[phenixbb] Failed to carry out AutoBuild

Tom Terwilliger terwilliger at lanl.gov
Wed Nov 12 09:55:20 PST 2008

Hi Joao,

I'm sorry for the trouble!

The error message you got I have not seen, and it is puzzling.  Is it  
possible that more than one job is being run in the same directory?   
If not, then if you are able to send me log file


and the directory listing

ls -lt /someplace/somedir/somedir2/AutoBuild_run_2_/TEMP0/

then I might be able to guess...

On the alignment, it should have worked, but it could depend on the  
presence of insertions/deletions.  Is there anything unusual about the  
formatting of MR.1.pdb?    If you can send this data I will check it  
out. Otherwise it is hard to see what is going wrong.

-Tom T

On Nov 11, 2008, at 10:24 AM, Joao Renato Carvalho Muniz wrote:

> Dear Phenix community,
> I started an AutoBuild run using the Phenix GUI (ver 1.3 final) on  
> linux.
> However, I noticed 2 weird things: 1st, Phenix seems that can not
> handle with alignment between the residues from pdb and sequence.seq,
> flagging the "Rebuild in place not recommended as identity *
> fraction_aligned is 0.0%" message but still trying to build the
> structure with the option "include_input_model=False" I guess(?)...
> and 2nd, after quite a while I obtained the following error message:
> ********************************************************************************
> Failed to carry out AutoBuild_build_cycle:
> child process stderr output:
>  command: 'csh /someplace/somedir/somedir2/AutoBuild_run_2_/TEMP0/ 
>  /someplace/somedir/somedir2/AutoBuild_run_2_/TEMP0/RUN_FILE_1.log:
> File exists.
> ********************************************************************************
> The alignment between MR.1.pdb and sequence.seq should be something  
> like 80%+!
> Also tried to run using the followed command line:
> phenix.autobuild data=MR.1.mtz model=MR.1.pdb include_input_model=True
> n_cycle_rebuild_max=5 seq_file=sequence.seq
> Same problem as above.
> Could anyone please tell me what to do to prevent this error and get
> phenix get its job finished?
> Many thanks in advance,
> Joao.
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