Tutorial: Can not open interpro output file. Job not scheduled.

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Tutorial: Can not open interpro output file. Job not scheduled.

Collett, James R-2
Hello,
 
I’m at the point in the tutorial where I’m trying to create an InterProScan analysis. When I finish filling in the form as per the instructions and click on “Save”, a new InterProScan analysis page is created, but it has the message “Can not open interpro output file. Job not scheduled.” at the top of the page.  Looking at the Jobs page, I can indeed see no job was created for the analysis.
 
I’m guessing that there is a problem with not having write permission to wherever the interproscan module sends its output, but I don’t know where that is.
 
Can you give me some leads on how to solve this problem?
 
Here below are the analysis details:
 
Analysis Name InterProScan of Dmel genes 3
Software iprscan (InterProScan 4.7)
Source FlyBase 2LHet genes FASTA file (FB2011_02)
Date performed 2011-08-18
Description InterProScan search of Dmel genes against all databases
InterProScan Arguments -goterms -ipr -format html
 
Thanks,
 
Jim
 
__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
 
Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, MSIN P8-60
Richland, WA  99352 USA
Tel:  509-372-6345
Fax: 509-372-4732
 
 
 

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
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Re: Tutorial: Can not open interpro output file. Job not scheduled.

Stephen Ficklin-2
Hi Jim,

Did you download the example InterPro output file in the demo?  The link for the data is at the top of the section:  http://gmod.org/wiki/Tripal_Tutorial_(v0.3.1b)#Loading_InterProScan_Results.  When you create your interpro analysis there is a field where you can enter the location where you downloaded and saved the file.  It works in the same way that the blast module worked in the previous step of the Tutorial.

Stephen

On 10/11/2011 6:20 PM, Collett, James R wrote:
Hello,
 
I’m at the point in the tutorial where I’m trying to create an InterProScan analysis. When I finish filling in the form as per the instructions and click on “Save”, a new InterProScan analysis page is created, but it has the message “Can not open interpro output file. Job not scheduled.” at the top of the page.  Looking at the Jobs page, I can indeed see no job was created for the analysis.
 
I’m guessing that there is a problem with not having write permission to wherever the interproscan module sends its output, but I don’t know where that is.
 
Can you give me some leads on how to solve this problem?
 
Here below are the analysis details:
 
Analysis Name InterProScan of Dmel genes 3
Software iprscan (InterProScan 4.7)
Source FlyBase 2LHet genes FASTA file (FB2011_02)
Date performed 2011-08-18
Description InterProScan search of Dmel genes against all databases
InterProScan Arguments -goterms -ipr -format html
 
Thanks,
 
Jim
 
__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
 
Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, MSIN P8-60
Richland, WA  99352 USA
Tel:  509-372-6345
Fax: 509-372-4732
 
 
 


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct


_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
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Re: Tutorial: Can not open interpro output file. Job not scheduled.

Collett, James R-2

Hi Stephen,

 

I’ve made some progress on getting the InterProScan extension to run, but I’m not quite there yet. 

 

I did download the correct file, but I noticed that the file path in the tutorial is listed as “/var/www/sites/default/files/flybase-tripal-demo.iprscan.xml.txt”, but the actual file that you download starts with a capital F - “Flybase-tripal-demo.iprscan.xml.txt”.

 

After several failures as described in my previous message, I got the job to run after logging of Drupal, clear my browser cache, and restarting firefox.  I don’t know if this was related to the problem, but the job started nonetheless with these job details:

 

Job 'Parse HTML interpro: Flybase-tripal-demo.iprscan.xml.txt' submitted. Check the jobs page for status

 

Calling: tripal_analysis_interpro_parseHTMLFile(16, /var/www/html/sites/default/files/Flybase-tripal-demo.iprscan.xml.txt, 1, 29)

Parsing File:/var/www/html/sites/default/files/Flybase-tripal-demo.iprscan.xml.txt ...

cvterm_id for analysis_interpro_output_iteration_hits is 37258

0 html tables to be processed.

Done.

Successful and failed entries have been saved in the log file:

/tmp/tripal_analysis_interpro_importZmtO5U

 

The log file only shows:

Tue Oct 11 21:46:12 2011. Loading /var/www/html/sites/default/files/Flybase-tripal-demo.iprscan.xml.txt

 

and there is still no link for an InterPro Report on the FBgn0039958 feature page.

 

Thanks,

 

Jim

 

 

From: Stephen Ficklin [mailto:[hidden email]]
Sent: Tuesday, October 11, 2011 3:45 PM
To: [hidden email]
Subject: Re: [Gmod-tripal] Tutorial: Can not open interpro output file. Job not scheduled.

 

Hi Jim,

Did you download the example InterPro output file in the demo?  The link for the data is at the top of the section:  http://gmod.org/wiki/Tripal_Tutorial_(v0.3.1b)#Loading_InterProScan_Results.  When you create your interpro analysis there is a field where you can enter the location where you downloaded and saved the file.  It works in the same way that the blast module worked in the previous step of the Tutorial.

Stephen

On 10/11/2011 6:20 PM, Collett, James R wrote:

Hello,

 

I’m at the point in the tutorial where I’m trying to create an InterProScan analysis. When I finish filling in the form as per the instructions and click on “Save”, a new InterProScan analysis page is created, but it has the message “Can not open interpro output file. Job not scheduled.” at the top of the page.  Looking at the Jobs page, I can indeed see no job was created for the analysis.

 

I’m guessing that there is a problem with not having write permission to wherever the interproscan module sends its output, but I don’t know where that is.

 

Can you give me some leads on how to solve this problem?

 

Here below are the analysis details:

 

Analysis Name InterProScan of Dmel genes 3

Software iprscan (InterProScan 4.7)

Source FlyBase 2LHet genes FASTA file (FB2011_02)

Date performed 2011-08-18

Description InterProScan search of Dmel genes against all databases

InterProScan Arguments -goterms -ipr -format html

 

Thanks,

 

Jim

 

__________________________________________________

James R. Collett, Ph.D.

Senior Scientist

Chemical and Biological Process Development Group

Energy and Environment Directorate

 

Pacific Northwest National Laboratory

902 Battelle Boulevard

P.O. Box 999, MSIN P8-60

Richland, WA  99352 USA

Tel:  509-372-6345

Fax: 509-372-4732

 

 

 




------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct




_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

 


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
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Re: Tutorial: Can not open interpro output file. Job not scheduled.

Stephen Ficklin-2
Hi Jim,

Unfortunately, the tutorial has a few mistakes at this point.  You are correct, the file name should be capitalized as you mentioned.   The InerPro output file is in XML fromat, not in HTML format, and the tutorial incorrectly states to check the box "The Input is in HTML format".  You should not check this box.   Also, there was one other setting that was missing.  The query type should be set to 'gene'.   I updated the tutorial and tested those settings on my own installation and they worked.  Can you try again and let me know if you have any other troubles.

Stephen

On 10/12/2011 1:40 AM, Collett, James R wrote:

Hi Stephen,

 

I’ve made some progress on getting the InterProScan extension to run, but I’m not quite there yet. 

 

I did download the correct file, but I noticed that the file path in the tutorial is listed as “/var/www/sites/default/files/flybase-tripal-demo.iprscan.xml.txt”, but the actual file that you download starts with a capital F - “Flybase-tripal-demo.iprscan.xml.txt”.

 

After several failures as described in my previous message, I got the job to run after logging of Drupal, clear my browser cache, and restarting firefox.  I don’t know if this was related to the problem, but the job started nonetheless with these job details:

 

Job 'Parse HTML interpro: Flybase-tripal-demo.iprscan.xml.txt' submitted. Check the jobs page for status

 

Calling: tripal_analysis_interpro_parseHTMLFile(16, /var/www/html/sites/default/files/Flybase-tripal-demo.iprscan.xml.txt, 1, 29)

Parsing File:/var/www/html/sites/default/files/Flybase-tripal-demo.iprscan.xml.txt ...

cvterm_id for analysis_interpro_output_iteration_hits is 37258

0 html tables to be processed.

Done.

Successful and failed entries have been saved in the log file:

/tmp/tripal_analysis_interpro_importZmtO5U

 

The log file only shows:

Tue Oct 11 21:46:12 2011. Loading /var/www/html/sites/default/files/Flybase-tripal-demo.iprscan.xml.txt

 

and there is still no link for an InterPro Report on the FBgn0039958 feature page.

 

Thanks,

 

Jim

 

 

From: Stephen Ficklin [[hidden email]]
Sent: Tuesday, October 11, 2011 3:45 PM
To: [hidden email]
Subject: Re: [Gmod-tripal] Tutorial: Can not open interpro output file. Job not scheduled.

 

Hi Jim,

Did you download the example InterPro output file in the demo?  The link for the data is at the top of the section:  http://gmod.org/wiki/Tripal_Tutorial_(v0.3.1b)#Loading_InterProScan_Results.  When you create your interpro analysis there is a field where you can enter the location where you downloaded and saved the file.  It works in the same way that the blast module worked in the previous step of the Tutorial.

Stephen

On 10/11/2011 6:20 PM, Collett, James R wrote:

Hello,

 

I’m at the point in the tutorial where I’m trying to create an InterProScan analysis. When I finish filling in the form as per the instructions and click on “Save”, a new InterProScan analysis page is created, but it has the message “Can not open interpro output file. Job not scheduled.” at the top of the page.  Looking at the Jobs page, I can indeed see no job was created for the analysis.

 

I’m guessing that there is a problem with not having write permission to wherever the interproscan module sends its output, but I don’t know where that is.

 

Can you give me some leads on how to solve this problem?

 

Here below are the analysis details:

 

Analysis Name InterProScan of Dmel genes 3

Software iprscan (InterProScan 4.7)

Source FlyBase 2LHet genes FASTA file (FB2011_02)

Date performed 2011-08-18

Description InterProScan search of Dmel genes against all databases

InterProScan Arguments -goterms -ipr -format html

 

Thanks,

 

Jim

 

__________________________________________________

James R. Collett, Ph.D.

Senior Scientist

Chemical and Biological Process Development Group

Energy and Environment Directorate

 

Pacific Northwest National Laboratory

902 Battelle Boulevard

P.O. Box 999, MSIN P8-60

Richland, WA  99352 USA

Tel:  509-372-6345

Fax: 509-372-4732

 

 

 




------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct




_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

 



------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct


_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal