Import old project to 5.0

V3eneno · February 1, 2026, 11:32pm

Hi everyone, I hate to say this, but I ran into issues with some projects after updating to version 5.0. I tried importing the projects (including the ones that were auto-detached) directly into 5.0, but I’m getting an error during import.

My questions are:

What should I do to recover the projects I already imported?
How can I fix the projects in the older version first and then upgrade them to 5.0 successfully?

Thanks in advance!

V3eneno · February 1, 2026, 11:37pm

The copy of validation report

P3
Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/models/mongo.py”, line 590, in to_mongo
return self.mongo_encode(self.model_dump(exclude={“id”}, by_alias=True))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/pydantic/main.py”, line 463, in model_dump
return self.pydantic_serializer.to_python(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/models/job.py”, line 697, in build_errors
return errors + self.spec.extra_build_errors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/compute/jobs/class3D/spec.py”, line 505, in extra_build_errors
if self.params.class3D_filter_hp_res and self.params.class3D_filter_hp_res <= self.params.class3D_target_res:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: ‘<=’ not supported between instances of ‘float’ and ‘NoneType’

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/cli/upgrade.py”, line 339, in validate_project
job.to_mongo()
File “/home/user/cryosparc/cryosparc_master/models/mongo.py”, line 592, in to_mongo
raise CSModelException(
models.error.CSModelException: Encountered serialization exception from Job with id 665deaf5bd184da59e432418 in collection jobs

P6

Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/models/mongo.py”, line 590, in to_mongo
return self.mongo_encode(self.model_dump(exclude={“id”}, by_alias=True))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/pydantic/main.py”, line 463, in model_dump
return self.pydantic_serializer.to_python(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/models/job.py”, line 697, in build_errors
return errors + self.spec.extra_build_errors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/compute/jobs/class3D/spec.py”, line 505, in extra_build_errors
if self.params.class3D_filter_hp_res and self.params.class3D_filter_hp_res <= self.params.class3D_target_res:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: ‘<=’ not supported between instances of ‘float’ and ‘NoneType’

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/cli/upgrade.py”, line 339, in validate_project
job.to_mongo()
File “/home/user/cryosparc/cryosparc_master/models/mongo.py”, line 592, in to_mongo
raise CSModelException(
models.error.CSModelException: Encountered serialization exception from Job with id 6676025327e630be6025a58a in collection jobs
Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/models/mongo.py”, line 590, in to_mongo
return self.mongo_encode(self.model_dump(exclude={“id”}, by_alias=True))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/pydantic/main.py”, line 463, in model_dump
return self.pydantic_serializer.to_python(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/models/job.py”, line 697, in build_errors
return errors + self.spec.extra_build_errors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/compute/jobs/class3D/spec.py”, line 505, in extra_build_errors
if self.params.class3D_filter_hp_res and self.params.class3D_filter_hp_res <= self.params.class3D_target_res:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: ‘<=’ not supported between instances of ‘float’ and ‘NoneType’

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/cli/upgrade.py”, line 339, in validate_project
job.to_mongo()
File “/home/user/cryosparc/cryosparc_master/models/mongo.py”, line 592, in to_mongo
raise CSModelException(
models.error.CSModelException: Encountered serialization exception from Job with id 6676069727e630be60364ee1 in collection jobs
Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/models/mongo.py”, line 590, in to_mongo
return self.mongo_encode(self.model_dump(exclude={“id”}, by_alias=True))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/pydantic/main.py”, line 463, in model_dump
return self.pydantic_serializer.to_python(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/models/job.py”, line 697, in build_errors
return errors + self.spec.extra_build_errors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/compute/jobs/class3D/spec.py”, line 505, in extra_build_errors
if self.params.class3D_filter_hp_res and self.params.class3D_filter_hp_res <= self.params.class3D_target_res:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: ‘<=’ not supported between instances of ‘float’ and ‘NoneType’

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/cli/upgrade.py”, line 339, in validate_project
job.to_mongo()
File “/home/user/cryosparc/cryosparc_master/models/mongo.py”, line 592, in to_mongo
raise CSModelException(
models.error.CSModelException: Encountered serialization exception from Job with id 667606c127e630be60370171 in collection jobs
Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/models/mongo.py”, line 590, in to_mongo
return self.mongo_encode(self.model_dump(exclude={“id”}, by_alias=True))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/pydantic/main.py”, line 463, in model_dump
return self.pydantic_serializer.to_python(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/models/job.py”, line 697, in build_errors
return errors + self.spec.extra_build_errors
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/compute/jobs/class3D/spec.py”, line 505, in extra_build_errors
if self.params.class3D_filter_hp_res and self.params.class3D_filter_hp_res <= self.params.class3D_target_res:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: ‘<=’ not supported between instances of ‘float’ and ‘NoneType’

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/cli/upgrade.py”, line 339, in validate_project
job.to_mongo()
File “/home/user/cryosparc/cryosparc_master/models/mongo.py”, line 592, in to_mongo
raise CSModelException(
models.error.CSModelException: Encountered serialization exception from Job with id 667606c227e630be603701cb in collection jobs

---

P20

```text
Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/models/mongo.py”, line 568, in from_mongo
model = cls.model_validate(data, context=context)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/pydantic/main.py”, line 705, in model_validate
return cls._pydantic_validator_.validate_python(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
pydantic_core._pydantic_core.ValidationError: 1 validation error for Job
outputs
Value should have at most 500 items after validation, not 1001 [type=too_long, input_value=Outputs(root={‘split_0’: …test_summary_stats={})}), input_type=Outputs]
For further information visit Redirecting...

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/models/job.py”, line 1209, in from_mongo
job = super().from_mongo(data, context=context, skip_copy=skip_copy)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/models/mongo.py”, line 570, in from_mongo
raise CSModelException(
models.error.CSModelException: Encountered validation exception from Job with id 68f93306f6ab5cf609e3b1dc in collection jobs

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/cli/upgrade.py”, line 331, in validate_project
job = Job.from_mongo(job_doc, context={“upgrade”: True})
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/models/job.py”, line 1213, in from_mongo
raise CSModelException(f"Failed to parse job {data.get(‘project_uid’)} {data.get(‘uid’)}") from e
models.error.CSModelException: Failed to parse job P20 J3211
``` :contentReference[oaicite:2]{index=2}

bsobol · February 2, 2026, 5:07pm

Look at the changelog of 5.0.1. Your issues look exactly like what was fixed.

wtempel · February 2, 2026, 7:12pm

@V3eneno Please let us know if you experience problems importing the affected projects after updating CryoSPARC to v5.0.1.

V3eneno · February 3, 2026, 3:51am

Thanks, but how can I rescue the failed import right now? The only option in Cryosparc now is delate from database.

wtempel · February 3, 2026, 10:53pm

@V3eneno Am I understanding the current status and question correctly:

In v5.0.0, attachment of the project directory as project P20 failed, leading to an incompletely attached project P20?
In v5.0.1, attachment of the same project was attempted again and succeeded.
You wish to remove database records for incompletely imported project P20

?
If so, please can you post the outputs of these commands:

old_puid="P20"
new_puid="P21" # change definition as needed
cryosparcm cli "api.projects.find_one('$old_puid')"
cryosparcm log api | grep $old_puid | tail -n 30
cryosparcm cli "api.projects.find_one('$new_puid')"
cryosparcm log api | grep $new_puid | tail -n 30

V3eneno · February 4, 2026, 9:42pm

Nope, both 5.0 and 5.0.1 fail. P20 has been detached by cryosparc when update to 5.0
P69 is the import in 5.0
P71 is 5.0.1
Non of them work.

P69
Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/tools/cryosparc/api.py”, line 238, in _call
return self._handle_response(_schema, res)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/tools/cryosparc/api.py”, line 158, in _handle_response
res.raise_for_status()
File “/home/user/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpx/_models.py”, line 829, in raise_for_status
raise HTTPStatusError(message, request=request, response=self)
httpx.HTTPStatusError: Client error ‘404 Not Found’ for url ‘http://galileo:39002/projects/P20’
For more information check: 404 Not Found - HTTP | MDN

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “”, line 198, in _run_module_ File “”, line 88, in _run_code
File “/home/user/cryosparc/cryosparc result = eval(sys.argv[1], {“api”: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File “”, line 1, in
File “/home/user/cryosparc/cryosparc return namespace._call(method, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File “/home/user/cryosparc/cryosparc raise APIError(“received error tools.cryosparc.errors.APIError: Response data:
{
“detail”: “Project P20 not found”
}
2026-02-04 15:38:30,229 app 2026-02-04 15:38:30,229 uvicorn.access {“id”: “697934b5e755bd1dd321fff4”, 2026-02-02 12:43:09,836 uvicorn.access 2026-02-02 12:43:09,877 uvicorn.access 2026-02-02 12:45:37,366 uvicorn.access 2026-02-02 14:11:28,476 uvicorn.access 2026-02-02 14:11:50,778 uvicorn.access 2026-02-02 16:56:35,397 uvicorn.access 2026-02-02 16:56:35,423 uvicorn.access 2026-02-02 16:56:41,576 uvicorn.access 2026-02-02 16:56:44,197 uvicorn.access 2026-02-02 16:56:44,252 uvicorn.access 2026-02-02 16:56:47,538 uvicorn.access 2026-02-02 16:56:47,954 uvicorn.access 2026-02-02 16:56:55,055 uvicorn.access 2026-02-02 16:57:58,784 uvicorn.access 2026-02-02 21:02:57,722 uvicorn.access 2026-02-02 21:02:57,740 uvicorn.access 2026-02-02 21:03:40,471 uvicorn.access 2026-02-02 21:45:05,910 uvicorn.access 2026-02-02 21:45:06,088 uvicorn.access 2026-02-02 21:46:03,668 uvicorn.access 2026-02-02 21:50:12,887 uvicorn.access 2026-02-03 12:29:37,119 uvicorn.access 2026-02-03 12:29:37,150 uvicorn.access 2026-02-03 14:30:19,946 uvicorn.access 2026-02-03 14:30:34,924 uvicorn.access 2026-02-03 15:14:47,610 uvicorn.access 2026-02-03 15:42:52,432 uvicorn.access 2026-02-03 15:52:29,972 uvicorn.access 2026-02-04 15:35:18,268 uvicorn.access 2026-02-04 15:38:33,105 uvicorn.access as_main
_master/cli/setup_client.py”, line 28, in
api, “db”: db, “gfs”: gfs}, {})
^^^^^^^^^^^^^^^^^^^
_master/tools/cryosparc/api.py”, line 324, in endpoint
path, schema, *args, **kwargs)
^^^^^^^^^^^^^^^^
_master/tools/cryosparc/api.py”, line 240, in _call
response”, res=err.response) from err
*** [API] (GET http://galileo:39002/projects/P20, code 404) received error response
cryosparc_except ERROR | GET http://galileo:39002/projects/P20 encountered 404 exception: Project P20 not found
send INFO | 127.0.0.1:34180 - “GET /projects/P20 HTTP/1.1” 404
“updated_at”: “2026-02-03T18:29:37.137000Z”, “created_at”: “2024-10-18T17:23:45.901000Z”, “autodump”: false, “uid”: “P69”, “project_dir”: “/home/user/Data/CS_Project_file/NFB/CS-n4-vrna-apo-and-p1-slac”, “owner_user_id”: “665112e30ec36e01397b8dde”, “title”: “N4_vRNA_Apo_and_P1_SLAC”, “description”: “Enter a description.”, “project_params_pdef”: {}, “queue_paused”: false, “deleted”: false, “deleting”: false, “users_with_access”: [“665112e30ec36e01397b8dde”], “size”: 0, “size_last_updated”: “2024-10-23T17:38:39.921000Z”, “last_accessed”: {“name”: “nfbellis”, “accessed_at”: “2026-02-03T18:29:37.137000Z”}, “archived”: false, “detached”: false, “generate_intermediate_results_settings”: {“class_2D_new”: false, “class_3D”: false, “var_3D_disp”: false}, “last_exp_group_id_used”: 4, “imported_at”: “2026-01-27T21:57:09.495000Z”, “import_status”: “failed”, “project_stats”: {“workspace_count”: 93, “session_count”: 2, “job_count”: 2643, “job_types”: {“select_2D”: 508, “class_2D_new”: 358, “homo_reconstruct”: 315, “homo_abinit”: 256, “nonuniform_refine_new”: 231, “new_local_refine”: 162, “class_3D”: 160, “import_volumes”: 65, “volume_tools”: 61, “rtp_worker”: 50, “extract_micrographs_multi”: 50, “hetero_refine”: 48, “align_3D_new”: 31, “particle_sets”: 25, “ctf_refine_local”: 24, “curate_exposures_v2”: 23, “template_picker_gpu”: 22, “inspect_picks_v2”: 19, “remove_duplicate_particles”: 18, “create_templates”: 16, “subset_particles”: 15, “cache_particles”: 14, “extract_micrographs_cpu_parallel”: 14, “downsample_particles”: 13, “topaz_extract”: 13, “local_resolution”: 12, “volume_alignment_tools”: 12, “reference_motion_correction”: 9, “homo_refine_new”: 8, “particle_subtract”: 8, “simulator_gpu”: 7, “blob_picker_gpu”: 7, “ctf_refine_global”: 6, “rebalance_3D”: 6, “autoselect_2D”: 5, “patch_ctf_estimation_multi”: 4, “exposure_sets”: 4, “orientation_diagnostics”: 4, “rebalance_classes_2D”: 4, “topaz_train”: 4, “reference_select_2D”: 4, “patch_motion_correction_multi”: 4, “export_live_exposures”: 3, “export_live_particles”: 3, “snowflake”: 2, “live_session”: 2, “var_3D”: 2, “manual_picker_v2”: 2, “class_2D_streaming”: 2, “reconstruct_2D”: 2, “junk_detector_v1”: 1, “var_3D_disp”: 1, “local_filter”: 1, “auto_blob_picker_gpu”: 1, “import_movies”: 1, “import_micrographs”: 1}, “job_sections”: {“import”: 67, “motion_correction”: 13, “ctf_estimation”: 4, “exposure_curation”: 24, “particle_picking”: 67, “extraction”: 77, “deep_picker”: 17, “particle_curation”: 897, “reconstruction”: 256, “refinement”: 602, “ctf_refinement”: 30, “variability”: 163, “postprocessing”: 17, “local_refinement”: 170, “utilities”: 167, “simulations”: 7, “live”: 60}, “job_status”: {“completed”: 2498, “building”: 140, “killed”: 5}, “updated_at”: “2026-01-28T16:30:08.236000Z”}, “created_at_version”: “v4.6.0”, “is_cleanup_in_progress”: false, “tags”: , “starred_by”: , “autodump_failed”: false, “autodump_errors”: , “uid_num”: 69}
send INFO | 127.0.0.1:46796 - “GET /projects/P69/generate_intermediate_results_settings HTTP/1.1” 200
send INFO | 127.0.0.1:46808 - “POST /projects/P69%3Aview HTTP/1.1” 200
send INFO | 127.0.0.1:56616 - “POST /projects/P69%3Astar HTTP/1.1” 422
send INFO | 127.0.0.1:57962 - “GET /projects/P69/generate_intermediate_results_settings HTTP/1.1” 200
send INFO | 127.0.0.1:53516 - “GET /projects/P69/generate_intermediate_results_settings HTTP/1.1” 200
send INFO | 127.0.0.1:34088 - “GET /projects/P69/generate_intermediate_results_settings HTTP/1.1” 200
send INFO | 127.0.0.1:34096 - “POST /projects/P69%3Aview HTTP/1.1” 200
send INFO | 127.0.0.1:47208 - “POST /projects/P69/workspaces/W52%3Aview HTTP/1.1” 200
send INFO | 127.0.0.1:47216 - “POST /projects/P69/workspaces/W30/jobs/J1063%3Aview HTTP/1.1” 200
send INFO | 127.0.0.1:47218 - “POST /projects/P69/workspaces/W30/jobs/J1063%3Aview HTTP/1.1” 200
send INFO | 127.0.0.1:47220 - “POST /projects/P69/workspaces/W52%3Aview HTTP/1.1” 200
send INFO | 127.0.0.1:55164 - “POST /projects/P69%3Aview HTTP/1.1” 200
send INFO | 127.0.0.1:55168 - “GET /projects/P69/generate_intermediate_results_settings HTTP/1.1” 200
send INFO | 127.0.0.1:38288 - “POST /projects/P69%3Aview HTTP/1.1” 200
send INFO | 127.0.0.1:55364 - “GET /projects/P69/generate_intermediate_results_settings HTTP/1.1” 200
send INFO | 127.0.0.1:55374 - “POST /projects/P69%3Aview HTTP/1.1” 200
send INFO | 127.0.0.1:48590 - “GET /projects/P69%3Apreview_delete HTTP/1.1” 200
send INFO | 127.0.0.1:52438 - “POST /projects/P69%3Aview HTTP/1.1” 200
send INFO | 127.0.0.1:52446 - “GET /projects/P69/generate_intermediate_results_settings HTTP/1.1” 200
send INFO | 127.0.0.1:38750 - “GET /projects/P69%3Apreview_delete HTTP/1.1” 200
send INFO | 127.0.0.1:43226 - “POST /projects/P69%3Aview HTTP/1.1” 200
send INFO | 127.0.0.1:42746 - “GET /projects/P69/generate_intermediate_results_settings HTTP/1.1” 200
send INFO | 127.0.0.1:42748 - “POST /projects/P69%3Aview HTTP/1.1” 200
send INFO | 127.0.0.1:56352 - “GET /projects/P69/generate_intermediate_results_settings HTTP/1.1” 200
send INFO | 127.0.0.1:56366 - “GET /projects/P69%3Apreview_delete HTTP/1.1” 200
send INFO | 127.0.0.1:42542 - “GET /projects/P69/generate_intermediate_results_settings HTTP/1.1” 200
send INFO | 127.0.0.1:59086 - “GET /projects/P69/generate_intermediate_results_settings HTTP/1.1” 200
send INFO | 127.0.0.1:44432 - “GET /projects/P69/generate_intermediate_results_settings HTTP/1.1” 200
send INFO | 127.0.0.1:38782 - “GET /projects/P69/generate_intermediate_results_settings HTTP/1.1” 200
send INFO | 127.0.0.1:34192 - “GET /projects/P69 HTTP/1.1” 200

P71
Traceback (most recent call last):
File “/home/user/cryosparc/cryosparc_master/tools/cryosparc/api.py”, line 238, in _call
return self._handle_response(_schema, res)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/tools/cryosparc/api.py”, line 158, in _handle_response
res.raise_for_status()
File “/home/user/cryosparc/cryosparc_master/.pixi/envs/master/lib/python3.12/site-packages/httpx/_models.py”, line 829, in raise_for_status
raise HTTPStatusError(message, request=request, response=self)
httpx.HTTPStatusError: Client error ‘404 Not Found’ for url ‘http://galileo:39002/projects/P20’
For more information check: 404 Not Found - HTTP | MDN

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “”, line 198, in _run_module_as_main
File “”, line 88, in _run_code
File “/home/user/cryosparc/cryosparc_master/cli/setup_client.py”, line 28, in
result = eval(sys.argv[1], {“api”: api, “db”: db, “gfs”: gfs}, {})
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “”, line 1, in
File “/home/user/cryosparc/cryosparc_master/tools/cryosparc/api.py”, line 324, in endpoint
return namespace._call(method, path, schema, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/home/user/cryosparc/cryosparc_master/tools/cryosparc/api.py”, line 240, in _call
raise APIError(“received error response”, res=err.response) from err
tools.cryosparc.errors.APIError: *** [API] (GET http://galileo:39002/projects/P20, code 404) received error response
Response data:
{
“detail”: “Project P20 not found”
}
2026-02-04 15:38:30,229 app cryosparc_except ERROR | GET http://galileo:39002/projects/P20 encountered 404 exception: Project P20 not found
2026-02-04 15:38:30,229 uvicorn.access send INFO | 127.0.0.1:34180 - “GET /projects/P20 HTTP/1.1” 404
2026-02-04 15:39:34,899 app cryosparc_except ERROR | GET http://galileo:39002/projects/P20 encountered 404 exception: Project P20 not found
2026-02-04 15:39:34,900 uvicorn.access send INFO | 127.0.0.1:42460 - “GET /projects/P20 HTTP/1.1” 404
{“id”: “69823b4881a30ded419251fc”, “updated_at”: “2026-02-03T18:55:39.401000Z”, “created_at”: “2024-10-18T17:23:45.901000Z”, “autodump”: false, “uid”: “P71”, “project_dir”: “/home/user/Data/CS_Project_file/NFB/CS-n4-vrna-apo-and-p1-slac”, “owner_user_id”: “665112e30ec36e01397b8dde”, “title”: “N4_vRNA_Apo_and_P1_SLAC”, “description”: “Enter a description.”, “project_params_pdef”: {}, “queue_paused”: false, “deleted”: false, “deleting”: false, “users_with_access”: [“665112e30ec36e01397b8dde”], “size”: 0, “size_last_updated”: “2024-10-23T17:38:39.921000Z”, “last_accessed”: {“name”: “nfbellis”, “accessed_at”: “2026-02-03T18:55:39.401000Z”}, “archived”: false, “detached”: false, “generate_intermediate_results_settings”: {“class_2D_new”: false, “class_3D”: false, “var_3D_disp”: false}, “last_exp_group_id_used”: 4, “imported_at”: “2026-02-03T18:15:36.536000Z”, “import_status”: “failed”, “project_stats”: {“workspace_count”: 93, “session_count”: 2, “job_count”: 2643, “job_types”: {“select_2D”: 508, “class_2D_new”: 358, “homo_reconstruct”: 315, “homo_abinit”: 256, “nonuniform_refine_new”: 231, “new_local_refine”: 162, “class_3D”: 160, “import_volumes”: 65, “volume_tools”: 61, “extract_micrographs_multi”: 50, “rtp_worker”: 50, “hetero_refine”: 48, “align_3D_new”: 31, “particle_sets”: 25, “ctf_refine_local”: 24, “curate_exposures_v2”: 23, “template_picker_gpu”: 22, “inspect_picks_v2”: 19, “remove_duplicate_particles”: 18, “create_templates”: 16, “subset_particles”: 15, “cache_particles”: 14, “extract_micrographs_cpu_parallel”: 14, “downsample_particles”: 13, “topaz_extract”: 13, “volume_alignment_tools”: 12, “local_resolution”: 12, “reference_motion_correction”: 9, “homo_refine_new”: 8, “particle_subtract”: 8, “simulator_gpu”: 7, “blob_picker_gpu”: 7, “ctf_refine_global”: 6, “rebalance_3D”: 6, “autoselect_2D”: 5, “reference_select_2D”: 4, “exposure_sets”: 4, “orientation_diagnostics”: 4, “patch_ctf_estimation_multi”: 4, “patch_motion_correction_multi”: 4, “rebalance_classes_2D”: 4, “topaz_train”: 4, “export_live_exposures”: 3, “export_live_particles”: 3, “snowflake”: 2, “reconstruct_2D”: 2, “manual_picker_v2”: 2, “var_3D”: 2, “live_session”: 2, “class_2D_streaming”: 2, “junk_detector_v1”: 1, “import_micrographs”: 1, “var_3D_disp”: 1, “auto_blob_picker_gpu”: 1, “import_movies”: 1, “local_filter”: 1}, “job_sections”: {“import”: 67, “motion_correction”: 13, “ctf_estimation”: 4, “exposure_curation”: 24, “particle_picking”: 67, “extraction”: 77, “deep_picker”: 17, “particle_curation”: 897, “reconstruction”: 256, “refinement”: 602, “ctf_refinement”: 30, “variability”: 163, “postprocessing”: 17, “local_refinement”: 170, “utilities”: 167, “simulations”: 7, “live”: 60}, “job_status”: {“completed”: 2498, “building”: 140, “killed”: 5}, “updated_at”: “2026-02-03T21:14:26.099000Z”}, “created_at_version”: “v4.6.0”, “is_cleanup_in_progress”: false, “tags”: , “starred_by”: , “autodump_failed”: false, “autodump_errors”: , “uid_num”: 71}
2026-02-03 12:54:12,545 core.data_management attach_jobs_data ERROR | Error importing job data for Job P71-J985 (Homogeneous Reconstruction Only)
2026-02-03 12:54:12,560 core.data_management _update_imported INFO | [IMPORT] Updated Job P71-J986 (3D Classification) asset references
2026-02-03 12:54:12,571 core.data_management attach_jobs_data ERROR | Error importing job data for Job P71-J987 (Non-uniform Refinement)
2026-02-03 12:54:12,587 core.data_management attach_jobs_data ERROR | Error importing job data for Job P71-J988 (Non-uniform Refinement)
2026-02-03 12:54:12,605 core.data_management attach_jobs_data ERROR | Error importing job data for Job P71-J989 (3D Classification)
2026-02-03 12:54:12,619 core.data_management _update_imported INFO | [IMPORT] Updated Job P71-J99 (Live Preprocessing Worker) asset references
2026-02-03 12:54:15,478 core.data_management _update_imported INFO | [IMPORT] Updated Job P71-J990 (Local Refinement) asset references
2026-02-03 12:54:15,486 core.data_management attach_jobs_data ERROR | Error importing job data for Job P71-J991 (Volume Tools)
2026-02-03 12:54:15,495 core.data_management attach_jobs_data ERROR | Error importing job data for Job P71-J992 (Local Refinement)
2026-02-03 12:54:15,509 core.data_management attach_jobs_data ERROR | Error importing job data for Job P71-J993 (Ab-Initio Reconstruction)
2026-02-03 12:54:15,520 core.data_management attach_jobs_data ERROR | Error importing job data for Job P71-J994 (Homogeneous Reconstruction Only)
2026-02-03 12:54:15,533 core.data_management attach_jobs_data ERROR | Error importing job data for Job P71-J995 (Homogeneous Reconstruction Only)
2026-02-03 12:54:15,547 core.data_management attach_jobs_data ERROR | Error importing job data for Job P71-J996 (Homogeneous Reconstruction Only)
2026-02-03 12:54:15,561 core.data_management attach_jobs_data ERROR | Error importing job data for Job P71-J997 (Non-uniform Refinement)
2026-02-03 12:54:15,579 core.data_management _update_imported INFO | [IMPORT] Updated Job P71-J998 (3D Classification) asset references
2026-02-03 12:54:15,589 core.data_management attach_jobs_data ERROR | Error importing job data for Job P71-J999 (Select 2D Classes)
2026-02-03 12:54:16,557 core.data_management attach_project_d ERROR | Not all job data could be loaded into Project P71, 766 failed to load.
2026-02-03 12:54:16,557 core.data_management attach_project_d ERROR | Not all jobs in the manifest were loaded into Project P71, 1 failed to load.
2026-02-03 12:55:22,414 uvicorn.access send INFO | 127.0.0.1:39914 - “GET /projects/P71/generate_intermediate_results_settings HTTP/1.1” 200
2026-02-03 12:55:22,485 uvicorn.access send INFO | 127.0.0.1:39924 - “POST /projects/P71%3Aview HTTP/1.1” 200
2026-02-03 12:55:23,559 uvicorn.access send INFO | 127.0.0.1:39926 - “GET /projects/P71/generate_intermediate_results_settings HTTP/1.1” 200
2026-02-03 12:55:23,593 uvicorn.access send INFO | 127.0.0.1:39934 - “POST /projects/P71%3Aview HTTP/1.1” 200
2026-02-03 12:55:37,780 uvicorn.access send INFO | 127.0.0.1:35286 - “POST /projects/P71%3Aview HTTP/1.1” 200
2026-02-03 12:55:39,411 uvicorn.access send INFO | 127.0.0.1:35296 - “POST /projects/P71%3Aview HTTP/1.1” 200
2026-02-03 14:29:06,616 uvicorn.access send INFO | 127.0.0.1:58334 - “GET /projects/P71/generate_intermediate_results_settings HTTP/1.1” 200
2026-02-03 14:37:35,337 uvicorn.access send INFO | 127.0.0.1:32914 - “POST /projects/P71/workspaces/W74%3Aview HTTP/1.1” 200
2026-02-03 15:14:28,517 uvicorn.access send INFO | 127.0.0.1:51724 - “GET /projects/P71/generate_intermediate_results_settings HTTP/1.1” 200
2026-02-03 15:14:33,626 uvicorn.access send INFO | 127.0.0.1:59358 - “POST /projects/P71/workspaces/W74%3Aview HTTP/1.1” 200
2026-02-03 15:37:59,918 uvicorn.access send INFO | 127.0.0.1:39296 - “GET /projects/P71/generate_intermediate_results_settings HTTP/1.1” 200
2026-02-04 15:39:37,769 uvicorn.access send INFO | 127.0.0.1:42462 - “GET /projects/P71 HTTP/1.1” 200

wtempel · February 4, 2026, 10:55pm

Thanks @V3eneno for these details.
Please can you create a copy of the api.log and share it with the developers:

# commands  to run on galileo
cd $(mktemp -d)
cp /home/user/cryosparc/cryosparc_master/run/api.log .
gzip api.log
realpath api.log.gz # note the path for file retrieval

and share the api.log.gz file with the CryoSPARC developers?

V3eneno · February 6, 2026, 4:05am

Can you give me an email address or anything you want?

wtempel · February 6, 2026, 2:32pm

@V3eneno I sent you a personal message regarding the email address. Did you receive it?
You can access My messages via the “hamburger” button near the upper right corner of the forum page.

V3eneno · February 23, 2026, 7:49pm

Hi, I send email a while ago, any feedback?

wtempel · March 3, 2026, 5:15pm

Thanks @V3eneno for sharing the logs. The project appears to contain thousands of jobs, of which hundreds fail to import due to errors reading metadata files (such as data plots) from the project directory. This suggests a systematic problem with the storage device itself or with the connection between the computer and the storage.
What type of device stores the project directory. The following command may provide some insight:

df -Th /home/user/Data/CS_Project_file/NFB/

V3eneno · March 3, 2026, 9:02pm

user@vivaldi:~$ df -Th /home/user/Data/CS_Project_file/NFB/
Filesystem Type Size Used Avail Use% Mounted on
galileo:/home/user/Data/CS_Project_file nfs4 304T 182T 122T 60% /home/user/Data/CS_Project_file

wtempel · March 16, 2026, 6:37pm

CryoSPARC currently bars the attachment of “incomplete” projects. For a future CryoSPARC minor release, we consider enabling users to optionally accept attaching an incomplete project. Even though routine processing may not work in such “incomplete” projects, the user may be able to export select jobs for import into an intact project.
Currently, some browsing is possible for a project whose import has failed. If you can identify a specific job whose data may be particular useful in continued processing, we may be able to help recover some of that job’s data so that you may continue processing in a new project.