Feature #1537
open
complete the frealign refinement uploader
Added by Amber Herold almost 13 years ago.
Updated over 10 years ago.
Description
using the following command for development:
uploadFrealignRefine.py --runname=frealign_recon1 --stackid=23 --modelid=1 --jobid=82 --contour=2.0 --zoom=1.0 --description="bin2 frealign test" --box=160 --apix=1.64 --rundir=/ami/data00/appion/12jan12z/recon/frealign_recon1 --projectid=234 --expId=9441 --jobtype=uploadrecon
developing this based on changes made in #1323
- Status changed from Assigned to In Code Review
- Assignee changed from Amber Herold to Anchi Cheng
- Status changed from In Code Review to In Test
- Status changed from In Test to Assigned
- Assignee changed from Anchi Cheng to Amber Herold
This does not work because frealign is now run through multiple qsub from the base node so it never creates job file. reconUploader checks for it and quit because it could not find job file. I was able to trick it by making a fake job file. Even so, it is a bad idea. We overwrite runname.appionsub.job generated by prepRefineWhatever, and then it is over-written by uploadRefineWhatever. The record is lost, non-reproducible.
We should discuss what to do. One possibility is for reconUploader check runname.appionsub.commands instead because that is always generated.
Found a minor bug with C1 symmetry conversion. committed the change in r17425
- Assignee changed from Amber Herold to Bradley Kearney
Brad, Assigning this to you. Don't know if it is still relevant.
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