Hi Alex, I'm sorry for both the failure and the lack of a clear message here! I will try to fix both. Is this running phenix-1.3-final? (If not, could you possibly run with that version so we are on the same version.) Can you possibly send me the end of the output in /someplace/home/someuser/ work/someproject/phenix2/AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/AutoBuild_run_1_1.log which I hope will have an actual error message to look at? The reason for the subdirectories is this: phenix.autobuild runs several jobs in parallel (if you have set nproc ) or one after the other (if you have not set nproc). These subdirectories contain those jobs...which are then combined together to give the final results in your overall AutoBuild_run_1_/ directory. I don't know the answer to the phenix.refine question...perhaps Pawel or Ralf can answer that one. All the best, Tom T
Dear phenix community,
I started an AutoBuild run using the phenix GUI (ver 1.3 rc4) on a linux cluster. It worked okay and all the refinement looked pretty decent. However, after quite a while I obtained the following error message (see below). Would anyone please tell me what to do to prevent this error and get phenix get its job finished?
Also, I don't understand why phenix AutoBuild creates 5 (or whatever number) AutoBuild_run_x in the AutoBuild-run_1/TEMP0 directory and not two dirs up in the tree. In other words in my /someplace/home/someuser/ work/someproject/phenix2/AutoBuild_run_1_/TEMP0 directory are more AutoBuild_run_x_ directories (with x=1 to 5). It is a bit confusing to me.
A final question: I realised that the phenix.refine drastically increases the number of outliers. I know that thare is a weighting term someplace ... but what was it again?
Many thanks in advance, Alex
warnings Failed to carry out AutoBuild_multiple_models: Sorry, subprocess failed...message is: ******************************************************************************** phenix.autobuild \
write_run_directory_to_file=/someplace/home/someuser/work/someproject/ phenix2/AutoBuild_run_1_/TEMP0/INFO_FILE_1
Reading effective parameters from /someplace/home/someuser/work/ someproject/phenix2/AutoBuild_run_1_/TEMP0/PARAMS_1.eff
Sending output to AutoBuild_run_1_/AutoBuild_run_1_1.log
********************************************************************************
Failed to carry out AutoBuild_build_cycle:
failure
********************************************************************************
********************************************************************************
work_pdb_file "AutoBuild_run_1_/edited_pdb.pdb" working_directory "/someplace/home/someuser/work/someproject/phenix2" worst_percent_res_rebuild 2.0
--------------------------------------------------- Alex Berndt MRC-Laboratory of Molecular Biology Hills Road Cambridge, CB2 0QH U.K.
phone: +44 (0)1223 402113 ---------------------------------------------------
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