[phenixbb] Autobuild error - bash/dash/sh

Thomas C. Terwilliger terwilliger at lanl.gov
Tue Oct 26 05:08:22 PDT 2010

Hi Stephen,
I'm sorry about the problem! I put in the "sh" with a bash system as you
guessed, and I must have used a non-generic command. I will have to check
this out on an ubuntu system.

No, unfortunately there is no easy way to get rid of the sh completely
(this is all there because I was trying to get rid of csh which is not in
ubuntu at all).  You can however go back to the last release version of
phenix (which used csh), then download csh and you should be in business.

On the sequence file, both fasta and pir should work...but try just a
plain sequence of letters, no headers, and that might solve the gui part
of this.

All the best,
Tom T

>> Hi there,
>> Apologies if this has been reported before, but the autobuild job I
>> tried to run last night failed after a short while...
>> The job was started from the command line using:
>> phenix.autobuild data=../mydata_free.mtz seq_file=../protein.fasta
>> map_file=../ccp4i/protein_phaser.1_parrot2.mtz
>> input_map_labels='parrot.F_phi.F parrot.F_phi.phi None'
>> And it got to the point where it was trying to submit the three jobs
>> before it died as follows:
>> Splitting work into 3 jobs and running with 1 processors using sh
>> background=False in
>> /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0
>> Starting job 1...Log will be:
>> /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.log
>> *************ERROR ENDING *******************
>> ********************************************************************************
>> Failed to carry out AutoBuild_build_cycle:
>> child process stderr output:
>>   command: 'sh
>> /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1'
>>   /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.sh:
>> 5: Syntax error: Bad fd number
>> ********************************************************************************
>> *************ERROR ENDING *******************
>> I think the problem might be that the RUN_FILE_1.sh script seems to
>> use a bash command/redirection that is not implemented in plain old
>> 'sh' spec, and thus not supported by dash (the lean version of sh that
>> ships with ubuntu)?  If I change the #! line of RUN_FILE_1.sh to call
>> /bin/bash rather than /bin/sh the script seems to run to completion...
>> Is there any easy way to change the script template to use /bin/bash
>> or remove the offending command?  I'm running phenix dev-550 on an x86
>> ubuntu 10.10 machine.
>> Thanks,
>> Stephen
>> P.S.  The reason I'm trying to run autobuild from the command line
>> rather from the GUI is that the GUI seems to crash every time I give
>> autobuild a sequence file in either the FASTA or PIR format.  Is there
>> another format I should be using?
>> --
>> Dr Stephen Graham
>> 1851 Research Fellow
>> Cambridge Institute for Medical Research
>> Wellcome Trust/MRC Building
>> Addenbrooke's Hospital, Hills Road
>> Cambridge, CB2 0XY, UK
>> Phone: +44 1223 762 638
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb

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