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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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Error when annotating more than 20 isoforms. #18

Open monicacecilia opened 10 years ago

monicacecilia commented 10 years ago

From Monical Poelchau: "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."

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)

monicacecilia commented 10 years ago

from Monica Poelchau: 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."

and a note from me: I also see that it is not possible to drag elements from the repeat track and drop them as new exons / gene models on the "U-cA" area. I also see that some of the snap exons also exhibit this behavior, and some don't. It is, however, possible to drag elements from the repeatmasker track and add it as an exon to any of the models already in the U-cA (drag and drop only after the "receiving" model has turned green" (User Guide - 4.3.3 Add an Exon).

nathandunn commented 9 years ago

I believe that this is related to the bug where if there is too many isoforms it becomes impossible to drag in the first place.