October 2022,09:44:56 prefect.ShellTask INFO preset 'initial styles' 'original look'
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| 8 | 27 October 2022,09:44:56 prefect.ShellTask INFO delete solvent
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| 9 | 27 October 2022,09:44:56 prefect.ShellTask INFO hide H|ligand|~(protein|nucleic-acid)
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| 10 | 27 October 2022,09:44:56 prefect.ShellTask INFO ~nuc
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| 11 | 27 October 2022,09:44:56 prefect.ShellTask INFO ~ribbon
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| 12 | 27 October 2022,09:44:56 prefect.ShellTask INFO ~display
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| 13 | 27 October 2022,09:44:56 prefect.ShellTask INFO surface #1 enclose #1 grid 2.5 sharp true
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| 14 | 27 October 2022,09:44:56 prefect.ShellTask INFO color magenta
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| 15 | 27 October 2022,09:44:56 prefect.ShellTask INFO color byattribute kd_hydrophobicity protein target rs palette 16,67,87:white:100,45,0 novalue magenta
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| 16 | 27 October 2022,09:44:56 prefect.ShellTask INFO
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| 17 | 27 October 2022,09:44:56 prefect.ShellTask INFO
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| 18 | 27 October 2022,09:44:56 prefect.ShellTask INFO
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| 19 | 27 October 2022,09:44:59 prefect.ShellTask INFO INFO:
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| 20 | 27 October 2022,09:44:59 prefect.ShellTask INFO Executing: view
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| 21 | 27 October 2022,09:45:02 prefect.ShellTask INFO INFO:
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| 22 | 27 October 2022,09:45:02 prefect.ShellTask INFO Executing: save 4V4U-surf-hydropathy_thumb_NIH3D.png width 512 height 512 supersample 3
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| 23 | 27 October 2022,09:48:19 prefect.ShellTask INFO INFO:
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| 24 | 27 October 2022,09:48:19 prefect.ShellTask INFO Executing: save 4V4U-surf-hydropathy_NIH3D.glb
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| 25 | 27 October 2022,09:48:25 prefect.ShellTask INFO INFO:
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| 26 | 27 October 2022,09:48:25 prefect.ShellTask INFO Executing: preset NIH3D "surface by chain"
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| 27 | 27 October 2022,09:48:25 prefect.ShellTask INFO INFO:
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| 28 | 27 October 2022,09:48:25 prefect.ShellTask INFO Using preset: NIH3D / Surface by Chain
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| 29 | 27 October 2022,09:48:29 prefect.ShellTask INFO STATUS:
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| 30 | 27 October 2022,09:48:29 prefect.ShellTask INFO Changed 5214540 atom radii, 5357280 bond radii, 4380 pseudobond radii
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| 31 | 27 October 2022,09:48:29 prefect.ShellTask INFO INFO:
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| 32 | 27 October 2022,09:48:29 prefect.ShellTask INFO Changed 5214540 atom radii, 5357280 bond radii, 4380 pseudobond radii
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| 33 | 27 October 2022,09:48:29 prefect.ShellTask INFO STATUS:
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| 34 | 27 October 2022,09:48:29 prefect.ShellTask INFO Changed 1 pseudobond dash
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| 35 | 27 October 2022,09:48:29 prefect.ShellTask INFO INFO:
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| 36 | 27 October 2022,09:48:29 prefect.ShellTask INFO Changed 1 pseudobond dash
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| 37 | 27 October 2022,09:48:29 prefect.ShellTask INFO INFO:
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| 38 | 27 October 2022,09:48:29 prefect.ShellTask INFO Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff
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| 39 | 27 October 2022,09:48:29 prefect.ShellTask INFO INFO:
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| 40 | 27 October 2022,09:48:29 prefect.ShellTask INFO Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22
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| 41 | 27 October 2022,09:48:29 prefect.ShellTask INFO INFO:
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| 42 | 27 October 2022,09:48:29 prefect.ShellTask INFO Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400
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| 43 | 27 October 2022,09:48:29 prefect.ShellTask INFO INFO:
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| 44 | 27 October 2022,09:48:29 prefect.ShellTask INFO Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd
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| 45 | 27 October 2022,09:48:29 prefect.ShellTask INFO INFO:
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| 46 | 27 October 2022,09:48:29 prefect.ShellTask INFO Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a
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| 47 | 27 October 2022,09:48:29 prefect.ShellTask INFO INFO:
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| 48 | 27 October 2022,09:48:29 prefect.ShellTask INFO Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090
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| 49 | 27 October 2022,09:48:29 prefect.ShellTask INFO INFO:
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| 50 | 27 October 2022,09:48:29 prefect.ShellTask INFO Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db
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| 51 | 27 October 2022,09:48:29 prefect.ShellTask INFO INFO:
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| 52 | 27 October 2022,09:48:29 prefect.ShellTask INFO Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a
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| 53 | 27 October 2022,09:48:29 prefect.ShellTask INFO INFO:
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| 54 | 27 October 2022,09:48:29 prefect.ShellTask INFO Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939
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| 55 | 27 October 2022,09:48:30 prefect.ShellTask INFO INFO:
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| 56 | 27 October 2022,09:48:30 prefect.ShellTask INFO Using preset: Initial Styles / Original Look
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| 57 | 27 October 2022,09:48:42 prefect.ShellTask INFO INFO:
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| 58 | 27 October 2022,09:48:42 prefect.ShellTask INFO Preset implemented in Python; no expansion to individual ChimeraX commands available.
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| 59 | 27 October 2022,11:26:50 prefect.ShellTask INFO /tmp/prefect-yq6ku7pa: 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_wv0sokow --voxel_size_file /tmp/nih3d_job_wv0sokow/voxel_size.json --pixel_spacing_file /tmp/nih3d_job_wv0sokow/pixel_spacing.json --molecule_size_file /tmp/nih3d_job_wv0sokow/molecule_size.json --pdb 4V4U'
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| 60 | 27 October 2022,11:26:50 prefect.ShellTask ERROR Command failed with exit code 137
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| 61 | 27 October 2022,11:26:50 prefect.CloudTaskRunner INFO FAIL signal raised: FAIL('Command failed with exit code 137')
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| 62 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'ShellTask': Finished task run for task with final state: 'Failed'
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| 63 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'collect_expected_output_suffixes': Starting task run...
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| 64 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'collect_expected_output_suffixes': Finished task run for task with final state: 'TriggerFailed'
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| 65 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'get_glb_fps': Starting task run...
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| 66 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'get_glb_fps': Finished task run for task with final state: 'TriggerFailed'
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| 67 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'gen_trimesh': Starting task run...
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| 68 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'gen_trimesh': Finished task run for task with final state: 'Failed'
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| 69 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Starting task run...
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| 70 | 27 October 2022,11:26:51 prefect.CloudTaskRunner ERROR Task 'FilterTask': Exception encountered during task execution!
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| 71 | Traceback (most recent call last):
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| 72 | File "/usr/local/lib/python3.9/site-packages/prefect/engine/task_runner.py", line 880, in get_task_run_state
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| 73 | value = prefect.utilities.executors.run_task_with_timeout(
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| 74 | File "/usr/local/lib/python3.9/site-packages/prefect/utilities/executors.py", line 468, in run_task_with_timeout
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| 75 | return task.run(*args, **kwargs) # type: ignore
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| 76 | File "/usr/local/lib/python3.9/site-packages/prefect/tasks/control_flow/filter.py", line 81, in run
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| 77 | filtered = [r for r in task_results if self.filter_func(r)]
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| 78 | TypeError: 'NoneType' object is not iterable
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| 79 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Finished task run for task with final state: 'Failed'
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| 80 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'gen_wrl': Starting task run...
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| 81 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'gen_wrl': Finished task run for task with final state: 'Failed'
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| 82 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Starting task run...
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| 83 | 27 October 2022,11:26:51 prefect.CloudTaskRunner ERROR Task 'FilterTask': Exception encountered during task execution!
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| 84 | Traceback (most recent call last):
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| 85 | File "/usr/local/lib/python3.9/site-packages/prefect/engine/task_runner.py", line 880, in get_task_run_state
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| 86 | value = prefect.utilities.executors.run_task_with_timeout(
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| 87 | File "/usr/local/lib/python3.9/site-packages/prefect/utilities/executors.py", line 468, in run_task_with_timeout
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| 88 | return task.run(*args, **kwargs) # type: ignore
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| 89 | File "/usr/local/lib/python3.9/site-packages/prefect/tasks/control_flow/filter.py", line 81, in run
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| 90 | filtered = [r for r in task_results if self.filter_func(r)]
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| 91 | TypeError: 'NoneType' object is not iterable
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| 92 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Finished task run for task with final state: 'Failed'
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| 93 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'gen_x3d': Starting task run...
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| 94 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'gen_x3d': Finished task run for task with final state: 'Failed'
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| 95 | 27 October 2022,11:26:51 prefect.CloudTaskRunner INFO Task 'FilterTask': Starting task run...
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| 96 | 27 October 2022,11:26:51 prefect.CloudTaskRunner ERROR Task 'FilterTask': Exception encountered during task execution!
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| 97 | Traceback (most recent call last):
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| 98 | File "/usr/local/lib/python3.9/site-packages/prefect/engine/task_runner.py", line 880, in get_task_run_state
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| 99 | value = prefect.utilities.executors.run_task_with_timeout(
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| 100 | File "/usr/local/lib/python3.9/site-packages/prefect/utilities/executors.py", line 468, in run_task_with_timeout
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| 101 | return task.run(*args, **kwargs) # type: ignore
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| 102 | File "/usr/local/lib/python3.9/site-packages/prefect/tasks/control_flow/filter.py", line 81, in run
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| 103 | filtered = [r for r in task_results if self.filter_func(r)]
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| 104 | TypeError: 'NoneType' object is not iterable
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| 105 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'FilterTask': Finished task run for task with final state: 'Failed'
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| 106 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'gen_stl': Starting task run...
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| 107 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'gen_stl': Finished task run for task with final state: 'Failed'
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| 108 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'process_thumbnail': Starting task run...
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| 109 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'is_quicksubmit': Starting task run...
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| 110 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'process_thumbnail': Finished task run for task with final state: 'TriggerFailed'
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| 111 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'validate_outputs': Starting task run...
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| 112 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'is_quicksubmit': Finished task run for task with final state: 'Success'
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| 113 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'validate_outputs': Finished task run for task with final state: 'TriggerFailed'
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| 114 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'case(False)': Starting task run...
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| 115 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'clean_up': Starting task run...
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| 116 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO SKIP signal raised: SKIP('Provided value "True" did not match "False"')
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| 117 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'clean_up': Finished task run for task with final state: 'TriggerFailed'
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| 118 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'case(False)': Finished task run for task with final state: 'Skipped'
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| 119 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'post_pixel_spacing_and_voxel_size': Starting task run...
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| 120 | 27 October 2022,11:26:52 prefect.CloudTaskRunner INFO Task 'post_pixel_spacing_and_voxel_size': Finished task run for task with final state: 'Skipped'
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| 121 | 27 October 2022,11:26:52 prefect.CloudFlowRunner INFO Flow run FAILED: some reference tasks failed.
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| 122 | 27 October 2022,11:26:52 prefect INFO Notifying NIH 3D API of status: Status.FAIL
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| 123 | 27 October 2022,11:26:52 prefect INFO POST (https://api-app-testing.threed.niaiddev.net/submissions/6590/runs/status): json={'message': 'placeholder', 'prefectRunId': '2b9fd51b-3961-430e-b7ff-580276b04e66', 'status': 'fail'}
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| 124 | 27 October 2022,11:26:53 prefect INFO POST successful: status_code=200
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