FASTA file loader error

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FASTA file loader error

azrinahmad
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.

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Re: FASTA file loader error

Stephen Ficklin-2

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.


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Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
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Re: FASTA file loader error

azrinahmad
Hi Stephen,

I already loaded the Sequence Ontology. Attached file is a screenshot of a job.

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:26 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.



------------------------------------------------------------------------------
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Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
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Re: FASTA file loader error

Stephen Ficklin-2

Hi Azrin,

The time it took to execute (submitted, started, ended times) is essentially zero.   I'm not sure why it says it succeeded.  We'll have to look into that as a bug, but the sequence ontology takes at least 20 minutes to load so I don't think it was loaded.  Can you try loading it again?

Stephen


On 6/23/2016 5:03 PM, Azrin Ahmad wrote:
Hi Stephen,

I already loaded the Sequence Ontology. Attached file is a screenshot of a job.

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:26 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.




------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
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Re: FASTA file loader error

azrinahmad
Hi Stephen,

I already reload the SO..it takes 1 hour and 30 minutes (from 15.44pm till 17.18pm - Malaysia time) to execute. but as you can see in the attached file (screenshot of the job), the time is zero. and when i load fasta file for scaffold sequence of Citrus sinensis, the error still there. 

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:06 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

The time it took to execute (submitted, started, ended times) is essentially zero.   I'm not sure why it says it succeeded.  We'll have to look into that as a bug, but the sequence ontology takes at least 20 minutes to load so I don't think it was loaded.  Can you try loading it again?

Stephen


On 6/23/2016 5:03 PM, Azrin Ahmad wrote:
Hi Stephen,

I already loaded the Sequence Ontology. Attached file is a screenshot of a job.

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:26 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.





------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
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Re: FASTA file loader error

Stephen Ficklin-2

Hi Arzin,

When you load the SO, are you using the drush command to do it?  If so, can you re-load it and cut-and-paste the contents of the terminal window? 

Thanks,

Stephen


On 6/24/2016 2:28 AM, Azrin Ahmad wrote:
Hi Stephen,

I already reload the SO..it takes 1 hour and 30 minutes (from 15.44pm till 17.18pm - Malaysia time) to execute. but as you can see in the attached file (screenshot of the job), the time is zero. and when i load fasta file for scaffold sequence of Citrus sinensis, the error still there. 

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:06 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

The time it took to execute (submitted, started, ended times) is essentially zero.   I'm not sure why it says it succeeded.  We'll have to look into that as a bug, but the sequence ontology takes at least 20 minutes to load so I don't think it was loaded.  Can you try loading it again?

Stephen


On 6/23/2016 5:03 PM, Azrin Ahmad wrote:
Hi Stephen,

I already loaded the Sequence Ontology. Attached file is a screenshot of a job.

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:26 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.






------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
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Re: FASTA file loader error

azrinahmad
Hi Stephen,

Yes, I'm using drush command when load the SO. Attached files are the screenshot of the terminal window. I'm using SO file in the new link (https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp.obo) as suggested in this link: https://www.drupal.org/node/2551697
It looks fine when loading SO for this time (almost 2 hours to execute the job but zero time in job status as can be seen in screenshot file) but when I submit the fasta file for scaffold Citrus sinensis,  the error is: 
Failed to find feature 'scaffold00001' ('') while matching on name. But, in status job, it says 100% completed. 

How can both job status and command execute status are not synchronized? How to solve this? 

Thanks,
Azrin.

On Sat, Jun 25, 2016 at 12:16 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

When you load the SO, are you using the drush command to do it?  If so, can you re-load it and cut-and-paste the contents of the terminal window? 

Thanks,

Stephen


On 6/24/2016 2:28 AM, Azrin Ahmad wrote:
Hi Stephen,

I already reload the SO..it takes 1 hour and 30 minutes (from 15.44pm till 17.18pm - Malaysia time) to execute. but as you can see in the attached file (screenshot of the job), the time is zero. and when i load fasta file for scaffold sequence of Citrus sinensis, the error still there. 

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:06 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

The time it took to execute (submitted, started, ended times) is essentially zero.   I'm not sure why it says it succeeded.  We'll have to look into that as a bug, but the sequence ontology takes at least 20 minutes to load so I don't think it was loaded.  Can you try loading it again?

Stephen


On 6/23/2016 5:03 PM, Azrin Ahmad wrote:
Hi Stephen,

I already loaded the Sequence Ontology. Attached file is a screenshot of a job.

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:26 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.







------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
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Re: FASTA file loader error

Stephen Ficklin-2

Hi Azrin,

The error message in the terminal window is that the OBO file is missing the 'default-namespace' and then it proceeds to load zero terms.  This makes me think that the OBO file is empty.  To make sure there's no bug in Tripal I just tested installing the SO on my machine and it loaded just fine.  But just to be sure, can you verify which version of Tripal you are using?  Is it 2.0 or the development 2.x version?

If I remember correctly, previously the OBO loader wasn't able to download for you and you had to download the file manually.  But in this screenshot it was downloaded automatically by the loader.  Did you have firewall issues that were adjusted? 

if you run this command do you get a full obo.file:

wget http://purl.obolibrary.org/obo/so.obo

Stephen



On 6/26/2016 7:54 PM, Azrin Ahmad wrote:
Hi Stephen,

Yes, I'm using drush command when load the SO. Attached files are the screenshot of the terminal window. I'm using SO file in the new link (https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp.obo) as suggested in this link: https://www.drupal.org/node/2551697
It looks fine when loading SO for this time (almost 2 hours to execute the job but zero time in job status as can be seen in screenshot file) but when I submit the fasta file for scaffold Citrus sinensis,  the error is: 
Failed to find feature 'scaffold00001' ('') while matching on name. But, in status job, it says 100% completed. 

How can both job status and command execute status are not synchronized? How to solve this? 

Thanks,
Azrin.

On Sat, Jun 25, 2016 at 12:16 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

When you load the SO, are you using the drush command to do it?  If so, can you re-load it and cut-and-paste the contents of the terminal window? 

Thanks,

Stephen


On 6/24/2016 2:28 AM, Azrin Ahmad wrote:
Hi Stephen,

I already reload the SO..it takes 1 hour and 30 minutes (from 15.44pm till 17.18pm - Malaysia time) to execute. but as you can see in the attached file (screenshot of the job), the time is zero. and when i load fasta file for scaffold sequence of Citrus sinensis, the error still there. 

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:06 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

The time it took to execute (submitted, started, ended times) is essentially zero.   I'm not sure why it says it succeeded.  We'll have to look into that as a bug, but the sequence ontology takes at least 20 minutes to load so I don't think it was loaded.  Can you try loading it again?

Stephen


On 6/23/2016 5:03 PM, Azrin Ahmad wrote:
Hi Stephen,

I already loaded the Sequence Ontology. Attached file is a screenshot of a job.

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:26 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.








------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
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Re: FASTA file loader error

azrinahmad
Hi Stephen,

Yup, im using Tripal 2.0. Nope, the SO OBO file was not automatically download. before this also i used a new ontology OBO reference and parse remote URL to download the SO OBO file (same link as you give). There is no firewall issues that were adjusted.

Thanks,
Azrin.

On Mon, Jun 27, 2016 at 11:12 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

The error message in the terminal window is that the OBO file is missing the 'default-namespace' and then it proceeds to load zero terms.  This makes me think that the OBO file is empty.  To make sure there's no bug in Tripal I just tested installing the SO on my machine and it loaded just fine.  But just to be sure, can you verify which version of Tripal you are using?  Is it 2.0 or the development 2.x version?

If I remember correctly, previously the OBO loader wasn't able to download for you and you had to download the file manually.  But in this screenshot it was downloaded automatically by the loader.  Did you have firewall issues that were adjusted? 

if you run this command do you get a full obo.file:

wget http://purl.obolibrary.org/obo/so.obo

Stephen



On 6/26/2016 7:54 PM, Azrin Ahmad wrote:
Hi Stephen,

Yes, I'm using drush command when load the SO. Attached files are the screenshot of the terminal window. I'm using SO file in the new link (https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp.obo) as suggested in this link: https://www.drupal.org/node/2551697
It looks fine when loading SO for this time (almost 2 hours to execute the job but zero time in job status as can be seen in screenshot file) but when I submit the fasta file for scaffold Citrus sinensis,  the error is: 
Failed to find feature 'scaffold00001' ('') while matching on name. But, in status job, it says 100% completed. 

How can both job status and command execute status are not synchronized? How to solve this? 

Thanks,
Azrin.

On Sat, Jun 25, 2016 at 12:16 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

When you load the SO, are you using the drush command to do it?  If so, can you re-load it and cut-and-paste the contents of the terminal window? 

Thanks,

Stephen


On 6/24/2016 2:28 AM, Azrin Ahmad wrote:
Hi Stephen,

I already reload the SO..it takes 1 hour and 30 minutes (from 15.44pm till 17.18pm - Malaysia time) to execute. but as you can see in the attached file (screenshot of the job), the time is zero. and when i load fasta file for scaffold sequence of Citrus sinensis, the error still there. 

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:06 PM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Azrin,

The time it took to execute (submitted, started, ended times) is essentially zero.   I'm not sure why it says it succeeded.  We'll have to look into that as a bug, but the sequence ontology takes at least 20 minutes to load so I don't think it was loaded.  Can you try loading it again?

Stephen


On 6/23/2016 5:03 PM, Azrin Ahmad wrote:
Hi Stephen,

I already loaded the Sequence Ontology. Attached file is a screenshot of a job.

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:26 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.









------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
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Re: FASTA file loader error

Stephen Ficklin-2

Hi Arzin,

I'm not able to reproduce the problem you're having so this is a bit hard to debug.  The OBO loader is trying to download the file but it seems as though the file is empty or it's in a format the loader can't read.  Can you re-load the SO and terminate the loader before it can finish on it's own (type Ctrl+C on the terminal before it completes).  This should leave the temporary SO OBO file that was downloaded.  The output in the terminal tells you where the file is downloaded to. Then can you go take a look at the file and make sure it looks correct?

Stephen


On 6/26/2016 8:46 PM, Azrin Ahmad wrote:
Hi Stephen,

Yup, im using Tripal 2.0. Nope, the SO OBO file was not automatically download. before this also i used a new ontology OBO reference and parse remote URL to download the SO OBO file (same link as you give). There is no firewall issues that were adjusted.

Thanks,
Azrin.

On Mon, Jun 27, 2016 at 11:12 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

The error message in the terminal window is that the OBO file is missing the 'default-namespace' and then it proceeds to load zero terms.  This makes me think that the OBO file is empty.  To make sure there's no bug in Tripal I just tested installing the SO on my machine and it loaded just fine.  But just to be sure, can you verify which version of Tripal you are using?  Is it 2.0 or the development 2.x version?

If I remember correctly, previously the OBO loader wasn't able to download for you and you had to download the file manually.  But in this screenshot it was downloaded automatically by the loader.  Did you have firewall issues that were adjusted? 

if you run this command do you get a full obo.file:

wget http://purl.obolibrary.org/obo/so.obo

Stephen



On 6/26/2016 7:54 PM, Azrin Ahmad wrote:
Hi Stephen,

Yes, I'm using drush command when load the SO. Attached files are the screenshot of the terminal window. I'm using SO file in the new link (https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp.obo) as suggested in this link: https://www.drupal.org/node/2551697
It looks fine when loading SO for this time (almost 2 hours to execute the job but zero time in job status as can be seen in screenshot file) but when I submit the fasta file for scaffold Citrus sinensis,  the error is: 
Failed to find feature 'scaffold00001' ('') while matching on name. But, in status job, it says 100% completed. 

How can both job status and command execute status are not synchronized? How to solve this? 

Thanks,
Azrin.

On Sat, Jun 25, 2016 at 12:16 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

When you load the SO, are you using the drush command to do it?  If so, can you re-load it and cut-and-paste the contents of the terminal window? 

Thanks,

Stephen


On 6/24/2016 2:28 AM, Azrin Ahmad wrote:
Hi Stephen,

I already reload the SO..it takes 1 hour and 30 minutes (from 15.44pm till 17.18pm - Malaysia time) to execute. but as you can see in the attached file (screenshot of the job), the time is zero. and when i load fasta file for scaffold sequence of Citrus sinensis, the error still there. 

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:06 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

The time it took to execute (submitted, started, ended times) is essentially zero.   I'm not sure why it says it succeeded.  We'll have to look into that as a bug, but the sequence ontology takes at least 20 minutes to load so I don't think it was loaded.  Can you try loading it again?

Stephen


On 6/23/2016 5:03 PM, Azrin Ahmad wrote:
Hi Stephen,

I already loaded the Sequence Ontology. Attached file is a screenshot of a job.

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:26 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.










------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
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Re: FASTA file loader error

azrinahmad
Hi Stephen,

Can you suggest, should i reload the SO using the saved ontology OBO reference or use a new ontology OBO reference? i had tried both, by using the saved ontology OBO reference, downloading URL is http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo and will get the error:
Couldn't find object term SO:0001411.
By using the new ontology OBO reference, it looks fine (100% completed and no error when execute using drush command) but finally get error when execute fasta file.

Thanks,
Azrin. 

On Mon, Jun 27, 2016 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

I'm not able to reproduce the problem you're having so this is a bit hard to debug.  The OBO loader is trying to download the file but it seems as though the file is empty or it's in a format the loader can't read.  Can you re-load the SO and terminate the loader before it can finish on it's own (type Ctrl+C on the terminal before it completes).  This should leave the temporary SO OBO file that was downloaded.  The output in the terminal tells you where the file is downloaded to. Then can you go take a look at the file and make sure it looks correct?

Stephen


On 6/26/2016 8:46 PM, Azrin Ahmad wrote:
Hi Stephen,

Yup, im using Tripal 2.0. Nope, the SO OBO file was not automatically download. before this also i used a new ontology OBO reference and parse remote URL to download the SO OBO file (same link as you give). There is no firewall issues that were adjusted.

Thanks,
Azrin.

On Mon, Jun 27, 2016 at 11:12 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

The error message in the terminal window is that the OBO file is missing the 'default-namespace' and then it proceeds to load zero terms.  This makes me think that the OBO file is empty.  To make sure there's no bug in Tripal I just tested installing the SO on my machine and it loaded just fine.  But just to be sure, can you verify which version of Tripal you are using?  Is it 2.0 or the development 2.x version?

If I remember correctly, previously the OBO loader wasn't able to download for you and you had to download the file manually.  But in this screenshot it was downloaded automatically by the loader.  Did you have firewall issues that were adjusted? 

if you run this command do you get a full obo.file:

wget http://purl.obolibrary.org/obo/so.obo

Stephen



On 6/26/2016 7:54 PM, Azrin Ahmad wrote:
Hi Stephen,

Yes, I'm using drush command when load the SO. Attached files are the screenshot of the terminal window. I'm using SO file in the new link (https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp.obo) as suggested in this link: https://www.drupal.org/node/2551697
It looks fine when loading SO for this time (almost 2 hours to execute the job but zero time in job status as can be seen in screenshot file) but when I submit the fasta file for scaffold Citrus sinensis,  the error is: 
Failed to find feature 'scaffold00001' ('') while matching on name. But, in status job, it says 100% completed. 

How can both job status and command execute status are not synchronized? How to solve this? 

Thanks,
Azrin.

On Sat, Jun 25, 2016 at 12:16 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Arzin,

When you load the SO, are you using the drush command to do it?  If so, can you re-load it and cut-and-paste the contents of the terminal window? 

Thanks,

Stephen


On 6/24/2016 2:28 AM, Azrin Ahmad wrote:
Hi Stephen,

I already reload the SO..it takes 1 hour and 30 minutes (from 15.44pm till 17.18pm - Malaysia time) to execute. but as you can see in the attached file (screenshot of the job), the time is zero. and when i load fasta file for scaffold sequence of Citrus sinensis, the error still there. 

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:06 PM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Azrin,

The time it took to execute (submitted, started, ended times) is essentially zero.   I'm not sure why it says it succeeded.  We'll have to look into that as a bug, but the sequence ontology takes at least 20 minutes to load so I don't think it was loaded.  Can you try loading it again?

Stephen


On 6/23/2016 5:03 PM, Azrin Ahmad wrote:
Hi Stephen,

I already loaded the Sequence Ontology. Attached file is a screenshot of a job.

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:26 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.











------------------------------------------------------------------------------
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Francisco, CA to explore cutting-edge tech and listen to tech luminaries
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everyone, including kids. Get more information and register today.
http://sdm.link/attshape
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Re: FASTA file loader error

Stephen Ficklin-2

Hi Azrin,

Try this one: http://purl.obolibrary.org/obo/so.obo

Although it looks fine (at 100% completed) it's lying to you.  The SO is not really being loaded.  The problem can be seen in the terminal window when the SO tries to load.  You'll see the error messages there.  I believe the downloaded file is empty or corrupted somehow.  Can you try my suggestion from the previous post?

Stephen


On 6/26/2016 11:26 PM, Azrin Ahmad wrote:
Hi Stephen,

Can you suggest, should i reload the SO using the saved ontology OBO reference or use a new ontology OBO reference? i had tried both, by using the saved ontology OBO reference, downloading URL is http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo and will get the error:
Couldn't find object term SO:0001411.
By using the new ontology OBO reference, it looks fine (100% completed and no error when execute using drush command) but finally get error when execute fasta file.

Thanks,
Azrin. 

On Mon, Jun 27, 2016 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

I'm not able to reproduce the problem you're having so this is a bit hard to debug.  The OBO loader is trying to download the file but it seems as though the file is empty or it's in a format the loader can't read.  Can you re-load the SO and terminate the loader before it can finish on it's own (type Ctrl+C on the terminal before it completes).  This should leave the temporary SO OBO file that was downloaded.  The output in the terminal tells you where the file is downloaded to. Then can you go take a look at the file and make sure it looks correct?

Stephen


On 6/26/2016 8:46 PM, Azrin Ahmad wrote:
Hi Stephen,

Yup, im using Tripal 2.0. Nope, the SO OBO file was not automatically download. before this also i used a new ontology OBO reference and parse remote URL to download the SO OBO file (same link as you give). There is no firewall issues that were adjusted.

Thanks,
Azrin.

On Mon, Jun 27, 2016 at 11:12 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

The error message in the terminal window is that the OBO file is missing the 'default-namespace' and then it proceeds to load zero terms.  This makes me think that the OBO file is empty.  To make sure there's no bug in Tripal I just tested installing the SO on my machine and it loaded just fine.  But just to be sure, can you verify which version of Tripal you are using?  Is it 2.0 or the development 2.x version?

If I remember correctly, previously the OBO loader wasn't able to download for you and you had to download the file manually.  But in this screenshot it was downloaded automatically by the loader.  Did you have firewall issues that were adjusted? 

if you run this command do you get a full obo.file:

wget http://purl.obolibrary.org/obo/so.obo

Stephen



On 6/26/2016 7:54 PM, Azrin Ahmad wrote:
Hi Stephen,

Yes, I'm using drush command when load the SO. Attached files are the screenshot of the terminal window. I'm using SO file in the new link (https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp.obo) as suggested in this link: https://www.drupal.org/node/2551697
It looks fine when loading SO for this time (almost 2 hours to execute the job but zero time in job status as can be seen in screenshot file) but when I submit the fasta file for scaffold Citrus sinensis,  the error is: 
Failed to find feature 'scaffold00001' ('') while matching on name. But, in status job, it says 100% completed. 

How can both job status and command execute status are not synchronized? How to solve this? 

Thanks,
Azrin.

On Sat, Jun 25, 2016 at 12:16 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

When you load the SO, are you using the drush command to do it?  If so, can you re-load it and cut-and-paste the contents of the terminal window? 

Thanks,

Stephen


On 6/24/2016 2:28 AM, Azrin Ahmad wrote:
Hi Stephen,

I already reload the SO..it takes 1 hour and 30 minutes (from 15.44pm till 17.18pm - Malaysia time) to execute. but as you can see in the attached file (screenshot of the job), the time is zero. and when i load fasta file for scaffold sequence of Citrus sinensis, the error still there. 

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:06 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

The time it took to execute (submitted, started, ended times) is essentially zero.   I'm not sure why it says it succeeded.  We'll have to look into that as a bug, but the sequence ontology takes at least 20 minutes to load so I don't think it was loaded.  Can you try loading it again?

Stephen


On 6/23/2016 5:03 PM, Azrin Ahmad wrote:
Hi Stephen,

I already loaded the Sequence Ontology. Attached file is a screenshot of a job.

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:26 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.












------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
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Re: FASTA file loader error

azrinahmad
Hi Stephen,

I already tried to load using this link http://purl.obolibrary.org/obo/so.obo and terminate the loader before it completes. i looked into temporary file and it is only loaded till this line:
[Term]
id: SO:0001904
name: antisense_lncRNA
def: "Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]
synonym: "antisense lncRNA" RELATED []
synonym: "natural anti

after that, i tried to load until it finish and it gives error:
Could not find object term SO:1000182
When i go through the file, the object term id is after the unfinish line in the file that has been downloaded. How can i solve this?Why it is not fully downloaded?It looks fine when i download other file from internet into my machine. I don't think it is because of firewall issues.

Thanks,
Azrin.

On Mon, Jun 27, 2016 at 11:20 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

Try this one: http://purl.obolibrary.org/obo/so.obo

Although it looks fine (at 100% completed) it's lying to you.  The SO is not really being loaded.  The problem can be seen in the terminal window when the SO tries to load.  You'll see the error messages there.  I believe the downloaded file is empty or corrupted somehow.  Can you try my suggestion from the previous post?

Stephen


On 6/26/2016 11:26 PM, Azrin Ahmad wrote:
Hi Stephen,

Can you suggest, should i reload the SO using the saved ontology OBO reference or use a new ontology OBO reference? i had tried both, by using the saved ontology OBO reference, downloading URL is http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo and will get the error:
Couldn't find object term SO:0001411.
By using the new ontology OBO reference, it looks fine (100% completed and no error when execute using drush command) but finally get error when execute fasta file.

Thanks,
Azrin. 

On Mon, Jun 27, 2016 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

I'm not able to reproduce the problem you're having so this is a bit hard to debug.  The OBO loader is trying to download the file but it seems as though the file is empty or it's in a format the loader can't read.  Can you re-load the SO and terminate the loader before it can finish on it's own (type Ctrl+C on the terminal before it completes).  This should leave the temporary SO OBO file that was downloaded.  The output in the terminal tells you where the file is downloaded to. Then can you go take a look at the file and make sure it looks correct?

Stephen


On 6/26/2016 8:46 PM, Azrin Ahmad wrote:
Hi Stephen,

Yup, im using Tripal 2.0. Nope, the SO OBO file was not automatically download. before this also i used a new ontology OBO reference and parse remote URL to download the SO OBO file (same link as you give). There is no firewall issues that were adjusted.

Thanks,
Azrin.

On Mon, Jun 27, 2016 at 11:12 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Azrin,

The error message in the terminal window is that the OBO file is missing the 'default-namespace' and then it proceeds to load zero terms.  This makes me think that the OBO file is empty.  To make sure there's no bug in Tripal I just tested installing the SO on my machine and it loaded just fine.  But just to be sure, can you verify which version of Tripal you are using?  Is it 2.0 or the development 2.x version?

If I remember correctly, previously the OBO loader wasn't able to download for you and you had to download the file manually.  But in this screenshot it was downloaded automatically by the loader.  Did you have firewall issues that were adjusted? 

if you run this command do you get a full obo.file:

wget http://purl.obolibrary.org/obo/so.obo

Stephen



On 6/26/2016 7:54 PM, Azrin Ahmad wrote:
Hi Stephen,

Yes, I'm using drush command when load the SO. Attached files are the screenshot of the terminal window. I'm using SO file in the new link (https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp.obo) as suggested in this link: https://www.drupal.org/node/2551697
It looks fine when loading SO for this time (almost 2 hours to execute the job but zero time in job status as can be seen in screenshot file) but when I submit the fasta file for scaffold Citrus sinensis,  the error is: 
Failed to find feature 'scaffold00001' ('') while matching on name. But, in status job, it says 100% completed. 

How can both job status and command execute status are not synchronized? How to solve this? 

Thanks,
Azrin.

On Sat, Jun 25, 2016 at 12:16 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Arzin,

When you load the SO, are you using the drush command to do it?  If so, can you re-load it and cut-and-paste the contents of the terminal window? 

Thanks,

Stephen


On 6/24/2016 2:28 AM, Azrin Ahmad wrote:
Hi Stephen,

I already reload the SO..it takes 1 hour and 30 minutes (from 15.44pm till 17.18pm - Malaysia time) to execute. but as you can see in the attached file (screenshot of the job), the time is zero. and when i load fasta file for scaffold sequence of Citrus sinensis, the error still there. 

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:06 PM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Azrin,

The time it took to execute (submitted, started, ended times) is essentially zero.   I'm not sure why it says it succeeded.  We'll have to look into that as a bug, but the sequence ontology takes at least 20 minutes to load so I don't think it was loaded.  Can you try loading it again?

Stephen


On 6/23/2016 5:03 PM, Azrin Ahmad wrote:
Hi Stephen,

I already loaded the Sequence Ontology. Attached file is a screenshot of a job.

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:26 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.













------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
Gmod-tripal mailing list
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Re: FASTA file loader error

Stephen Ficklin-2

Hi Arzin,

I have no idea why the file is not fully downloaded.  Do you have some on-site IT staff who may be able to help you look into it.  I don't think this is an  issue with Tripal as we've been loading SO into Tripal sites the last few days with no problems.

Stephen


On 6/27/2016 5:47 PM, Azrin Ahmad wrote:
Hi Stephen,

I already tried to load using this link http://purl.obolibrary.org/obo/so.obo and terminate the loader before it completes. i looked into temporary file and it is only loaded till this line:
[Term]
id: SO:0001904
name: antisense_lncRNA
def: "Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]
synonym: "antisense lncRNA" RELATED []
synonym: "natural anti

after that, i tried to load until it finish and it gives error:
Could not find object term SO:1000182
When i go through the file, the object term id is after the unfinish line in the file that has been downloaded. How can i solve this?Why it is not fully downloaded?It looks fine when i download other file from internet into my machine. I don't think it is because of firewall issues.

Thanks,
Azrin.

On Mon, Jun 27, 2016 at 11:20 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

Try this one: http://purl.obolibrary.org/obo/so.obo

Although it looks fine (at 100% completed) it's lying to you.  The SO is not really being loaded.  The problem can be seen in the terminal window when the SO tries to load.  You'll see the error messages there.  I believe the downloaded file is empty or corrupted somehow.  Can you try my suggestion from the previous post?

Stephen


On 6/26/2016 11:26 PM, Azrin Ahmad wrote:
Hi Stephen,

Can you suggest, should i reload the SO using the saved ontology OBO reference or use a new ontology OBO reference? i had tried both, by using the saved ontology OBO reference, downloading URL is http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo and will get the error:
Couldn't find object term SO:0001411.
By using the new ontology OBO reference, it looks fine (100% completed and no error when execute using drush command) but finally get error when execute fasta file.

Thanks,
Azrin. 

On Mon, Jun 27, 2016 at 2:09 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

I'm not able to reproduce the problem you're having so this is a bit hard to debug.  The OBO loader is trying to download the file but it seems as though the file is empty or it's in a format the loader can't read.  Can you re-load the SO and terminate the loader before it can finish on it's own (type Ctrl+C on the terminal before it completes).  This should leave the temporary SO OBO file that was downloaded.  The output in the terminal tells you where the file is downloaded to. Then can you go take a look at the file and make sure it looks correct?

Stephen


On 6/26/2016 8:46 PM, Azrin Ahmad wrote:
Hi Stephen,

Yup, im using Tripal 2.0. Nope, the SO OBO file was not automatically download. before this also i used a new ontology OBO reference and parse remote URL to download the SO OBO file (same link as you give). There is no firewall issues that were adjusted.

Thanks,
Azrin.

On Mon, Jun 27, 2016 at 11:12 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

The error message in the terminal window is that the OBO file is missing the 'default-namespace' and then it proceeds to load zero terms.  This makes me think that the OBO file is empty.  To make sure there's no bug in Tripal I just tested installing the SO on my machine and it loaded just fine.  But just to be sure, can you verify which version of Tripal you are using?  Is it 2.0 or the development 2.x version?

If I remember correctly, previously the OBO loader wasn't able to download for you and you had to download the file manually.  But in this screenshot it was downloaded automatically by the loader.  Did you have firewall issues that were adjusted? 

if you run this command do you get a full obo.file:

wget http://purl.obolibrary.org/obo/so.obo

Stephen



On 6/26/2016 7:54 PM, Azrin Ahmad wrote:
Hi Stephen,

Yes, I'm using drush command when load the SO. Attached files are the screenshot of the terminal window. I'm using SO file in the new link (https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp.obo) as suggested in this link: https://www.drupal.org/node/2551697
It looks fine when loading SO for this time (almost 2 hours to execute the job but zero time in job status as can be seen in screenshot file) but when I submit the fasta file for scaffold Citrus sinensis,  the error is: 
Failed to find feature 'scaffold00001' ('') while matching on name. But, in status job, it says 100% completed. 

How can both job status and command execute status are not synchronized? How to solve this? 

Thanks,
Azrin.

On Sat, Jun 25, 2016 at 12:16 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

When you load the SO, are you using the drush command to do it?  If so, can you re-load it and cut-and-paste the contents of the terminal window? 

Thanks,

Stephen


On 6/24/2016 2:28 AM, Azrin Ahmad wrote:
Hi Stephen,

I already reload the SO..it takes 1 hour and 30 minutes (from 15.44pm till 17.18pm - Malaysia time) to execute. but as you can see in the attached file (screenshot of the job), the time is zero. and when i load fasta file for scaffold sequence of Citrus sinensis, the error still there. 

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:06 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

The time it took to execute (submitted, started, ended times) is essentially zero.   I'm not sure why it says it succeeded.  We'll have to look into that as a bug, but the sequence ontology takes at least 20 minutes to load so I don't think it was loaded.  Can you try loading it again?

Stephen


On 6/23/2016 5:03 PM, Azrin Ahmad wrote:
Hi Stephen,

I already loaded the Sequence Ontology. Attached file is a screenshot of a job.

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:26 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.














------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
Reply | Threaded
Open this post in threaded view
|

Re: FASTA file loader error

azrinahmad
Hi Stephen,

I got new error: "Could not fill cvtermpath table". But again, in web browser, it's status is 100% completed. How to solve this error?

Thanks.
Azrin.

On Fri, Jul 1, 2016 at 12:48 AM, Stephen Ficklin <[hidden email]> wrote:

Hi Arzin,

I have no idea why the file is not fully downloaded.  Do you have some on-site IT staff who may be able to help you look into it.  I don't think this is an  issue with Tripal as we've been loading SO into Tripal sites the last few days with no problems.

Stephen


On 6/27/2016 5:47 PM, Azrin Ahmad wrote:
Hi Stephen,

I already tried to load using this link http://purl.obolibrary.org/obo/so.obo and terminate the loader before it completes. i looked into temporary file and it is only loaded till this line:
[Term]
id: SO:0001904
name: antisense_lncRNA
def: "Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]
synonym: "antisense lncRNA" RELATED []
synonym: "natural anti

after that, i tried to load until it finish and it gives error:
Could not find object term SO:1000182
When i go through the file, the object term id is after the unfinish line in the file that has been downloaded. How can i solve this?Why it is not fully downloaded?It looks fine when i download other file from internet into my machine. I don't think it is because of firewall issues.

Thanks,
Azrin.

On Mon, Jun 27, 2016 at 11:20 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Azrin,

Try this one: http://purl.obolibrary.org/obo/so.obo

Although it looks fine (at 100% completed) it's lying to you.  The SO is not really being loaded.  The problem can be seen in the terminal window when the SO tries to load.  You'll see the error messages there.  I believe the downloaded file is empty or corrupted somehow.  Can you try my suggestion from the previous post?

Stephen


On 6/26/2016 11:26 PM, Azrin Ahmad wrote:
Hi Stephen,

Can you suggest, should i reload the SO using the saved ontology OBO reference or use a new ontology OBO reference? i had tried both, by using the saved ontology OBO reference, downloading URL is http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo and will get the error:
Couldn't find object term SO:0001411.
By using the new ontology OBO reference, it looks fine (100% completed and no error when execute using drush command) but finally get error when execute fasta file.

Thanks,
Azrin. 

On Mon, Jun 27, 2016 at 2:09 PM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Arzin,

I'm not able to reproduce the problem you're having so this is a bit hard to debug.  The OBO loader is trying to download the file but it seems as though the file is empty or it's in a format the loader can't read.  Can you re-load the SO and terminate the loader before it can finish on it's own (type Ctrl+C on the terminal before it completes).  This should leave the temporary SO OBO file that was downloaded.  The output in the terminal tells you where the file is downloaded to. Then can you go take a look at the file and make sure it looks correct?

Stephen


On 6/26/2016 8:46 PM, Azrin Ahmad wrote:
Hi Stephen,

Yup, im using Tripal 2.0. Nope, the SO OBO file was not automatically download. before this also i used a new ontology OBO reference and parse remote URL to download the SO OBO file (same link as you give). There is no firewall issues that were adjusted.

Thanks,
Azrin.

On Mon, Jun 27, 2016 at 11:12 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Azrin,

The error message in the terminal window is that the OBO file is missing the 'default-namespace' and then it proceeds to load zero terms.  This makes me think that the OBO file is empty.  To make sure there's no bug in Tripal I just tested installing the SO on my machine and it loaded just fine.  But just to be sure, can you verify which version of Tripal you are using?  Is it 2.0 or the development 2.x version?

If I remember correctly, previously the OBO loader wasn't able to download for you and you had to download the file manually.  But in this screenshot it was downloaded automatically by the loader.  Did you have firewall issues that were adjusted? 

if you run this command do you get a full obo.file:

wget http://purl.obolibrary.org/obo/so.obo

Stephen



On 6/26/2016 7:54 PM, Azrin Ahmad wrote:
Hi Stephen,

Yes, I'm using drush command when load the SO. Attached files are the screenshot of the terminal window. I'm using SO file in the new link (https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp.obo) as suggested in this link: https://www.drupal.org/node/2551697
It looks fine when loading SO for this time (almost 2 hours to execute the job but zero time in job status as can be seen in screenshot file) but when I submit the fasta file for scaffold Citrus sinensis,  the error is: 
Failed to find feature 'scaffold00001' ('') while matching on name. But, in status job, it says 100% completed. 

How can both job status and command execute status are not synchronized? How to solve this? 

Thanks,
Azrin.

On Sat, Jun 25, 2016 at 12:16 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Arzin,

When you load the SO, are you using the drush command to do it?  If so, can you re-load it and cut-and-paste the contents of the terminal window? 

Thanks,

Stephen


On 6/24/2016 2:28 AM, Azrin Ahmad wrote:
Hi Stephen,

I already reload the SO..it takes 1 hour and 30 minutes (from 15.44pm till 17.18pm - Malaysia time) to execute. but as you can see in the attached file (screenshot of the job), the time is zero. and when i load fasta file for scaffold sequence of Citrus sinensis, the error still there. 

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:06 PM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Azrin,

The time it took to execute (submitted, started, ended times) is essentially zero.   I'm not sure why it says it succeeded.  We'll have to look into that as a bug, but the sequence ontology takes at least 20 minutes to load so I don't think it was loaded.  Can you try loading it again?

Stephen


On 6/23/2016 5:03 PM, Azrin Ahmad wrote:
Hi Stephen,

I already loaded the Sequence Ontology. Attached file is a screenshot of a job.

Thanks,
Azrin.

On Fri, Jun 24, 2016 at 12:26 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:

Hi Azrin,

It looks as though you have not yet loaded the Sequence Ontology.   Can you check?

Stephen


On 6/22/2016 9:34 PM, Azrin Ahmad wrote:
Hi,

I tried to setup of an example genomics site (Citrus sinensis) by following your tutorial. I have successfully loaded gff file but failed for both fasta files (scaffold sequence and mRNA sequences). The error is: 
  • The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another.
How to solve this problem?

Thanks in advance.

Best regards,
Azrin.















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