[Iplant-api-dev] seqtk_seq-1.0.76

[Matthew Vaughn]

I misspoke. The API was indeed backed up yesterday. We don’t do a full phase change from PENDING to SUBMITTED until we’ve had a chance to confirm availability of various files etc. Sometimes, when things are busy that still takes a while.

> On May 11, 2015, at 4:53 PM, Wang, Liya <wangli at cshl.edu> wrote:
> 
> Matt,
> 
> This app is utilizing the Cshl server. My experience is that it usually moves quickly from submission to running.
> 
> Liya
> 
> Sent from my iPhone
> 
>> On May 11, 2015, at 5:03 PM, Matthew Vaughn <vaughn at tacc.utexas.edu> wrote:
>> 
>> The job has been accepted if it is sitting at the Submitted stage. We are just waiting in line to move the data into the system before it enters the HPC queue. 
>> 
>> 
>> 
>>> On May 11, 2015, at 4:00 PM, Wang, Liya <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>>
>>> 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>>, "Lu, Jerry" <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
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On 5/11/15, 1:23 PM, "Wang, Liya" <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> 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]
>>> Sent: Monday, May 11, 2015 2:00 PM
>>> To: Lu, Jerry
>>> Cc: 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> wrote:
>>> 
>>> Hi Martha,
>>> Yes, both Liya and I helped him.
>>> 
>>> Zhenyuan
>>> 
>>> ________________________________
>>> From: Martha Narro [narro at iplantcollaborative.org]
>>> Sent: Monday, May 11, 2015 1:40 PM
>>> To: 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>>
>>> Date: Monday, May 11, 2015
>>> Subject: seqtk_seq-1.0.76
>>> To:
>>> "info at iplantcollaborative.org<mailto:info at iplantcollaborative.org>"
>>> <info at iplantcollaborative.org<mailto:info at iplantcollaborative.org>>
>>> Cc: "Lu, Jerry" <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<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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