[Bioperl-l] Re: [Bioperl-pipeline] need help with biopipe

[Shawn Hoon]

On Tuesday, November 18, 2003, at 7:11AM, matthieu CONTE wrote:

> I'm trying to work with biopipe , i'm using the example program:
> Blast_file_pipeline.xml
> I use the command
> "perl PipelineManager -xml /home/conte/xml/test_blast_pipe.xml -dbname
> biopipe -dbpass biopipe -dbuser biopipe"
> in bioperl-pipeline/scripts
> and I have :
> "Retrying........
> Fetched 0 completed jobs
> Going to snooze for 3 seconds...
> Waking up and run again!
> Fetching Jobs...
> Fetched 1 incomplete jobs
> "
> so ???Does anybody know what it means?
>

This is the output from PipelineManager that describes whether it is 
fetching/running jobs etc. PipelineManager
cycles through a series of steps:
	1) Fetched Failed or New Jobs in batches (the number u can specify in 
PipeConf.pm)
	2) Run these Jobs
	3)Fetched Completed Jobs and remove them from the job table into the 
completed_jobs table

To figure out whether the individual jobs are failing, you can look up 
the job table for its status and look up the  stderr log
file to see any other error messages.

shawn

>
>
>
> Matthieu CONTE
> 23 route d'EUS
> 66500 CATLLAR
> Tel
> 0468962854
> m_conte at hotmail.com
>
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