[Iplant-api-dev] Fwd: seqtk_seq-1.0.76

Tue May 12 12:00:25 MST 2015

Thanks Liya. Rion said Zhangou’s jobs are staging in to stampede and archiving from CSHL now. So they have not yet run, but will before too long.

Martha 

On May 12, 2015, at 11:57 AM, Wang, Liya <wangli at cshl.edu> wrote:

> I can confirm that Agave is responding very fast now. However, the analysis status in DE is not synchronized with Agave. My latest testing job finished 10 minutes ago but the status in DE is still ’submitted’. DE was down a few hours ago not sure whether it is related.
> 
> For Zhanguo, you may want to check whether you got the results back, although the status is still ‘submitted’.
> 
> Liya
> On May 12, 2015, at 2:36 PM, Martha Narro <narro at iplantcollaborative.org<mailto:narro at iplantcollaborative.org>> wrote:
> 
> Liya and Zhanguo,
> 
> Can you confirm that your jobs ran once the back log in the Agave queue cleared up?
> 
> Martha
> 
> Martha Narro
> Senior Project Coordinator
> iPlant Collaborative
> Keating 445
> University of Arizona
> 520-626-6814
> 
> On May 11, 2015, at 1:59 PM, Wang, Liya <wangli at cshl.edu<mailto:wangli at cshl.edu>> wrote:
> 
> It seems that Agave job submission sever is busy. The following job and my testing jobs have been held in pending status for a while. Can anybody check it?
> 
> Thanks,
> Liya
> Begin forwarded message:
> 
> From: "Xin, Zhanguo" <Zhanguo.Xin at ARS.USDA.GOV<mailto:Zhanguo.Xin at ARS.USDA.GOV><mailto:Zhanguo.Xin at ARS.USDA.GOV>>
> Subject: Re: seqtk_seq-1.0.76
> Date: May 11, 2015 at 4:46:45 PM EDT
> To: "Wang, Liya" <wangli at cshl.edu<mailto:wangli at cshl.edu><mailto:wangli at cshl.edu>>, "Lu, Jerry" <luj at cshl.edu<mailto:luj at cshl.edu><mailto:luj at cshl.edu>>
> 
> Hi Liya,
> 
> I re-submitted the APP seqtk_seq-1.0.76 to DE using a folder that contains
> the zipped file. This time, it never runs but remains at submitted status.
> Can you what I entered wrong.
> 
> https://de.iplantcollaborative.org/de/?type=data&folder=/iplant/home/xinzha
> nguo/analyses
> 
> Thanks,
> 
> 
> Zhanguo Xin
> 
> USDA-ARS
> 3810 4th Street
> Lubbock, TX 79415
> Ph: 806-749-5560Fax: 806-723-5272
> E-mail:  Zhanguo.Xin at ars.usda.gov<mailto:Zhanguo.Xin at ars.usda.gov>
> 
> 
> 
> 
> 
> 
> On 5/11/15, 1:23 PM, "Wang, Liya" <wangli at cshl.edu<mailto:wangli at cshl.edu>> wrote:
> 
> The seqtk app expects a folder as input. When Zhanguo selected a gzipped
> fastq file as input, the app couldn¹t handle it.
> 
> Liya
> On May 11, 2015, at 2:08 PM, Lu, Jerry <luj at cshl.edu<mailto:luj at cshl.edu>> wrote:
> 
> Yes. As I understand, there is some miscommunication on what should be
> the input for the app. Liya could give more details if needed.
> 
> Zhenyuan
> ________________________________________
> From: Martha Narro [narro at iplantcollaborative.org<mailto:narro at iplantcollaborative.org>]
> Sent: Monday, May 11, 2015 2:00 PM
> To: Lu, Jerry
> Cc: Zhanguo.Xin at ars.usda.gov<mailto:Zhanguo.Xin at ars.usda.gov>; Wang, Liya
> Subject: Re: seqtk_seq-1.0.76
> 
> Hi Zhenyuan,
> 
> Does that mean you and/or Liya solved the problem Zhanguo was having?
> Whether the answer is yes or no, could you describe what you and Liya
> did so I understand and close the ticket (or not)?
> 
> Martha
> 
> On May 11, 2015, at 10:55 AM, Lu, Jerry <luj at cshl.edu<mailto:luj at cshl.edu>> wrote:
> 
> Hi Martha,
> Yes, both Liya and I helped him.
> 
> Zhenyuan
> 
> ________________________________
> From: Martha Narro [narro at iplantcollaborative.org<mailto:narro at iplantcollaborative.org>]
> Sent: Monday, May 11, 2015 1:40 PM
> To: Zhanguo.Xin at ars.usda.gov<mailto:Zhanguo.Xin at ars.usda.gov>; Lu, Jerry
> Subject: Fwd: seqtk_seq-1.0.76
> 
> Hi Zhenyuan,
> 
> Can you help troubleshoot Zhanguo¹s problem described below? Zhanguo
> will first need to share the analysis run details with you via the DE.
> 
> Zhenyuan, real NGS data files should run on your account in iPlant.
> There is no "small files only² type of account.
> 
> Martha
> 
> 
> ---------- Forwarded message ----------
> From: Xin, Zhanguo
> <Zhanguo.Xin at ars.usda.gov<mailto:Zhanguo.Xin at ars.usda.gov><mailto:Zhanguo.Xin at ars.usda.gov>>
> Date: Monday, May 11, 2015
> Subject: seqtk_seq-1.0.76
> To:
> "info at iplantcollaborative.org<mailto:info at iplantcollaborative.org><mailto:info at iplantcollaborative.org>"
> <info at iplantcollaborative.org<mailto:info at iplantcollaborative.org><mailto:info at iplantcollaborative.org>>
> Cc: "Lu, Jerry" <luj at cshl.edu<mailto:luj at cshl.edu><mailto:luj at cshl.edu>>
> 
> 
> Hi Support,
> 
> I am trying to run the first step in variant calling to convert a
> fastq to a fasta file with the data I loaded in DE for the Santa Fe
> workshop. The program ran for two days without completion. I canceled
> and re-submitted last night. It is still running. What could be wrong.
> 
> My iPlant user ID: xinzhanguo. I am wondering if my account is limited
> to run small size of files. The data I loaded is a real NGS data with a
> size about 6 Gb in zipped file. If my account is indeed limited, how
> can I remove the limitation.
> 
> Thanks,
> 
> Zhanguo Xin
> 
> USDA-ARS
> 3810 4th Street
> Lubbock, TX 79415
> Ph: 806-749-5560
> Fax: 806-723-5272
> E-mail:  Zhanguo.Xin at ars.usda.gov<mailto:Zhanguo.Xin at ars.usda.gov><http://Zhanguo.Xin@ars.usda.gov/>
> 
> 
> 
> 
> --
> Mary Margaret Sprinkle
> Project Coordinator
> iPlant Collaborative
> http://www.iplantcollaborative.org<http://www.iplantcollaborative.org/>
> marys at iplantcollaborative.org<mailto:marys at iplantcollaborative.org>
> TEL: +1-520-626-4219
> FAX: +1-520-626-4824
> 
> 
> 
> 
> 
> 
> 
> 
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