is there a limit to the number of isoforms that can be annotated?

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is there a limit to the number of isoforms that can be annotated?

Monica Poelchau
Hi everyone,

One of our annotators is working on a gene model with ~20 isoforms. When attempting to drag more evidence into the user-created annotations track in the area of this gene model, we get the error 'Error writing transcript:null'. Catalina.out output is pasted below. Any ideas?

Thanks!

Monica

java.lang.NullPointerException

        at org.gmod.gbol.bioObject.CDS.overlaps(CDS.java:187)

        at org.bbop.apollo.web.overlap.OrfOverlapper.overlaps(OrfOverlapper.java:28)

        at org.bbop.apollo.web.overlap.OrfOverlapper.overlaps(OrfOverlapper.java:17)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:3892)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1202)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1186)

        at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:403)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)

        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)

        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)

        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)

        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)

        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)

        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)

        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)

        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)

        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)

        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)

        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)

        at java.lang.Thread.run(Thread.java:724)


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Re: is there a limit to the number of isoforms that can be annotated?

Monica Munoz-Torres
Hola Monica, 

To the best of my knowledge there is not a limit in the number of isoforms you can annotate. I have worked with over 30 isoforms for a gene product, and was able to drag additional evidence (in that case, Illumina contigs), and partial gene models onto the same region, as well as drag other gene models around it. 

Just to test, I went back and added evidence in support of "non-transcribed" models in the same region and regions around it. I have not been able to recreate an error doing this. 

Sorry I don't have much light to shed on this right now. I've created a GitHub issue with your note, and we will look into this as soon as possible. 

cheers, 
~moni. 


On Mon, Aug 18, 2014 at 5:07 PM, Monica Poelchau <[hidden email]> wrote:
Hi everyone,

One of our annotators is working on a gene model with ~20 isoforms. When attempting to drag more evidence into the user-created annotations track in the area of this gene model, we get the error 'Error writing transcript:null'. Catalina.out output is pasted below. Any ideas?

Thanks!

Monica

java.lang.NullPointerException

        at org.gmod.gbol.bioObject.CDS.overlaps(CDS.java:187)

        at org.bbop.apollo.web.overlap.OrfOverlapper.overlaps(OrfOverlapper.java:28)

        at org.bbop.apollo.web.overlap.OrfOverlapper.overlaps(OrfOverlapper.java:17)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:3892)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1202)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1186)

        at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:403)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)

        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)

        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)

        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)

        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)

        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)

        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)

        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)

        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)

        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)

        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)

        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)

        at java.lang.Thread.run(Thread.java:724)





--
 Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
Google Scholar Profile: http://goo.gl/sXYTE

Mailing Address:
Joint Genome Institute (400-0415)
for the US Department of Energy
2800 Mitchell Dr. Ste 100
Walnut Creek, CA 94598-1631
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Re: is there a limit to the number of isoforms that can be annotated?

Colin
Hi all,
I am just curious, are all the evidence features being sourced from the same GFF? If not, are there possibly any strand differences in the source GFF that might be causing the errors?

One of the things noted on the github issue says:

"I get the above error when I use glyphs from the repeatmasker track, but I can drag entire gene models from the augustus and snap tracks into that field. Then again, some individual exons from the augustus and snap tracks can be loaded, but other generate the same error. The resulting gff3 file seems to be fine."

If the gff does not have a standard structure with mRNA->exon,etc then it has the potential to cause some problems.


-Colin


On Mon, Aug 18, 2014 at 7:34 PM, Monica Munoz-Torres <[hidden email]> wrote:
Hola Monica, 

To the best of my knowledge there is not a limit in the number of isoforms you can annotate. I have worked with over 30 isoforms for a gene product, and was able to drag additional evidence (in that case, Illumina contigs), and partial gene models onto the same region, as well as drag other gene models around it. 

Just to test, I went back and added evidence in support of "non-transcribed" models in the same region and regions around it. I have not been able to recreate an error doing this. 

Sorry I don't have much light to shed on this right now. I've created a GitHub issue with your note, and we will look into this as soon as possible. 

cheers, 
~moni. 


On Mon, Aug 18, 2014 at 5:07 PM, Monica Poelchau <[hidden email]> wrote:
Hi everyone,

One of our annotators is working on a gene model with ~20 isoforms. When attempting to drag more evidence into the user-created annotations track in the area of this gene model, we get the error 'Error writing transcript:null'. Catalina.out output is pasted below. Any ideas?

Thanks!

Monica

java.lang.NullPointerException

        at org.gmod.gbol.bioObject.CDS.overlaps(CDS.java:187)

        at org.bbop.apollo.web.overlap.OrfOverlapper.overlaps(OrfOverlapper.java:28)

        at org.bbop.apollo.web.overlap.OrfOverlapper.overlaps(OrfOverlapper.java:17)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:3892)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1202)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1186)

        at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:403)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)

        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)

        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)

        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)

        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)

        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)

        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)

        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)

        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)

        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)

        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)

        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)

        at java.lang.Thread.run(Thread.java:724)





--
 Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
Google Scholar Profile: http://goo.gl/sXYTE

Mailing Address:
Joint Genome Institute (400-0415)
for the US Department of Energy
2800 Mitchell Dr. Ste 100
Walnut Creek, CA 94598-1631

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Re: is there a limit to the number of isoforms that can be annotated?

Colin
I meant to say strange differences, not strand differences, in my last email, apologies.

-Colin


On Tue, Aug 19, 2014 at 3:26 PM, Colin <[hidden email]> wrote:
Hi all,
I am just curious, are all the evidence features being sourced from the same GFF? If not, are there possibly any strand differences in the source GFF that might be causing the errors?

One of the things noted on the github issue says:

"I get the above error when I use glyphs from the repeatmasker track, but I can drag entire gene models from the augustus and snap tracks into that field. Then again, some individual exons from the augustus and snap tracks can be loaded, but other generate the same error. The resulting gff3 file seems to be fine."

If the gff does not have a standard structure with mRNA->exon,etc then it has the potential to cause some problems.


-Colin


On Mon, Aug 18, 2014 at 7:34 PM, Monica Munoz-Torres <[hidden email]> wrote:
Hola Monica, 

To the best of my knowledge there is not a limit in the number of isoforms you can annotate. I have worked with over 30 isoforms for a gene product, and was able to drag additional evidence (in that case, Illumina contigs), and partial gene models onto the same region, as well as drag other gene models around it. 

Just to test, I went back and added evidence in support of "non-transcribed" models in the same region and regions around it. I have not been able to recreate an error doing this. 

Sorry I don't have much light to shed on this right now. I've created a GitHub issue with your note, and we will look into this as soon as possible. 

cheers, 
~moni. 


On Mon, Aug 18, 2014 at 5:07 PM, Monica Poelchau <[hidden email]> wrote:
Hi everyone,

One of our annotators is working on a gene model with ~20 isoforms. When attempting to drag more evidence into the user-created annotations track in the area of this gene model, we get the error 'Error writing transcript:null'. Catalina.out output is pasted below. Any ideas?

Thanks!

Monica

java.lang.NullPointerException

        at org.gmod.gbol.bioObject.CDS.overlaps(CDS.java:187)

        at org.bbop.apollo.web.overlap.OrfOverlapper.overlaps(OrfOverlapper.java:28)

        at org.bbop.apollo.web.overlap.OrfOverlapper.overlaps(OrfOverlapper.java:17)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:3892)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1202)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1186)

        at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:403)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)

        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)

        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)

        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)

        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)

        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)

        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)

        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)

        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)

        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)

        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)

        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)

        at java.lang.Thread.run(Thread.java:724)





--
 Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
Google Scholar Profile: http://goo.gl/sXYTE

Mailing Address:
Joint Genome Institute (400-0415)
for the US Department of Energy
2800 Mitchell Dr. Ste 100
Walnut Creek, CA 94598-1631


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Re: is there a limit to the number of isoforms that can be annotated?

Monica Poelchau
In reply to this post by Colin
Hi Colin,

Not sure. Here's a gff snippet from one of the repeatmasker features that won't load, but it seems to be formatted fine:

Scaffold366     repeatmasker    match   699498  699601  310     +       .       ID=Scaffold366:hit:9926:1.3.0.6;Name=species:rnd-6_family-695|genus:Unknown;Target=species:rnd-6_family-695|genus:Unknown 210 313 +

Scaffold366     repeatmasker    match_part      699498  699601  310     +       .       ID=Scaffold366:hsp:17308:1.3.0.6;Parent=Scaffold366:hit:9926:1.3.0.6;Target=species:rnd-6_family-695|genus:Unknown 210 313 +


There's a slight oddity with the snap track - the match_part features are ordered by coordinate, and are not necessarily grouped by parent feature. In the following example, the first, second, and sixth line belong to the same feature. I can load the entire feature into the user-created annotations track, as well as the second match-part feature, but not the first. 

Scaffold366     snap_masked     match   695629  700182  24.373  +       .       ID=Scaffold366:hit:12724:4.5.0.7;Name=snap_masked-Scaffold366-abinit-gene-7.7-mRNA-1

Scaffold366     snap_masked     match_part      695629  695676  9.627   +       .       ID=Scaffold366:hsp:25290:4.5.0.7;Parent=Scaffold366:hit:12724:4.5.0.7;Target=snap_masked-Scaffold366-abinit-gene-7.7-mRNA-1 1 48 +;Gap=M48

Scaffold366     snap_masked     match   695724  718360  84.161  -       .       ID=Scaffold366:hit:12725:4.5.0.7;Name=snap_masked-Scaffold366-abinit-gene-7.8-mRNA-1

Scaffold366     snap_masked     match_part      695724  695911  23.022  -       .       ID=Scaffold366:hsp:25297:4.5.0.7;Parent=Scaffold366:hit:12725:4.5.0.7;Target=snap_masked-Scaffold366-abinit-gene-7.8-mRNA-1 1 188 +;Gap=M188

Scaffold366     snap_masked     match_part      699780  699878  14.582  -       .       ID=Scaffold366:hsp:25296:4.5.0.7;Parent=Scaffold366:hit:12725:4.5.0.7;Target=snap_masked-Scaffold366-abinit-gene-7.8-mRNA-1 189 287 +;Gap=M99

Scaffold366     snap_masked     match_part      699919  700182  14.746  +       .       ID=Scaffold366:hsp:25291:4.5.0.7;Parent=Scaffold366:hit:12724:4.5.0.7;Target=snap_masked-Scaffold366-abinit-gene-7.7-mRNA-1 49 312 +;Gap=M264


Hth...


Monica



On Tue, Aug 19, 2014 at 4:26 PM, Colin <[hidden email]> wrote:
Hi all,
I am just curious, are all the evidence features being sourced from the same GFF? If not, are there possibly any strand differences in the source GFF that might be causing the errors?

One of the things noted on the github issue says:

"I get the above error when I use glyphs from the repeatmasker track, but I can drag entire gene models from the augustus and snap tracks into that field. Then again, some individual exons from the augustus and snap tracks can be loaded, but other generate the same error. The resulting gff3 file seems to be fine."

If the gff does not have a standard structure with mRNA->exon,etc then it has the potential to cause some problems.


-Colin


On Mon, Aug 18, 2014 at 7:34 PM, Monica Munoz-Torres <[hidden email]> wrote:
Hola Monica, 

To the best of my knowledge there is not a limit in the number of isoforms you can annotate. I have worked with over 30 isoforms for a gene product, and was able to drag additional evidence (in that case, Illumina contigs), and partial gene models onto the same region, as well as drag other gene models around it. 

Just to test, I went back and added evidence in support of "non-transcribed" models in the same region and regions around it. I have not been able to recreate an error doing this. 

Sorry I don't have much light to shed on this right now. I've created a GitHub issue with your note, and we will look into this as soon as possible. 

cheers, 
~moni. 


On Mon, Aug 18, 2014 at 5:07 PM, Monica Poelchau <[hidden email]> wrote:
Hi everyone,

One of our annotators is working on a gene model with ~20 isoforms. When attempting to drag more evidence into the user-created annotations track in the area of this gene model, we get the error 'Error writing transcript:null'. Catalina.out output is pasted below. Any ideas?

Thanks!

Monica

java.lang.NullPointerException

        at org.gmod.gbol.bioObject.CDS.overlaps(CDS.java:187)

        at org.bbop.apollo.web.overlap.OrfOverlapper.overlaps(OrfOverlapper.java:28)

        at org.bbop.apollo.web.overlap.OrfOverlapper.overlaps(OrfOverlapper.java:17)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:3892)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1202)

        at org.bbop.apollo.web.AnnotationEditorService.addTranscript(AnnotationEditorService.java:1186)

        at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:403)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)

        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)

        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)

        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)

        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)

        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)

        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)

        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)

        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)

        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)

        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)

        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)

        at java.lang.Thread.run(Thread.java:724)





--
 Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
Google Scholar Profile: http://goo.gl/sXYTE

Mailing Address:
Joint Genome Institute (400-0415)
for the US Department of Energy
2800 Mitchell Dr. Ste 100
Walnut Creek, CA 94598-1631