Hi all,

I am trying to run phenix.mr_rosetta using the following script for rebuilding the model with Rosetta before MR from phenix website except omitting specifying ncs_copies number. Following is the script I am using:

phenix.mr_rosetta \

seq_file = seq.dat \

data=coords1.mtz \  

search_models=coords1.pdb \  

run_prerefine=True \  

number_of_prerefine_models=1000 \  

fragment_files = test3.gz \  

fragment_files = test9.gz \ 

rescore_mr.relax=False \ 

rosetta_models=20 \  

space_group=p222  \  

use_all_plausible_sg=False \ 

nproc=4 \  

group_run_command=qsub\

 

When I run the above script, it gives the following error message:

child process stderr output:

  command: 'qsub /home/wei/MR_ROSETTA_14/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1'

  /bin/sh: qsub: not found

Then, I omit the last line in the command �group_run_command=qsub\�. MR_ROSETTA seems to be running.  But, it takes forever to run.

My questions is:

1.     Does anyone happen to know why it tells me �qsub: not found� when I include  �group_run_command=qsub� in my script?

2.     When I omit �group_run_command=qsub� in the script, mr_rosetta seems to be running.  But it just gives me the following message and it takes forever to run. Almost 10h later, no job is finished. I don�t know whether this is normal. If not, any idea about why it�s so slow and any suggestions about how to speed up the run? Thank you so much!

 

Splitting work into 1 jobs and running with 4 processors using sh

background=True in /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1

 

Starting job 1...Log will be: /home/wei/MR_ROSETTA_15/GROUP_OF_PLACE_MODEL_1/RUN_FILE_1.log

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