[Iplant-api-dev] Unable to stage inputs for job after 3 attempts. Job cancelled

[Barthelson, Roger A - (rogerab)]

My Tophat jobs, which also have been failing, have a single folder with about 20 sequencing files in them. I understand this can be a challenge for iRODS.

Roger

Sent from my iPad

> On Nov 11, 2015, at 8:06 AM, "Ghiban, Cornel" <ghiban at cshl.edu> wrote:
> 
> Hi Matt,
> 
> One of the differences from the other apps we have in Agave is that
> cuffdiff may take many input files (some quite large) and I think this
> could be the main reason these jobs fail.
> 
> Cornel
> 
>> On Wed, 2015-11-11 at 14:57 +0000, Matthew Vaughn wrote:
>> Thanks for the job IDs. We’re looking into it. Very curious that it’s just Richard’s jobs. Permissions look OK, and there’s no obvious log info. Let me see if I can replicate it by running a job of his myself.
>> 
>> Matt
>> 
>>> On Nov 11, 2015, at 8:34 AM, Ghiban, Cornel <ghiban at cshl.edu> wrote:
>>> 
>>> Hi,
>>> 
>>> I have a user has keeps getting errors on his final step of his
>>> analysis. Just to give you an idea, he started his project at the end of
>>> July and he's trying to compare the spaceflight transcriptome of four
>>> commonly used Arabidopsis thaliana ecotypes.
>>> 
>>> Here are the last 5 CUFFDIFF jobs that failed with the error "Unable to
>>> stage inputs for job after 3 attempts. Job cancelled.":
>>> 
>>> 5502699045213966821-e0bd34dffff8de6-0001-007
>>> 5742354097154626021-e0bd34dffff8de6-0001-007
>>> 7819059084788428315-e0bd34dffff8de6-0001-007
>>> 6417341257285037595-e0bd34dffff8de6-0001-007
>>> 6944550352745599461-e0bd34dffff8de6-0001-007
>>> 
>>> There's been other users that successfully finished their CUFFDIFF jobs,
>>> so it's not an app issue.
>>> 
>>> Thank you,
>>> Cornel
>>> 
>>> -------- Forwarded Message --------
>>> From: Richard Barker <dr.richard.barker at gmail.com>
>>> To: "Ghiban, Cornel" <ghiban at cshl.edu>
>>> Subject: Re: DNASUBWAY is back online
>>> Date: Wed, 11 Nov 2015 09:20:28 -0500
>>> 
>>> Hi Cornel
>>> 
>>> 
>>> My final run keeps failing, it says in the message section of the
>>> failure report that "Unable to stage inputs for job after 3 attempts.
>>> Job cancelled."
>>> 
>>> I'm not sure what else to try?
>>> 
>>> 
>>> Best wishes, Richard
>>> 
>>> 
>>> On 10 November 2015 at 14:03, Richard Barker
>>> <dr.richard.barker at gmail.com> wrote:
>>>       That's great, i just up loaded the final cuffdiff analysis, and
>>>       will be showing it to the NASA team in a couple of hours... :)
>>> 
>>> 
>>>       On 10 November 2015 at 12:21, Ghiban, Cornel <ghiban at cshl.edu>
>>>       wrote:
>>>               Hi Richard,
>>> 
>>>               The greenline is up and running. Let us know if you
>>>               encounter any
>>>               issues.
>>> 
>>>               Cornel
>>> 
>>> 
>>> 
>>> 
>>>       -- 
>>>       Richard Barker, PhD
>>>       Post doctoral research associate
>>>       Gilroy Lab - B121 Birge Hall
>>>       430 Lincoln Drive
>>>       Madison,
>>>       WI, 53706, USA
>>> 
>>>       Mobile: (608) 515 0516
>>>       Personal website: https://drrichardbarker.wordpress.com/
>>>       Gilroy Lab: http://www.botany.wisc.edu/gilroy/
>>>       GeneLab: http://genelab.nasa.gov/
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> Richard Barker, PhD
>>> Post doctoral research associate
>>> Gilroy Lab - B121 Birge Hall
>>> 430 Lincoln Drive
>>> Madison,
>>> WI, 53706, USA
>>> 
>>> Mobile: (608) 515 0516
>>> Personal website: https://drrichardbarker.wordpress.com/
>>> Gilroy Lab: http://www.botany.wisc.edu/gilroy/
>>> GeneLab: http://genelab.nasa.gov/
>>> 
>>> 
>>> 
>>> 
>>> 
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> 
> 
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