Unable to do blob picking

Particle Picking
1

Hi everyone,

I import micrographs into cryosparc v4.1.2 and do Patch CTF estimation and manually curate exposures.
But I’m not able to run blob picking with imported micrographs from curate exposures job (see below)

License is valid.

Launching job on lane default target u124172 …

Running job on master node hostname u124172

[CPU: 194.9 MB Avail: 301.94 GB]
Job J26 Started

[CPU: 194.9 MB Avail: 301.94 GB]
Master running v4.1.2, worker running v4.1.2

[CPU: 194.9 MB Avail: 301.93 GB]
Working in directory: /data/editosome-pncc/CS-editosome-pncc/J26

[CPU: 194.9 MB Avail: 301.93 GB]
Running on lane default

[CPU: 194.9 MB Avail: 301.93 GB]
Resources allocated:

[CPU: 194.9 MB Avail: 301.93 GB]
Worker: u124172

[CPU: 194.9 MB Avail: 301.93 GB]
CPU : [0, 1, 2, 3]

[CPU: 194.9 MB Avail: 301.93 GB]
GPU : [0]

[CPU: 194.9 MB Avail: 301.93 GB]
RAM : [0]

[CPU: 194.9 MB Avail: 301.93 GB]
SSD : False

[CPU: 194.9 MB Avail: 301.94 GB]

[CPU: 194.9 MB Avail: 301.94 GB]
Importing job module for job type blob_picker_gpu…

[CPU: 293.4 MB Avail: 302.23 GB]
Job ready to run

[CPU: 293.4 MB Avail: 302.23 GB]

[CPU: 377.8 MB Avail: 302.14 GB]
Computing cc with FFT size 432

[CPU: 377.8 MB Avail: 302.14 GB]
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 96, in cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/template_picker_gpu/run.py”, line 61, in cryosparc_compute.jobs.template_picker_gpu.run.run
File “cryosparc_master/cryosparc_compute/jobs/template_picker_gpu/run.py”, line 237, in cryosparc_compute.jobs.template_picker_gpu.run.do_pick
File “cryosparc_master/cryosparc_compute/jobs/template_picker_gpu/template_pick_gpu.py”, line 168, in cryosparc_compute.jobs.template_picker_gpu.template_pick_gpu.rotate_downsample
IndexError: list index out of range.

Do I miss anything? Thank you!

2

Please can you post:

  • The expanded Inputs section (under the Inputs and Parameters tab) for this job.
  • Relevant messages from the job log, accessible via Metadata|Log.
    image
    image864×230 13.4 KB
3

1
12150×887 60.1 KB

2
22144×912 59.7 KB

4

Have you enabled one of the
Use [circular|elliptical|ring] blob options?
image

5

Yes, I enabled the “Use circular blob”.

6

Please can you share the P10 J26 job report with us, if the job is still in the failed state that you reported earlier.

7

Thanks for sending us the two job reports. In both cases, the respective job document indicated that use circular blob was disabled. To rule out an error or bug in the GUI, please can you double-check, under Inputs and Parameters, that Use circular blob was really toggled to the right, as shown below:
image

8

It’s quite strange. In both jobs, this option looks the same (see picture).

picking-issue
picking-issue826×305 18.5 KB

9

What happens when you clone the job, toggle Use circular blob to on/right, and run the job again?

10

It works well when toggle the blob to on/right.