Unable to load Jbrowse / WebApollo - tracks.conf

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Unable to load Jbrowse / WebApollo - tracks.conf

Shane McCoy
I was checking in on my Jbrowse / WebApollo site and found it would not load (was fine a couple days ago). For Jbrowse I get the:

"Congratulations, JBrowse is on the web!However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error." 

or a timed out browser message.
Going directly to WebApollo times out.

Logging into the backend, everything looks fine, tracks.conf is where it should be.
I am not finding any one w/ same issue in the lists.
Any thoughts of what I should do?

Thank you!
Shane M.




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: Unable to load Jbrowse / WebApollo - tracks.conf

nathandunn

If you are using Apollo2, my only guesses are:

1) you are logged out and the server isn’t telling you (then just do a refresh)
2) is that the organism preferences is somehow not set and you just select one from the drop-down at the top or click on a scaffold from the reference sequence tab.

If it is #1 (most likely), I would click on the “remember-me” option when you login.  We’re still working on making the “logout” a bit more obvious when doing a timeout, but we’re not quite there yet. 

Nathan

On Sep 14, 2015, at 5:16 AM, Shane McCoy <[hidden email]> wrote:

I was checking in on my Jbrowse / WebApollo site and found it would not load (was fine a couple days ago). For Jbrowse I get the:

"Congratulations, JBrowse is on the web!However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error." 

or a timed out browser message.
Going directly to WebApollo times out.

Logging into the backend, everything looks fine, tracks.conf is where it should be.
I am not finding any one w/ same issue in the lists.
Any thoughts of what I should do?

Thank you!
Shane M.



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: Unable to load Jbrowse / WebApollo - tracks.conf

Colin
If you are seeing things like timeouts, you might also have a tomcat issue.

If you can check the log files for things like PermGen errors out OutOfMemory errors, then this will typically just require a tomcat restart.

Sometimes tuning tomcat parameters can help with these issues if you see are seeing them frequently, and our troubleshooting guide goes over some recommended JAVA_OPTS.


-Colin

On Mon, Sep 14, 2015 at 11:39 AM, Nathan Dunn <[hidden email]> wrote:

If you are using Apollo2, my only guesses are:

1) you are logged out and the server isn’t telling you (then just do a refresh)
2) is that the organism preferences is somehow not set and you just select one from the drop-down at the top or click on a scaffold from the reference sequence tab.

If it is #1 (most likely), I would click on the “remember-me” option when you login.  We’re still working on making the “logout” a bit more obvious when doing a timeout, but we’re not quite there yet. 

Nathan

On Sep 14, 2015, at 5:16 AM, Shane McCoy <[hidden email]> wrote:

I was checking in on my Jbrowse / WebApollo site and found it would not load (was fine a couple days ago). For Jbrowse I get the:

"Congratulations, JBrowse is on the web!However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error." 

or a timed out browser message.
Going directly to WebApollo times out.

Logging into the backend, everything looks fine, tracks.conf is where it should be.
I am not finding any one w/ same issue in the lists.
Any thoughts of what I should do?

Thank you!
Shane M.



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: Unable to load Jbrowse / WebApollo - tracks.conf

Shane McCoy
Thanks! I will have to try resetting Tomcat and see if that works. Appreciate the help and i'll post back soon,

Shane

On Mon, Sep 14, 2015 at 12:55 PM, Colin <[hidden email]> wrote:
If you are seeing things like timeouts, you might also have a tomcat issue.

If you can check the log files for things like PermGen errors out OutOfMemory errors, then this will typically just require a tomcat restart.

Sometimes tuning tomcat parameters can help with these issues if you see are seeing them frequently, and our troubleshooting guide goes over some recommended JAVA_OPTS.


-Colin


On Mon, Sep 14, 2015 at 11:39 AM, Nathan Dunn <[hidden email]> wrote:

If you are using Apollo2, my only guesses are:

1) you are logged out and the server isn’t telling you (then just do a refresh)
2) is that the organism preferences is somehow not set and you just select one from the drop-down at the top or click on a scaffold from the reference sequence tab.

If it is #1 (most likely), I would click on the “remember-me” option when you login.  We’re still working on making the “logout” a bit more obvious when doing a timeout, but we’re not quite there yet. 

Nathan

On Sep 14, 2015, at 5:16 AM, Shane McCoy <[hidden email]> wrote:

I was checking in on my Jbrowse / WebApollo site and found it would not load (was fine a couple days ago). For Jbrowse I get the:

"Congratulations, JBrowse is on the web!However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error." 

or a timed out browser message.
Going directly to WebApollo times out.

Logging into the backend, everything looks fine, tracks.conf is where it should be.
I am not finding any one w/ same issue in the lists.
Any thoughts of what I should do?

Thank you!
Shane M.



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.

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Re: Unable to load Jbrowse / WebApollo - tracks.conf

Shane McCoy
Quick fix! Restarting Tomcat resolved the issue.
Much thanks again!
Shane

On Mon, Sep 14, 2015 at 2:00 PM, Shane McCoy <[hidden email]> wrote:
Thanks! I will have to try resetting Tomcat and see if that works. Appreciate the help and i'll post back soon,

Shane

On Mon, Sep 14, 2015 at 12:55 PM, Colin <[hidden email]> wrote:
If you are seeing things like timeouts, you might also have a tomcat issue.

If you can check the log files for things like PermGen errors out OutOfMemory errors, then this will typically just require a tomcat restart.

Sometimes tuning tomcat parameters can help with these issues if you see are seeing them frequently, and our troubleshooting guide goes over some recommended JAVA_OPTS.


-Colin


On Mon, Sep 14, 2015 at 11:39 AM, Nathan Dunn <[hidden email]> wrote:

If you are using Apollo2, my only guesses are:

1) you are logged out and the server isn’t telling you (then just do a refresh)
2) is that the organism preferences is somehow not set and you just select one from the drop-down at the top or click on a scaffold from the reference sequence tab.

If it is #1 (most likely), I would click on the “remember-me” option when you login.  We’re still working on making the “logout” a bit more obvious when doing a timeout, but we’re not quite there yet. 

Nathan

On Sep 14, 2015, at 5:16 AM, Shane McCoy <[hidden email]> wrote:

I was checking in on my Jbrowse / WebApollo site and found it would not load (was fine a couple days ago). For Jbrowse I get the:

"Congratulations, JBrowse is on the web!However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error." 

or a timed out browser message.
Going directly to WebApollo times out.

Logging into the backend, everything looks fine, tracks.conf is where it should be.
I am not finding any one w/ same issue in the lists.
Any thoughts of what I should do?

Thank you!
Shane M.



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.

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Re: Unable to load Jbrowse / WebApollo - tracks.conf

nathandunn

If it gets in this state again (or before) you may want to check your tomcat logs (catalina.out usually, but not always).   As Colin alluded to, it might have been due to a OutOfMemory / PermGen error (which it will say in the log).   You will have to increase memory in that case.   

Nathan


On Sep 14, 2015, at 11:53 AM, Shane McCoy <[hidden email]> wrote:

Quick fix! Restarting Tomcat resolved the issue.
Much thanks again!
Shane

On Mon, Sep 14, 2015 at 2:00 PM, Shane McCoy <[hidden email]> wrote:
Thanks! I will have to try resetting Tomcat and see if that works. Appreciate the help and i'll post back soon,

Shane

On Mon, Sep 14, 2015 at 12:55 PM, Colin <[hidden email]> wrote:
If you are seeing things like timeouts, you might also have a tomcat issue.

If you can check the log files for things like PermGen errors out OutOfMemory errors, then this will typically just require a tomcat restart.

Sometimes tuning tomcat parameters can help with these issues if you see are seeing them frequently, and our troubleshooting guide goes over some recommended JAVA_OPTS.


-Colin


On Mon, Sep 14, 2015 at 11:39 AM, Nathan Dunn <[hidden email]> wrote:

If you are using Apollo2, my only guesses are:

1) you are logged out and the server isn’t telling you (then just do a refresh)
2) is that the organism preferences is somehow not set and you just select one from the drop-down at the top or click on a scaffold from the reference sequence tab.

If it is #1 (most likely), I would click on the “remember-me” option when you login.  We’re still working on making the “logout” a bit more obvious when doing a timeout, but we’re not quite there yet. 

Nathan

On Sep 14, 2015, at 5:16 AM, Shane McCoy <[hidden email]> wrote:

I was checking in on my Jbrowse / WebApollo site and found it would not load (was fine a couple days ago). For Jbrowse I get the:

"Congratulations, JBrowse is on the web!However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error." 

or a timed out browser message.
Going directly to WebApollo times out.

Logging into the backend, everything looks fine, tracks.conf is where it should be.
I am not finding any one w/ same issue in the lists.
Any thoughts of what I should do?

Thank you!
Shane M.



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.






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.