Nate, 

this error is intermittent. You resubmit the same job twice or three time and 
then it works.  Once we are over the midterm exams - which use galaxy - we will 
try to switch the filesystem from autofs to hard mount. We suspect this to be 
the issue.  

Could we suppress e and o SGE style to resolve this issue, or Galaxy wants the 
o? 


Do you have an idea about the url build for galaxy - ucsc page return when the 
url is :8080/galaxy and not just /galaxy? 

thanks,
joe

________________________________________
From: Nate Coraor [n...@bx.psu.edu]
Sent: Friday, October 21, 2011 10:26 AM
To: Joseph Hargitai
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Job output not returned from cluster

Joseph Hargitai wrote:
>
> Hi,
>
> i was browsing through the list and found many entries for this issue but not 
> a definite answer.
>
> We are actually running into this error for simple file uploads from the 
> internal filesystem.

Hi Joe,

This error occurs when the job's standard output and error files are not
found where Galaxy expects them, namely:

    <cluster_files_directory>/<job_id>.o
    <cluster_files_directory>/<job_id>.e

Please check your queueing system to make sure it can correctly deliver
these back from the execution hosts to the specified filesystem.

--nate

>
> thanks,
> joe
>

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