Error: Missing 3DFSC file during Refine3D

[Tom Laughlin]

Hello!

I have been really happy with the results of the anisotropy correction module and wanted to see whether the misalignment correction module could push my map further.

However, I encounter an error when the HEALPIX order reaches the ISONET_START_HEALPIX value during relion_refine:

FileNotFoundError: [Errno 2] No such file or directory: 'Refine3D/job020/run_it008_3DFSC.mrc'

Any ideas why the 3DFSC.mrc is not being generated and how I can troubleshoot/fix?

Thanks for your help!
-Tom

[YUNTAO LIU]

Hi Tom,

I do not have a clear idea of how this happened.  Is there other information or log info during the processing? 

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Best Regards,

Yuntao Liu,  Postdoc.

California NanoSystem Institute

University of California Los Angeles

[Tom Laughlin]

Hi Yuntao,

Thank you for the prompt reply!

I've attached my note.txt, run.err, and the last 2 interations of the .out.
Relion and spisonet are being run through sbgrid, but I get the same result with a standalone spisonet install (Relion still through sbgrid).

Thanks for your help,
-Tom

[YUNTAO LIU]

Hi Tom,

I went through the error, but still can not find the reason that the 3DFSC did not execute properly. I will think about it.

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[Tom Laughlin]

Thanks!

For now, I am setting the ISONET_START_HEALPIX=8 for the misalignment correction and then running the anisotropy correction once refinement has finished.
Perhaps sub-optimal, but it is improving the interpretability of the map so seems to be sufficient for my task.

Let me know if you have an idea of a potential solution to running the anisotropy correction module, and I will post back if I arrive at a solution as well.

Thanks for the software and help!
-Tom