Failed to carry out AutoBuild
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/RUN_FILE_1' /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.
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 /someplace/somedir/somedir2/AutoBuild_run_2_/AutoBuild_run_2_1.log 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. Thanks! -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/ RUN_FILE_1' /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. _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (2)
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Joao Renato Carvalho Muniz -
Tom Terwilliger