[Iplant-api-dev] DO NOT REPLY "problem running cloudSTRUCTURE"

[Cornel Ghiban]

None of the jobs our systems/users submitted since "Tue Jan 13 2015 09:31:01"
has finished. All (most) are in QUEUED.

Cornel

On 01/16/2015 05:25 PM, Wang, Liya wrote:
> Thanks Dennis. I tried to re-submit several jobs outside of DE and all of them are pending (for several public apps). Attached please find the screenshot. Hope it is helpful for debugging. I know in the past this will happen right after the Lonestar maintenance.
> 
>  Liya
> 
> [cid:30FE2F83-F5A5-429E-8DA9-D6DFDCC49155 at cshl.edu]
> On Jan 16, 2015, at 5:10 PM, Dennis Roberts <dennis at iplantcollaborative.org<mailto:dennis at iplantcollaborative.org>>
>  wrote:
> 
> Hi Liya,
> 
> I found the job submission and retrieved some information about the job submission from the Foundation API. I’m afraid this is as much troubleshooting as I can do from the DE side. Please let me know if more information is needed.
> 
> 
> 
> Thanks,
> Dennis
> 
>> On Jan 16, 2015, at 10:21 AM, Wang, Liya <wangli at cshl.edu<mailto:wangli at cshl.edu>> wrote:
>>
>> This Foundation app runs on Lonestar. I just tested it and it runs for ever from DE.
>>
>> Begin forwarded message:
>>
>> From: <ask at iplantcollaborative.org<mailto:ask at iplantcollaborative.org><mailto:ask at iplantcollaborative.org>>
>> Subject: DO NOT REPLY "problem running cloudSTRUCTURE"
>> Date: January 16, 2015 4:32:43 AM EST
>> To: <wangli at cshl.edu<mailto:wangli at cshl.edu><mailto:wangli at cshl.edu>>
>> Reply-To: <ask at iplantcollaborative.org<mailto:ask at iplantcollaborative.org><mailto:ask at iplantcollaborative.org>>
>>
>>
>>
>> sopicq<http://ask.iplantcollaborative.org/users/573/sopicq/> posted a question<http://ask.iplantcollaborative.org/question/2912/problem-running-cloudstructure/>.
>>
>> Question : problem running cloudSTRUCTURE
>>
>> Asked by sopicq:
>>
>> Tags: DataStore, DiscoveryEnvironment.
>>
>> I am having problems running cloudSTRUCTURE, even with the test data provided. The problem is that regardless of how much maximum run time I select, the status of the analysis does not change from 'Running' and no output is saved ever. I am not sure if the analysis is actually running or not as I don't get any error messages.
>>
>> For the test data, these are the settings I used: input file: /iplant/home/shared/iplantcollaborative/example_data/GWAS/Structure/input/marker_numerical.txt
>>
>> maximum populations 3, 12982 as number of loci, 310 as number of samples
>>
>> File information was left with default settings: Input file contains individual labels, Input file contains row of marker names, Store data for individuals in a single line
>>
>> Maximum Run time: 4 hours
>>
>> Thank you for your help !
>>
>> Sophie
>>
>> ======= Full thread summary =======
>>
>> Question : problem running cloudSTRUCTURE
>>
>> Asked by sopicq:
>>
>> Tags: DataStore, DiscoveryEnvironment.
>>
>> I am having problems running cloudSTRUCTURE, even with the test data provided. The problem is that regardless of how much maximum run time I select, the status of the analysis does not change from 'Running' and no output is saved ever. I am not sure if the analysis is actually running or not as I don't get any error messages.
>>
>> For the test data, these are the settings I used: input file: /iplant/home/shared/iplantcollaborative/example_data/GWAS/Structure/input/marker_numerical.txt
>>
>> maximum populations 3, 12982 as number of loci, 310 as number of samples
>>
>> File information was left with default settings: Input file contains individual labels, Input file contains row of marker names, Store data for individuals in a single line
>>
>> Maximum Run time: 4 hours
>>
>> Thank you for your help !
>>
>> Sophie
>>
>> Please note - you can easily change<http://ask.iplantcollaborative.org/users/101/lwang/subscriptions/> how often you receive these notifications or unsubscribe. Thank you for your interest in our forum!
>>
>>
>> ________________________________
>>
>> Sincerely,
>> Administrator
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Iplant-api-dev Mailing List: Iplant-api-dev at iplantcollaborative.org<mailto:Iplant-api-dev at iplantcollaborative.org>
>> List Info and Archives: http://mail.iplantcollaborative.org/mailman/listinfo/iplant-api-dev
>> One-click Unsubscribe: http://mail.iplantcollaborative.org/mailman/options/iplant-api-dev/dennis%40iplantcollaborative.org?unsub=1&unsubconfirm=1
> 
> <cloud-structure.json>
> 
> 
> 
> 
> _______________________________________________
> Iplant-api-dev Mailing List: Iplant-api-dev at iplantcollaborative.org
> List Info and Archives: http://mail.iplantcollaborative.org/mailman/listinfo/iplant-api-dev  
> One-click Unsubscribe: http://mail.iplantcollaborative.org/mailman/options/iplant-api-dev/ungreen%40gmail.com?unsub=1&unsubconfirm=1 
>