Cryosparc 3.1.0 CTF index 1 is out of bounds for axis 0 with size 1

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1

Hello everyone, We have just updated to v3.1.0 to fix the motion error, and then a CTF error occurred.
Here’s the error message:
Traceback (most recent call last):
File “/opt/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 1726, in run_with_except_hook
run_old(*args, **kw)
File “/opt/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/threading.py”, line 870, in run
self._target(*self._args, **self._kwargs)
File “/opt/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 186, in thread_work
work = processor.exec(item)
File “/opt/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 43, in exec
return self.process(item)
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py”, line 112, in cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py”, line 118, in cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py”, line 119, in cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/patchctf.py”, line 71, in cryosparc_compute.jobs.ctf_estimation.patchctf.patchctf_v217
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/patchctf.py”, line 832, in cryosparc_compute.jobs.ctf_estimation.patchctf.patchctf_v217
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/patchctf.py”, line 781, in cryosparc_compute.jobs.ctf_estimation.patchctf.patchctf_v217.compute_cc_fit
IndexError: index 1 is out of bounds for axis 0 with size 1
I have found similar error in v2.14.0 and v2.15.0 update log said this error was repaired. Our data was collected at 22.5kx.
Thanks!

2

Thanks. I tried to install the patch for v2.14.2, however, it was not work in our case for v3.1.0. We have processed 3 motion-corrected datasets, and the error often occured in ~180 pictures. Should I provide any more info?

3

Hello, I have the same problem when trying patch ctf estimation with cryosparc v3.1.0.
This is K3 motion-corrected micrographs from super resolution movies.
I tried the solution from v2.14 and it does not solve the problem.

Traceback (most recent call last):
File “/home/adrian/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 1726, in run_with_except_hook
run_old(*args, **kw)
File “/home/adrian/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/threading.py”, line 870, in run
self._target(*self._args, **self._kwargs)
File “/home/adrian/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 186, in thread_work
work = processor.exec(item)
File “/home/adrian/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 43, in exec
return self.process(item)
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py”, line 112, in cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py”, line 118, in cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py”, line 119, in cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/patchctf.py”, line 71, in cryosparc_compute.jobs.ctf_estimation.patchctf.patchctf_v217
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/patchctf.py”, line 832, in cryosparc_compute.jobs.ctf_estimation.patchctf.patchctf_v217
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/patchctf.py”, line 781, in cryosparc_compute.jobs.ctf_estimation.patchctf.patchctf_v217.compute_cc_fit
IndexError: index 1 is out of bounds for axis 0 with size 1

Traceback (most recent call last):
File “/home/adrian/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 1726, in run_with_except_hook
run_old(*args, **kw)
File “/home/adrian/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/threading.py”, line 870, in run
self._target(*self._args, **self._kwargs)
File “/home/adrian/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 186, in thread_work
work = processor.exec(item)
File “/home/adrian/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 43, in exec
return self.process(item)
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py”, line 209, in cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
AssertionError: Job is not in running state - worker thread with PID 14393 terminating self.
Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 84, in cryosparc_compute.run.main
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py”, line 256, in cryosparc_compute.jobs.ctf_estimation.run.run
AssertionError: Child process with PID 14393 has terminated unexpectedly!

4

I also encounter the same issue:
[CPU: 941.9 MB] Traceback (most recent call last):
File “/home/lrss/softwares/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 1726, in run_with_except_hook
run_old(*args, **kw)
File “/home/lrss/softwares/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/threading.py”, line 870, in run
self._target(*self._args, **self._kwargs)
File “/home/lrss/softwares/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 186, in thread_work
work = processor.exec(item)
File “/home/lrss/softwares/cryosparc/cryosparc_worker/cryosparc_compute/jobs/pipeline.py”, line 43, in exec
return self.process(item)
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py”, line 112, in cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py”, line 118, in cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/run.py”, line 119, in cryosparc_compute.jobs.ctf_estimation.run.run.ctfworker.process
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/patchctf.py”, line 71, in cryosparc_compute.jobs.ctf_estimation.patchctf.patchctf_v217
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/patchctf.py”, line 832, in cryosparc_compute.jobs.ctf_estimation.patchctf.patchctf_v217
File “cryosparc_worker/cryosparc_compute/jobs/ctf_estimation/patchctf.py”, line 781, in cryosparc_compute.jobs.ctf_estimation.patchctf.patchctf_v217.compute_cc_fit
IndexError: index 1 is out of bounds for axis 0 with size 1

any suggestion? thanks

5

I also have the same issue with patch CTF estimation in v3.1.0 and the v2.14 patch does not fix issue.

6

Hi everyone,

This is a known bug having to do with high magnification. We are working on a fix and will include it in the next release. Sorry for the inconvenience.

Harris

7

A patch is now available that fixes this issue. Please see: Patch 210216 available for v3.1.0 - Fixes CPU extraction bug and Patch CTF bug

8

Thanks. We have applied the patch and bug fixed.

9

@spunjani, I ran into the same issue “IndexError: index 1 is out of bounds for axis 0 with size 1”. I updated to v3.2.0 and applied the patch. Same error still occurred. Strange thing is that I processed the same dataset using v3.1.0 to 2D classification without any problem. The reason I started all over is because I used a wrong total dose and activated phase plate by error. During the reprocess, I ran into the following problems: 1. PMC failed after ~3000 out of 6000 micrographs. That is when I updated to V3.2.0 and applied the patch and continued with the second half of the movies. 2. Patch CTF failed with the above message at movie #565. I checked, there is no new patch to V3.2.0. Is there anyway I can delete a specific movie after PMC or how could I fix this? Please advice. Thanks.