Error during per-particle CTF

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#1

Hi all,

I am trying to estimate CTFs for my tilted-data particles within Cryosparc by using the GCTF option prior to the 3D steps. All the steps up until 2D classification have been done within Cryosparc, including picking.

After manually generating _automatch.box separate particle coordinate files for each micrograph, I have run a GCTF local refine and I am getting the following error:

Traceback (most recent call last):
  File "cryosparc2_worker/cryosparc2_compute/run.py", line 78, in cryosparc2_compute.run.main (/home/installtest/deps_manage/cryosparc2_package/deploy/stage/cryosparc2_worker/cryosparc2_compute/run.c:3954)
  File "cryosparc2_compute/jobs/ctf/run.py", line 861, in run_ctf_estimation_gctf
    local_ctf_df = starfile.read_star_file(local_ctf_path)
  File "cryosparc2_compute/metaio/starfile.py", line 29, in read_star_file
    with open(fname, 'r') as f:
IOError: [Errno 2] No such file or directory: u'/data/XXX/YYY/ZZZ/P7/J339/imported/0002_frames_local.star'

If I am not mistaken, frames_local.star is generated AFTER local refinement, so…how can I approach this in order to succeed in the per-particle CTF step? I have checked the input options and it seems that even though I unchecked the “Refine Input CTF” section, it is now automatically checked. Does it have something to do with this issue?

Most of the other values are default except “do local refine” and “boxsuffix”, which is set to _automatch.box.

Thank you very much in advance.

David