Skyline document import - Site54_Study9-1_SSS_111611_QCED_2016-03-22_16-28-31.sky.zip: /Panorama Public/2017/Schilling

Skyline document import - Site54_Study9-1_SSS_111611_QCED_2016-03-22_16-28-31.sky.zip

Site 54

Job Status

Created:

2017-06-27 13:10:59

Modified:

2020-04-20 17:09:20

Email:

vsharma@uw.edu

Status:

ERROR

Info:

Uncaught exception in PipelineJob: (DONE) Skyline document import - Site54_Study9-1_SSS_111611_QCED_2016-03-22_16-28-31.sky.zip

Description:

Skyline document import - Site54_Study9-1_SSS_111611_QCED_2016-03-22_16-28-31.sky.zip

File Path:

/data/labkey/files/Panorama Public/2017/Schilling - Longitudinal SSS/Site 54/@files/Site54_Study9-1_SSS_111611_QCED_2016-03-22_16-28-31.sky.log

Files:

Site54_Study9-1_SSS_111611_QCED_2016-03-22_16-28-31.sky.log

Join job:

Status	Description

Split jobs:

Status	Description

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Log File

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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)