[phenixbb] Autobuild error message

Tom Terwilliger terwilliger at lanl.gov
Fri Aug 13 13:39:09 PDT 2010


Hi again Bryan,

Thank you for sending in your data; I have found the problem and fixed  
it. The problem is that the "phenix_refine.eff" file that you supplied  
was not properly handled by AutoBuild and using it removed some  
defaults for maps that should be present. Tomorrow's version should be  
ok.

Thanks very much for letting me know of the problem!

All the best,
Tom T

On Aug 13, 2010, at 1:03 PM, Tom Terwilliger wrote:

> Hi Bryan,
> I'm sorry for the trouble!
>
> AutoBuild is running phenix.refine and asking it to write out  
> "refine_pdb_in.mtz".  After phenix.refine is done, it looks for this  
> file and if it is missing it will stop.
>
> There are two possibilities. Can you check if the file is really  
> missing or not:
>
> ls -ltr AutoBuild_run_2_/TEMP0/refine_pdb_in.mtz
>
>
> 1. AutoBuild_run_2_/TEMP0/refine_pdb_in.mtz really is missing:  This  
> means that something has gone wrong that is not anticipated. Can you  
> in this case send me the data to run here?  If not, have a look at  
> the last set of files written in AutoBuild_run_2_/TEMP0/ ... do  
> these log files help in any way?
>
> 2.  AutoBuild_run_2_/TEMP0/refine_pdb_in.mtz is not missing, it was  
> just written after the check for its presence was over.  This can  
> happen if you are on an nfs file system and it is slow.  I have just  
> finished adding code to AutoBuild to wait for files to appear to get  
> around this problem...so if you try tomorrow's build it is possible  
> this will be fixed. You may need to change the parameter  
> "max_wait_time" to a longer time (default=0.1 sec).
>
> Let me know if this doesn't do it!
> All the best,
> Tom T
>
>
> On Aug 13, 2010, at 12:46 PM, <bschmidt at berkeley.edu> wrote:
>
>> Hello all,
>>
>> I am trying to use phenix.autobuild from the command line to  
>> generate either composite omit maps or prime and switch maps. In  
>> either case, when I try, the program starts to run for a while  
>> before failing and giving me the following error message:
>>
>> "Failed to carry out AutoBuild_build_cycle:
>>
>> Sorry...the file AutoBuild_run_2_/TEMP0/refine_pdb_in.mtz is  
>> missing..."
>>
>> I'm not sure why that would be the case, or where that mtz is  
>> supposed to come from. Can anyone explain what might be the problem?
>>
>> Thanks,
>>
>> Bryan
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
> Thomas C. Terwilliger
> Mail Stop M888
> Los Alamos National Laboratory
> Los Alamos, NM 87545
>
> Tel:  505-667-0072                 email: terwilliger at LANL.gov
> Fax: 505-665-3024                 SOLVE web site: http:// 
> solve.lanl.gov
> PHENIX web site: http:www.phenix-online.org
> ISFI Integrated Center for Structure and Function Innovation web  
> site: http://techcenter.mbi.ucla.edu
> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/ 
> cbss
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb


Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100813/ba61645d/attachment-0003.htm>


More information about the phenixbb mailing list