Error during extract from micrographs jobs

[Nicholas]

Hello, I have been getting the following error when trying to extract from micrographs. I have had no problems with any other data sets collected at the same time as this one, and processed in the exact same way. The same error occurs for every micrograph in the data set.

Does anyone have an idea what is going on with this?

[wtempel]

Hi @Nicholas

Please can you post:

1. the text of the error message (why not just a screenshot?)
2. expanded inputs from the Inputs and Parameters tab
   
   
3. the job types from which the inputs were connected

[Nicholas]

Hi, please see below:
1.

[CPU: 400.0 MB]  Error occurred while processing micrograph J4/motioncorrected/017355273394818217867_23nov13c_reelinlrp8_00011gr_00027sq_v02_00002hln_00004enn.frames_patch_aligned_doseweighted.mrc
Traceback (most recent call last):
  File "/cm/shared/apps/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py", line 60, in exec
    return self.process(item)
  File "/cm/shared/apps/cryosparc/cryosparc_worker/cryosparc_compute/jobs/extract/run.py", line 486, in process
    path_abs = os.path.join(proj_dir_abs, micrograph['background_blob/path'])
KeyError: 'background_blob/path'

Marking J4/motioncorrected/017355273394818217867_23nov13c_reelinlrp8_00011gr_00027sq_v02_00002hln_00004enn.frames_patch_aligned_doseweighted.mrc as incomplete and continuing...

3. the previous 3 jobs were a) import movies,b) patch motion correction (multi) c) patch CTF correction (multi) d) blob picker

[wtempel]

Thanks @Nicholas. Please can you expand the micrographs and particles sections by clicking on the respective > symbols.

I wanted to see whether the J6.micrographs.background_blob subsection is missing.
Please can you also post

• a screenshot of the Outputs section of upstream job J6
• the job type of of J6

[Nicholas]

Hi- sorry for the late reply I have been on vacation.

Please the the screenshot of the Outputs section for J6 below. J6 is an Blob Picker job.

[Nicholas]

The micrographs section is below:

[wtempel]

Interesting. You may want to check in which upstream job

@Nicholas

b) patch motion correction (multi) c) patch CTF correction (multi) d) blob picker

outputs like background_blob went missing. Below is a screenshot of outputs from a Blob Picker job within the CryoSPARC v4.4.1 Extensive Validation.