Feature #2044
closedAdd Relion single model refinement to appion pipeline
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Description
While adding this refinement, I am updating documentation with general steps for adding a new refinement here: http://emg.nysbc.org/projects/appion/wiki/Refine_Refactor_documentation
Relion is installed on huey. Start the gui with
/usr/local/relion-1.1/gui/gui
Updated by Amber Herold about 12 years ago
Arne, r17112 contains all the pieces for the prep step. You should be able to create the prep command from the web page and run the prepRefineRelion.py file. I have NOT made changes to the python file to remove the stack inversion step and add the awk command.
Updated by Amber Herold about 12 years ago
r17113 includes the form for the run step. Still need to write the python class for the run step.
Updated by Amber Herold over 10 years ago
- Status changed from Assigned to In Test
- Assignee changed from Amber Herold to David Veesler
Hey David,
Would you be able to try running Relion refine from the gui to test it out?
It should be available from betamyamiweb on Guppy tomorrow for small tests.
Sargis is checking in some code later today that he would like on Garibaldi, so when he is done, we will have Garibaldi updated as well.
Updated by Clint Potter almost 10 years ago
Neil has made changes. Neil will upload his changes to trunk. Kids will test.
Updated by Neil Voss almost 10 years ago
- Related to Feature #2954: faster methods for prep RELION added
Updated by Clint Potter over 9 years ago
- Assignee changed from David Veesler to Sargis Dallakyan
Updated by Neil Voss over 9 years ago
- Related to Bug #2939: Appion Developers Conference Call Notes added
Updated by Neil Voss over 9 years ago
An error was reported for this, can I get the error message.
Updated by Yong Zi Tan over 9 years ago
Jana and I have tried to use Relion in the Appion pipeline in December 2014 unsuccessfully.
I had the job prepared (with a template), but when I ran it none of the iterations went through. The directory on fishtail is: /ami/data15/appion/14nov19f/recon/relion_recon1/relion_recon1.appionsub.job
Thank you.
Updated by Sargis Dallakyan over 9 years ago
Thank you. I see this in one of the *.o files:
MetaDataTable::read: File /ami/data15/appion/14nov19f/recon/relion_recon1/all_images.star does not exists
r18777 fixes this. Appion doesn't check the output of relion_refine_mpi. At this point, users would need to read latest .o file before starting upload jobs. After fixing 'all_images.star does not exists' I tried another Relion refinement and saw this in the output:
MlOptimiserMpi::initialiseWorkLoad: at least 3 MPI processes are required when splitting data into random halves
I then modified relion_recon*.appionsub.job, replaced "mpirun -np 2 `which relion_refine_mpi` ..." with "mpirun -np 4 `which relion_refine_mpi` ..." and did qsub relion_recon*.appionsub.job. This went further, but failed again with another error:
=>> PBS: job killed: mem job total 5258200 kb exceeded limit 4194304 kb
I might try running this an another machine with larger RAM, if I get a chance.
Updated by Neil Voss over 7 years ago
- Related to Feature #4849: Is uploadRelionRefine.py implemented? added
Updated by Anchi Cheng over 6 years ago
- Status changed from In Test to Won't Fix or Won't Do
no one use this