Dear,

We are having some issues in submiting the skyline file to Panorama. We are receiving the error below. Could you please help us to troubleshoot this issue? Thank you very much. Best, Daniela

08 Aug 2024 05:17:48,369 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
08 Aug 2024 05:17:48,370 INFO : Starting to import Skyline document from Corridas_PRM_Amostras_Injeçao1e2_184pepsquantificados_2024-08-08_09-14-59.sky.zip
08 Aug 2024 05:17:48,370 INFO : Expanding Peps_Mix_Saliva_PRM_Unscheduled_364peps_17fev23.blib
08 Aug 2024 05:17:50,589 INFO : Expanding PRM_Final_21_07_23.blib
08 Aug 2024 05:17:55,067 INFO : Expanding PRM_Final_21_07_23.redundant.blib
08 Aug 2024 05:18:16,718 ERROR: Import failed
java.lang.IllegalArgumentException: malformed input off : 26, length : 1
at java.base/java.lang.String.throwMalformed(String.java:1242)
at java.base/java.lang.String.decodeUTF8_UTF16(String.java:1198)
at java.base/java.lang.String.newStringUTF8NoRepl(String.java:732)
at java.base/java.lang.System$2.newStringUTF8NoRepl(System.java:2398)
at java.base/java.util.zip.ZipCoder$UTF8ZipCoder.toString(ZipCoder.java:199)
at java.base/java.util.zip.ZipCoder.toString(ZipCoder.java:66)
at java.base/java.util.zip.ZipInputStream.readLOC(ZipInputStream.java:302)
at java.base/java.util.zip.ZipInputStream.getNextEntry(ZipInputStream.java:124)
at org.labkey.api.writer.ZipUtil.unzipToDirectory(ZipUtil.java:106)
at org.labkey.api.writer.ZipUtil.unzipToDirectory(ZipUtil.java:82)
at org.labkey.api.writer.ZipUtil.unzipToDirectory(ZipUtil.java:69)
at org.labkey.api.writer.ZipUtil.unzipToDirectory(ZipUtil.java:64)
at org.labkey.targetedms.SkylineDocImporter.extractIfZip(SkylineDocImporter.java:1005)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:317)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:249)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:833)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1075)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1156.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$CallerRunsPolicy.rejectedExecution(ThreadPoolExecutor.java:1486)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:391)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:865)
at org.mule.impl.work.ScheduleWorkExecutor.doExecute(ScheduleWorkExecutor.java:39)
at org.mule.impl.work.MuleWorkManager.executeWork(MuleWorkManager.java:277)
at org.mule.impl.work.MuleWorkManager.scheduleWork(MuleWorkManager.java:244)
at org.mule.impl.model.seda.SedaComponent.run(SedaComponent.java:483)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.nio.charset.MalformedInputException: Input length = 1
... 39 more
08 Aug 2024 05:18:16,745 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
08 Aug 2024 05:18:16,747 ERROR: malformed input off : 26, length : 1
org.labkey.api.pipeline.PipelineJobException: malformed input off : 26, length : 1
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:276)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:63)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:833)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1075)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1156.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$CallerRunsPolicy.rejectedExecution(ThreadPoolExecutor.java:1486)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:391)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:865)
at org.mule.impl.work.ScheduleWorkExecutor.doExecute(ScheduleWorkExecutor.java:39)
at org.mule.impl.work.MuleWorkManager.executeWork(MuleWorkManager.java:277)
at org.mule.impl.work.MuleWorkManager.scheduleWork(MuleWorkManager.java:244)
at org.mule.impl.model.seda.SedaComponent.run(SedaComponent.java:483)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.IllegalArgumentException: malformed input off : 26, length : 1
at java.base/java.lang.String.throwMalformed(String.java:1242)
at java.base/java.lang.String.decodeUTF8_UTF16(String.java:1198)
at java.base/java.lang.String.newStringUTF8NoRepl(String.java:732)
at java.base/java.lang.System$2.newStringUTF8NoRepl(System.java:2398)
at java.base/java.util.zip.ZipCoder$UTF8ZipCoder.toString(ZipCoder.java:199)
at java.base/java.util.zip.ZipCoder.toString(ZipCoder.java:66)
at java.base/java.util.zip.ZipInputStream.readLOC(ZipInputStream.java:302)
at java.base/java.util.zip.ZipInputStream.getNextEntry(ZipInputStream.java:124)
at org.labkey.api.writer.ZipUtil.unzipToDirectory(ZipUtil.java:106)
at org.labkey.api.writer.ZipUtil.unzipToDirectory(ZipUtil.java:82)
at org.labkey.api.writer.ZipUtil.unzipToDirectory(ZipUtil.java:69)
at org.labkey.api.writer.ZipUtil.unzipToDirectory(ZipUtil.java:64)
at org.labkey.targetedms.SkylineDocImporter.extractIfZip(SkylineDocImporter.java:1005)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:317)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:249)
... 24 more
Caused by: java.nio.charset.MalformedInputException: Input length = 1
... 39 more