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

Tue May 12 11:57:32 MST 2015

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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