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via labkey.org by Unknown author, 1 year ago
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via labkey.org by Unknown author, 2 years ago
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java.lang.NullPointerException: 	at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:160)	at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)	at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)	at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)	at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)	at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)	at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)	at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)	at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)	at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)	at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)	at org.labkey.pipeline.analysis.FileAnalysisJob.findFile(FileAnalysisJob.java:134)	at org.labkey.pipeline.analysis.FileAnalysisJob.findInputFile(FileAnalysisJob.java:81)	at org.labkey.pipeline.api.AbstractWorkDirectory.getDir(AbstractWorkDirectory.java:157)	at org.labkey.pipeline.api.AbstractWorkDirectory.newFile(AbstractWorkDirectory.java:180)	at org.labkey.pipeline.analysis.CommandTaskImpl.newWorkFile(CommandTaskImpl.java:306)	at org.labkey.pipeline.analysis.CommandTaskImpl.getWorkFiles(CommandTaskImpl.java:295)	at org.labkey.pipeline.analysis.CommandTaskImpl.getProcessPaths(CommandTaskImpl.java:277)	at org.labkey.api.pipeline.cmd.TaskPathToCommandArgs.getPaths(TaskPathToCommandArgs.java:57)	at org.labkey.api.pipeline.cmd.PathToCommandArgs.toArgsInner(PathToCommandArgs.java:28)	at org.labkey.api.pipeline.cmd.TaskToCommandArgs.toArgs(TaskToCommandArgs.java:61)	at org.labkey.api.pipeline.cmd.ListToCommandArgs.toArgsInner(ListToCommandArgs.java:70)	at org.labkey.api.pipeline.cmd.TaskToCommandArgs.toArgs(TaskToCommandArgs.java:61)	at org.labkey.api.pipeline.cmd.EnumToCommandArgs.toArgsInner(EnumToCommandArgs.java:67)	at org.labkey.api.pipeline.cmd.TaskToCommandArgs.toArgs(TaskToCommandArgs.java:61)	at org.labkey.pipeline.analysis.CommandTaskImpl$Factory.isParticipant(CommandTaskImpl.java:189)	at org.labkey.api.pipeline.PipelineJob.findRunnableTask(PipelineJob.java:716)	at org.labkey.api.pipeline.PipelineJob.runStateMachine(PipelineJob.java:659)	at org.labkey.api.pipeline.PipelineJob.setQueue(PipelineJob.java:473)	at org.labkey.pipeline.api.PipelineQueueImpl.addJob(PipelineQueueImpl.java:83)	at org.labkey.pipeline.api.PipelineServiceImpl.queueJob(PipelineServiceImpl.java:290)	at org.labkey.pipeline.analysis.AnalysisController$StartAnalysisAction.execute(AnalysisController.java:211)	at org.labkey.pipeline.analysis.AnalysisController$AbstractAnalysisApiAction.execute(AnalysisController.java:271)	at org.labkey.pipeline.analysis.AnalysisController$AbstractAnalysisApiAction.execute(AnalysisController.java:251)	at org.labkey.api.action.ApiAction.handlePost(ApiAction.java:144)	at org.labkey.api.action.ApiAction.handleRequest(ApiAction.java:95)	at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:167)	at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)	at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:349)	at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:756)	at org.labkey.api.view.ViewServlet.service(ViewServlet.java:166)	at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)	at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:36)	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)	at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)	at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:603)	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)	at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:138)	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:210)	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174)	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:151)	at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870)	at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)	at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)	at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)	at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685)	at java.lang.Thread.run(Thread.java:619)