[GE users] Standard output file

wagoodman wgoodman at jcvi.org
Thu Jul 1 14:59:05 BST 2010


Thanks for getting back to me, but I found out that
the problem was in the user's environment setting. Problem
resolve. Thank for your help.

Bill

-----Original Message-----
From: reuti [mailto:reuti at staff.uni-marburg.de] 
Sent: Monday, June 28, 2010 5:19 PM
To: users at gridengine.sunsource.net
Subject: Re: [GE users] Standard output file

Hi,

Am 28.06.2010 um 23:11 schrieb wagoodman:

> This is a command line submission:
>
> qsub -P ${PRJ_CODE} -N ALIGNMENT -hold_jid BWA_align_jobs.txt -o  
> output.sam /usr/local/devel/BCIS/external_software/bwa-0.5.8a/bwa  
> sampe /usr/local/projects/REF_DBS/human_b37/chr1.fa file1.sai  
> file2.sai file1.fastq file2.fastq
>
> Because this script depends on the out of another script the login  
> STDOUT causes jobs to fail downstream. Is
> there a CLI to suppress the successful login jargon.

for `qsub` there shouldn't be any output of the chosen node at all. Is  
there any prolog on a global or queue level defined?

-- Reuti


>
> Bill
>
> -----Original Message-----
> From: reuti [mailto:reuti at staff.uni-marburg.de]
> Sent: Monday, June 28, 2010 12:52 PM
> To: users at gridengine.sunsource.net
> Subject: Re: [GE users] Standard output file
>
> Am 28.06.2010 um 17:37 schrieb wagoodman:
>
>> A command I am trying to run on the grid has its output directed to  
>> STDOUT and normally I need to redirect it to a file. With the qsub  
>> I tried to use the -o flag to redirect the STDOUT to a file but  
>> even though the output of the program gets written to that file,  
>> but so does the login message I get when the job get a node. How  
>> can I save the STDOUT of the application I am running without  
>> having the login message in the file that is generated?
>
> You mean, this is an interactive job?
>
> -- Reuti
>
>>
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