users getting logged off

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users getting logged off

kemi

Hello,


I’m experiencing the following issue:

Users can log in to the ‘Select track’ page but once they select a scaffold they get logged off on the ‘JBrowse' page. All the tracks appear correctly but users cannot log in. Also, when I zoom in, there are questions marks in place of the 3-frame reference sequence translations (please see attached image).

I checked users’ read/write permissions and info in config.xml as suggested in http://gmod.827538.n3.nabble.com/user-created-annotation-track-and-login-disappear-for-certain-scaffolds-td4040214.html but that didn’t help.


Please let me know if you have any suggestions.


Thanks,

Kemi Abolude

Institute for Genome Sciences

University of Maryland


apolloscreenshot.png (299K) Download Attachment
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Re: users getting logged off

nathandunn

Do you have the javascript/console and tomcat/catalina.out logs? 

When going to the JBrowse page there are a series of login / data absorption steps.   If any of them fails then you won’t be logged in.  

Nathan

On Oct 29, 2014, at 1:40 PM, Abolude, Kemi <[hidden email]> wrote:

Hello,

I’m experiencing the following issue:
Users can log in to the ‘Select track’ page but once they select a scaffold they get logged off on the ‘JBrowse' page. All the tracks appear correctly but users cannot log in. Also, when I zoom in, there are questions marks in place of the 3-frame reference sequence translations (please see attached image).
I checked users’ read/write permissions and info in config.xml as suggested in http://gmod.827538.n3.nabble.com/user-created-annotation-track-and-login-disappear-for-certain-scaffolds-td4040214.html but that didn’t help.

Please let me know if you have any suggestions.

Thanks,
Kemi Abolude
Institute for Genome Sciences
University of Maryland
<apolloscreenshot.png>

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Re: users getting logged off

kemi

Thanks,
Kemi
From: Nathan Dunn <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Wednesday, October 29, 2014 at 4:48 PM
To: "[hidden email]" <[hidden email]>
Subject: Re: [apollo] users getting logged off


Do you have the javascript/console and tomcat/catalina.out logs? 

When going to the JBrowse page there are a series of login / data absorption steps.   If any of them fails then you won’t be logged in.  

Nathan

On Oct 29, 2014, at 1:40 PM, Abolude, Kemi <[hidden email]> wrote:

Hello,

I’m experiencing the following issue:
Users can log in to the ‘Select track’ page but once they select a scaffold they get logged off on the ‘JBrowse' page. All the tracks appear correctly but users cannot log in. Also, when I zoom in, there are questions marks in place of the 3-frame reference sequence translations (please see attached image).
I checked users’ read/write permissions and info in config.xml as suggested in http://gmod.827538.n3.nabble.com/user-created-annotation-track-and-login-disappear-for-certain-scaffolds-td4040214.html but that didn’t help.

Please let me know if you have any suggestions.

Thanks,
Kemi Abolude
Institute for Genome Sciences
University of Maryland
<apolloscreenshot.png>

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Re: users getting logged off

nathandunn

I’m not sure if this is the error or not, but it appears that you are trying to run two tomcat’s on the same server and port.

You’ll want to kill both and start over.  

To confirm that they’re dead:

ps -ef | grep -i catalina
netstat -tan | grep 8080 | grep LISTEN

You may have to explicitly kill the PID.  

Nathan

On Oct 30, 2014, at 6:55 AM, Abolude, Kemi <[hidden email]> wrote:


Thanks,
Kemi
From: Nathan Dunn <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Wednesday, October 29, 2014 at 4:48 PM
To: "[hidden email]" <[hidden email]>
Subject: Re: [apollo] users getting logged off


Do you have the javascript/console and tomcat/catalina.out logs? 

When going to the JBrowse page there are a series of login / data absorption steps.   If any of them fails then you won’t be logged in.  

Nathan

On Oct 29, 2014, at 1:40 PM, Abolude, Kemi <[hidden email]> wrote:

Hello,

I’m experiencing the following issue:
Users can log in to the ‘Select track’ page but once they select a scaffold they get logged off on the ‘JBrowse' page. All the tracks appear correctly but users cannot log in. Also, when I zoom in, there are questions marks in place of the 3-frame reference sequence translations (please see attached image).
I checked users’ read/write permissions and info in config.xml as suggested in http://gmod.827538.n3.nabble.com/user-created-annotation-track-and-login-disappear-for-certain-scaffolds-td4040214.html but that didn’t help.

Please let me know if you have any suggestions.

Thanks,
Kemi Abolude
Institute for Genome Sciences
University of Maryland
<apolloscreenshot.png>


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Re: users getting logged off

kemi
I tried the following but still having the same issue:

[root@bcaballi-curation ~]# ps -ef | grep -i catalina

tomcat   20707     1  0 Sep04 ?        01:53:00 /usr/java/jre1.7.0_45/bin/java -Djava.util.logging.config.file=/opt/apache-tomcat-7.0.47/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/opt/apache-tomcat-7.0.47/endorsed -classpath /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bin/tomcat-juli.jar -Dcatalina.base=/opt/apache-tomcat-7.0.47 -Dcatalina.home=/opt/apache-tomcat-7.0.47 -Djava.io.tmpdir=/opt/apache-tomcat-7.0.47/temp org.apache.catalina.startup.Bootstrap start

root     57725 57503  0 11:17 pts/1    00:00:00 grep -i catalina

[root@bcaballi-curation ~]# netstat -tan | grep 8080 | grep LISTEN

tcp        0      0 :::8080                     :::*                        LISTEN      

[root@bcaballi-curation ~]# kill -9 20707

[root@bcaballi-curation ~]# ps -ef  | grep tomcat 

root     57747 57503  0 11:25 pts/1    00:00:00 grep tomcat

[root@bcaballi-curation ~]# netstat -tan | grep 8080 | grep LISTEN

[root@bcaballi-curation data]# service tomcat start

Starting Tomcat7: 

Using CATALINA_BASE:   /opt/apache-tomcat-7.0.47

Using CATALINA_HOME:   /opt/apache-tomcat-7.0.47

Using CATALINA_TMPDIR: /opt/apache-tomcat-7.0.47/temp

Using JRE_HOME:        /usr/java/jre1.7.0_45

Using CLASSPATH:       /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bin/tomcat-juli.jar


[root@bcaballi-curation data]# netstat -tan | grep 8080 | grep LISTEN

tcp        0      0 :::8080                     :::*                        LISTEN      

[root@bcaballi-curation data]# ps -ef | grep -i catalina

tomcat   57779     1 57 11:28 ?        00:00:16 /usr/java/jre1.7.0_45/bin/java -Djava.util.logging.config.file=/opt/apache-tomcat-7.0.47/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/opt/apache-tomcat-7.0.47/endorsed -classpath /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bin/tomcat-juli.jar -Dcatalina.base=/opt/apache-tomcat-7.0.47 -Dcatalina.home=/opt/apache-tomcat-7.0.47 -Djava.io.tmpdir=/opt/apache-tomcat-7.0.47/temp org.apache.catalina.startup.Bootstrap start

root     57807 57503  0 11:28 pts/1    00:00:00 grep -i catalina



From: Nathan Dunn <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Thursday, October 30, 2014 at 11:01 AM
To: "[hidden email]" <[hidden email]>
Subject: Re: [apollo] users getting logged off


I’m not sure if this is the error or not, but it appears that you are trying to run two tomcat’s on the same server and port.

You’ll want to kill both and start over.  

To confirm that they’re dead:

ps -ef | grep -i catalina
netstat -tan | grep 8080 | grep LISTEN

You may have to explicitly kill the PID.  

Nathan

On Oct 30, 2014, at 6:55 AM, Abolude, Kemi <[hidden email]> wrote:


Thanks,
Kemi
From: Nathan Dunn <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Wednesday, October 29, 2014 at 4:48 PM
To: "[hidden email]" <[hidden email]>
Subject: Re: [apollo] users getting logged off


Do you have the javascript/console and tomcat/catalina.out logs? 

When going to the JBrowse page there are a series of login / data absorption steps.   If any of them fails then you won’t be logged in.  

Nathan

On Oct 29, 2014, at 1:40 PM, Abolude, Kemi <[hidden email]> wrote:

Hello,

I’m experiencing the following issue:
Users can log in to the ‘Select track’ page but once they select a scaffold they get logged off on the ‘JBrowse' page. All the tracks appear correctly but users cannot log in. Also, when I zoom in, there are questions marks in place of the 3-frame reference sequence translations (please see attached image).
I checked users’ read/write permissions and info in config.xml as suggested in http://gmod.827538.n3.nabble.com/user-created-annotation-track-and-login-disappear-for-certain-scaffolds-td4040214.html but that didn’t help.

Please let me know if you have any suggestions.

Thanks,
Kemi Abolude
Institute for Genome Sciences
University of Maryland
<apolloscreenshot.png>


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Re: users getting logged off

nathandunn

Do you have a new catalina.out / javascript console when you startup the server and login? 

If you are getting the exact same thing that means you have some other service running on 8080 and it needs to be killed or you need to run tomcat on a different port.  

Nathan

On Oct 30, 2014, at 8:34 AM, Abolude, Kemi <[hidden email]> wrote:

I tried the following but still having the same issue:

[root@bcaballi-curation ~]# ps -ef | grep -i catalina
tomcat   20707     1  0 Sep04 ?        01:53:00 /usr/java/jre1.7.0_45/bin/java -Djava.util.logging.config.file=/opt/apache-tomcat-7.0.47/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/opt/apache-tomcat-7.0.47/endorsed -classpath /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bin/tomcat-juli.jar -Dcatalina.base=/opt/apache-tomcat-7.0.47 -Dcatalina.home=/opt/apache-tomcat-7.0.47 -Djava.io.tmpdir=/opt/apache-tomcat-7.0.47/temp org.apache.catalina.startup.Bootstrap start
root     57725 57503  0 11:17 pts/1    00:00:00 grep -i catalina
[root@bcaballi-curation ~]# netstat -tan | grep 8080 | grep LISTEN

tcp        0      0 :::8080                     :::*                        LISTEN      
[root@bcaballi-curation ~]# kill -9 20707
[root@bcaballi-curation ~]# ps -ef  | grep tomcat 
root     57747 57503  0 11:25 pts/1    00:00:00 grep tomcat
[root@bcaballi-curation ~]# netstat -tan | grep 8080 | grep LISTEN
[root@bcaballi-curation data]# service tomcat start
Starting Tomcat7: 
Using CATALINA_BASE:   /opt/apache-tomcat-7.0.47
Using CATALINA_HOME:   /opt/apache-tomcat-7.0.47
Using CATALINA_TMPDIR: /opt/apache-tomcat-7.0.47/temp
Using JRE_HOME:        /usr/java/jre1.7.0_45
Using CLASSPATH:       /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bin/tomcat-juli.jar

[root@bcaballi-curation data]# netstat -tan | grep 8080 | grep LISTEN
tcp        0      0 :::8080                     :::*                        LISTEN      
[root@bcaballi-curation data]# ps -ef | grep -i catalina
tomcat   57779     1 57 11:28 ?        00:00:16 /usr/java/jre1.7.0_45/bin/java -Djava.util.logging.config.file=/opt/apache-tomcat-7.0.47/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/opt/apache-tomcat-7.0.47/endorsed -classpath /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bin/tomcat-juli.jar -Dcatalina.base=/opt/apache-tomcat-7.0.47 -Dcatalina.home=/opt/apache-tomcat-7.0.47 -Djava.io.tmpdir=/opt/apache-tomcat-7.0.47/temp org.apache.catalina.startup.Bootstrap start

root     57807 57503  0 11:28 pts/1    00:00:00 grep -i catalina


From: Nathan Dunn <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Thursday, October 30, 2014 at 11:01 AM
To: "[hidden email]" <[hidden email]>
Subject: Re: [apollo] users getting logged off


I’m not sure if this is the error or not, but it appears that you are trying to run two tomcat’s on the same server and port.

You’ll want to kill both and start over.  

To confirm that they’re dead:

ps -ef | grep -i catalina
netstat -tan | grep 8080 | grep LISTEN

You may have to explicitly kill the PID.  

Nathan

On Oct 30, 2014, at 6:55 AM, Abolude, Kemi <[hidden email]> wrote:


Thanks,
Kemi
From: Nathan Dunn <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Wednesday, October 29, 2014 at 4:48 PM
To: "[hidden email]" <[hidden email]>
Subject: Re: [apollo] users getting logged off


Do you have the javascript/console and tomcat/catalina.out logs? 

When going to the JBrowse page there are a series of login / data absorption steps.   If any of them fails then you won’t be logged in.  

Nathan

On Oct 29, 2014, at 1:40 PM, Abolude, Kemi <[hidden email]> wrote:

Hello,

I’m experiencing the following issue:
Users can log in to the ‘Select track’ page but once they select a scaffold they get logged off on the ‘JBrowse' page. All the tracks appear correctly but users cannot log in. Also, when I zoom in, there are questions marks in place of the 3-frame reference sequence translations (please see attached image).
I checked users’ read/write permissions and info in config.xml as suggested in http://gmod.827538.n3.nabble.com/user-created-annotation-track-and-login-disappear-for-certain-scaffolds-td4040214.html but that didn’t help.

Please let me know if you have any suggestions.

Thanks,
Kemi Abolude
Institute for Genome Sciences
University of Maryland
<apolloscreenshot.png>



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Re: users getting logged off

kemi
Hi Nathan,

Yes, same  javascript console errors.
catalina.out has this in addition:

Oct 30, 2014 1:04:21 PM org.apache.coyote.AbstractProtocol pause

INFO: Pausing ProtocolHandler ["ajp-bio-8009"]

Oct 30, 2014 1:04:21 PM org.apache.catalina.core.StandardService stopInternal

INFO: Stopping service Catalina

Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future

Oct 30, 2014 1:04:21 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc

SEVERE: The web application [/WebApollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.

Oct 30, 2014 1:04:21 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads

SEVERE: The web application [/WebApollo] appears to have started a thread named [Thread-4] but has failed to stop it. This is very likely to create a memory leak.

Oct 30, 2014 1:04:33 PM org.apache.catalina.startup.ContextConfig validateSecurityRoles

WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>


I tried killing all processes running on 8080 and restarting but that didn’t help.

Also, (not sure if this is related..) when I run add_transcripts_from_gff3_to_annotations.pl
It reports an error for each gene:

Error writing 3943_g: Refseq unitig_55|quiver does not exist [3943_g, 6112, 6500, -1]

Then…

No genes of type "gene" or transcripts of type "transcript|mRNA" found


Thanks for your help,
Kemi
From: Nathan Dunn <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Thursday, October 30, 2014 at 4:24 PM
To: "[hidden email]" <[hidden email]>
Subject: Re: [apollo] users getting logged off


Do you have a new catalina.out / javascript console when you startup the server and login? 

If you are getting the exact same thing that means you have some other service running on 8080 and it needs to be killed or you need to run tomcat on a different port.  

Nathan

On Oct 30, 2014, at 8:34 AM, Abolude, Kemi <[hidden email]> wrote:

I tried the following but still having the same issue:

[root@bcaballi-curation ~]# ps -ef | grep -i catalina
tomcat   20707     1  0 Sep04 ?        01:53:00 /usr/java/jre1.7.0_45/bin/java -Djava.util.logging.config.file=/opt/apache-tomcat-7.0.47/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/opt/apache-tomcat-7.0.47/endorsed -classpath /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bin/tomcat-juli.jar -Dcatalina.base=/opt/apache-tomcat-7.0.47 -Dcatalina.home=/opt/apache-tomcat-7.0.47 -Djava.io.tmpdir=/opt/apache-tomcat-7.0.47/temp org.apache.catalina.startup.Bootstrap start
root     57725 57503  0 11:17 pts/1    00:00:00 grep -i catalina
[root@bcaballi-curation ~]# netstat -tan | grep 8080 | grep LISTEN

tcp        0      0 :::8080                     :::*                        LISTEN      
[root@bcaballi-curation ~]# kill -9 20707
[root@bcaballi-curation ~]# ps -ef  | grep tomcat 
root     57747 57503  0 11:25 pts/1    00:00:00 grep tomcat
[root@bcaballi-curation ~]# netstat -tan | grep 8080 | grep LISTEN
[root@bcaballi-curation data]# service tomcat start
Starting Tomcat7: 
Using CATALINA_BASE:   /opt/apache-tomcat-7.0.47
Using CATALINA_HOME:   /opt/apache-tomcat-7.0.47
Using CATALINA_TMPDIR: /opt/apache-tomcat-7.0.47/temp
Using JRE_HOME:        /usr/java/jre1.7.0_45
Using CLASSPATH:       /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bin/tomcat-juli.jar

[root@bcaballi-curation data]# netstat -tan | grep 8080 | grep LISTEN
tcp        0      0 :::8080                     :::*                        LISTEN      
[root@bcaballi-curation data]# ps -ef | grep -i catalina
tomcat   57779     1 57 11:28 ?        00:00:16 /usr/java/jre1.7.0_45/bin/java -Djava.util.logging.config.file=/opt/apache-tomcat-7.0.47/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/opt/apache-tomcat-7.0.47/endorsed -classpath /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bin/tomcat-juli.jar -Dcatalina.base=/opt/apache-tomcat-7.0.47 -Dcatalina.home=/opt/apache-tomcat-7.0.47 -Djava.io.tmpdir=/opt/apache-tomcat-7.0.47/temp org.apache.catalina.startup.Bootstrap start

root     57807 57503  0 11:28 pts/1    00:00:00 grep -i catalina


From: Nathan Dunn <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Thursday, October 30, 2014 at 11:01 AM
To: "[hidden email]" <[hidden email]>
Subject: Re: [apollo] users getting logged off


I’m not sure if this is the error or not, but it appears that you are trying to run two tomcat’s on the same server and port.

You’ll want to kill both and start over.  

To confirm that they’re dead:

ps -ef | grep -i catalina
netstat -tan | grep 8080 | grep LISTEN

You may have to explicitly kill the PID.  

Nathan

On Oct 30, 2014, at 6:55 AM, Abolude, Kemi <[hidden email]> wrote:


Thanks,
Kemi
From: Nathan Dunn <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Wednesday, October 29, 2014 at 4:48 PM
To: "[hidden email]" <[hidden email]>
Subject: Re: [apollo] users getting logged off


Do you have the javascript/console and tomcat/catalina.out logs? 

When going to the JBrowse page there are a series of login / data absorption steps.   If any of them fails then you won’t be logged in.  

Nathan

On Oct 29, 2014, at 1:40 PM, Abolude, Kemi <[hidden email]> wrote:

Hello,

I’m experiencing the following issue:
Users can log in to the ‘Select track’ page but once they select a scaffold they get logged off on the ‘JBrowse' page. All the tracks appear correctly but users cannot log in. Also, when I zoom in, there are questions marks in place of the 3-frame reference sequence translations (please see attached image).
I checked users’ read/write permissions and info in config.xml as suggested in http://gmod.827538.n3.nabble.com/user-created-annotation-track-and-login-disappear-for-certain-scaffolds-td4040214.html but that didn’t help.

Please let me know if you have any suggestions.

Thanks,
Kemi Abolude
Institute for Genome Sciences
University of Maryland
<apolloscreenshot.png>



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Re: users getting logged off

nathandunn

Kemi,

You catalina.out looks fine now.   A few things.

1 - Would it be possible for you to send me (separately) a login to your server to see if I can’t see the errors in more details?   I want to see which call its getting the 500 errors on.
2 - If you can send me the annotation files, that might be helpful, but hopefully I can figure it out with #1.
3 - WRT to the add_transcripts_from_gff3_to_annotations.pl error. .  ., I would need to see the command and maybe the first few lines of the GFF3 file.  If you want to open up a separate email thread for that, that would be great.

Thanks,

Nathan


> On Oct 31, 2014, at 7:31 AM, Abolude, Kemi <[hidden email]> wrote:
>
> Hi Nathan,
>
> Yes, same  javascript console errors.
> catalina.out has this in addition:
> Oct 30, 2014 1:04:21 PM org.apache.coyote.AbstractProtocol pause
> INFO: Pausing ProtocolHandler ["ajp-bio-8009"]
> Oct 30, 2014 1:04:21 PM org.apache.catalina.core.StandardService stopInternal
> INFO: Stopping service Catalina
> Please use CMSClassUnloadingEnabled in place of CMSPermGenSweepingEnabled in the future
> Oct 30, 2014 1:04:21 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
> SEVERE: The web application [/WebApollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
> Oct 30, 2014 1:04:21 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
> SEVERE: The web application [/WebApollo] appears to have started a thread named [Thread-4] but has failed to stop it. This is very likely to create a memory leak.
> Oct 30, 2014 1:04:33 PM org.apache.catalina.startup.ContextConfig validateSecurityRoles
> WARNING: Security role name NobodyHasThisRole used in an <auth-constraint> without being defined in a <security-role>
>
> I tried killing all processes running on 8080 and restarting but that didn’t help.
>
> Also, (not sure if this is related..) when I run add_transcripts_from_gff3_to_annotations.pl
> It reports an error for each gene:
> Error writing 3943_g: Refseq unitig_55|quiver does not exist [3943_g, 6112, 6500, -1]
> Then…
> No genes of type "gene" or transcripts of type "transcript|mRNA" found
>
> Thanks for your help,
> Kemi
> From: Nathan Dunn <[hidden email]>
> Reply-To: "[hidden email]" <[hidden email]>
> Date: Thursday, October 30, 2014 at 4:24 PM
> To: "[hidden email]" <[hidden email]>
> Subject: Re: [apollo] users getting logged off
>
>
> Do you have a new catalina.out / javascript console when you startup the server and login?
>
> If you are getting the exact same thing that means you have some other service running on 8080 and it needs to be killed or you need to run tomcat on a different port.  
>
> Nathan
>
>> On Oct 30, 2014, at 8:34 AM, Abolude, Kemi <[hidden email]> wrote:
>>
>> I tried the following but still having the same issue:
>>
>> [root@bcaballi-curation ~]# ps -ef | grep -i catalina
>> tomcat   20707     1  0 Sep04 ?        01:53:00 /usr/java/jre1.7.0_45/bin/java -Djava.util.logging.config.file=/opt/apache-tomcat-7.0.47/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/opt/apache-tomcat-7.0.47/endorsed -classpath /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bin/tomcat-juli.jar -Dcatalina.base=/opt/apache-tomcat-7.0.47 -Dcatalina.home=/opt/apache-tomcat-7.0.47 -Djava.io.tmpdir=/opt/apache-tomcat-7.0.47/temp org.apache.catalina.startup.Bootstrap start
>> root     57725 57503  0 11:17 pts/1    00:00:00 grep -i catalina
>> [root@bcaballi-curation ~]# netstat -tan | grep 8080 | grep LISTEN
>> tcp        0      0 :::8080                     :::*                        LISTEN      
>> [root@bcaballi-curation ~]# kill -9 20707
>> [root@bcaballi-curation ~]# ps -ef  | grep tomcat
>> root     57747 57503  0 11:25 pts/1    00:00:00 grep tomcat
>> [root@bcaballi-curation ~]# netstat -tan | grep 8080 | grep LISTEN
>> [root@bcaballi-curation data]# service tomcat start
>> Starting Tomcat7:
>> Using CATALINA_BASE:   /opt/apache-tomcat-7.0.47
>> Using CATALINA_HOME:   /opt/apache-tomcat-7.0.47
>> Using CATALINA_TMPDIR: /opt/apache-tomcat-7.0.47/temp
>> Using JRE_HOME:        /usr/java/jre1.7.0_45
>> Using CLASSPATH:       /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bin/tomcat-juli.jar
>>
>> [root@bcaballi-curation data]# netstat -tan | grep 8080 | grep LISTEN
>> tcp        0      0 :::8080                     :::*                        LISTEN      
>> [root@bcaballi-curation data]# ps -ef | grep -i catalina
>> tomcat   57779     1 57 11:28 ?        00:00:16 /usr/java/jre1.7.0_45/bin/java -Djava.util.logging.config.file=/opt/apache-tomcat-7.0.47/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/opt/apache-tomcat-7.0.47/endorsed -classpath /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bin/tomcat-juli.jar -Dcatalina.base=/opt/apache-tomcat-7.0.47 -Dcatalina.home=/opt/apache-tomcat-7.0.47 -Djava.io.tmpdir=/opt/apache-tomcat-7.0.47/temp org.apache.catalina.startup.Bootstrap start
>> root     57807 57503  0 11:28 pts/1    00:00:00 grep -i catalina
>>
>>
>> From: Nathan Dunn <[hidden email]>
>> Reply-To: "[hidden email]" <[hidden email]>
>> Date: Thursday, October 30, 2014 at 11:01 AM
>> To: "[hidden email]" <[hidden email]>
>> Subject: Re: [apollo] users getting logged off
>>
>>
>> I’m not sure if this is the error or not, but it appears that you are trying to run two tomcat’s on the same server and port.
>>
>> You’ll want to kill both and start over.  
>>
>> To confirm that they’re dead:
>>
>> ps -ef | grep -i catalina
>> netstat -tan | grep 8080 | grep LISTEN
>>
>> You may have to explicitly kill the PID.  
>>
>> Nathan
>>
>>> On Oct 30, 2014, at 6:55 AM, Abolude, Kemi <[hidden email]> wrote:
>>>
>>> Javascript console: http://pastie.org/pastes/9684199/text
>>> catalina.out: http://pastie.org/9685532
>>>
>>> Thanks,
>>> Kemi
>>> From: Nathan Dunn <[hidden email]>
>>> Reply-To: "[hidden email]" <[hidden email]>
>>> Date: Wednesday, October 29, 2014 at 4:48 PM
>>> To: "[hidden email]" <[hidden email]>
>>> Subject: Re: [apollo] users getting logged off
>>>
>>>
>>> Do you have the javascript/console and tomcat/catalina.out logs?
>>>
>>> When going to the JBrowse page there are a series of login / data absorption steps.   If any of them fails then you won’t be logged in.  
>>>
>>> Nathan
>>>
>>>> On Oct 29, 2014, at 1:40 PM, Abolude, Kemi <[hidden email]> wrote:
>>>>
>>>> Hello,
>>>>
>>>> I’m experiencing the following issue:
>>>> Users can log in to the ‘Select track’ page but once they select a scaffold they get logged off on the ‘JBrowse' page. All the tracks appear correctly but users cannot log in. Also, when I zoom in, there are questions marks in place of the 3-frame reference sequence translations (please see attached image).
>>>> I checked users’ read/write permissions and info in config.xml as suggested in http://gmod.827538.n3.nabble.com/user-created-annotation-track-and-login-disappear-for-certain-scaffolds-td4040214.html but that didn’t help.
>>>>
>>>> Please let me know if you have any suggestions.
>>>>
>>>> Thanks,
>>>> Kemi Abolude
>>>> Institute for Genome Sciences
>>>> University of Maryland
>>>> <apolloscreenshot.png>
>>>
>>
>


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Re: users getting logged off

kemi
It¹s fixed!
I expanded the javascript console errors and saw an error that it could
not find /export/genome_annotations/Annotations-unitig_7|quiver
Then I saw that /export/genome_annotations was empty..I guessed it had
something to with the permissions so I did chmod 777 on genome_annotations
and reran add_transcripts_from_gff3_to_annotations.pl
Now everything looks right.

Thanks so much for your help!
Kemi


On 10/31/14, 11:57 AM, "Nathan Dunn" <[hidden email]> wrote:

>
>Kemi,
>
>You catalina.out looks fine now.   A few things.
>
>1 - Would it be possible for you to send me (separately) a login to your
>server to see if I can¹t see the errors in more details?   I want to see
>which call its getting the 500 errors on.
>2 - If you can send me the annotation files, that might be helpful, but
>hopefully I can figure it out with #1.
>3 - WRT to the add_transcripts_from_gff3_to_annotations.pl error. .  ., I
>would need to see the command and maybe the first few lines of the GFF3
>file.  If you want to open up a separate email thread for that, that
>would be great.
>
>Thanks,
>
>Nathan
>
>
>> On Oct 31, 2014, at 7:31 AM, Abolude, Kemi <[hidden email]>
>>wrote:
>>
>> Hi Nathan,
>>
>> Yes, same  javascript console errors.
>> catalina.out has this in addition:
>> Oct 30, 2014 1:04:21 PM org.apache.coyote.AbstractProtocol pause
>> INFO: Pausing ProtocolHandler ["ajp-bio-8009"]
>> Oct 30, 2014 1:04:21 PM org.apache.catalina.core.StandardService
>>stopInternal
>> INFO: Stopping service Catalina
>> Please use CMSClassUnloadingEnabled in place of
>>CMSPermGenSweepingEnabled in the future
>> Oct 30, 2014 1:04:21 PM org.apache.catalina.loader.WebappClassLoader
>>clearReferencesJdbc
>> SEVERE: The web application [/WebApollo] registered the JDBC driver
>>[org.postgresql.Driver] but failed to unregister it when the web
>>application was stopped. To prevent a memory leak, the JDBC Driver has
>>been forcibly unregistered.
>> Oct 30, 2014 1:04:21 PM org.apache.catalina.loader.WebappClassLoader
>>clearReferencesThreads
>> SEVERE: The web application [/WebApollo] appears to have started a
>>thread named [Thread-4] but has failed to stop it. This is very likely
>>to create a memory leak.
>> Oct 30, 2014 1:04:33 PM org.apache.catalina.startup.ContextConfig
>>validateSecurityRoles
>> WARNING: Security role name NobodyHasThisRole used in an
>><auth-constraint> without being defined in a <security-role>
>>
>> I tried killing all processes running on 8080 and restarting but that
>>didn¹t help.
>>
>> Also, (not sure if this is related..) when I run
>>add_transcripts_from_gff3_to_annotations.pl
>> It reports an error for each gene:
>> Error writing 3943_g: Refseq unitig_55|quiver does not exist [3943_g,
>>6112, 6500, -1]
>> ThenŠ
>> No genes of type "gene" or transcripts of type "transcript|mRNA" found
>>
>> Thanks for your help,
>> Kemi
>> From: Nathan Dunn <[hidden email]>
>> Reply-To: "[hidden email]" <[hidden email]>
>> Date: Thursday, October 30, 2014 at 4:24 PM
>> To: "[hidden email]" <[hidden email]>
>> Subject: Re: [apollo] users getting logged off
>>
>>
>> Do you have a new catalina.out / javascript console when you startup
>>the server and login?
>>
>> If you are getting the exact same thing that means you have some other
>>service running on 8080 and it needs to be killed or you need to run
>>tomcat on a different port.
>>
>> Nathan
>>
>>> On Oct 30, 2014, at 8:34 AM, Abolude, Kemi
>>><[hidden email]> wrote:
>>>
>>> I tried the following but still having the same issue:
>>>
>>> [root@bcaballi-curation ~]# ps -ef | grep -i catalina
>>> tomcat   20707     1  0 Sep04 ?        01:53:00
>>>/usr/java/jre1.7.0_45/bin/java
>>>-Djava.util.logging.config.file=/opt/apache-tomcat-7.0.47/conf/logging.p
>>>roperties
>>>-Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
>>>-Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled
>>>-XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC
>>>-XX:MaxPermSize=256m
>>>-Djava.endorsed.dirs=/opt/apache-tomcat-7.0.47/endorsed -classpath
>>>/opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bi
>>>n/tomcat-juli.jar -Dcatalina.base=/opt/apache-tomcat-7.0.47
>>>-Dcatalina.home=/opt/apache-tomcat-7.0.47
>>>-Djava.io.tmpdir=/opt/apache-tomcat-7.0.47/temp
>>>org.apache.catalina.startup.Bootstrap start
>>> root     57725 57503  0 11:17 pts/1    00:00:00 grep -i catalina
>>> [root@bcaballi-curation ~]# netstat -tan | grep 8080 | grep LISTEN
>>> tcp        0      0 :::8080                     :::*
>>>     LISTEN    
>>> [root@bcaballi-curation ~]# kill -9 20707
>>> [root@bcaballi-curation ~]# ps -ef  | grep tomcat
>>> root     57747 57503  0 11:25 pts/1    00:00:00 grep tomcat
>>> [root@bcaballi-curation ~]# netstat -tan | grep 8080 | grep LISTEN
>>> [root@bcaballi-curation data]# service tomcat start
>>> Starting Tomcat7:
>>> Using CATALINA_BASE:   /opt/apache-tomcat-7.0.47
>>> Using CATALINA_HOME:   /opt/apache-tomcat-7.0.47
>>> Using CATALINA_TMPDIR: /opt/apache-tomcat-7.0.47/temp
>>> Using JRE_HOME:        /usr/java/jre1.7.0_45
>>> Using CLASSPATH:
>>>/opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bi
>>>n/tomcat-juli.jar
>>>
>>> [root@bcaballi-curation data]# netstat -tan | grep 8080 | grep LISTEN
>>> tcp        0      0 :::8080                     :::*
>>>     LISTEN    
>>> [root@bcaballi-curation data]# ps -ef | grep -i catalina
>>> tomcat   57779     1 57 11:28 ?        00:00:16
>>>/usr/java/jre1.7.0_45/bin/java
>>>-Djava.util.logging.config.file=/opt/apache-tomcat-7.0.47/conf/logging.p
>>>roperties
>>>-Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
>>>-Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled
>>>-XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC
>>>-XX:MaxPermSize=256m
>>>-Djava.endorsed.dirs=/opt/apache-tomcat-7.0.47/endorsed -classpath
>>>/opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bi
>>>n/tomcat-juli.jar -Dcatalina.base=/opt/apache-tomcat-7.0.47
>>>-Dcatalina.home=/opt/apache-tomcat-7.0.47
>>>-Djava.io.tmpdir=/opt/apache-tomcat-7.0.47/temp
>>>org.apache.catalina.startup.Bootstrap start
>>> root     57807 57503  0 11:28 pts/1    00:00:00 grep -i catalina
>>>
>>>
>>> From: Nathan Dunn <[hidden email]>
>>> Reply-To: "[hidden email]" <[hidden email]>
>>> Date: Thursday, October 30, 2014 at 11:01 AM
>>> To: "[hidden email]" <[hidden email]>
>>> Subject: Re: [apollo] users getting logged off
>>>
>>>
>>> I¹m not sure if this is the error or not, but it appears that you are
>>>trying to run two tomcat¹s on the same server and port.
>>>
>>> You¹ll want to kill both and start over.
>>>
>>> To confirm that they¹re dead:
>>>
>>> ps -ef | grep -i catalina
>>> netstat -tan | grep 8080 | grep LISTEN
>>>
>>> You may have to explicitly kill the PID.
>>>
>>> Nathan
>>>
>>>> On Oct 30, 2014, at 6:55 AM, Abolude, Kemi
>>>><[hidden email]> wrote:
>>>>
>>>> Javascript console: http://pastie.org/pastes/9684199/text
>>>> catalina.out: http://pastie.org/9685532
>>>>
>>>> Thanks,
>>>> Kemi
>>>> From: Nathan Dunn <[hidden email]>
>>>> Reply-To: "[hidden email]" <[hidden email]>
>>>> Date: Wednesday, October 29, 2014 at 4:48 PM
>>>> To: "[hidden email]" <[hidden email]>
>>>> Subject: Re: [apollo] users getting logged off
>>>>
>>>>
>>>> Do you have the javascript/console and tomcat/catalina.out logs?
>>>>
>>>> When going to the JBrowse page there are a series of login / data
>>>>absorption steps.   If any of them fails then you won¹t be logged in.
>>>>
>>>> Nathan
>>>>
>>>>> On Oct 29, 2014, at 1:40 PM, Abolude, Kemi
>>>>><[hidden email]> wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> I¹m experiencing the following issue:
>>>>> Users can log in to the ŒSelect track¹ page but once they select a
>>>>>scaffold they get logged off on the ŒJBrowse' page. All the tracks
>>>>>appear correctly but users cannot log in. Also, when I zoom in, there
>>>>>are questions marks in place of the 3-frame reference sequence
>>>>>translations (please see attached image).
>>>>> I checked users¹ read/write permissions and info in config.xml as
>>>>>suggested in
>>>>>http://gmod.827538.n3.nabble.com/user-created-annotation-track-and-log
>>>>>in-disappear-for-certain-scaffolds-td4040214.html but that didn¹t
>>>>>help.
>>>>>
>>>>> Please let me know if you have any suggestions.
>>>>>
>>>>> Thanks,
>>>>> Kemi Abolude
>>>>> Institute for Genome Sciences
>>>>> University of Maryland
>>>>> <apolloscreenshot.png>
>>>>
>>>
>>
>
>


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Re: users getting logged off

nathandunn
Glad it worked out.  Thanks for your persistence!

Nathan

> On Oct 31, 2014, at 9:39 AM, Abolude, Kemi <[hidden email]> wrote:
>
> It¹s fixed!
> I expanded the javascript console errors and saw an error that it could
> not find /export/genome_annotations/Annotations-unitig_7|quiver
> Then I saw that /export/genome_annotations was empty..I guessed it had
> something to with the permissions so I did chmod 777 on genome_annotations
> and reran add_transcripts_from_gff3_to_annotations.pl
> Now everything looks right.
>
> Thanks so much for your help!
> Kemi
>
>
> On 10/31/14, 11:57 AM, "Nathan Dunn" <[hidden email]> wrote:
>
>>
>> Kemi,
>>
>> You catalina.out looks fine now.   A few things.
>>
>> 1 - Would it be possible for you to send me (separately) a login to your
>> server to see if I can¹t see the errors in more details?   I want to see
>> which call its getting the 500 errors on.
>> 2 - If you can send me the annotation files, that might be helpful, but
>> hopefully I can figure it out with #1.
>> 3 - WRT to the add_transcripts_from_gff3_to_annotations.pl error. .  ., I
>> would need to see the command and maybe the first few lines of the GFF3
>> file.  If you want to open up a separate email thread for that, that
>> would be great.
>>
>> Thanks,
>>
>> Nathan
>>
>>
>>> On Oct 31, 2014, at 7:31 AM, Abolude, Kemi <[hidden email]>
>>> wrote:
>>>
>>> Hi Nathan,
>>>
>>> Yes, same  javascript console errors.
>>> catalina.out has this in addition:
>>> Oct 30, 2014 1:04:21 PM org.apache.coyote.AbstractProtocol pause
>>> INFO: Pausing ProtocolHandler ["ajp-bio-8009"]
>>> Oct 30, 2014 1:04:21 PM org.apache.catalina.core.StandardService
>>> stopInternal
>>> INFO: Stopping service Catalina
>>> Please use CMSClassUnloadingEnabled in place of
>>> CMSPermGenSweepingEnabled in the future
>>> Oct 30, 2014 1:04:21 PM org.apache.catalina.loader.WebappClassLoader
>>> clearReferencesJdbc
>>> SEVERE: The web application [/WebApollo] registered the JDBC driver
>>> [org.postgresql.Driver] but failed to unregister it when the web
>>> application was stopped. To prevent a memory leak, the JDBC Driver has
>>> been forcibly unregistered.
>>> Oct 30, 2014 1:04:21 PM org.apache.catalina.loader.WebappClassLoader
>>> clearReferencesThreads
>>> SEVERE: The web application [/WebApollo] appears to have started a
>>> thread named [Thread-4] but has failed to stop it. This is very likely
>>> to create a memory leak.
>>> Oct 30, 2014 1:04:33 PM org.apache.catalina.startup.ContextConfig
>>> validateSecurityRoles
>>> WARNING: Security role name NobodyHasThisRole used in an
>>> <auth-constraint> without being defined in a <security-role>
>>>
>>> I tried killing all processes running on 8080 and restarting but that
>>> didn¹t help.
>>>
>>> Also, (not sure if this is related..) when I run
>>> add_transcripts_from_gff3_to_annotations.pl
>>> It reports an error for each gene:
>>> Error writing 3943_g: Refseq unitig_55|quiver does not exist [3943_g,
>>> 6112, 6500, -1]
>>> ThenŠ
>>> No genes of type "gene" or transcripts of type "transcript|mRNA" found
>>>
>>> Thanks for your help,
>>> Kemi
>>> From: Nathan Dunn <[hidden email]>
>>> Reply-To: "[hidden email]" <[hidden email]>
>>> Date: Thursday, October 30, 2014 at 4:24 PM
>>> To: "[hidden email]" <[hidden email]>
>>> Subject: Re: [apollo] users getting logged off
>>>
>>>
>>> Do you have a new catalina.out / javascript console when you startup
>>> the server and login?
>>>
>>> If you are getting the exact same thing that means you have some other
>>> service running on 8080 and it needs to be killed or you need to run
>>> tomcat on a different port.
>>>
>>> Nathan
>>>
>>>> On Oct 30, 2014, at 8:34 AM, Abolude, Kemi
>>>> <[hidden email]> wrote:
>>>>
>>>> I tried the following but still having the same issue:
>>>>
>>>> [root@bcaballi-curation ~]# ps -ef | grep -i catalina
>>>> tomcat   20707     1  0 Sep04 ?        01:53:00
>>>> /usr/java/jre1.7.0_45/bin/java
>>>> -Djava.util.logging.config.file=/opt/apache-tomcat-7.0.47/conf/logging.p
>>>> roperties
>>>> -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
>>>> -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled
>>>> -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC
>>>> -XX:MaxPermSize=256m
>>>> -Djava.endorsed.dirs=/opt/apache-tomcat-7.0.47/endorsed -classpath
>>>> /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bi
>>>> n/tomcat-juli.jar -Dcatalina.base=/opt/apache-tomcat-7.0.47
>>>> -Dcatalina.home=/opt/apache-tomcat-7.0.47
>>>> -Djava.io.tmpdir=/opt/apache-tomcat-7.0.47/temp
>>>> org.apache.catalina.startup.Bootstrap start
>>>> root     57725 57503  0 11:17 pts/1    00:00:00 grep -i catalina
>>>> [root@bcaballi-curation ~]# netstat -tan | grep 8080 | grep LISTEN
>>>> tcp        0      0 :::8080                     :::*
>>>>    LISTEN    
>>>> [root@bcaballi-curation ~]# kill -9 20707
>>>> [root@bcaballi-curation ~]# ps -ef  | grep tomcat
>>>> root     57747 57503  0 11:25 pts/1    00:00:00 grep tomcat
>>>> [root@bcaballi-curation ~]# netstat -tan | grep 8080 | grep LISTEN
>>>> [root@bcaballi-curation data]# service tomcat start
>>>> Starting Tomcat7:
>>>> Using CATALINA_BASE:   /opt/apache-tomcat-7.0.47
>>>> Using CATALINA_HOME:   /opt/apache-tomcat-7.0.47
>>>> Using CATALINA_TMPDIR: /opt/apache-tomcat-7.0.47/temp
>>>> Using JRE_HOME:        /usr/java/jre1.7.0_45
>>>> Using CLASSPATH:
>>>> /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bi
>>>> n/tomcat-juli.jar
>>>>
>>>> [root@bcaballi-curation data]# netstat -tan | grep 8080 | grep LISTEN
>>>> tcp        0      0 :::8080                     :::*
>>>>    LISTEN    
>>>> [root@bcaballi-curation data]# ps -ef | grep -i catalina
>>>> tomcat   57779     1 57 11:28 ?        00:00:16
>>>> /usr/java/jre1.7.0_45/bin/java
>>>> -Djava.util.logging.config.file=/opt/apache-tomcat-7.0.47/conf/logging.p
>>>> roperties
>>>> -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
>>>> -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled
>>>> -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC
>>>> -XX:MaxPermSize=256m
>>>> -Djava.endorsed.dirs=/opt/apache-tomcat-7.0.47/endorsed -classpath
>>>> /opt/apache-tomcat-7.0.47/bin/bootstrap.jar:/opt/apache-tomcat-7.0.47/bi
>>>> n/tomcat-juli.jar -Dcatalina.base=/opt/apache-tomcat-7.0.47
>>>> -Dcatalina.home=/opt/apache-tomcat-7.0.47
>>>> -Djava.io.tmpdir=/opt/apache-tomcat-7.0.47/temp
>>>> org.apache.catalina.startup.Bootstrap start
>>>> root     57807 57503  0 11:28 pts/1    00:00:00 grep -i catalina
>>>>
>>>>
>>>> From: Nathan Dunn <[hidden email]>
>>>> Reply-To: "[hidden email]" <[hidden email]>
>>>> Date: Thursday, October 30, 2014 at 11:01 AM
>>>> To: "[hidden email]" <[hidden email]>
>>>> Subject: Re: [apollo] users getting logged off
>>>>
>>>>
>>>> I¹m not sure if this is the error or not, but it appears that you are
>>>> trying to run two tomcat¹s on the same server and port.
>>>>
>>>> You¹ll want to kill both and start over.
>>>>
>>>> To confirm that they¹re dead:
>>>>
>>>> ps -ef | grep -i catalina
>>>> netstat -tan | grep 8080 | grep LISTEN
>>>>
>>>> You may have to explicitly kill the PID.
>>>>
>>>> Nathan
>>>>
>>>>> On Oct 30, 2014, at 6:55 AM, Abolude, Kemi
>>>>> <[hidden email]> wrote:
>>>>>
>>>>> Javascript console: http://pastie.org/pastes/9684199/text
>>>>> catalina.out: http://pastie.org/9685532
>>>>>
>>>>> Thanks,
>>>>> Kemi
>>>>> From: Nathan Dunn <[hidden email]>
>>>>> Reply-To: "[hidden email]" <[hidden email]>
>>>>> Date: Wednesday, October 29, 2014 at 4:48 PM
>>>>> To: "[hidden email]" <[hidden email]>
>>>>> Subject: Re: [apollo] users getting logged off
>>>>>
>>>>>
>>>>> Do you have the javascript/console and tomcat/catalina.out logs?
>>>>>
>>>>> When going to the JBrowse page there are a series of login / data
>>>>> absorption steps.   If any of them fails then you won¹t be logged in.
>>>>>
>>>>> Nathan
>>>>>
>>>>>> On Oct 29, 2014, at 1:40 PM, Abolude, Kemi
>>>>>> <[hidden email]> wrote:
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I¹m experiencing the following issue:
>>>>>> Users can log in to the ŒSelect track¹ page but once they select a
>>>>>> scaffold they get logged off on the ŒJBrowse' page. All the tracks
>>>>>> appear correctly but users cannot log in. Also, when I zoom in, there
>>>>>> are questions marks in place of the 3-frame reference sequence
>>>>>> translations (please see attached image).
>>>>>> I checked users¹ read/write permissions and info in config.xml as
>>>>>> suggested in
>>>>>> http://gmod.827538.n3.nabble.com/user-created-annotation-track-and-log
>>>>>> in-disappear-for-certain-scaffolds-td4040214.html but that didn¹t
>>>>>> help.
>>>>>>
>>>>>> Please let me know if you have any suggestions.
>>>>>>
>>>>>> Thanks,
>>>>>> Kemi Abolude
>>>>>> Institute for Genome Sciences
>>>>>> University of Maryland
>>>>>> <apolloscreenshot.png>
>>>>>
>>>>
>>>
>>
>>
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