I am trying to generate 2D projections from a 3D volume I’ve imported. I have followed the “typical workflow” of particle picking using a 3D map (Particle picking using 3D map), and gotten to the template picker. Here, I input my selected 2D templates from "Select 2D) and my exposures from “patch CTF”. When I queue the job, however, I get the following error:
Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 85, in cryosparc2_compute.run.main
File “cryosparc2_worker/cryosparc2_compute/jobs/template_picker_gpu/run.py”, line 62, in cryosparc2_compute.jobs.template_picker_gpu.run.run
File “cryosparc2_worker/cryosparc2_compute/jobs/template_picker_gpu/run.py”, line 119, in cryosparc2_compute.jobs.template_picker_gpu.run.do_pick
IndexError: list index out of range
I have tried running it on separate/individual GPUs, various particle dimensions, various lowpass filter, various angular sampling values, with/without CTF filter, and all yields the same error.
Other threads advice that similar errors is due to not having a worker node setup ('List index out of range' during Import Particles - v2.12.4), however I am remote accessing our main master workstation for this job, so I don’t think this error is applicable.
What was the size/pixel size of the micrographs that you are connecting to the template picker? Also what lowpass resolution was set in the template picker job?
The error is actually happening because for some reason the combination of micrograph input size, pixel size, and lowpass resolution as causing the job to think it needs to store the micrograph in a size larger than 4096x4096 during processing (this is the max size). This would only happen if the micrograph was extremely large, was very low magnification, and the lowpass res was set to a very high res.
The pixel size of my micrographs is 1.07 Å. The magnification is 130kx.
For lowpass filter in I have tried several different values, but most recently, causing the same error, 2 Å.
Attempting to find the pixel size, I looked at the “metadata” of my “import movies” job, and found the following excerpt:
},
“psize_A”: {
“title”: “Raw pixel size (A)”,
“section”: “import”,
“value”: null,
“hidden”: false,
“type”: “number”,
“order”: 5,
“advanced”: false,
“desc”: “Pixel size of the raw movie data in Angstroms”
Is the fact that the value here is “null”, or the pixel size otherwise not reported, part of the issue?