Error when running Symmetry Search Utility

[TatBRU]

Hello,

I started using cryoSPARC recently to process helical samples. I was trying to run a Symmetry Search Utility job but it always fails and outputs this error message:

" Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 115, in cryosparc_master.cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/helix/run_utils.py”, line 499, in cryosparc_master.cryosparc_compute.jobs.helix.run_utils.run_search
AttributeError: ‘NoneType’ object has no attribute ‘split’ "

This is with varying parameters, both in pitch and rise mode and using different models and/or masks. We are using the latest cryoSPARC release.

I was wondering if anyone had had this issue previously and if they had found a way to solve this. Is the issue due to the data used or to the cryoSPARC installation?

Any suggestion would be appreciated. Thank you.

Tatiana

[wtempel]

@TatBRU Please can you post the output of this command

cryosparcm cli "get_job('P12', 'J934', 'job_type', 'version', 'params_spec', 'instance_information', 'input_slot_groups')"

substituting the failed job’s actual project and job IDs for P12 and J934, respectively.

[TatBRU]

@wtempel

Please can you post the output of this command

Hello @wtempel,

Here is the output I get while running this command:

" cryosparcm cli “get_job(‘P26’, ‘J142’, ‘job_type’, ‘version’, ‘params_spec’, ‘instance_information’, ‘input_slot_groups’)”

{‘_id’: ‘664f31060cacd60bc465b247’, ‘input_slot_groups’: [{‘connections’: [{‘group_name’: ‘volume’, ‘job_uid’: ‘J135’, ‘slots’: [{‘group_name’: ‘volume’, ‘job_uid’: ‘J135’, ‘result_name’: ‘map’, ‘result_type’: ‘volume.blob’, ‘slot_name’: ‘map’, ‘version’: ‘F’}, {‘group_name’: ‘volume’, ‘job_uid’: ‘J135’, ‘result_name’: ‘map_sharp’, ‘result_type’: ‘volume.blob’, ‘slot_name’: ‘map_sharp’, ‘version’: ‘F’}, {‘group_name’: ‘volume’, ‘job_uid’: ‘J135’, ‘result_name’: ‘map_half_A’, ‘result_type’: ‘volume.blob’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘volume’, ‘job_uid’: ‘J135’, ‘result_name’: ‘map_half_B’, ‘result_type’: ‘volume.blob’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘volume’, ‘job_uid’: ‘J135’, ‘result_name’: ‘mask_refine’, ‘result_type’: ‘volume.blob’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘volume’, ‘job_uid’: ‘J135’, ‘result_name’: ‘mask_fsc’, ‘result_type’: ‘volume.blob’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘volume’, ‘job_uid’: ‘J135’, ‘result_name’: ‘mask_fsc_auto’, ‘result_type’: ‘volume.blob’, ‘slot_name’: None, ‘version’: ‘F’}, {‘group_name’: ‘volume’, ‘job_uid’: ‘J135’, ‘result_name’: ‘precision’, ‘result_type’: ‘volume.blob’, ‘slot_name’: None, ‘version’: ‘F’}]}], ‘count_max’: 1, ‘count_min’: 1, ‘description’: ‘Volume’, ‘name’: ‘volume’, ‘repeat_allowed’: False, ‘slots’: [{‘description’: ‘’, ‘name’: ‘map’, ‘optional’: True, ‘title’: ‘Volume raw data’, ‘type’: ‘volume.blob’}, {‘description’: ‘’, ‘name’: ‘map_sharp’, ‘optional’: True, ‘title’: ‘Volume raw data’, ‘type’: ‘volume.blob’}, {‘description’: ‘’, ‘name’: ‘symmetry’, ‘optional’: True, ‘title’: ‘Volume symmetry data’, ‘type’: ‘volume.symmetry’}], ‘title’: ‘Volume’, ‘type’: ‘volume’}, {‘connections’: , ‘count_max’: 1, ‘count_min’: 0, ‘description’: ‘Mask’, ‘name’: ‘mask’, ‘repeat_allowed’: False, ‘slots’: [{‘description’: ‘’, ‘name’: ‘mask’, ‘optional’: True, ‘title’: ‘Mask raw data’, ‘type’: ‘volume.blob’}], ‘title’: ‘Mask’, ‘type’: ‘mask’}], ‘instance_information’: {‘CUDA_version’: ‘11.8’, ‘available_memory’: ‘119.15GB’, ‘cpu_model’: ‘Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz’, ‘driver_version’: ‘12.4’, ‘gpu_info’: [{‘id’: 0, ‘mem’: 8500609024, ‘name’: ‘NVIDIA GeForce GTX 1080’, ‘pcie’: ‘0000:02:00’}, {‘id’: 1, ‘mem’: 8500609024, ‘name’: ‘NVIDIA GeForce GTX 1080’, ‘pcie’: ‘0000:04:00’}, {‘id’: 2, ‘mem’: 8500609024, ‘name’: ‘NVIDIA GeForce GTX 1080’, ‘pcie’: ‘0000:83:00’}, {‘id’: 3, ‘mem’: 8500609024, ‘name’: ‘NVIDIA GeForce GTX 1080’, ‘pcie’: ‘0000:84:00’}], ‘ofd_hard_limit’: 1048576, ‘ofd_soft_limit’: 1024, ‘physical_cores’: 16, ‘platform_architecture’: ‘x86_64’, ‘platform_node’: ‘gpu4-bioc’, ‘platform_release’: ‘5.10.0-26-amd64’, ‘platform_version’: ‘#1 SMP Debian 5.10.197-1 (2023-09-29)’, ‘total_memory’: ‘125.67GB’, ‘used_memory’: ‘5.49GB’}, ‘job_type’: ‘helix_search’, ‘params_spec’: {‘search_sym_mode’: {‘value’: ‘rise’}, ‘vol_to_search’: {‘value’: ‘map’}}, ‘project_uid’: ‘P26’, ‘uid’: ‘J142’, ‘version’: ‘v4.5.1’} "

[mmclean]

Hi @TatBRU,

Could you check the value of the parameters entitled “Search min and max over ___” (either pitch/number of subunits per turn, or rise/twist, depending on the search mode selected), and ensure that these are set to a comma separated pair of values specifying the desired min,max search range of the symmetry parameter? The job’s info page on our guide has a bit more details on the two search modes.

Best,
Michael

[TatBRU]

Hello @mmclean,

I re-ran the job with both modes and the values separated with a comma but I get the same error message.

Tatiana

[mmclean]

Hello Tatiana,

Thanks for the parameter information. I believe the job also needs the Search min and max over helical twist (degrees) param (if in ‘rise’ mode), or the Search min and max over number of subunits per turn param (if in ‘pitch’ mode) to be set, but it looks like these are not currently set based on the custom parameters.

Best,
Michael

[TatBRU]

Hello @mmclean,

After adding these parameters, the job is now working. Thank you for your help.

Tatiana