Hello,
I recently ran a patch motion job that failed due to hard drive disk space availability. My original plan was to mark the job as complete and use the incomplete micrographs output as input for another patch motion and just continue with CTF estimation with the successful micrographs. However, I could not mark the job as complete and use the complete/incomplete micrographs for further processing.
How can I import patch motion corrected files properly into CryoSPARC? I can import the DW and non-DW micrographs easily through the import micrograph job, but I don’t want to lose the other files (bending_traj.npy. rigid_traj.npy and background.mrc) which I believe may be needed for local motion correction. How can I import them all simultaneously?
Thanks,
Karl
Hi Karl,
Did the attempt to mark the job as complete fail due to insufficient disk space?
If you were able to make more space available, it may be easiest to repeat the motion correction for the entire movie set.
Hi wtempel,
Yes, that is what happened.
Unfortunately, the only way to make room for more disk space is to delete the imported movies, which would not allow us to repeat the entire motion correction job. Usually, we run motion correction and immediately transfer our movies to our research storage server for permanent storage of raw movies.
The import should be preceded by an export operation (guide). This operation should create folders inside an exports subdirectory of your project directory. Note that the folders include symbolic links. Be sure to dereference those links in case data are transferred to other storage for subsequent import.
I have tried that, but exporting was not successful for whatever reason. I saved the motioncorrection folder that was generated from the failed job and kept the successfully processed movies. I guess I can forget about local motion at this point, but which processed micrograph would be best to keep using forward? I know CTF estimation used the non-DW micrographs, but it seems most downstream applications use the DW micrographs. If I import both, how can I make sure they are both being utilized properly?
Alternatively, Is it possible to re-create a .csg file from this motioncorrection job so that I can import the micrographs with all .npy/mrc files?