Problems with displaying scaffolds and fasta export

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Dom
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Problems with displaying scaffolds and fasta export

Dom
Hi,

my previous problem concerning gff3 export was solved by the patch you recommended.

However I still have 2 problems:

####
1.
####

When trying to export all peptides I get the following error:

java.lang.NullPointerException
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterations(AnnotationSession.java:253)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterations(AnnotationSession.java:235)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterationsAndFrameshifts(AnnotationSession.java:222)
        at org.bbop.apollo.web.dataadapter.fasta.FastaIO.getUpdatedSequence(FastaIO.java:67)
        at org.bbop.apollo.web.dataadapter.fasta.FastaIO.writeFeatures(FastaIO.java:53)
        at org.bbop.apollo.web.dataadapter.fasta.FastaJEDatabaseIO.writeFeatures(FastaJEDatabaseIO.java:48)
        at org.bbop.apollo.web.dataadapter.fasta.FastaDataAdapter.write(FastaDataAdapter.java:197)
        at org.bbop.apollo.web.dataadapter.IOService.doPost(IOService.java:191)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:641)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:169)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:701)

when trying to export all cDNA I get :

java.lang.StringIndexOutOfBoundsException: String index out of range: -777
        at java.lang.AbstractStringBuilder.substring(AbstractStringBuilder.java:877)
        at java.lang.StringBuilder.substring(StringBuilder.java:72)
        at org.bbop.apollo.web.data.FeatureLazyResidues.getResidues(FeatureLazyResidues.java:37)
        at org.gmod.gbol.bioObject.AbstractSingleLocationBioFeature.getResidues(AbstractSingleLocationBioFeature.java:292)
        at org.gmod.gbol.bioObject.Transcript.getResidues(Transcript.java:362)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterations(AnnotationSession.java:253)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterations(AnnotationSession.java:235)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterationsAndFrameshifts(AnnotationSession.java:222)
        at org.bbop.apollo.web.dataadapter.fasta.FastaIO.getUpdatedSequence(FastaIO.java:104)
        at org.bbop.apollo.web.dataadapter.fasta.FastaIO.writeFeatures(FastaIO.java:53)
        at org.bbop.apollo.web.dataadapter.fasta.FastaJEDatabaseIO.writeFeatures(FastaJEDatabaseIO.java:48)
        at org.bbop.apollo.web.dataadapter.fasta.FastaDataAdapter.write(FastaDataAdapter.java:197)
        at org.bbop.apollo.web.dataadapter.IOService.doPost(IOService.java:191)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:641)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:169)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:701)

and when exporting CDS:

java.lang.NullPointerException
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterations(AnnotationSession.java:253)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterations(AnnotationSession.java:235)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterationsAndFrameshifts(AnnotationSession.java:222)
        at org.bbop.apollo.web.dataadapter.fasta.FastaIO.getUpdatedSequence(FastaIO.java:112)
        at org.bbop.apollo.web.dataadapter.fasta.FastaIO.writeFeatures(FastaIO.java:53)
        at org.bbop.apollo.web.dataadapter.fasta.FastaJEDatabaseIO.writeFeatures(FastaJEDatabaseIO.java:48)
        at org.bbop.apollo.web.dataadapter.fasta.FastaDataAdapter.write(FastaDataAdapter.java:197)
        at org.bbop.apollo.web.dataadapter.IOService.doPost(IOService.java:191)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:641)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:169)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:701)

I can export some annotations as fasta from some scaffolds but not from all of them…
 
####
2. 
####

When looking at the gff3 file of all scaffolds I noticed that there are 67 duplicated lines on 5 scaffolds (the duplicated lines do all refer either to exons or CDS). 

When inspecting the scaffolds in webapollo I encounter the following error in the regions described by the duplicated annotations:



Some of these scaffolds do not allow export of peptides/etc, but some do … but export of peptides/etc fails even when all five scaffolds are excluded from the export. 

Do you have any suggestion on how to deal with these problems? 

I am not that worried about the first problem, but I would be happy if I could solve the second problem as fast as possible ...

Thanks in advance, 

dom

On 16 May 2014, at 00:07, Dominik R Laetsch <[hidden email]> wrote:

Cool!

thanks, 

dom

On 16 May 2014, at 00:02, Ed Lee <[hidden email]> wrote:

Hi Dom,

Looking at the timestamp for the GiaB 2.05 release, it's not using the most current WebApollo release (which fixed this issue).  I'm not sure when a new version will be released with the current version of WebApollo.  There are two ways to handle this:

1) Upgrade your WebApollo instance in GiaB to the 2014-04-03 release (you'll need to following the server installation guide)

2) Run the patch for the 2013-11-22 release that addresses this issue:
http://genomearchitect.org/webapollo/releases/patches/2013-11-22/owner_date_last_modified_patch.tgz

$ tar -xvzf owner_date_last_modified_patch.tgz
$ cd owner_date_last_modified_patch
$ sudo ./apply_patch.sh /var/lib/tomcat7/webapps/WebApollo
$ sudo service tomcat7 restart

Cheers,
Ed


On Thu, May 15, 2014 at 3:46 PM, Dominik R Laetsch <[hidden email]> wrote:
Hi Ed,

we used the GMOD_in_a_Box_2.05.ova VM from ftp://ftp.gmod.org//pub/gmod/GMODinaBox

cheers,

dom

On 15 May 2014, at 23:34, Ed Lee <[hidden email]> wrote:

Hi Dom,

Which version of WebApollo are you running?

Cheers,
Ed


On Thu, May 15, 2014 at 2:54 PM, Dominik R Laetsch <[hidden email]> wrote:
Hi,

we have trouble exporting annotations.

tomcat reports this :

java.lang.NullPointerException
       at org.gmod.gbol.bioObject.io.GFF3Handler.extractAttributes(GFF3Handler.java:354)
       at org.gmod.gbol.bioObject.io.GFF3Handler.convertToEntry(GFF3Handler.java:216)
       at org.gmod.gbol.bioObject.io.GFF3Handler.convertToEntry(GFF3Handler.java:223)
       at org.gmod.gbol.bioObject.io.GFF3Handler.convertToEntry(GFF3Handler.java:223)
       at org.gmod.gbol.bioObject.io.GFF3Handler.convertToEntry(GFF3Handler.java:193)
       at org.gmod.gbol.bioObject.io.GFF3Handler.writeFeature(GFF3Handler.java:153)
       at org.gmod.gbol.bioObject.io.GFF3Handler.writeFeatures(GFF3Handler.java:134)
       at org.bbop.apollo.web.dataadapter.gff3.Gff3IO.writeFeatures(Gff3IO.java:29)
       at org.bbop.apollo.web.dataadapter.gff3.Gff3JEDatabaseIO.writeFeatures(Gff3JEDatabaseIO.java:47)
       at org.bbop.apollo.web.dataadapter.gff3.Gff3DataAdapter.write(Gff3DataAdapter.java:171)
       at org.bbop.apollo.web.dataadapter.IOService.doPost(IOService.java:191)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:641)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
       at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224)
       at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:169)
       at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
       at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168)
       at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
       at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
       at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
       at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
       at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
       at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
       at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
       at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
       at java.lang.Thread.run(Thread.java:701)

which resembles the problem reported here :

http://gmod.827538.n3.nabble.com/GFF-export-foiled-by-non-canonical-splice-sites-td4039946.html

Is a patch available? any suggestions?

thanks in advance,

dom



--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.





--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.






The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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Re: Problems with displaying scaffolds and fasta export

Colin
Hello,
I apologize for not replying to this email sooner.

For your second question, this seems to be related to "orphan" features. There are a couple of recent threads about this

http://gmod.827538.n3.nabble.com/Single-Contig-Error-s-td4043053.html
http://gmod.827538.n3.nabble.com/Corrupted-annotation-db-files-td4044029.html

The best thing to do currently is to use the tool remove_orphan_features.sh to remove the orphan feature manually.

I can't be certain about the first problem that you had, but if you have problems with this still let me know. If you want help with removing orphan features let me know as well.

Again sorry for the delay

Thanks
-Colin


On Fri, May 23, 2014 at 5:33 AM, Dominik R Laetsch <[hidden email]> wrote:
Hi,

my previous problem concerning gff3 export was solved by the patch you recommended.

However I still have 2 problems:

####
1.
####

When trying to export all peptides I get the following error:

java.lang.NullPointerException
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterations(AnnotationSession.java:253)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterations(AnnotationSession.java:235)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterationsAndFrameshifts(AnnotationSession.java:222)
        at org.bbop.apollo.web.dataadapter.fasta.FastaIO.getUpdatedSequence(FastaIO.java:67)
        at org.bbop.apollo.web.dataadapter.fasta.FastaIO.writeFeatures(FastaIO.java:53)
        at org.bbop.apollo.web.dataadapter.fasta.FastaJEDatabaseIO.writeFeatures(FastaJEDatabaseIO.java:48)
        at org.bbop.apollo.web.dataadapter.fasta.FastaDataAdapter.write(FastaDataAdapter.java:197)
        at org.bbop.apollo.web.dataadapter.IOService.doPost(IOService.java:191)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:641)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:169)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:701)

when trying to export all cDNA I get :

java.lang.StringIndexOutOfBoundsException: String index out of range: -777
        at java.lang.AbstractStringBuilder.substring(AbstractStringBuilder.java:877)
        at java.lang.StringBuilder.substring(StringBuilder.java:72)
        at org.bbop.apollo.web.data.FeatureLazyResidues.getResidues(FeatureLazyResidues.java:37)
        at org.gmod.gbol.bioObject.AbstractSingleLocationBioFeature.getResidues(AbstractSingleLocationBioFeature.java:292)
        at org.gmod.gbol.bioObject.Transcript.getResidues(Transcript.java:362)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterations(AnnotationSession.java:253)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterations(AnnotationSession.java:235)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterationsAndFrameshifts(AnnotationSession.java:222)
        at org.bbop.apollo.web.dataadapter.fasta.FastaIO.getUpdatedSequence(FastaIO.java:104)
        at org.bbop.apollo.web.dataadapter.fasta.FastaIO.writeFeatures(FastaIO.java:53)
        at org.bbop.apollo.web.dataadapter.fasta.FastaJEDatabaseIO.writeFeatures(FastaJEDatabaseIO.java:48)
        at org.bbop.apollo.web.dataadapter.fasta.FastaDataAdapter.write(FastaDataAdapter.java:197)
        at org.bbop.apollo.web.dataadapter.IOService.doPost(IOService.java:191)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:641)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:169)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:701)

and when exporting CDS:

java.lang.NullPointerException
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterations(AnnotationSession.java:253)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterations(AnnotationSession.java:235)
        at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterationsAndFrameshifts(AnnotationSession.java:222)
        at org.bbop.apollo.web.dataadapter.fasta.FastaIO.getUpdatedSequence(FastaIO.java:112)
        at org.bbop.apollo.web.dataadapter.fasta.FastaIO.writeFeatures(FastaIO.java:53)
        at org.bbop.apollo.web.dataadapter.fasta.FastaJEDatabaseIO.writeFeatures(FastaJEDatabaseIO.java:48)
        at org.bbop.apollo.web.dataadapter.fasta.FastaDataAdapter.write(FastaDataAdapter.java:197)
        at org.bbop.apollo.web.dataadapter.IOService.doPost(IOService.java:191)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:641)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:169)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:701)

I can export some annotations as fasta from some scaffolds but not from all of them…
 
####
2. 
####

When looking at the gff3 file of all scaffolds I noticed that there are 67 duplicated lines on 5 scaffolds (the duplicated lines do all refer either to exons or CDS). 

When inspecting the scaffolds in webapollo I encounter the following error in the regions described by the duplicated annotations:



Some of these scaffolds do not allow export of peptides/etc, but some do … but export of peptides/etc fails even when all five scaffolds are excluded from the export. 

Do you have any suggestion on how to deal with these problems? 

I am not that worried about the first problem, but I would be happy if I could solve the second problem as fast as possible ...

Thanks in advance, 

dom

On 16 May 2014, at 00:07, Dominik R Laetsch <[hidden email]> wrote:

Cool!

thanks, 

dom

On 16 May 2014, at 00:02, Ed Lee <[hidden email]> wrote:

Hi Dom,

Looking at the timestamp for the GiaB 2.05 release, it's not using the most current WebApollo release (which fixed this issue).  I'm not sure when a new version will be released with the current version of WebApollo.  There are two ways to handle this:

1) Upgrade your WebApollo instance in GiaB to the 2014-04-03 release (you'll need to following the server installation guide)

2) Run the patch for the 2013-11-22 release that addresses this issue:
http://genomearchitect.org/webapollo/releases/patches/2013-11-22/owner_date_last_modified_patch.tgz

$ tar -xvzf owner_date_last_modified_patch.tgz
$ cd owner_date_last_modified_patch
$ sudo ./apply_patch.sh /var/lib/tomcat7/webapps/WebApollo
$ sudo service tomcat7 restart

Cheers,
Ed


On Thu, May 15, 2014 at 3:46 PM, Dominik R Laetsch <[hidden email]> wrote:
Hi Ed,

we used the GMOD_in_a_Box_2.05.ova VM from ftp://ftp.gmod.org//pub/gmod/GMODinaBox

cheers,

dom

On 15 May 2014, at 23:34, Ed Lee <[hidden email]> wrote:

Hi Dom,

Which version of WebApollo are you running?

Cheers,
Ed


On Thu, May 15, 2014 at 2:54 PM, Dominik R Laetsch <[hidden email]> wrote:
Hi,

we have trouble exporting annotations.

tomcat reports this :

java.lang.NullPointerException
       at org.gmod.gbol.bioObject.io.GFF3Handler.extractAttributes(GFF3Handler.java:354)
       at org.gmod.gbol.bioObject.io.GFF3Handler.convertToEntry(GFF3Handler.java:216)
       at org.gmod.gbol.bioObject.io.GFF3Handler.convertToEntry(GFF3Handler.java:223)
       at org.gmod.gbol.bioObject.io.GFF3Handler.convertToEntry(GFF3Handler.java:223)
       at org.gmod.gbol.bioObject.io.GFF3Handler.convertToEntry(GFF3Handler.java:193)
       at org.gmod.gbol.bioObject.io.GFF3Handler.writeFeature(GFF3Handler.java:153)
       at org.gmod.gbol.bioObject.io.GFF3Handler.writeFeatures(GFF3Handler.java:134)
       at org.bbop.apollo.web.dataadapter.gff3.Gff3IO.writeFeatures(Gff3IO.java:29)
       at org.bbop.apollo.web.dataadapter.gff3.Gff3JEDatabaseIO.writeFeatures(Gff3JEDatabaseIO.java:47)
       at org.bbop.apollo.web.dataadapter.gff3.Gff3DataAdapter.write(Gff3DataAdapter.java:171)
       at org.bbop.apollo.web.dataadapter.IOService.doPost(IOService.java:191)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:641)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
       at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224)
       at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:169)
       at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
       at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168)
       at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
       at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
       at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
       at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
       at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
       at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
       at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
       at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
       at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
       at java.lang.Thread.run(Thread.java:701)

which resembles the problem reported here :

http://gmod.827538.n3.nabble.com/GFF-export-foiled-by-non-canonical-splice-sites-td4039946.html

Is a patch available? any suggestions?

thanks in advance,

dom



--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.





--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.






The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.