Hello!
I am running into an issue with the new Micrograph Junk Detector, where the job runs like normal and then runs into an index error after the last example micrograph appears in the event log. Below is the relevant information and image of the error:
Input: Micrographs and particles from Inspect Picks of a Template Picker
Error:
(IndexError: index 632 is out of bounds for axis 1 with size 632)
Anyone have an idea as to what this means?
@perrottza Please can you post the outputs of these commands (replacing P99 and J999 with the relevant project and job IDs):
csprojectid="P99"
csjobid="J999"
cryosparcm cli "get_job('$csprojectid', '$csjobid', 'job_type', 'version', 'instance_information', 'status', 'params_spec', 'errors_run', 'input_slot_groups', 'started_at')"
cryosparcm joblog $csprojectid $csjobid | tail -n 40
cryosparcm eventlog $csprojectid $csjobid | tail -n 40
@perrottza thanks for reporting this. We’ve looked into it and unfortunately this is a bug. It will be fixed in a future release. In the meantime, you may be able to work around it by excluding particle picks that are near to the far +X and +Y edges of the micrographs. You could do this using the “subset particles” job, filtering by X and Y fractional location. Try a manual threshold of 0.9 or so.
– Harris
@perrottza CryoSPARC v4.7.1 contains a fix for this issue. Happy data processing.
Hi, i am still getting this error. I am running junk detector without associated particles on PatchCTF corrected micrographs. Any insights what could cause this>
Traceback (most recent call last):
File "cryosparc_master/cryosparc_compute/run.py", line 129, in cryosparc_master.cryosparc_compute.run.main
File "cryosparc_master/cryosparc_compute/jobs/micrograph_analysis/run_junk_detector.py", line 289, in cryosparc_master.cryosparc_compute.jobs.micrograph_analysis.run_junk_detector.run_junk_detector_v1
File "cryosparc_master/cryosparc_compute/jobs/micrograph_analysis/run_junk_detector.py", line 187, in cryosparc_master.cryosparc_compute.jobs.micrograph_analysis.run_junk_detector.prep_junkseg_train
IndexError: index 0 is out of bounds for axis 0 with size 0
We are running cryosparc 4.7.1 +251124. Thank you!
Update:
Update: The issue was MRC files with a corrupted header (re-processed data form EMPIAR, starting with motioncorrected micrographs and ran the junk detector directly on those imported micrgraphs)
Thanks for the update. To confirm: Were you able to work around this issue?
Yes - I used the cstools combined with a coding agent to find and remove the faulty micrographs. I assume if I had run Patch CTF before Junk detector the faulty micrographs would have been flagged/removed? Would be useful to get a clearer error message from Junk Detector (i,e the UID of the micrograph with the corrupted header) for better debugging.
Cheers,
Matthias
Correct. Patch CTF Estimation would have caught the corrupt micrographs.
