user annotation track not showing for one of the sequences

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user annotation track not showing for one of the sequences

Pedrolance
Hi,

I am running a webapollo V1.0  instance for Botrytis cinerea and the users are now unable to see the User-annotation track for one of the 18 sequences. Any ideas what may be causing the problem? I checked the user database and everything looks good regarding permissions.

Any help much appreciated.

Cheers

Helder Pedro

*******************************************
               Hélder Pedro
     PhytoPath Bioinformatician
            EnsemblGenomes

European Bioinformatics Institute     
Wellcome Trust Genome Campus 
        Hinxton  CB10 1SD - UK 

Phone: +44.1223.49.25.92
********************************************











This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: user annotation track not showing for one of the sequences

Monica Poelchau
Hi Helder,

We see that a lot, too. Try removing the .lck files from the offending sequence's annotation directory. (Probably best to back up the directory first...).

Monica

On Mon, Nov 16, 2015 at 5:02 AM, Helder Pedro <[hidden email]> wrote:
Hi,

I am running a webapollo V1.0  instance for Botrytis cinerea and the users are now unable to see the User-annotation track for one of the 18 sequences. Any ideas what may be causing the problem? I checked the user database and everything looks good regarding permissions.

Any help much appreciated.

Cheers

Helder Pedro

*******************************************
               Hélder Pedro
     PhytoPath Bioinformatician
            EnsemblGenomes

European Bioinformatics Institute     
Wellcome Trust Genome Campus 
        Hinxton  CB10 1SD - UK 

Phone: +44.1223.49.25.92
********************************************











This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: user annotation track not showing for one of the sequences

Pedrolance
Thanks Monica. That worked. 

Any idea what is causing it? Is happening again for other chromosomes.

Cheers

Helder Pedro

*******************************************
               Hélder Pedro
     PhytoPath Bioinformatician
            EnsemblGenomes

European Bioinformatics Institute     
Wellcome Trust Genome Campus 
        Hinxton  CB10 1SD - UK 

Phone: +44.1223.49.25.92
********************************************







On 16 Nov 2015, at 15:21, Monica Poelchau <[hidden email]> wrote:

Hi Helder,

We see that a lot, too. Try removing the .lck files from the offending sequence's annotation directory. (Probably best to back up the directory first...).

Monica

On Mon, Nov 16, 2015 at 5:02 AM, Helder Pedro <[hidden email]> wrote:
Hi,

I am running a webapollo V1.0  instance for Botrytis cinerea and the users are now unable to see the User-annotation track for one of the 18 sequences. Any ideas what may be causing the problem? I checked the user database and everything looks good regarding permissions.

Any help much appreciated.

Cheers

Helder Pedro

*******************************************
               Hélder Pedro
     PhytoPath Bioinformatician
            EnsemblGenomes

European Bioinformatics Institute     
Wellcome Trust Genome Campus 
        Hinxton  CB10 1SD - UK 

Phone: +44.1223.49.25.92
********************************************











This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: user annotation track not showing for one of the sequences

nathandunn

I don’t think that the older versions of Apollo (1.x and earlier) did not necessarily clean up properly after certain operations (maybe not consistently thread-safe?).   

I would definitely try moving towards a 2.0 version when you have a chance. 

Nathan

On Nov 18, 2015, at 1:59 AM, Helder Pedro <[hidden email]> wrote:

Thanks Monica. That worked. 

Any idea what is causing it? Is happening again for other chromosomes.

Cheers

Helder Pedro

*******************************************
               Hélder Pedro
     PhytoPath Bioinformatician
            EnsemblGenomes

European Bioinformatics Institute     
Wellcome Trust Genome Campus 
        Hinxton  CB10 1SD - UK 

Phone: +44.1223.49.25.92
********************************************







On 16 Nov 2015, at 15:21, Monica Poelchau <[hidden email]> wrote:

Hi Helder,

We see that a lot, too. Try removing the .lck files from the offending sequence's annotation directory. (Probably best to back up the directory first...).

Monica

On Mon, Nov 16, 2015 at 5:02 AM, Helder Pedro <[hidden email]> wrote:
Hi,

I am running a webapollo V1.0  instance for Botrytis cinerea and the users are now unable to see the User-annotation track for one of the 18 sequences. Any ideas what may be causing the problem? I checked the user database and everything looks good regarding permissions.

Any help much appreciated.

Cheers

Helder Pedro

*******************************************
               Hélder Pedro
     PhytoPath Bioinformatician
            EnsemblGenomes

European Bioinformatics Institute     
Wellcome Trust Genome Campus 
        Hinxton  CB10 1SD - UK 

Phone: +44.1223.49.25.92
********************************************











This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.