[phenixbb] Autobuild error message, please help!!!

Thomas C. Terwilliger terwilliger at lanl.gov
Thu Jun 10 02:53:46 PDT 2010


Hi Inchul,
Can you try running with "debug=True" and see if the output has more
helpful information?
Also can you verify that you have a very recent version of phenix (there
is a version from yesterday now available).
If these are not helpful, can you send me (not the list) your full output
file AutoMR_run_xx_/AutoMR_run_xx.log and also the last log file in an
AutoBuild_run_xx_/TEMP0/AutoBuild_run_yy_/AutoBuild_run_yy_1.log or
similar file.  The work is being done in this subdirectory of the
AutoBuild directory. This may have useful information
Thanks!
All the best,
Tom T

>> Hi, everyone
>>
>>
>>
>> I have a problem in running phenix.automr
>>
>>
>>
>> I started AutoMR with the command:
>>
>> ----------------------------------------------------------------------------
>> -----
>>
>> phenix.automr build=True data=ZZZZZZ_H-Nat_x22_P3221_from_P321.sca   \
>>
>> coords='1_SMsp.pdb 2_SMsp.pdb 3_SMsp.pdb 4_SMsp.pdb'   \
>>
>> identity='40 32 29 27' seq_file=ZZZZZZ_seq.dat
>> input_seq_file=ZZZZZZ_seq.dat   \
>>
>> copies=4
>>
>> ----------------------------------------------------------------------------
>> ------
>>
>>
>>
>> AutoMR process seems to be done without any error
>>
>>
>>
>> but during autobuild process, I encounterd an error message as follows
>>
>>
>>
>> ----------------------------------------------------------------------------
>> -----
>>
>> Re-using input PDB coordinates in build this cycle
>>
>>
>>
>> Running  3 parallel build jobs
>>
>>
>>
>> Standard build in parallel  starting with  refine.pdb_1
>>
>> This is the first try at building this model
>>
>>
>>
>> Setting background=False as nproc=1
>>
>> Try:  1 building 1 model
>>
>> Try:  2 building 1 model
>>
>> Try:  3 building 1 model
>>
>> Running up to  1  jobs in parallel... with total of  3  jobs
>>
>> Splitting work into 3 jobs and running 1 at a time with csh in
>>
>> /data1/disk02/icshin/UGI/MR/PHENIX_MR_8/AutoBuild_run_1_/TEMP0
>>
>>
>>
>> Starting job 1...
>>
>>
>>
>> ****************************************************************************
>> ****
>>
>> Failed to carry out AutoBuild_build_cycle:
>>
>>
>>
>> child process stderr output:
>>
>>   command: 'csh
>> /data1/disk02/icshin/ZZZ/MR/PHENIX_MR_8/AutoBuild_run_1_/TEMP0/RUN_FILE_1'
>>
>>   icshin_com: No such file or directory.
>>
>> ****************************************************************************
>> ****
>>
>> ----------------------------------------------------------------------------
>> ----------------------------------------------------------
>>
>>
>>
>> What am I supposed to do? Please, help me!
>>
>>
>>
>>
>>
>> -------------------------------------------------------
>>
>> Inchul Shin
>>
>> Structural Biology Lab. CALS. Seoul Nationl Univ.
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>




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