Assertion error in local refinement

Troubleshooting
1

Hello, I am attempting to run local refinement following particle subtraction. In both the new and legacy local refinement jobs I receive an assertion error after several iterations have passed. Any help would be much appreciated! Here is an error message I received on one of these jobs:

[CPU: 3.80 GB] Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 88, in cryosparc_compute.run.main
File “/home/cryosparc2/cryosparc2_worker/cryosparc_compute/jobs/runcommon.py”, line 908, in passthrough_outputs
dset = load_input_group(input_group_name, passthrough_result_names, allow_passthrough=True)
File “/home/cryosparc2/cryosparc2_worker/cryosparc_compute/jobs/runcommon.py”, line 556, in load_input_group
dsets = [load_input_connection_slots(input_group_name, keep_slot_names, idx, allow_passthrough=allow_passthrough) for idx in range(num_connections)]
File “/home/cryosparc2/cryosparc2_worker/cryosparc_compute/jobs/runcommon.py”, line 556, in
dsets = [load_input_connection_slots(input_group_name, keep_slot_names, idx, allow_passthrough=allow_passthrough) for idx in range(num_connections)]
File “/home/cryosparc2/cryosparc2_worker/cryosparc_compute/jobs/runcommon.py”, line 527, in load_input_connection_slots
dsets = [load_input_connection_single_slot(input_group_name, slot_name, connection_idx, allow_passthrough=allow_passthrough) for slot_name in slot_names]
File “/home/cryosparc2/cryosparc2_worker/cryosparc_compute/jobs/runcommon.py”, line 527, in
dsets = [load_input_connection_single_slot(input_group_name, slot_name, connection_idx, allow_passthrough=allow_passthrough) for slot_name in slot_names]
File “/home/cryosparc2/cryosparc2_worker/cryosparc_compute/jobs/runcommon.py”, line 517, in load_input_connection_single_slot
output_result = com.query(otherjob[‘output_results’], lambda r : r[‘group_name’] == slotconnection[‘group_name’] and r[‘name’] == slotconnection[‘result_name’], error=‘No match for %s.%s in job %s’ % (slotconnection[‘group_name’], slotconnection[‘result_name’], job[‘uid’]))
File “/home/cryosparc2/cryosparc2_worker/cryosparc_compute/jobs/common.py”, line 406, in query
assert res != default, error
AssertionError: No match for particles.alignments_class_0 in job J533

2

After retrying these jobs I realized the error occurs after the final iteration, when the particle outputs are being generated. The issue was related to the particle stack I used.

3

Hi @DavidYanofsky,

Thanks for the report – just confirming, were you able to work around the issue?

Best,
Michael

4

Hi Michael, yes it worked out. I think it was a fairly unique problem.

My map did not have the correct axis of symmetry after ab initio so I refined my particles against an imported volume that had the correct axis. Then I ran symmetry expansion to take advantage of the symmetry.

For some reason, these symmetry expanded particles gave the error I posted about during local refinement. Repeating the same set of jobs without symmetry expansion gave me a working result. This is true even when symmetry was enforced in the new local refinement.