IndexError: index 3 is out of bounds for axis 0 with size 0 while preprocessing moves through live in v4.1.2

CryoSPARC Live
1

Hi everybody,

I have a CS live session running smoothly until, at some point, all movies started to fail with this error.

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/jobs/rtp_workers/run.py”, line 371, in cryosparc_compute.jobs.rtp_workers.run.rtp_worker
File “cryosparc_master/cryosparc_compute/jobs/rtp_workers/run.py”, line 434, in cryosparc_compute.jobs.rtp_workers.run.process_movie
File “cryosparc_master/cryosparc_compute/jobs/rtp_workers/run.py”, line 950, in cryosparc_compute.jobs.rtp_workers.run.do_pick
File “/data/software/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/dataset.py”, line 1251, in take
return type(self)([(f, self[f][indices]) for f in self])
File “/data/software/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/dataset.py”, line 1251, in
return type(self)([(f, self[f][indices]) for f in self])
IndexError: index 3 is out of bounds for axis 0 with size 0

I am wondering if somebody else has encountered this error. The collected movies seem to be okay, so I don’t know if it’s a hidden defect with the movies or if it’s maybe a bug from the program. I am using v4.1.2

I have also restarted CS and the Live session several times already.

Best, and thanks!
Armando

2

Hi everybody,

I got the issue resolved!

It turns out it was a problem with the particle picking being set to zero that made the CTFs bug out and, consequently, make the preprocessing fail in live.

To save space, I reduced the picking thresholds to zero, so I wouldn’t pick any particles in live (I had started to do it at first, but then I stopped). I think what happened is that, as Daniel Asarnow said in the last comment in this post Delete extracted particles from cryosparc live? - #4 by wtempel since these new movies didn’t get the particles picked to start with the CTFs must’ve not been displayed properly, and the movies were failing.

I hope this helps somebody.

Best and thanks,
Armando