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Feature #2044

closed

Add Relion single model refinement to appion pipeline

Added by Amber Herold about 12 years ago. Updated almost 7 years ago.

Status:
Won't Fix or Won't Do
Priority:
Normal
Assignee:
Sargis Dallakyan
Category:
-
Target version:
Start date:
09/13/2012
Due date:
% Done:

0%

Estimated time:

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


Related issues 3 (3 open0 closed)

Related to Appion - Feature #2954: faster methods for prep RELIONIn Test10/09/2014

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Related to Appion - Bug #2939: Appion Developers Conference Call NotesNew09/24/2014

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Related to Appion - Feature #4849: Is uploadRelionRefine.py implemented?NewNeil Voss03/22/2017

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Actions #1

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.

Actions #2

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.

Actions #3

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.

Actions #4

Updated by Clint Potter about 10 years ago

Neil has made changes. Neil will upload his changes to trunk. Kids will test.

Actions #5

Updated by Neil Voss about 10 years ago

Actions #6

Updated by Clint Potter almost 10 years ago

  • Assignee changed from David Veesler to Sargis Dallakyan
Actions #7

Updated by Neil Voss almost 10 years ago

  • Related to Bug #2939: Appion Developers Conference Call Notes added
Actions #8

Updated by Neil Voss over 9 years ago

An error was reported for this, can I get the error message.

Actions #9

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.

Actions #10

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.

Actions #11

Updated by Clint Potter over 9 years ago

Bridget will take on testing.

Actions #12

Updated by Neil Voss over 7 years ago

  • Related to Feature #4849: Is uploadRelionRefine.py implemented? added
Actions #13

Updated by Anchi Cheng almost 7 years ago

  • Status changed from In Test to Won't Fix or Won't Do

no one use this

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