Blob Picker Job Error (Bug?): index 0 is out of bounds for axis 0 with size 0


Encountered the following error (below) while running Blob Picker following Patch Motion and Patch CTF jobs. The job would consistently fail on the same micrograph. I went back to the output of the Patch CTF job, and ran Curate Exposures to get rid of all bad micrographs with high CTF Fits and that seems to have solved the problem. My interpretation of the error is that the Blob Picker job will fail if it encounters any micrograph it cannot pick particles from.


PS running 2.8.3

Completed 54 of 6194 : J8/motioncorrected/FoilHole_30146799_Data_30141907_30141908_20190131_1257_Fractions_patch_aligned_doseweighted.mrc
Picked 0 particles in 0.10s (9.28s total)

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/”, line 78, in (/home/installtest/deps_manage/cryosparc2_package/deploy/stage/cryosparc2_worker/cryosparc2_compute/run.c:3954)
File “cryosparc2_worker/cryosparc2_compute/jobs/template_picker_gpu/”, line 58, in (/home/installtest/deps_manage/cryosparc2_package/deploy/stage/cryosparc2_worker/cryosparc2_compute/jobs/template_picker_gpu/run.c:2723)
File “cryosparc2_worker/cryosparc2_compute/jobs/template_picker_gpu/”, line 184, in (/home/installtest/deps_manage/cryosparc2_package/deploy/stage/cryosparc2_worker/cryosparc2_compute/jobs/template_picker_gpu/run.c:14270)
File “cryosparc2_worker/cryosparc2_compute/jobs/template_picker_gpu/”, line 396, in (/home/installtest/deps_manage/cryosparc2_package/deploy/stage/cryosparc2_worker/cryosparc2_compute/jobs/template_picker_gpu/run.c:13809)
File “cryosparc2_compute/jobs/ctf_estimation/”, line 15, in extract_ctf
micshape =[‘location/micrograph_shape’][0]
IndexError: index 0 is out of bounds for axis 0 with size 0

Hi @Yazan,

Thank you for reporting this error. We’ve identified the issue and a fix will be released soon!