Ticket #16034: 3NIR_chimerax_error.txt

File 3NIR_chimerax_error.txt, 9.5 KB (added by Tom Goddard, 14 months ago)

Error output from Mike Bopf

Line 
1
2INFO prefect.ShellTask:shell.py:151 Executing: save 3NIR-ribbon-vis_NIH3D.glb
3INFO prefect.ShellTask:shell.py:151 ERROR:
4INFO prefect.ShellTask:shell.py:151 Traceback (most recent call last):
5INFO prefect.ShellTask:shell.py:151 File "/var/lib/actions-runner/_work/nih_3d_workflows/nih_3d_workflows/nih_3d_workflows/cli_scripts/cx_unified.py", line 817, in <module>
6INFO prefect.ShellTask:shell.py:151 process_macro_model(model)
7INFO prefect.ShellTask:shell.py:151 File "/var/lib/actions-runner/_work/nih_3d_workflows/nih_3d_workflows/nih_3d_workflows/cli_scripts/cx_unified.py", line 588, in process_macro_model
8INFO prefect.ShellTask:shell.py:151 export_scene(appendix="ribbon-vis")
9INFO prefect.ShellTask:shell.py:151 File "/var/lib/actions-runner/_work/nih_3d_workflows/nih_3d_workflows/nih_3d_workflows/cli_scripts/cx_unified.py", line 468, in export_scene
10INFO prefect.ShellTask:shell.py:151 run(session, export_cmd)
11INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run
12INFO prefect.ShellTask:shell.py:151 results = command.run(text, log=log, return_json=return_json)
13INFO prefect.ShellTask:shell.py:151 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
14INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
15INFO prefect.ShellTask:shell.py:151 result = ci.function(session, **kw_args)
16INFO prefect.ShellTask:shell.py:151 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
17INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86, in cmd_save
18INFO prefect.ShellTask:shell.py:151 Command(session, registry=registry).run(provider_cmd_text, log=log)
19INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
20INFO prefect.ShellTask:shell.py:151 result = ci.function(session, **kw_args)
21INFO prefect.ShellTask:shell.py:151 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
22INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101, in provider_save
23INFO prefect.ShellTask:shell.py:151 saver_info.save(session, path, **provider_kw)
24INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/gltf/__init__.py", line 52, in save
25INFO prefect.ShellTask:shell.py:151 gltf.write_gltf(session, path, models, **kw)
26INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/gltf/gltf.py", line 454, in write_gltf
27INFO prefect.ShellTask:shell.py:151 center_nodes_and_meshes(nodes, meshes, buffers)
28INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/gltf/gltf.py", line 517, in center_nodes_and_meshes
29INFO prefect.ShellTask:shell.py:151 check_node_centering_possible(nodes, meshes)
30INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/gltf/gltf.py", line 633, in check_node_centering_possible
31INFO prefect.ShellTask:shell.py:151 raise UserError('Cannot center nodes because a node has both a mesh and children')
32INFO prefect.ShellTask:shell.py:151 chimerax.core.errors.UserError: Cannot center nodes because a node has both a mesh and children
33INFO prefect.ShellTask:shell.py:151
34INFO prefect.ShellTask:shell.py:151 Traceback (most recent call last):
35INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/scripting.py", line 95, in open_python_script
36INFO prefect.ShellTask:shell.py:151 _exec_python(session, code, argv)
37INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/scripting.py", line 72, in _exec_python
38INFO prefect.ShellTask:shell.py:151 exec(code, sandbox.__dict__)
39INFO prefect.ShellTask:shell.py:151 File "/var/lib/actions-runner/_work/nih_3d_workflows/nih_3d_workflows/nih_3d_workflows/cli_scripts/cx_unified.py", line 817, in <module>
40INFO prefect.ShellTask:shell.py:151 process_macro_model(model)
41INFO prefect.ShellTask:shell.py:151 File "/var/lib/actions-runner/_work/nih_3d_workflows/nih_3d_workflows/nih_3d_workflows/cli_scripts/cx_unified.py", line 588, in process_macro_model
42INFO prefect.ShellTask:shell.py:151 export_scene(appendix="ribbon-vis")
43INFO prefect.ShellTask:shell.py:151 File "/var/lib/actions-runner/_work/nih_3d_workflows/nih_3d_workflows/nih_3d_workflows/cli_scripts/cx_unified.py", line 468, in export_scene
44INFO prefect.ShellTask:shell.py:151 run(session, export_cmd)
45INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run
46INFO prefect.ShellTask:shell.py:151 results = command.run(text, log=log, return_json=return_json)
47INFO prefect.ShellTask:shell.py:151 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
48INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
49INFO prefect.ShellTask:shell.py:151 result = ci.function(session, **kw_args)
50INFO prefect.ShellTask:shell.py:151 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
51INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86, in cmd_save
52INFO prefect.ShellTask:shell.py:151 Command(session, registry=registry).run(provider_cmd_text, log=log)
53INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
54INFO prefect.ShellTask:shell.py:151 result = ci.function(session, **kw_args)
55INFO prefect.ShellTask:shell.py:151 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
56INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101, in provider_save
57INFO prefect.ShellTask:shell.py:151 saver_info.save(session, path, **provider_kw)
58INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/gltf/__init__.py", line 52, in save
59INFO prefect.ShellTask:shell.py:151 gltf.write_gltf(session, path, models, **kw)
60INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/gltf/gltf.py", line 454, in write_gltf
61INFO prefect.ShellTask:shell.py:151 center_nodes_and_meshes(nodes, meshes, buffers)
62INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/gltf/gltf.py", line 517, in center_nodes_and_meshes
63INFO prefect.ShellTask:shell.py:151 check_node_centering_possible(nodes, meshes)
64INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/gltf/gltf.py", line 633, in check_node_centering_possible
65INFO prefect.ShellTask:shell.py:151 raise UserError('Cannot center nodes because a node has both a mesh and children')
66INFO prefect.ShellTask:shell.py:151 chimerax.core.errors.UserError: Cannot center nodes because a node has both a mesh and children
67INFO prefect.ShellTask:shell.py:151
68INFO prefect.ShellTask:shell.py:151 During handling of the above exception, another exception occurred:
69INFO prefect.ShellTask:shell.py:151
70INFO prefect.ShellTask:shell.py:151 Traceback (most recent call last):
71INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 878, in init
72INFO prefect.ShellTask:shell.py:151 run(sess, "runscript %s" % script)
73INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run
74INFO prefect.ShellTask:shell.py:151 results = command.run(text, log=log, return_json=return_json)
75INFO prefect.ShellTask:shell.py:151 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
76INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run
77INFO prefect.ShellTask:shell.py:151 result = ci.function(session, **kw_args)
78INFO prefect.ShellTask:shell.py:151 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
79INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/runscript.py", line 49, in runscript
80INFO prefect.ShellTask:shell.py:151 open_python_script(session, open(script_file, 'rb'), script_file, argv=argv)
81INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/scripting.py", line 101, in open_python_script
82INFO prefect.ShellTask:shell.py:151 raise UserError('Error opening python file %s' % stream.name)
83INFO prefect.ShellTask:shell.py:151 chimerax.core.errors.UserError: Error opening python file /var/lib/actions-runner/_work/nih_3d_workflows/nih_3d_workflows/nih_3d_workflows/cli_scripts/cx_unified.py