27 Jun 2017 13:10:59,309 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
27 Jun 2017 13:10:59,313 INFO : Starting to import Skyline document from Site54_Study9-1_SSS_111611_QCED_2016-03-22_16-28-31.sky.zip
27 Jun 2017 13:10:59,313 INFO : Expanding Site54_Study9-1_SSS_111611_QCED.skyd
27 Jun 2017 13:10:59,649 INFO : Expanding Site54_Study9-1_SSS_111611_QCED.sky.view
27 Jun 2017 13:10:59,650 INFO : Expanding Site54_Study9-1_SSS_111611_QCED.sky
27 Jun 2017 13:10:59,839 INFO : Updating previously imported data for sample file C:\Documents and Settings\Simon\My Documents\Simon\CPTAC\Verification Group\Site 54 Study 9-1\9-1_Site54_SSS_run_224.wiff in QC folder.
27 Jun 2017 13:10:59,861 INFO : Inserting 2194089|Beta
27 Jun 2017 13:11:11,805 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
27 Jun 2017 13:11:11,806 ERROR: Uncaught exception in PipelineJob: (DONE) Skyline document import - Site54_Study9-1_SSS_111611_QCED_2016-03-22_16-28-31.sky.zip
org.postgresql.util.PSQLException: ERROR: insert or update on table "generalmoleculechrominfo" violates foreign key constraint "fk_gmchrominfo_samplefile"
Detail: Key (samplefileid)=(419241) is not present in table "samplefile".
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2155)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:288)
at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:430)
at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:356)
at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:168)
at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:116)
at org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
at org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
at org.labkey.api.data.dialect.StatementWrapper.executeQuery(StatementWrapper.java:1157)
at org.labkey.core.dialect.PostgreSql91Dialect.executeWithResults(PostgreSql91Dialect.java:286)
at org.labkey.core.dialect.PostgreSql92Dialect.executeWithResults(PostgreSql92Dialect.java:28)
at org.labkey.api.data.Table.insert(Table.java:763)
at org.labkey.targetedms.SkylineDocImporter.insertGeneralMoleculeChromInfos(SkylineDocImporter.java:1400)
at org.labkey.targetedms.SkylineDocImporter.insertPeptideOrSmallMolecule(SkylineDocImporter.java:1058)
at org.labkey.targetedms.SkylineDocImporter.insertPeptideGroup(SkylineDocImporter.java:947)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:530)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:153)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:61)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:710)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:941)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
27 Jun 2017 14:13:54,421 INFO : Retrying job.
27 Jun 2017 14:13:54,421 DEBUG: Database indicates active task ID is org.labkey.targetedms.pipeline.TargetedMSImportTask
27 Jun 2017 14:13:54,421 DEBUG: Retry details: Old Job ID: 3ab5eb54-3da0-1035-a2e7-3013bb9b8b42
27 Jun 2017 14:13:54,428 INFO : Starting to run task 'org.labkey.targetedms.pipeline.TargetedMSImportTask' at location 'webserver-high-priority'
27 Jun 2017 14:13:54,436 INFO : Starting to import Skyline document from Site54_Study9-1_SSS_111611_QCED_2016-03-22_16-28-31.sky.zip
27 Jun 2017 14:13:54,436 INFO : Expanding Site54_Study9-1_SSS_111611_QCED.skyd
27 Jun 2017 14:13:54,801 INFO : Expanding Site54_Study9-1_SSS_111611_QCED.sky.view
27 Jun 2017 14:13:54,802 INFO : Expanding Site54_Study9-1_SSS_111611_QCED.sky
27 Jun 2017 14:13:54,992 INFO : Updating previously imported data for sample file C:\Documents and Settings\Simon\My Documents\Simon\CPTAC\Verification Group\Site 54 Study 9-1\9-1_Site54_SSS_run_224.wiff in QC folder.
27 Jun 2017 14:13:55,013 INFO : Inserting 2194089|Beta
27 Jun 2017 14:14:07,007 INFO : Failed to complete task 'org.labkey.targetedms.pipeline.TargetedMSImportTask'
27 Jun 2017 14:14:07,007 ERROR: Uncaught exception in PipelineJob: (DONE) Skyline document import - Site54_Study9-1_SSS_111611_QCED_2016-03-22_16-28-31.sky.zip
org.postgresql.util.PSQLException: ERROR: insert or update on table "generalmoleculechrominfo" violates foreign key constraint "fk_gmchrominfo_samplefile"
Detail: Key (samplefileid)=(419662) is not present in table "samplefile".
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2455)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2155)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:288)
at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:430)
at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:356)
at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:168)
at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:116)
at org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
at org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:96)
at org.labkey.api.data.dialect.StatementWrapper.executeQuery(StatementWrapper.java:1157)
at org.labkey.core.dialect.PostgreSql91Dialect.executeWithResults(PostgreSql91Dialect.java:286)
at org.labkey.core.dialect.PostgreSql92Dialect.executeWithResults(PostgreSql92Dialect.java:28)
at org.labkey.api.data.Table.insert(Table.java:763)
at org.labkey.targetedms.SkylineDocImporter.insertGeneralMoleculeChromInfos(SkylineDocImporter.java:1400)
at org.labkey.targetedms.SkylineDocImporter.insertPeptideOrSmallMolecule(SkylineDocImporter.java:1058)
at org.labkey.targetedms.SkylineDocImporter.insertPeptideGroup(SkylineDocImporter.java:947)
at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:530)
at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:153)
at org.labkey.targetedms.pipeline.TargetedMSImportTask.run(TargetedMSImportTask.java:61)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:710)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:941)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)