2014-02-13 11:48:14,DEBUG,com.nimblegen.common.config.impl.ApplicationLogConfiguration, Application logging has been successfully configured
2014-02-13 11:48:14,DEBUG,com.nimblegen.deva.projectmanager.settings.Settings, Settings successfully saved to Java properties.
2014-02-13 11:48:14,DEBUG,com.nimblegen.deva.projectmanager.ui.ProjectManagerMainPanel, Running DbMigrate and then DEVA on directory: 'Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA'
2014-02-13 11:48:14,DEBUG,com.nimblegen.deva.projectmanager.settings.MemoryProbe, Java Command Line: C:\Deva\jre\bin\java
2014-02-13 11:48:15,INFO,com.nimblegen.deva.projectmanager.settings.MemoryProbe, MemoryProbe has found the total physical memory to be 8189 megabytes.
2014-02-13 11:48:17,INFO,com.nimblegen.deva.projectmanager.settings.MemoryProbe, In 11 trials, MemoryProbe has found the "borderline" memory setting to be 7157 megabytes.
2014-02-13 11:48:17,DEBUG,com.nimblegen.deva.projectmanager.settings.MemoryProbe, Finished determineBorderlineMemorySettingInMegabytes()
2014-02-13 11:48:17,INFO,com.nimblegen.deva.projectmanager.settings.MemoryProbe, MemoryProbe has set the highest recommended memory setting to 7150 megabytes.
2014-02-13 11:48:17,INFO,com.nimblegen.deva.projectmanager.launcher.CombinedLauncher, CombinedLauncher starting.
2014-02-13 11:48:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.CombinedLauncher, CombinedLauncher is in Jar mode.
2014-02-13 11:48:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.CombinedLauncher, Command: java -Duser.language=en -Duser.region=US -cp C:\Deva\DEVA.jar com.nimblegen.deva.dbmigrate.RunDBMigrate -D -v=h
2014-02-13 11:48:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.CombinedLauncher, Project directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA
2014-02-13 11:48:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.CombinedLauncher, Working directory: C:\Deva
2014-02-13 11:48:17,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, StreamWorker 1871045134 starting.
2014-02-13 11:48:17,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, Error StreamLogger 568699335 starting.
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:17,944 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:17,944 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:17,944 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/C:/Deva/DEVA.jar!/logback.xml]
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:17,960 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@33010058 - URL [jar:file:/C:/Deva/DEVA.jar!/logback.xml] is not of type file
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:18,090 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:18,093 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [STDOUT]
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:18,130 |-INFO in ch.qos.logback.classic.joran.action.LevelAction - com.nimblegen level set to DEBUG
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:18,130 |-INFO in ch.qos.logback.classic.joran.action.LevelAction - com.nimblegen.common.jobcontroller level set to ERROR
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:18,130 |-INFO in ch.qos.logback.classic.joran.action.LevelAction - ROOT level set to ERROR
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:18,131 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [STDOUT] to Logger[ROOT]
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:18,132 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:48:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 5Command line arguments retrieved.
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:18 AM org.springframework.context.support.AbstractApplicationContext prepareRefresh
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@4c331059: startup date [Thu Feb 13 11:48:18 PST 2014]; root of context hierarchy
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:18 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Loading XML bean definitions from class path resource [com/nimblegen/deva/dbmigrate/DataSourceFactory_h2.xml]
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:18 AM org.springframework.beans.factory.support.DefaultListableBeanFactory preInstantiateSingletons
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@73c6641: defining beans [db_connection_driver_class_name,db_connection_protocol,db_vendor,database_name,db_directory,db_user_default_name,db_user_default_password,sql_create_role,sql_set_schema,sql_create_schema,sql_drop_role,sql_create_version,sql_insert_version]; root of factory hierarchy
2014-02-13 11:48:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 673 [main] INFO com.nimblegen.deva.dbmigrate.DataSourceFactory - Using: org.h2.Driver
2014-02-13 11:48:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 15MigrationFramework initialized.
2014-02-13 11:48:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1266 [main] DEBUG com.nimblegen.common.services.ServiceProvider - Starting H2 in EMBEDDED mode.
2014-02-13 11:48:19,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:19 AM org.springframework.context.support.AbstractApplicationContext prepareRefresh
2014-02-13 11:48:19,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@2d1e233: startup date [Thu Feb 13 11:48:19 PST 2014]; root of context hierarchy
2014-02-13 11:48:19,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:19 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
2014-02-13 11:48:19,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Loading XML bean definitions from class path resource [com/nimblegen/common/spring/services_h2_embedded.xml]
2014-02-13 11:48:19,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:19 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
2014-02-13 11:48:19,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Loading XML bean definitions from class path resource [com/nimblegen/common/spring/services.xml]
2014-02-13 11:48:19,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:19 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
2014-02-13 11:48:19,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Loading XML bean definitions from class path resource [com/nimblegen/common/spring/daos.xml]
2014-02-13 11:48:19,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:19 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
2014-02-13 11:48:19,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Loading XML bean definitions from URL [file:Z:/users/c/csather/TO_BE_REVIEWED_SCANS/02132014/ClaireOlson/DEVA/config/sys_config/db/h2-embedded-datasource.xml]
2014-02-13 11:48:19,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:19 AM org.springframework.beans.factory.support.DefaultListableBeanFactory preInstantiateSingletons
2014-02-13 11:48:20,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@6da0d866: defining beans [org.springframework.context.annotation.internalConfigurationAnnotationProcessor,org.springframework.context.annotation.internalAutowiredAnnotationProcessor,org.springframework.context.annotation.internalRequiredAnnotationProcessor,org.springframework.context.annotation.internalCommonAnnotationProcessor,fileTokenFactory,fileTokenDao,organismFactory,organismDao,genomeSourceFactory,genomeSourceDao,genomeAssyFactory,genomeAssyDao,sampleFactory,sampleDao,arrayDesignFactory,arrayDesignDao,arrayResultFactory,arrayResultDao,sampleTrackingControlSetFactory,sampleTrackingControlSetDao,labeledSampleFactory,labeledSampleDao,slideDesignFactory,slideDesignDao,slideResultFactory,slideResultDao,arrayTiffFactory,arrayTiffDao,decodedNumberFactory,decodedNumberDao,analysisWorkflowFactory,analysisWorkflowDao,workflowDataFactory,workflowDataDao,monitoredFileFactory,monitoredFileDao,importedFileAssociationsDao,genomeAssemblySequenceFactory,genomeAssemblySequenceDao,settingFactory,settingDao,workflowTemplateFactory,workflowTemplateDao,visualizationFactory,visualizationDao,genomeDatasetDboFactory,genomeDatasetDao,valuedGenomeDatasetAttributesDao,genomeDatasetCacheDboFactory,genomeDatasetCacheDao,exportFactory,exportDao,containerGenomeDatasetDao,segmntStatsFactory,segmntStatsDao,designAnnotationFactory,designAnnotationDao,jobsRecoveryDao,activityStatusDao,qualityControlReportFactory,qualityControlReportDao,genomeDatasetPioService,slideService,analysisWorkflowService,workflowTransportService,workflowTemplateService,visualizationService,qualityControlReportService,snpHeterozygosityFrequencyService,genomeDatasetCacheService,fileMoverFactory,fileService,filePioService,genomeAssyService,genomeAssyPioService,applicationConfiguration,systemConfiguration,designAnnotationService,devaArchiveImportService,genomeAssemblySequenceService,sequenceStatsService,systemConfigurationService,dataWriterFactory,xysExporter,gffDataExporter,jobsRecoveryService,trackSettingsService,paneSettingsService,plotSettingsService,genomeAssemblyController,tiffImportMonitor,manualAlignmentController,tiffImportController,slidesTableController,genomeDatasetController,slideResultSearchController,arrayResultSearchController,exportService,jobStatusDetailController,propertyConfigurer,h2datasource,datasource,dialect,template]; root of factory hierarchy
2014-02-13 11:48:20,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:20 AM java.util.prefs.WindowsPreferences
2014-02-13 11:48:20,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5.
2014-02-13 11:48:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2820 [main] DEBUG com.nimblegen.common.services.ServiceProvider - Temporary working directory cleared (total time:112ms)
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3322 [main] DEBUG com.nimblegen.deva.common.jobservice.JobService - job service resource limit for ESTIMATED_MEMORY_IN_KB is set to 1524932.
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3380 [main] DEBUG com.nimblegen.deva.dbmigrate.RunDBMigrate - deleting all files in store directory[Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore].
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3387 [main] DEBUG com.nimblegen.deva.dbmigrate.RunDBMigrate - 0 files and 0 directories successfully deleted in store directory[Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore].
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 17Store folder deleted.
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3387 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationFrameworkFacade - deleting all files in database directory[Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\datastore].
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3395 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationFrameworkFacade - 0 files and 0 directories successfully deleted in database directory[Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\datastore].
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 17Database deleted.
2014-02-13 11:48:21,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:21 AM org.springframework.jdbc.datasource.DriverManagerDataSource setDriverClassName
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3396 [main] DEBUG com.nimblegen.deva.dbmigrate.DataSourceFactory - jdbc:h2:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\datastore\rng_database
2014-02-13 11:48:21,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Loaded JDBC driver: org.h2.Driver
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3662 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - Executing CREATE TABLE version_info ( id BIGINT AUTO_INCREMENT PRIMARY KEY, version INT NOT NULL, updated TIMESTAMP DEFAULT CURRENT TIMESTAMP );
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3672 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - Initialization is complete.
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 50Framework initialized
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3731 [main] DEBUG com.nimblegen.deva.dbmigrate.RunDBMigrate - Fired up a database Migrator.
2014-02-13 11:48:21,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3731 [main] INFO com.nimblegen.deva.dbmigrate.RunDBMigrate - Current database version: 0
2014-02-13 11:48:21,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3731 [main] INFO com.nimblegen.deva.dbmigrate.RunDBMigrate - Destination version: 10000
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3902 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationFactory - Found and created 39 new Migrations.
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 51Stage 1 of 39 done
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3911 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE filetoken ( id_filetoken BIGINT AUTO_INCREMENT PRIMARY KEY, path_relative_to_store_directory VARCHAR(512) NULL , file_name VARCHAR(128) NOT NULL UNIQUE , original_file_name VARCHAR(256) NOT NULL , num_references INTEGER NOT NULL , md5_value VARCHAR(128) UNIQUE NOT NULL , stored_at TIMESTAMP NOT NULL DEFAULT current_timestamp )
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3949 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (1)
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 52Stage 2 of 39 done
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3952 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE organism ( id_organism BIGINT AUTO_INCREMENT PRIMARY KEY, ncbi_taxon_id INT NOT NULL , scientific_name VARCHAR(128) NOT NULL , common_name VARCHAR(128) , is_user_defined INT NOT NULL DEFAULT 0 , created_at TIMESTAMP NOT NULL DEFAULT current_timestamp )
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4032 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE genome_source ( id_genome_source BIGINT AUTO_INCREMENT PRIMARY KEY, name VARCHAR(64) NOT NULL , description VARCHAR(512), created_at TIMESTAMP NOT NULL DEFAULT current_timestamp )
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4047 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE genome_assembly ( id_genome_assembly BIGINT AUTO_INCREMENT PRIMARY KEY, genome_assembly_name VARCHAR(32) , accession_identifier VARCHAR(132) , is_user_defined INT NOT NULL DEFAULT 0 , id_organism BIGINT NOT NULL , id_genome_source BIGINT NOT NULL , created_at TIMESTAMP NOT NULL DEFAULT current_timestamp , CONSTRAINT fk_gnmssy_rgn FOREIGN KEY (id_organism) REFERENCES organism (id_organism) , CONSTRAINT fk_gnmssy_gnmsrc FOREIGN KEY (id_genome_source) REFERENCES genome_source (id_genome_source) , CONSTRAINT unq_gnmssy_lbl UNIQUE (genome_assembly_name) )
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4053 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (2)
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 53Stage 3 of 39 done
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4055 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: INSERT INTO organism ( ncbi_taxon_id , scientific_name , common_name ) VALUES ( 32644 , 'Unspecified' , 'Unspecified' ), ( 3702 , 'Arabidopsis thaliana' , 'Thale-cress'), ( 9913 , 'Bos taurus' , 'Domestic cow' ), ( 6239 , 'Caenorhabditis elegans' , 'Nematode' ), ( 7955 , 'Danio rerio' , 'Zebrafish' ), ( 7227 , 'Drosophila melanogaster' , 'Fruit fly' ), ( 9606 , 'Homo sapiens' , 'Human' ), ( 10090 , 'Mus musculus' , 'House mouse' ), ( 10116 , 'Rattus norvegicus' , 'Norway rat' ), ( 4932 , 'Saccharomyces cerevisiae' , 'Yeast' ), ( 9685 , 'Xenopus tropicalis' , 'Frog' ) , ( 9615 , 'Canis familiaris' , 'Dog' ), ( 9823 , 'Sus scrofa' , 'Pig' ), ( 9031 , 'Gallus gallus' , 'Chicken' ), ( 9796 , 'Equus caballus' , 'Horse' )
2014-02-13 11:48:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4058 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: INSERT INTO genome_source ( name , description ) VALUES ( 'UCSC' , 'Genome Bioinformatics at the University of California at Santa Clara. Provides assembly releases of popular genomes.' ), ( 'GenBank' , 'GenBank is a resource for genomic information at the National Center for Bioinformatics (NIH).'), ( 'Flybase' , 'A project supported by a consortium of Drosophila researchers and computer scientists at Harvard University, the University of Cambridge (UK), and Indiana University.'), ( 'TAIR' , 'The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.' ), ( 'Unknown' , 'Unknown' ), ( 'Customer' , 'Customer supplied' )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4067 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: INSERT INTO genome_assembly ( genome_assembly_name , id_organism , id_genome_source ) VALUES ( 'Unspecified' , 1 , 5 ) , ( 'TAIR9' , 2 , 4 ) , ( 'bosTau4' , 3 , 1 ) , ( 'ce6' , 4 , 1 ), ( 'ce4' , 4 , 1 ) , ( 'danRer6' , 5 , 1 ) , ( 'dm3' , 6 , 1 ) , ( 'hg19' , 7 , 1 ) , ( 'hg18' , 7 , 1 ) , ( 'hg17' , 7 , 1 ) , ( 'mm9' , 8 , 1 ) , ( 'mm8' , 8 , 1 ) , ( 'mm7' , 8 , 1 ) , ( 'rn4' , 9 , 1 ) , ( 'sacCer2' , 10 , 1 ) , ( 'xenTro2' , 11 , 1 ) , ( 'canFam2' , 12 , 1 ) , ( 'susScr2' , 13 , 1 ) , ( 'galGal3' , 14 , 1 ) , ( 'equCab2' , 15 , 1 )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4078 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE VIEW vw_genome_assembly AS SELECT ga.id_genome_assembly , genome_assembly_name , accession_identifier , ga.is_user_defined AS genome_assembly_is_user_defined , ga.created_at AS genome_assembly_created_at , gs.id_genome_source , gs.name AS genome_source_name , gs.description AS genome_source_description , org.id_organism , org.is_user_defined AS organism_is_user_defined , scientific_name , common_name , ncbi_taxon_id FROM genome_assembly AS ga , genome_source AS gs , organism AS org WHERE ga.id_organism = org.id_organism AND ga.id_genome_source = gs.id_genome_source
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4111 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (3)
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 54Stage 4 of 39 done
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4113 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE genome_dataset ( id_genome_dataset BIGINT AUTO_INCREMENT PRIMARY KEY , original_file_name VARCHAR(128) , data_type VARCHAR(128) NOT NULL , id_genome_assembly BIGINT REFERENCES genome_assembly , is_import SMALLINT NOT NULL DEFAULT 0 , is_annotation SMALLINT NOT NULL DEFAULT 0 , stored_at TIMESTAMP NOT NULL DEFAULT current_timestamp )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4120 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE genome_dataset_container ( id_genome_dataset_container BIGINT AUTO_INCREMENT PRIMARY KEY , id_genome_dataset_parent BIGINT REFERENCES genome_dataset , container_name VARCHAR (128) , id_genome_dataset BIGINT REFERENCES genome_dataset )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4122 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE chromosome_data_file ( id_chromosome_data_file BIGINT AUTO_INCREMENT PRIMARY KEY , id_filetoken BIGINT NOT NULL REFERENCES filetoken (id_filetoken) , id_attributes_filetoken BIGINT NOT NULL REFERENCES filetoken (id_filetoken) , id_position_key_filetoken BIGINT NOT NULL REFERENCES filetoken (id_filetoken) , chromosome_name VARCHAR(64) NOT NULL , num_records BIGINT NOT NULL , min_value FLOAT , first_quartile FLOAT , median FLOAT , third_quartile FLOAT , max_value FLOAT , min_position BIGINT NOT NULL , max_position BIGINT NOT NULL , stored_at TIMESTAMP NOT NULL DEFAULT current_timestamp )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4125 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE chromosome_dataset ( id_chromosome_dataset BIGINT NOT NULL AUTO_INCREMENT PRIMARY KEY , id_genome_dataset BIGINT NOT NULL REFERENCES genome_dataset (id_genome_dataset) ON DELETE CASCADE , id_chromosome_data_file BIGINT NOT NULL UNIQUE REFERENCES chromosome_data_file (id_chromosome_data_file) , id_filetoken_lucene_anchor BIGINT REFERENCES filetoken (id_filetoken) )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4146 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE VIEW vw_gds_ga AS SELECT id_genome_dataset , original_file_name AS gds_original_filename , data_type AS gds_data_type , is_import AS gds_is_import , stored_at AS gds_stored_at , is_annotation AS gds_is_annotation , vw_genome_assembly.id_genome_assembly , genome_assembly_name , accession_identifier , genome_assembly_is_user_defined , genome_assembly_created_at , id_genome_source , genome_source_description , genome_source_name , id_organism , organism_is_user_defined , scientific_name , common_name , ncbi_taxon_id FROM genome_dataset INNER JOIN vw_genome_assembly ON genome_dataset.id_genome_assembly = vw_genome_assembly.id_genome_assembly
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4148 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE VIEW vw_chromosome_dataset AS SELECT cds.id_chromosome_dataset , cds.id_genome_dataset , cds.id_chromosome_data_file , cds.id_filetoken_lucene_anchor , cds.id_filetoken_lucene_anchor AS lucene_anchor_ft_id , data_file.id_chromosome_data_file AS data_file_id , data_file.chromosome_name , data_file.num_records AS data_file_num_records , data_file.min_value , data_file.first_quartile , data_file.median , data_file.third_quartile , data_file.max_value , data_file.min_position , data_file.max_position , data_file.num_records , data_file.id_filetoken AS data_filetoken_id , data_file.id_attributes_filetoken AS attributes_filetoken_id , data_file.id_position_key_filetoken AS position_key_filetoken_id FROM chromosome_dataset AS cds , chromosome_data_file AS data_file WHERE cds.id_chromosome_data_file = data_file.id_chromosome_data_file
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4156 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE VIEW vw_genome_dataset AS SELECT gds.id_genome_dataset , gds.gds_original_filename , gds.gds_data_type , gds.gds_is_import , gds.gds_is_annotation , gds.gds_stored_at , gds.id_genome_assembly , gds.genome_assembly_name , gds.accession_identifier , gds.genome_assembly_created_at , gds.genome_assembly_is_user_defined , gds.id_genome_source , gds.genome_source_description , gds.genome_source_name , gds.id_organism , gds.scientific_name , gds.common_name , gds.ncbi_taxon_id , gds.organism_is_user_defined , cds.id_chromosome_dataset , data_file.chromosome_name , data_file.id_chromosome_data_file AS data_file_id , data_file.id_filetoken AS data_filetoken_id , data_file.id_attributes_filetoken AS attributes_filetoken_id , data_file.id_position_key_filetoken AS position_key_filetoken_id , data_file.min_value , data_file.first_quartile , data_file.median , data_file.third_quartile , data_file.max_value , data_file.min_position , data_file.max_position , data_file.num_records , cds.id_filetoken_lucene_anchor AS lucene_anchor_ft_id FROM vw_gds_ga as gds LEFT OUTER JOIN chromosome_dataset AS cds ON gds.id_genome_dataset = cds.id_genome_dataset LEFT OUTER JOIN chromosome_data_file AS data_file ON cds.id_chromosome_data_file = data_file.id_chromosome_data_file
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4157 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE valued_genome_dataset_attributes ( id_valued_genome_dataset_attributes BIGINT AUTO_INCREMENT PRIMARY KEY , attribute_name VARCHAR(128) NOT NULL , id_genome_dataset BIGINT NOT NULL)
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4159 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (4)
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 55Stage 5 of 39 done
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4160 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE monitored_file ( id_monitored_file BIGINT AUTO_INCREMENT PRIMARY KEY , created TIMESTAMP NOT NULL , found_at TIMESTAMP NOT NULL , file_path VARCHAR(512) NOT NULL , file_name VARCHAR(128) NOT NULL , file_size BIGINT NOT NULL)
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4161 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE imported_file_associations ( id_imported_file_associations BIGINT AUTO_INCREMENT PRIMARY KEY , md5_value VARCHAR(128) NOT NULL , id_genome_dataset BIGINT REFERENCES genome_dataset )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4162 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (5)
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 56Stage 6 of 39 done
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4164 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE workflow_visualization ( id_workflow_visualization BIGINT AUTO_INCREMENT PRIMARY KEY , visualization_name VARCHAR(100) UNIQUE , visualization_xml CLOB NOT NULL )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4166 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE workflow_template ( id_workflow_template BIGINT AUTO_INCREMENT PRIMARY KEY, experiment_type VARCHAR(64) NOT NULL, workflow_name VARCHAR(512) NOT NULL UNIQUE, workflow_xml CLOB NOT NULL, id_workflow_visualization BIGINT , status_type VARCHAR(64) NOT NULL , active_type VARCHAR(64) NOT NULL , CONSTRAINT fk_workflow_visualization FOREIGN KEY (id_workflow_visualization) REFERENCES workflow_visualization (id_workflow_visualization) )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4167 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE rng_workflow ( id_workflow BIGINT AUTO_INCREMENT PRIMARY KEY, name VARCHAR(512) , description VARCHAR(256) , workflow CLOB , id_workflow_template BIGINT , dye_mapping VARCHAR(128) , is_complete SMALLINT NOT NULL , experiment_type VARCHAR(64) NOT NULL , array_name VARCHAR(256) , created_at TIMESTAMP NOT NULL DEFAULT current_timestamp , CONSTRAINT fk_workflow_template FOREIGN KEY (id_workflow_template) REFERENCES workflow_template (id_workflow_template) )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4169 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE slide_design ( id_slide_design BIGINT AUTO_INCREMENT PRIMARY KEY , marketing_format_name VARCHAR(128) , slide_barcode VARCHAR(128) NOT NULL , id_filetoken_ncd BIGINT , is_local_alignment_used SMALLINT NOT NULL , is_old SMALLINT NOT NULL DEFAULT 0 , alignment_border_in_pixels SMALLINT NOT NULL , is_bursting_performed SMALLINT NOT NULL , feature_size_in_microns FLOAT NOT NULL , created_at TIMESTAMP NOT NULL DEFAULT current_timestamp , CONSTRAINT fk_filetoken_ncd FOREIGN KEY (id_filetoken_ncd) REFERENCES filetoken (id_filetoken) )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4174 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE array_design ( id_array_design BIGINT AUTO_INCREMENT PRIMARY KEY, well_name VARCHAR(128) NOT NULL , experiment_type VARCHAR(64) NOT NULL , id_filetoken_ndf BIGINT , id_filetoken_pos BIGINT , id_slide_design BIGINT NOT NULL , id_genome_assembly BIGINT NOT NULL , created_at TIMESTAMP NOT NULL DEFAULT current_timestamp , CONSTRAINT fk_slide_design FOREIGN KEY (id_slide_design) REFERENCES slide_design (id_slide_design) , CONSTRAINT fk_genome_assembly FOREIGN KEY (id_genome_assembly) REFERENCES genome_assembly (id_genome_assembly) , CONSTRAINT fk_filetoken_ndf FOREIGN KEY (id_filetoken_ndf) REFERENCES filetoken (id_filetoken) , CONSTRAINT fk_filetoken_pos FOREIGN KEY (id_filetoken_pos) REFERENCES filetoken (id_filetoken) )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4179 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE slide_result ( id_slide_result BIGINT AUTO_INCREMENT PRIMARY KEY, slide_result_name VARCHAR(128), slide_scan_tag VARCHAR(128) , slide_result_description VARCHAR(128), id_filetoken_cy3tiff BIGINT , id_filetoken_cy5tiff BIGINT , id_filetoken_twochanneltiff BIGINT , id_slide_design BIGINT NOT NULL , scanned_date_cy3tiff TIMESTAMP , scanned_date_cy5tiff TIMESTAMP , scanned_date_twochanneltiff TIMESTAMP , cy3_slide_status VARCHAR(24) , cy5_slide_status VARCHAR(24) , serialized_slide_result BLOB NOT NULL, created_at TIMESTAMP NOT NULL DEFAULT current_timestamp , CONSTRAINT fk_slide_design1 FOREIGN KEY (id_slide_design) REFERENCES slide_design (id_slide_design) , CONSTRAINT fk_filetoken_cy3tiff1 FOREIGN KEY (id_filetoken_cy3tiff) REFERENCES filetoken (id_filetoken) , CONSTRAINT fk_filetoken_cy5tiff1 FOREIGN KEY (id_filetoken_cy5tiff) REFERENCES filetoken (id_filetoken) , CONSTRAINT fk_filetoken_twochanneltiff1 FOREIGN KEY (id_filetoken_twochanneltiff) REFERENCES filetoken (id_filetoken) )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4183 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE array_result ( id_array_result BIGINT AUTO_INCREMENT PRIMARY KEY, array_result_name VARCHAR(128), array_result_description VARCHAR(128), dye_mapping VARCHAR(128) NOT NULL, is_analysis_disabled SMALLINT NOT NULL DEFAULT 0 , id_slide_result BIGINT NOT NULL , id_array_design BIGINT NOT NULL , id_default_workflow BIGINT , created_at TIMESTAMP NOT NULL DEFAULT current_timestamp , CONSTRAINT fk_slide_result FOREIGN KEY (id_slide_result) REFERENCES slide_result (id_slide_result) , CONSTRAINT fk_array_design FOREIGN KEY (id_array_design) REFERENCES array_design (id_array_design) , CONSTRAINT fk_rng_workflow FOREIGN KEY (id_default_workflow) REFERENCES rng_workflow (id_workflow) )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4197 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE array_tiff ( id_array_tiff BIGINT AUTO_INCREMENT PRIMARY KEY , id_array_tiff_filetoken BIGINT , id_thumbnail_filetoken BIGINT REFERENCES filetoken , id_thumbnail_upper_left_filetoken BIGINT , id_thumbnail_upper_right_filetoken BIGINT , id_thumbnail_lower_left_filetoken BIGINT , id_thumbnail_lower_right_filetoken BIGINT , id_alignment_filetoken BIGINT , precision_score FLOAT , alignment_status VARCHAR(64) , CONSTRAINT fk_at_af FOREIGN KEY (id_alignment_filetoken) REFERENCES filetoken (id_filetoken) , CONSTRAINT fk_at_ft FOREIGN KEY (id_array_tiff_filetoken) REFERENCES filetoken (id_filetoken) , CONSTRAINT fk_at_ft_ul FOREIGN KEY (id_thumbnail_upper_left_filetoken) REFERENCES filetoken (id_filetoken) , CONSTRAINT fk_at_ft_ur FOREIGN KEY (id_thumbnail_upper_right_filetoken) REFERENCES filetoken (id_filetoken) , CONSTRAINT fk_at_ft_ll FOREIGN KEY (id_thumbnail_lower_left_filetoken) REFERENCES filetoken (id_filetoken) , CONSTRAINT fk_at_ft_lr FOREIGN KEY (id_thumbnail_lower_right_filetoken) REFERENCES filetoken (id_filetoken) )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4205 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE labeled_sample ( id_labeled_sample BIGINT AUTO_INCREMENT PRIMARY KEY, dye VARCHAR(16) , CHECK(dye in ('Cy3','Cy5')), sample_id VARCHAR(128) NOT NULL, description VARCHAR(128) NOT NULL, dna_amount VARCHAR(64) NOT NULL, tissue VARCHAR(64) NOT NULL, bursting_failure VARCHAR(64) NOT NULL, alignment_failure VARCHAR(64) NOT NULL, extraction_failure VARCHAR(64) NOT NULL, storing_failure VARCHAR(64) NOT NULL, id_organism BIGINT REFERENCES organism , id_filetoken_xys BIGINT , id_array_result BIGINT NOT NULL , id_array_tiff BIGINT , id_genome_dataset BIGINT REFERENCES genome_dataset , is_manually_aligned SMALLINT DEFAULT 0 , created_at TIMESTAMP NOT NULL DEFAULT current_timestamp , CONSTRAINT fk_filetoken_xys FOREIGN KEY (id_filetoken_xys) REFERENCES filetoken (id_filetoken) , CONSTRAINT fk_array_result FOREIGN KEY (id_array_result) REFERENCES array_result (id_array_result) , CONSTRAINT fk_array_tiff FOREIGN KEY (id_array_tiff) REFERENCES array_tiff (id_array_tiff) )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4209 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE rng_workflow_data ( id_workflow_data BIGINT AUTO_INCREMENT PRIMARY KEY, id_workflow BIGINT , original_output_dockbinding CLOB NOT NULL , next_input_dockbinding CLOB NOT NULL , datatype VARCHAR(128) NOT NULL , id_genome_dataset BIGINT REFERENCES genome_dataset , id_labeled_sample BIGINT REFERENCES labeled_sample , id_array_tiff_during_analysis BIGINT REFERENCES array_tiff , CONSTRAINT fk_workflow FOREIGN KEY (id_workflow) REFERENCES rng_workflow (id_workflow) )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4210 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE setting ( id_setting BIGINT AUTO_INCREMENT PRIMARY KEY, setting_type VARCHAR(64) NOT NULL, setting_name VARCHAR(128) NOT NULL, setting_value CLOB NOT NULL)
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4211 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (6)
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 57Stage 7 of 39 done
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4212 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE file_export ( id_file_export BIGINT AUTO_INCREMENT PRIMARY KEY , filename VARCHAR(128) NOT NULL , filesize_in_kb BIGINT NOT NULL , absolute_path VARCHAR(512) NOT NULL , created_at TIMESTAMP NOT NULL )
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 4213 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (7)
2014-02-13 11:48:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 58Stage 8 of 39 done
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 5551 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (8)
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 59Stage 9 of 39 done
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 5554 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE genome_assembly_sequence ( id_genome_assembly_sequence BIGINT AUTO_INCREMENT PRIMARY KEY , id_filetoken_fasta BIGINT NOT NULL, chromosome VARCHAR(512) NOT NULL , id_genome_assembly BIGINT NOT NULL , CONSTRAINT fk_filetoken_genome_assembly_sequence FOREIGN KEY (id_filetoken_fasta) REFERENCES filetoken (id_filetoken) , CONSTRAINT fk_genome_assembly_genome_assembly_sequence FOREIGN KEY (id_genome_assembly) REFERENCES genome_assembly (id_genome_assembly) )
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 5556 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (9)
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 60Stage 10 of 39 done
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 5559 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE segmntstats ( id_segmntstats BIGINT AUTO_INCREMENT PRIMARY KEY, id_array_result BIGINT NOT NULL , id_workflow BIGINT NOT NULL , xshift DOUBLE NOT NULL , mad1dr DOUBLE NOT NULL , CONSTRAINT fk_workflow_segmntstats FOREIGN KEY (id_workflow) REFERENCES rng_workflow (id_workflow) , CONSTRAINT fk_array_result_segmentstats FOREIGN KEY (id_array_result) REFERENCES array_result (id_array_result) )
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 5560 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (10)
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 61Stage 11 of 39 done
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 5561 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE genome_dataset_for_design ( id_genome_dataset_for_design BIGINT AUTO_INCREMENT PRIMARY KEY , id_slide_design BIGINT NOT NULL REFERENCES slide_design( id_slide_design ) , id_genome_dataset BIGINT NOT NULL REFERENCES genome_dataset( id_genome_dataset ) )
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 5562 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (11)
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 62Stage 12 of 39 done
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 5563 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE submitted_jobs ( job_id BIGINT NOT NULL PRIMARY KEY, serialized_job_file_token_id BIGINT NOT NULL)
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 5564 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (12)
2014-02-13 11:48:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 63Stage 13 of 39 done
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 6766 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE workflow_template ADD REQUIRED_INPUT_TYPE VARCHAR(64) NOT NULL default 'TEST_AND_REFERENCE'
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 6767 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (13)
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 64Stage 14 of 39 done
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 6768 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE stc (id_stc BIGINT AUTO_INCREMENT PRIMARY KEY, id_stc_set BIGINT NOT NULL, stc BIGINT NOT NULL)
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 6912 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE array_result ADD expected_id_stc_set BIGINT
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 6989 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE array_result ADD actual_id_stc_set BIGINT
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 6992 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE VIEW vw_stc AS SELECT DISTINCT id_stc_set,(SELECT GROUP_CONCAT(stc SEPARATOR ',') FROM stc WHERE id_stc_set=top.id_stc_set) AS stcs FROM stc AS top UNION SELECT DISTINCT expected_id_stc_set, '' AS stcs FROM array_result WHERE expected_id_stc_set NOT IN (SELECT DISTINCT ID_STC_SET FROM STC) UNION SELECT DISTINCT actual_id_stc_set, '' AS stcs FROM array_result WHERE actual_id_stc_set NOT IN (SELECT DISTINCT ID_STC_SET FROM STC) ORDER BY id_stc_set
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 6996 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (14)
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 65Stage 15 of 39 done
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 6998 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (16)
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 66Stage 16 of 39 done
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7000 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE decoded_number ( id_decoded_number BIGINT AUTO_INCREMENT PRIMARY KEY , id_array_tiff BIGINT NOT NULL , series_name VARCHAR(50) NOT NULL , name VARCHAR(50) NOT NULL , value VARCHAR(50) NOT NULL , created_at TIMESTAMP NOT NULL DEFAULT current_timestamp , CONSTRAINT fk_array_tiff_decoded_num FOREIGN KEY (id_array_tiff) REFERENCES array_tiff (id_array_tiff) , CONSTRAINT unq_id_array_tiff_name UNIQUE (id_array_tiff,name) )
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7001 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (17)
2014-02-13 11:48:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 67Stage 17 of 39 done
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7086 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE array_tiff ADD COLUMN alignment_outcome VARCHAR(50)
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7088 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: UPDATE array_tiff SET alignment_outcome = 'NONE'
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7090 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER table array_tiff ALTER COLUMN alignment_outcome SET NOT NULL
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7092 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (18)
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 68Stage 18 of 39 done
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7093 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE quality_control_metrics ( id_quality_control BIGINT AUTO_INCREMENT PRIMARY KEY , id_labeled_sample BIGINT NOT NULL , slope DOUBLE , inter_quartile_density DOUBLE , noise DOUBLE , created_at TIMESTAMP NOT NULL DEFAULT current_timestamp )
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7094 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (19)
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 69Stage 19 of 39 done
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7097 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE activity_status ( id_activity_status BIGINT AUTO_INCREMENT PRIMARY KEY , activity_status_detail_filetoken BIGINT , description VARCHAR(512) , job_type VARCHAR(128) , status VARCHAR(128) , percent_complete DOUBLE , date_submitted TIMESTAMP , created_at TIMESTAMP NOT NULL DEFAULT current_timestamp , CONSTRAINT fk_activity_status_detail_filetoken FOREIGN KEY (activity_status_detail_filetoken) REFERENCES filetoken (id_filetoken) )
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7100 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (21)
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 70Stage 20 of 39 done
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7149 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE slide_result ADD COLUMN id_filetoken_cy3tiff_checksum BIGINT
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7197 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE slide_result ADD COLUMN id_filetoken_cy5tiff_checksum BIGINT
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7258 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE slide_result ADD COLUMN id_filetoken_twochanneltiff_checksum BIGINT
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7259 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER table slide_result add CONSTRAINT fk_filetoken_cy3tiff_chksum1 FOREIGN KEY (id_filetoken_cy3tiff_checksum) REFERENCES filetoken (id_filetoken)
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7260 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE slide_result ADD CONSTRAINT fk_filetoken_cy5tiff_chksum1 FOREIGN KEY ( id_filetoken_cy3tiff_checksum ) REFERENCES FILETOKEN ( id_filetoken )
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7261 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE slide_result ADD CONSTRAINT fk_filetoken_twochanneltiff_chksum1 FOREIGN KEY ( id_filetoken_twochanneltiff_checksum ) REFERENCES FILETOKEN ( id_filetoken )
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7262 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (22)
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 71Stage 21 of 39 done
2014-02-13 11:48:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 7842 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE workflow_template ADD COLUMN WORKFLOW_IDENTIFIER VARCHAR(512)
2014-02-13 11:48:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 8577 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE workflow_template ADD COLUMN WORKFLOW_VERSION DOUBLE
2014-02-13 11:48:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 8580 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (25)
2014-02-13 11:48:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 72Stage 22 of 39 done
2014-02-13 11:48:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 8583 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 8769 [main] DEBUG com.nimblegen.deva.dbmigrate.rng.M_0026_insert_loh_alter_cgh_workflows - test name: LOH-SNP-WORKFLOW-TEST
2014-02-13 11:48:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 9003 [main] DEBUG com.nimblegen.deva.dbmigrate.rng.M_0026_insert_loh_alter_cgh_workflows - reference name: LOH-SNP-WORKFLOW-TEST
2014-02-13 11:48:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 9693 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 10322 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 10697 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11010 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11207 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11359 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11539 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11761 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11777 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (26)
2014-02-13 11:48:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 73Stage 23 of 39 done
2014-02-13 11:48:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 12081 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (27)
2014-02-13 11:48:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 74Stage 24 of 39 done
2014-02-13 11:48:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 12181 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (28)
2014-02-13 11:48:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 75Stage 25 of 39 done
2014-02-13 11:48:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 12196 [main] DEBUG com.nimblegen.deva.dbmigrate.rng.M_0029_update_workflow_visualizations_for_versioning - Updating workflow visualization XML for visualization name 'DNA-METHYLATION-WORKFLOW'.
2014-02-13 11:48:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 12665 [main] DEBUG com.nimblegen.deva.dbmigrate.rng.M_0029_update_workflow_visualizations_for_versioning - Updating workflow visualization XML for visualization name 'CHIP-CHIP-WORKFLOW'.
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13103 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (29)
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 76Stage 26 of 39 done
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13104 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (30)
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 77Stage 27 of 39 done
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13274 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE array_design ADD COLUMN id_filetoken_gc_statistics BIGINT
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13275 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE array_design ADD CONSTRAINT id_filetoken_gc_statistics FOREIGN KEY ( id_filetoken_gc_statistics ) REFERENCES FILETOKEN ( id_filetoken )
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13276 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (31)
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 78Stage 28 of 39 done
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13278 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: select 1 from dual
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13279 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (32)
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 79Stage 29 of 39 done
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13391 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: DROP TABLE SUBMITTED_JOBS
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13394 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE SUBMITTED_JOBS ( UNIQUE_JOB_ID VARCHAR(100) PRIMARY KEY , SERIALIZED_JOB_FILE_TOKEN_ID BIGINT NOT NULL , ID_ACTIVITY_STATUS BIGINT , CREATED_AT TIMESTAMP NOT NULL DEFAULT current_timestamp , CONSTRAINT FK_SERIALIZED_JOB_FILE_TOKEN_ID FOREIGN KEY (SERIALIZED_JOB_FILE_TOKEN_ID) REFERENCES FILETOKEN (ID_FILETOKEN) , CONSTRAINT FK_ID_ACTIVITY_STATUS FOREIGN KEY (ID_ACTIVITY_STATUS) REFERENCES ACTIVITY_STATUS (ID_ACTIVITY_STATUS) )
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13395 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (34)
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 80Stage 30 of 39 done
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13434 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (35)
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 81Stage 31 of 39 done
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13434 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13673 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (1200)
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 82Stage 32 of 39 done
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13680 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13812 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 13946 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 14070 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 14228 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (1204)
2014-02-13 11:48:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 83Stage 33 of 39 done
2014-02-13 11:48:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 17077 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE workflow_template ADD COLUMN modified_outside_of_deva VARCHAR(64) default 'FALSE' not null
2014-02-13 11:48:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 17078 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (1206)
2014-02-13 11:48:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 84Stage 34 of 39 done
2014-02-13 11:48:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 17086 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 17448 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 17894 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 18255 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 18560 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 18807 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 18975 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19190 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19334 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19472 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (1208)
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 85Stage 35 of 39 done
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19473 [main] DEBUG com.nimblegen.deva.dbmigrate.rng.M_1210_remove_unused_genome_data - Genome dataset ids used by labeled samples: []
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19473 [main] DEBUG com.nimblegen.deva.dbmigrate.rng.M_1210_remove_unused_genome_data - Number of xys token id: 0
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19473 [main] DEBUG com.nimblegen.deva.dbmigrate.rng.M_1210_remove_unused_genome_data - Number of position key file token ids: 0
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19474 [main] DEBUG com.nimblegen.deva.dbmigrate.rng.M_1210_remove_unused_genome_data - Orphaned genome dataset ids: []
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19476 [main] DEBUG com.nimblegen.deva.dbmigrate.rng.M_1210_remove_unused_genome_data - Orphaned xys file token ids: []
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19477 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (1210)
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 86Stage 36 of 39 done
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19478 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE labeled_sample drop constraint FK_FILETOKEN_XYS;
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19604 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: alter table labeled_sample drop column id_filetoken_xys;
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19701 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: alter table labeled_sample drop column storing_failure;
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19804 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: alter table labeled_sample drop column extraction_failure;
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19805 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE labeled_sample ALTER COLUMN bursting_failure RENAME TO bursting_status;
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19910 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER table array_tiff DROP COLUMN alignment_status
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19912 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE labeled_sample ALTER COLUMN alignment_failure RENAME TO alignment_status;
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 19912 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: alter table labeled_sample drop constraint CONSTRAINT_16724;
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20010 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: alter table labeled_sample drop column id_genome_dataset;
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20012 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (1212)
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 87Stage 37 of 39 done
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20013 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: DROP VIEW vw_chromosome_dataset IF EXISTS;
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20013 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: DROP VIEW vw_gds_ga IF EXISTS;
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20013 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: DROP VIEW vw_genome_dataset IF EXISTS;
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20014 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE CHROMOSOME_DATASET RENAME TO CHROMOSOME_DATASET_OLD;
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20017 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE CHROMOSOME_DATASET ( ID_CHROMOSOME_DATASET bigint AUTO_INCREMENT PRIMARY KEY , ID_FILETOKEN bigint DEFAULT NULL, ID_ATTRIBUTES_FILETOKEN bigint DEFAULT NULL, CHROMOSOME_NAME varchar(64) NOT NULL, NUM_RECORDS bigint NOT NULL, MIN_VALUE FLOAT, FIRST_QUARTILE FLOAT, MEDIAN FLOAT, THIRD_QUARTILE FLOAT, MAX_VALUE FLOAT, MIN_POSITION bigint NOT NULL, MAX_POSITION bigint NOT NULL, STORED_AT timestamp DEFAULT CURRENT_TIMESTAMP() NOT NULL, RECORD_START_INDEX BIGINT NOT NULL DEFAULT 0, ID_GENOME_DATASET BIGINT NOT NULL, ID_FILETOKEN_LUCENE_ANCHOR BIGINT, CONSTRAINT FK_ID_FILETOKEN FOREIGN KEY (ID_FILETOKEN) REFERENCES FILETOKEN (ID_FILETOKEN), CONSTRAINT FK_ID_ATTRIBUTES_FILETOKEN FOREIGN KEY (ID_ATTRIBUTES_FILETOKEN) REFERENCES FILETOKEN (ID_FILETOKEN), CONSTRAINT FK_ID_GENOME_DATASET FOREIGN KEY (ID_GENOME_DATASET) REFERENCES GENOME_DATASET (ID_GENOME_DATASET), );
2014-02-13 11:48:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20020 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: INSERT INTO CHROMOSOME_DATASET ( ID_CHROMOSOME_DATASET,ID_FILETOKEN,ID_ATTRIBUTES_FILETOKEN, CHROMOSOME_NAME,NUM_RECORDS,MIN_VALUE, FIRST_QUARTILE,MEDIAN,THIRD_QUARTILE, MAX_VALUE,MIN_POSITION,MAX_POSITION, STORED_AT,ID_GENOME_DATASET,ID_FILETOKEN_LUCENE_ANCHOR) SELECT cdf.ID_CHROMOSOME_DATA_FILE,cdf.ID_FILETOKEN,cdf.ID_ATTRIBUTES_FILETOKEN, CHROMOSOME_NAME,NUM_RECORDS,MIN_VALUE, FIRST_QUARTILE,MEDIAN,THIRD_QUARTILE, MAX_VALUE,MIN_POSITION,MAX_POSITION, STORED_AT, cd.ID_GENOME_DATASET,cd.ID_FILETOKEN_LUCENE_ANCHOR FROM chromosome_data_file cdf, CHROMOSOME_DATASET_OLD cd WHERE cdf.id_chromosome_data_file=cd.id_chromosome_data_file;
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20106 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: drop table CHROMOSOME_DATASET_OLD;
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20196 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: drop table chromosome_data_file;
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20325 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE genome_dataset ADD id_filetoken_lucene_anchor BIGINT NULL DEFAULT NULL;
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20437 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE genome_dataset ADD id_filetoken_data BIGINT DEFAULT NULL;
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20534 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: ALTER TABLE genome_dataset ADD id_filetoken_attributes BIGINT DEFAULT NULL;
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20536 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE VIEW vw_chromosome_dataset AS SELECT cds.id_chromosome_dataset , cds.id_genome_dataset , cds.id_filetoken_lucene_anchor , cds.id_filetoken_lucene_anchor AS lucene_anchor_ft_id , cds.chromosome_name , cds.num_records AS data_file_num_records , cds.min_value , cds.first_quartile , cds.median , cds.third_quartile , cds.max_value , cds.min_position , cds.max_position , cds.record_start_index , cds.num_records , cds.id_filetoken AS data_filetoken_id , cds.id_attributes_filetoken AS attributes_filetoken_id FROM chromosome_dataset AS cds
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20543 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE VIEW vw_gds_ga AS SELECT id_genome_dataset , original_file_name AS gds_original_filename , data_type AS gds_data_type , is_import AS gds_is_import , stored_at AS gds_stored_at , is_annotation AS gds_is_annotation , id_filetoken_lucene_anchor AS genome_dataset_lucene_anchor_ft_id , id_filetoken_data AS genome_dataset_data_ft_id , id_filetoken_attributes AS genome_dataset_attributes_ft_id , vw_genome_assembly.id_genome_assembly , genome_assembly_name , accession_identifier , genome_assembly_is_user_defined , genome_assembly_created_at , id_genome_source , genome_source_description , genome_source_name , id_organism , organism_is_user_defined , scientific_name , common_name , ncbi_taxon_id FROM genome_dataset INNER JOIN vw_genome_assembly ON genome_dataset.id_genome_assembly = vw_genome_assembly.id_genome_assembly
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20549 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE VIEW vw_genome_dataset AS SELECT gds.id_genome_dataset , gds.gds_original_filename , gds.gds_data_type , gds.gds_is_import , gds.gds_is_annotation , gds.gds_stored_at , gds.id_genome_assembly , gds.genome_assembly_name , gds.accession_identifier , gds.genome_assembly_created_at , gds.genome_assembly_is_user_defined , gds.id_genome_source , gds.genome_source_description , gds.genome_source_name , gds.id_organism , gds.scientific_name , gds.common_name , gds.ncbi_taxon_id , gds.organism_is_user_defined , cds.id_chromosome_dataset , cds.chromosome_name , coalesce(cds.id_filetoken, gds.genome_dataset_data_ft_id) AS data_filetoken_id , coalesce(cds.id_attributes_filetoken, gds.genome_dataset_attributes_ft_id) AS attributes_filetoken_id , cds.min_value , cds.first_quartile , cds.median , cds.third_quartile , cds.max_value , cds.min_position , cds.max_position , cds.record_start_index , cds.num_records , cds.id_filetoken_lucene_anchor AS chromosome_dataset_lucene_anchor_ft_id , gds.genome_dataset_lucene_anchor_ft_id AS genome_dataset_lucene_anchor_ft_id , gds.genome_dataset_data_ft_id , gds.genome_dataset_attributes_ft_id FROM vw_gds_ga as gds LEFT OUTER JOIN chromosome_dataset AS cds ON gds.id_genome_dataset = cds.id_genome_dataset
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20551 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (1218)
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 88Stage 38 of 39 done
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20552 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE TABLE GENOME_DATASET_CACHE ( ID_GENOME_DATASET_CACHE bigint AUTO_INCREMENT PRIMARY KEY NOT NULL, CACHE_KEY bigint NOT NULL, ID_GENOME_DATASET bigint, CREATED_AT timestamp DEFAULT CURRENT_TIMESTAMP() NOT NULL, CONSTRAINT FK_GDS_CACHE FOREIGN KEY (ID_GENOME_DATASET) REFERENCES GENOME_DATASET(ID_GENOME_DATASET) ON DELETE CASCADE );
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20553 [main] DEBUG com.nimblegen.deva.dbmigrate.Migration - QUERY: CREATE UNIQUE INDEX GDS_CACHE_IDX01 ON GENOME_DATASET_CACHE(CACHE_KEY, ID_GENOME_DATASET);
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20554 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (1225)
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 90Stage 39 of 39 done
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20560 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20717 [main] DEBUG com.nimblegen.common.util.versionidentifier.VersionIdentifierUtil - convertVersionIdentifierToDouble for '1.2.1' returning 1.21
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20858 [main] DEBUG com.nimblegen.deva.dbmigrate.MigrationWorker - QUERY (rng): INSERT INTO version_info ( version ) VALUES (1226)
2014-02-13 11:48:38,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:38 AM com.nimblegen.deva.dbmigrate.Migrator doMigrations
2014-02-13 11:48:38,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Updated to version 1226
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20903 [main] DEBUG com.nimblegen.common.services.ServiceProvider - Temporary working directory cleared (total time:44ms)
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20937 [main] DEBUG com.nimblegen.deva.common.configuration.DevaConfigurationUtil - A version.properties file has been created with project.type=DEVA and project.version=1.2.1
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Finished driving progress bar.
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Removed an expired listener.
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Progress bar being left intact for further processing.
2014-02-13 11:48:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 100Database installed
2014-02-13 11:48:38,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 20937 [main] INFO com.nimblegen.deva.dbmigrate.RunDBMigrate - runDbMigrate completed.
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, Error StreamLogger 568699335 ending.
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, StreamWorker 1871045134 ending.
2014-02-13 11:48:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.CombinedLauncher, DBMigrate ran successfully.
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.CombinedLauncher, DBMigrate is finished. Now launching DEVA...
2014-02-13 11:48:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.CombinedLauncher, Command: java -Xms7150m -Xmx7150m -Dsun.java2d.opengl=false -Dsun.java2d.nodraw=false -Dsun.java2d.d3d=false -Duser.language=en -Duser.region=US -cp C:\Deva\DEVA.jar com.nimblegen.deva.app.RunDevaApp
2014-02-13 11:48:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.CombinedLauncher, Project directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA
2014-02-13 11:48:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.CombinedLauncher, Working directory: C:\Deva
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, StreamWorker 1658284560 starting.
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, Error StreamLogger 288543739 starting.
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.CombinedLauncher, CombinedLauncher ending.
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:39,709 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:39,709 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:39,709 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/C:/Deva/DEVA.jar!/logback.xml]
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:39,720 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@4c5e176f - URL [jar:file:/C:/Deva/DEVA.jar!/logback.xml] is not of type file
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:39,845 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:39,848 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [STDOUT]
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:39,878 |-INFO in ch.qos.logback.classic.joran.action.LevelAction - com.nimblegen level set to DEBUG
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:39,878 |-INFO in ch.qos.logback.classic.joran.action.LevelAction - com.nimblegen.common.jobcontroller level set to ERROR
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:39,878 |-INFO in ch.qos.logback.classic.joran.action.LevelAction - ROOT level set to ERROR
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:39,879 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [STDOUT] to Logger[ROOT]
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 11:48:39,880 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:48:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 250 [main] DEBUG com.nimblegen.common.services.ServiceProvider - Starting H2 in EMBEDDED mode.
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:39 AM org.springframework.context.support.AbstractApplicationContext prepareRefresh
2014-02-13 11:48:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Refreshing org.springframework.context.support.ClassPathXmlApplicationContext@72e6f7d2: startup date [Thu Feb 13 11:48:39 PST 2014]; root of context hierarchy
2014-02-13 11:48:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:40 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
2014-02-13 11:48:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Loading XML bean definitions from class path resource [com/nimblegen/common/spring/services_h2_embedded.xml]
2014-02-13 11:48:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:40 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
2014-02-13 11:48:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Loading XML bean definitions from class path resource [com/nimblegen/common/spring/services.xml]
2014-02-13 11:48:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:40 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
2014-02-13 11:48:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Loading XML bean definitions from class path resource [com/nimblegen/common/spring/daos.xml]
2014-02-13 11:48:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:40 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
2014-02-13 11:48:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Loading XML bean definitions from URL [file:Z:/users/c/csather/TO_BE_REVIEWED_SCANS/02132014/ClaireOlson/DEVA/config/sys_config/db/h2-embedded-datasource.xml]
2014-02-13 11:48:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:40 AM org.springframework.beans.factory.support.DefaultListableBeanFactory preInstantiateSingletons
2014-02-13 11:48:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) INFO: Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@35cf7491: defining beans [org.springframework.context.annotation.internalConfigurationAnnotationProcessor,org.springframework.context.annotation.internalAutowiredAnnotationProcessor,org.springframework.context.annotation.internalRequiredAnnotationProcessor,org.springframework.context.annotation.internalCommonAnnotationProcessor,fileTokenFactory,fileTokenDao,organismFactory,organismDao,genomeSourceFactory,genomeSourceDao,genomeAssyFactory,genomeAssyDao,sampleFactory,sampleDao,arrayDesignFactory,arrayDesignDao,arrayResultFactory,arrayResultDao,sampleTrackingControlSetFactory,sampleTrackingControlSetDao,labeledSampleFactory,labeledSampleDao,slideDesignFactory,slideDesignDao,slideResultFactory,slideResultDao,arrayTiffFactory,arrayTiffDao,decodedNumberFactory,decodedNumberDao,analysisWorkflowFactory,analysisWorkflowDao,workflowDataFactory,workflowDataDao,monitoredFileFactory,monitoredFileDao,importedFileAssociationsDao,genomeAssemblySequenceFactory,genomeAssemblySequenceDao,settingFactory,settingDao,workflowTemplateFactory,workflowTemplateDao,visualizationFactory,visualizationDao,genomeDatasetDboFactory,genomeDatasetDao,valuedGenomeDatasetAttributesDao,genomeDatasetCacheDboFactory,genomeDatasetCacheDao,exportFactory,exportDao,containerGenomeDatasetDao,segmntStatsFactory,segmntStatsDao,designAnnotationFactory,designAnnotationDao,jobsRecoveryDao,activityStatusDao,qualityControlReportFactory,qualityControlReportDao,genomeDatasetPioService,slideService,analysisWorkflowService,workflowTransportService,workflowTemplateService,visualizationService,qualityControlReportService,snpHeterozygosityFrequencyService,genomeDatasetCacheService,fileMoverFactory,fileService,filePioService,genomeAssyService,genomeAssyPioService,applicationConfiguration,systemConfiguration,designAnnotationService,devaArchiveImportService,genomeAssemblySequenceService,sequenceStatsService,systemConfigurationService,dataWriterFactory,xysExporter,gffDataExporter,jobsRecoveryService,trackSettingsService,paneSettingsService,plotSettingsService,genomeAssemblyController,tiffImportMonitor,manualAlignmentController,tiffImportController,slidesTableController,genomeDatasetController,slideResultSearchController,arrayResultSearchController,exportService,jobStatusDetailController,propertyConfigurer,h2datasource,datasource,dialect,template]; root of factory hierarchy
2014-02-13 11:48:41,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:41 AM java.util.prefs.WindowsPreferences
2014-02-13 11:48:41,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5.
2014-02-13 11:48:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2007 [main] DEBUG com.nimblegen.common.services.ServiceProvider - Temporary working directory cleared (total time:53ms)
2014-02-13 11:48:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337 [main] DEBUG com.nimblegen.deva.common.jobservice.JobService - job service resource limit for ESTIMATED_MEMORY_IN_KB is set to 6800973.
2014-02-13 11:48:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 10Startup has begun
2014-02-13 11:48:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 25Fonts are loaded
2014-02-13 11:48:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 55SlideMainTabPanel initialized
2014-02-13 11:48:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 60TemplateTabPanel finished
2014-02-13 11:48:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 70AnalysisPanel finished
2014-02-13 11:48:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 75AnnotationPanel finished
2014-02-13 11:48:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 80ExternalDataPanel finished
2014-02-13 11:48:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 85ExportPanel finished
2014-02-13 11:48:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 95JobsPanel finished
2014-02-13 11:48:44,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 5029 [AWT-EventQueue-0] INFO com.nimblegen.common.app.guicomponents.AppMainFrame - Roche NimbleGen, Inc. DEVA 1.2.1 2012-0426-1812-3714
2014-02-13 11:48:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 5047 [AWT-EventQueue-0] DEBUG com.nimblegen.common.app.guicomponents.AppMainFrame - frame size from persistence is maximized:true width:1024.0 height:768.0
2014-02-13 11:48:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 97MainFrame is finished
2014-02-13 11:48:45,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:45 AM org.jdesktop.application.LocalStorage getId
2014-02-13 11:48:45,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) WARNING: unspecified resource Application.id using RunDevaApp
2014-02-13 11:48:45,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Feb 13, 2014 11:48:45 AM org.jdesktop.application.LocalStorage getId
2014-02-13 11:48:45,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) WARNING: unspecified resource Application.vendorId using UnknownApplicationVendor
2014-02-13 11:48:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Finished driving progress bar.
2014-02-13 11:48:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Removed an expired listener.
2014-02-13 11:48:45,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Closing progress bar.
2014-02-13 11:48:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 100Startup complete
2014-02-13 11:48:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 5647 [AWT-EventQueue-0] DEBUG com.nimblegen.deva.app.RunDevaApp$1 - Project upgrade argument has been set to: false
2014-02-13 11:51:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 159416 [AWT-EventQueue-0] DEBUG com.nimblegen.deva.app.guicomponents.dialog.ManualDesignArchiveAndTiffImportDialog - creating design import worker in event handler for DESIGN ONLY.
2014-02-13 11:51:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 159427 [SwingWorker-pool-5-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - new Attempting slide import, barcode = 546409.
2014-02-13 11:51:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 160008 [SwingWorker-pool-5-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - new Attempting slide import, barcode = 558216.
2014-02-13 11:51:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 160387 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Importing NCD file: Z:\NimbleScanFiles\121101_OysterV9_MG_meth_HX3.ncd
2014-02-13 11:51:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 160665 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Importing NDF file: Z:\NimbleScanFiles\121101_OysterV9_MG_meth.ndf
2014-02-13 11:51:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 160830 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Importing POS file: Z:\NimbleScanFiles\121101_OysterV9_MG_meth.pos
2014-02-13 11:51:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 185702 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ControlProbeExtractor - Non-experimental probes extracted.
2014-02-13 11:51:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187061 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - Creating new slide result.
2014-02-13 11:51:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187063 [Directory Monitor] DEBUG com.nimblegen.common.services.controllers.TiffImportController - Starting import of TIFF file:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3_635.tif
2014-02-13 11:51:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187083 [SwingWorker-pool-5-thread-2] DEBUG com.nimblegen.common.services.controllers.TiffImportController$TiffImporter$1 - Importing TIFF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3_635.tif
2014-02-13 11:51:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187093 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - saving new STC set (STC set id = 1)
2014-02-13 11:51:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187098 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - saving new STC set (STC set id = 2)
2014-02-13 11:51:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187105 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - saving new STC set (STC set id = 3)
2014-02-13 11:51:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187107 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - saving new STC set (STC set id = 4)
2014-02-13 11:51:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187111 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - saving new STC set (STC set id = 5)
2014-02-13 11:51:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187129 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - saving new STC set (STC set id = 6)
2014-02-13 11:51:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187160 [Directory Monitor] DEBUG com.nimblegen.common.services.controllers.TiffImportController - Starting import of TIFF file:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3_532.tif
2014-02-13 11:51:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187161 [SwingWorker-pool-5-thread-2] DEBUG com.nimblegen.common.services.model.impl.SlideService - Did not find an existing result that matches barcode: 546409 and scan tag: ClaireOlson_1_2_3 trying to find a placeholder slide result
2014-02-13 11:51:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187162 [SwingWorker-pool-5-thread-3] DEBUG com.nimblegen.common.services.controllers.TiffImportController$TiffImporter$1 - Importing TIFF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3_532.tif
2014-02-13 11:51:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187164 [SwingWorker-pool-5-thread-2] DEBUG com.nimblegen.common.services.model.impl.SlideService - Found a placeholder slide result for barcode: 546409 and scan tag: ClaireOlson_1_2_3
2014-02-13 11:51:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187847 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Importing design for slide barcode 546409[COMPLETED] was removed from submitted tasks.
2014-02-13 11:51:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187856 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 11:51:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187903 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 11:51:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 187903 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Importing design for slide barcode 546409[COMPLETED] was removed from job service submissions.
2014-02-13 11:51:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 188210 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Importing NCD file: Z:\NimbleScanFiles\121101_OysterV9_MG_meth_HX3.ncd
2014-02-13 11:51:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 188357 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Importing NDF file: Z:\NimbleScanFiles\121101_OysterV9_MG_meth.ndf
2014-02-13 11:51:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 188512 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Importing POS file: Z:\NimbleScanFiles\121101_OysterV9_MG_meth.pos
2014-02-13 11:51:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 192355 [SwingWorker-pool-5-thread-2] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy5] was saved from [EMPTY] to [IMAGE_FOUND].
2014-02-13 11:51:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 193129 [SwingWorker-pool-5-thread-3] DEBUG com.nimblegen.common.services.model.impl.SlideService - Found 1 existing slide results that match barcode: 546409 and scan tag: ClaireOlson_1_2_3
2014-02-13 11:51:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 193173 [SwingWorker-pool-5-thread-3] DEBUG com.nimblegen.common.services.model.impl.SlideService - Found an existing result that matches barcode: 546409 and scan tag: ClaireOlson_1_2_3 that has no image for dye: 532
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198379 [SwingWorker-pool-5-thread-3] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy3] was saved from [EMPTY] to [IMAGE_FOUND].
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198396 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - Creating new slide result.
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198399 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - saving new STC set (STC set id = 7)
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198400 [Directory Monitor] DEBUG com.nimblegen.common.services.controllers.TiffImportController - Starting import of TIFF file:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6_635.tif
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198402 [SwingWorker-pool-5-thread-5] DEBUG com.nimblegen.common.services.controllers.TiffImportController$TiffImporter$1 - Importing TIFF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6_635.tif
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198402 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - saving new STC set (STC set id = 8)
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198407 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - saving new STC set (STC set id = 9)
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198409 [Directory Monitor] DEBUG com.nimblegen.common.services.controllers.TiffImportController - Starting import of TIFF file:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6_532.tif
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198409 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - saving new STC set (STC set id = 10)
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198410 [SwingWorker-pool-5-thread-6] DEBUG com.nimblegen.common.services.controllers.TiffImportController$TiffImporter$1 - Importing TIFF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6_532.tif
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198413 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - saving new STC set (STC set id = 11)
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198414 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - saving new STC set (STC set id = 12)
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198852 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Importing design for slide barcode 558216[COMPLETED] was removed from submitted tasks.
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198877 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198877 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Importing design for slide barcode 558216[COMPLETED] was removed from job service submissions.
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198930 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.GffFileImporter - Importing GFF file: Z:\NimbleScanFiles\121101_OysterV9_MG_meth.gff
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198938 [SwingWorker-pool-5-thread-6] DEBUG com.nimblegen.common.services.model.impl.SlideService - Did not find an existing result that matches barcode: 558216 and scan tag: ClaireOlson_4_5_6 trying to find a placeholder slide result
2014-02-13 11:51:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 198939 [SwingWorker-pool-5-thread-6] DEBUG com.nimblegen.common.services.model.impl.SlideService - Found a placeholder slide result for barcode: 558216 and scan tag: ClaireOlson_4_5_6
2014-02-13 11:51:59,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 199615 [pool-1-thread-1] INFO com.nimblegen.common.services.infrastructure.GffFileImporter - Lines imported: 28027 from file: Z:\NimbleScanFiles\121101_OysterV9_MG_meth.gff
2014-02-13 11:51:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 199729 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:93
2014-02-13 11:52:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 205501 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:5865
2014-02-13 11:52:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 206287 [SwingWorker-pool-5-thread-6] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy3] was saved from [EMPTY] to [IMAGE_FOUND].
2014-02-13 11:52:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 207907 [SwingWorker-pool-5-thread-5] DEBUG com.nimblegen.common.services.model.impl.SlideService - Found 1 existing slide results that match barcode: 558216 and scan tag: ClaireOlson_4_5_6
2014-02-13 11:52:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 207926 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:8290
2014-02-13 11:52:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 207933 [SwingWorker-pool-5-thread-5] DEBUG com.nimblegen.common.services.model.impl.SlideService - Found an existing result that matches barcode: 558216 and scan tag: ClaireOlson_4_5_6 that has no image for dye: 635
2014-02-13 11:52:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 207960 [pool-1-thread-1] DEBUG com.nimblegen.common.jobservice.jobs.FileImportTask - Associating annotation dataset id = {1} with slide design {RngSlideDesign[slide barcode: 546409, marketing format name: 3x720K]}.
2014-02-13 11:52:08,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 209242 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.GenomeDatasetDao - time to GenomeDatasetDao.findById:1281
2014-02-13 11:52:08,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 209265 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.DesignAnnotationDboFactory - INSERT INTO genome_dataset_for_design ( id_slide_design , id_genome_dataset ) VALUES ( ?, ? ) 0
2014-02-13 11:52:08,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 209267 [pool-1-thread-1] DEBUG com.nimblegen.common.jobservice.jobs.FileImportTask - Associating annotation dataset id = {1} with md5sum{699ad175b89c25e105912dcf28a5083e}.
2014-02-13 11:52:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 209416 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Importing Annotation from [121101_OysterV9_MG_meth.gff][COMPLETED] was removed from submitted tasks.
2014-02-13 11:52:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 209418 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 11:52:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 209453 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 11:52:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 209454 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Importing Annotation from [121101_OysterV9_MG_meth.gff][COMPLETED] was removed from job service submissions.
2014-02-13 11:52:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 209523 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.GffFileImporter - Importing GFF file: Z:\NimbleScanFiles\121101_OysterV9_MG_meth.gff
2014-02-13 11:52:09,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 209821 [pool-1-thread-1] INFO com.nimblegen.common.services.infrastructure.GffFileImporter - Lines imported: 28027 from file: Z:\NimbleScanFiles\121101_OysterV9_MG_meth.gff
2014-02-13 11:52:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 209886 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:52
2014-02-13 11:52:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 212576 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:2742
2014-02-13 11:52:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 213438 [SwingWorker-pool-5-thread-5] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy5] was saved from [EMPTY] to [IMAGE_FOUND].
2014-02-13 11:52:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 214054 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:4220
2014-02-13 11:52:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 214078 [pool-1-thread-1] DEBUG com.nimblegen.common.jobservice.jobs.FileImportTask - Associating annotation dataset id = {2} with slide design {RngSlideDesign[slide barcode: 558216, marketing format name: 3x720K]}.
2014-02-13 11:52:14,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 214954 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.GenomeDatasetDao - time to GenomeDatasetDao.findById:876
2014-02-13 11:52:14,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 214955 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.DesignAnnotationDboFactory - INSERT INTO genome_dataset_for_design ( id_slide_design , id_genome_dataset ) VALUES ( ?, ? ) 0
2014-02-13 11:52:14,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 214956 [pool-1-thread-1] DEBUG com.nimblegen.common.jobservice.jobs.FileImportTask - Associating annotation dataset id = {2} with md5sum{699ad175b89c25e105912dcf28a5083e}.
2014-02-13 11:52:14,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 215060 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Importing Annotation from [121101_OysterV9_MG_meth.gff][COMPLETED] was removed from submitted tasks.
2014-02-13 11:52:14,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 215064 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 11:52:14,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 215081 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 11:52:14,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 215082 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Importing Annotation from [121101_OysterV9_MG_meth.gff][COMPLETED] was removed from job service submissions.
2014-02-13 11:52:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 215328 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing slide for barcode: 546409 dye: Cy5.
2014-02-13 11:52:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 215359 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - No NDF provided. Bursting does not require NDF file. Using NCD as NDF file.
2014-02-13 11:52:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 215366 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:52:20,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321109425A03_463749748.tif
2014-02-13 11:52:21,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Error: Could not load mediaLib accelerator wrapper classes. Continuing in pure Java mode.
2014-02-13 11:52:21,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) Occurs in: com.sun.media.jai.mlib.MediaLibAccessor
2014-02-13 11:52:21,INFO,com.nimblegen.deva.projectmanager.launcher.StreamLogger, (error stream) com.sun.media.jai.mlib.MediaLibLoadException
2014-02-13 11:52:24,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321109425A02_463749748.tif
2014-02-13 11:52:27,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321109425A01_463749748.tif
2014-02-13 11:52:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 232855 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy5] was saved from [IMAGE_FOUND] to [IMAGE_FOUND].
2014-02-13 11:52:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 234594 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy5] was saved from [IMAGE_FOUND] to [IMAGE_FOUND].
2014-02-13 11:52:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 236149 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy5] was saved from [IMAGE_FOUND] to [BURSTED].
2014-02-13 11:52:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 236254 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy5] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:52:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 236370 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done bursting slide into array image(s) for barcode: 546409 dye: Cy5
2014-02-13 11:52:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 236371 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:burst slide tiff[546409] dye[Cy5].[COMPLETED] was removed from submitted tasks.
2014-02-13 11:52:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 236510 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Aligning sample for 546409 array:A03 dye:Cy5.
2014-02-13 11:52:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 236530 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:52:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 236530 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:52:46,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Looking for fiducial corners...
2014-02-13 11:52:47,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperLeft
2014-02-13 11:52:47,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperRight
2014-02-13 11:52:47,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerLeft
2014-02-13 11:52:48,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerRight
2014-02-13 11:52:48,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Fine tuning...
2014-02-13 11:52:49,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:52:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 251032 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Evaluating accuracy of autoalignment
2014-02-13 11:53:01,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 261351 [pool-1-thread-1] INFO com.nimblegen.common.jobservice.jobs.AlignmentCheckUtil - finished confirming alignment for 546409:A03:Cy5. matches [UR,LR,LL,UL]: [[2, 1, 3, 2]] confirmed: true
2014-02-13 11:53:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 261464 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Outcome of auto-alignment confirmation: PASS
2014-02-13 11:53:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 261576 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Generating thumbnail images
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262524 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>1 name=>DESIGN_ID value=>577051
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262524 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>2 name=>DESIGN_ID1_A01 value=>577051
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262525 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>3 name=>DESIGN_ID2_A01 value=>577051
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262525 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>4 name=>SAMPLE_TRACKING value=>1
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262526 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>5 name=>control:sample_tracking:A_A01 value=>None
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262526 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>6 name=>control:sample_tracking:B_A01 value=>1
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262527 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>7 name=>MAGIC_ALIGNMENT value=>6581857
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262528 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>8 name=>MAGIC_ALIGNMENT1_A01 value=>6581857
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262529 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>9 name=>MAGIC_ALIGNMENT2_A01 value=>6581857
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262529 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>10 name=>MAGIC_ALIGNMENT3_A01 value=>6581857
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262533 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>11 name=>MAGIC_ALIGNMENT4_A01 value=>6581857
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262533 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>12 name=>CHIP_ID value=>546409
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262534 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>13 name=>CHIP_ID1_A01 value=>546409
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262535 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>1 id=>14 name=>CHIP_ID2_A01 value=>546409
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262638 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy5] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262748 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - alignment file for labeled sample[6] dye[Cy5]:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321151487_1842096315.tif.properties is stored as Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321170771_1840641015.properties
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262863 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Finished aligning array for 546409 arrayA03 dye:Cy5
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262967 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy5] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 262967 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:auto align tiff files for labeled sample:6.[COMPLETED] was removed from submitted tasks.
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 263105 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Aligning sample for 546409 array:A01 dye:Cy5.
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 263131 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:53:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 263131 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:53:13,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Looking for fiducial corners...
2014-02-13 11:53:13,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperLeft
2014-02-13 11:53:13,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperRight
2014-02-13 11:53:13,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerLeft
2014-02-13 11:53:14,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerRight
2014-02-13 11:53:14,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Fine tuning...
2014-02-13 11:53:15,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:53:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 277062 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Evaluating accuracy of autoalignment
2014-02-13 11:53:27,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 287474 [pool-1-thread-1] INFO com.nimblegen.common.jobservice.jobs.AlignmentCheckUtil - finished confirming alignment for 546409:A01:Cy5. matches [UR,LR,LL,UL]: [[2, 1, 3, 1]] confirmed: true
2014-02-13 11:53:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 287610 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Outcome of auto-alignment confirmation: PASS
2014-02-13 11:53:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 287734 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Generating thumbnail images
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288386 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>15 name=>DESIGN_ID value=>577051
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288386 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>16 name=>DESIGN_ID1_A01 value=>577051
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288386 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>17 name=>DESIGN_ID2_A01 value=>577049
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288386 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>18 name=>SAMPLE_TRACKING value=>17
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288387 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>19 name=>control:sample_tracking:A_A01 value=>None
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288388 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>20 name=>control:sample_tracking:B_A01 value=>17
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288389 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>21 name=>MAGIC_ALIGNMENT value=>6581857
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288392 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>22 name=>MAGIC_ALIGNMENT1_A01 value=>6581857
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288393 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>23 name=>MAGIC_ALIGNMENT2_A01 value=>6581857
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288393 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>24 name=>MAGIC_ALIGNMENT3_A01 value=>6581857
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288398 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>25 name=>MAGIC_ALIGNMENT4_A01 value=>6581857
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288398 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>26 name=>CHIP_ID value=>546409
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288398 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>27 name=>CHIP_ID1_A01 value=>546409
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288401 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>3 id=>28 name=>CHIP_ID2_A01 value=>546409
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288508 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy5] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288621 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - alignment file for labeled sample[4] dye[Cy5]:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321154837_774399534.tif.properties is stored as Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321196799_958206262.properties
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288734 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Finished aligning array for 546409 arrayA01 dye:Cy5
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288836 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy5] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288836 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:auto align tiff files for labeled sample:4.[COMPLETED] was removed from submitted tasks.
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288954 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Aligning sample for 546409 array:A02 dye:Cy5.
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288977 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:53:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 288977 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:53:39,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Looking for fiducial corners...
2014-02-13 11:53:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperLeft
2014-02-13 11:53:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperRight
2014-02-13 11:53:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerLeft
2014-02-13 11:53:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerRight
2014-02-13 11:53:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Fine tuning...
2014-02-13 11:53:41,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:53:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 303242 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Evaluating accuracy of autoalignment
2014-02-13 11:53:53,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 313995 [pool-1-thread-1] INFO com.nimblegen.common.jobservice.jobs.AlignmentCheckUtil - finished confirming alignment for 546409:A02:Cy5. matches [UR,LR,LL,UL]: [[2, 1, 3, 2]] confirmed: true
2014-02-13 11:53:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314106 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Outcome of auto-alignment confirmation: PASS
2014-02-13 11:53:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314218 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Generating thumbnail images
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314827 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>29 name=>DESIGN_ID value=>577051
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314827 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>30 name=>DESIGN_ID1_A01 value=>577051
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314828 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>31 name=>DESIGN_ID2_A01 value=>577051
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314828 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>32 name=>SAMPLE_TRACKING value=>None
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314829 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>33 name=>control:sample_tracking:A_A01 value=>None
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314829 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>34 name=>control:sample_tracking:B_A01 value=>None
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314829 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>35 name=>MAGIC_ALIGNMENT value=>6581857
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314832 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>36 name=>MAGIC_ALIGNMENT1_A01 value=>6581857
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314832 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>37 name=>MAGIC_ALIGNMENT2_A01 value=>6581857
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314833 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>38 name=>MAGIC_ALIGNMENT3_A01 value=>6581857
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314833 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>39 name=>MAGIC_ALIGNMENT4_A01 value=>6581857
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314833 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>40 name=>CHIP_ID value=>546409
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314834 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>41 name=>CHIP_ID1_A01 value=>546409
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314835 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>2 id=>42 name=>CHIP_ID2_A01 value=>546409
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 314937 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy5] was saved from [BURSTED] to [COMPLETE].
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 315049 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - alignment file for labeled sample[2] dye[Cy5]:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321153073_1131389620.tif.properties is stored as Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321222986_726991319.properties
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 315163 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Finished aligning array for 546409 arrayA02 dye:Cy5
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 315271 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy5] was saved from [COMPLETE] to [COMPLETE].
2014-02-13 11:53:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 315271 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:auto align tiff files for labeled sample:2.[COMPLETED] was removed from submitted tasks.
2014-02-13 11:53:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 315569 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Analysis attempted for labeled sample id[6], but stopped because control alignment is not set.
2014-02-13 11:53:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 316212 [pool-1-thread-1] DEBUG com.nimblegen.common.jobservice.jobs.RunDefaultAnalysisWorkflowForLabeledSampleJob - Analysis attempted for labeled sample id[6], but stopped because control alignment is not set.
2014-02-13 11:53:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 316961 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:start analysis workflow[COMPLETED] was removed from submitted tasks.
2014-02-13 11:53:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 317177 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Analysis attempted for labeled sample id[4], but stopped because control alignment is not set.
2014-02-13 11:53:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 317178 [pool-1-thread-1] DEBUG com.nimblegen.common.jobservice.jobs.RunDefaultAnalysisWorkflowForLabeledSampleJob - Analysis attempted for labeled sample id[4], but stopped because control alignment is not set.
2014-02-13 11:53:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 317905 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:start analysis workflow[COMPLETED] was removed from submitted tasks.
2014-02-13 11:53:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 318076 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Analysis attempted for labeled sample id[2], but stopped because control alignment is not set.
2014-02-13 11:53:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 318076 [pool-1-thread-1] DEBUG com.nimblegen.common.jobservice.jobs.RunDefaultAnalysisWorkflowForLabeledSampleJob - Analysis attempted for labeled sample id[2], but stopped because control alignment is not set.
2014-02-13 11:53:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 318789 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:start analysis workflow[COMPLETED] was removed from submitted tasks.
2014-02-13 11:53:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 318790 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 11:53:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 318893 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 11:53:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 318893 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:Importing Image for slide barcode 546409 dye:Cy5[COMPLETED] was removed from job service submissions.
2014-02-13 11:53:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 319128 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing slide for barcode: 546409 dye: Cy3.
2014-02-13 11:53:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 319134 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - No NDF provided. Bursting does not require NDF file. Using NCD as NDF file.
2014-02-13 11:53:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 319139 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:54:04,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321115346A03_28755627.tif
2014-02-13 11:54:08,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321115346A02_28755627.tif
2014-02-13 11:54:11,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321115346A01_28755627.tif
2014-02-13 11:54:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 336745 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy3] was saved from [IMAGE_FOUND] to [IMAGE_FOUND].
2014-02-13 11:54:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 338322 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy3] was saved from [IMAGE_FOUND] to [IMAGE_FOUND].
2014-02-13 11:54:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 340092 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy3] was saved from [IMAGE_FOUND] to [BURSTED].
2014-02-13 11:54:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 340198 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy3] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:54:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 340318 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done bursting slide into array image(s) for barcode: 546409 dye: Cy3
2014-02-13 11:54:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 340318 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:burst slide tiff[546409] dye[Cy3].[COMPLETED] was removed from submitted tasks.
2014-02-13 11:54:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 340445 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Aligning sample for 546409 array:A03 dye:Cy3.
2014-02-13 11:54:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 340459 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:54:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 340459 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:54:31,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Looking for fiducial corners...
2014-02-13 11:54:31,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperLeft
2014-02-13 11:54:31,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperRight
2014-02-13 11:54:32,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerLeft
2014-02-13 11:54:32,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerRight
2014-02-13 11:54:32,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Fine tuning...
2014-02-13 11:54:32,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:54:33,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 354280 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Evaluating accuracy of autoalignment
2014-02-13 11:54:43,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 364265 [pool-1-thread-1] INFO com.nimblegen.common.jobservice.jobs.AlignmentCheckUtil - finished confirming alignment for 546409:A03:Cy3. matches [UR,LR,LL,UL]: [[2, 1, 3, 2]] confirmed: true
2014-02-13 11:54:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 364381 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Outcome of auto-alignment confirmation: PASS
2014-02-13 11:54:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 364494 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Generating thumbnail images
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365683 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>43 name=>DESIGN_ID value=>577051
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365683 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>44 name=>DESIGN_ID1_A01 value=>577051
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365683 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>45 name=>DESIGN_ID2_A01 value=>577051
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365683 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>46 name=>SAMPLE_TRACKING value=>None
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365684 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>47 name=>control:sample_tracking:A_A01 value=>None
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365684 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>48 name=>control:sample_tracking:B_A01 value=>None
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365684 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>49 name=>MAGIC_ALIGNMENT value=>6581857
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>50 name=>MAGIC_ALIGNMENT1_A01 value=>6581857
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>51 name=>MAGIC_ALIGNMENT2_A01 value=>6581857
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>52 name=>MAGIC_ALIGNMENT3_A01 value=>6581857
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365687 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>53 name=>MAGIC_ALIGNMENT4_A01 value=>6581857
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365687 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>54 name=>CHIP_ID value=>546409
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365688 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>55 name=>CHIP_ID1_A01 value=>546409
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365689 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>4 id=>56 name=>CHIP_ID2_A01 value=>546409
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365794 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy3] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 365905 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - alignment file for labeled sample[5] dye[Cy3]:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321255435_1709097168.tif.properties is stored as Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321274020_1991082097.properties
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 366015 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Finished aligning array for 546409 arrayA03 dye:Cy3
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 366120 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy3] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 366120 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:auto align tiff files for labeled sample:5.[COMPLETED] was removed from submitted tasks.
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 366244 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Aligning sample for 546409 array:A01 dye:Cy3.
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 366266 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:54:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 366266 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:54:56,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Looking for fiducial corners...
2014-02-13 11:54:56,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperLeft
2014-02-13 11:54:57,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperRight
2014-02-13 11:54:57,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerLeft
2014-02-13 11:54:57,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerRight
2014-02-13 11:54:57,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Fine tuning...
2014-02-13 11:54:57,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:54:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 379591 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Evaluating accuracy of autoalignment
2014-02-13 11:55:10,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 390406 [pool-1-thread-1] INFO com.nimblegen.common.jobservice.jobs.AlignmentCheckUtil - finished confirming alignment for 546409:A01:Cy3. matches [UR,LR,LL,UL]: [[2, 1, 3, 2]] confirmed: true
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 390518 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Outcome of auto-alignment confirmation: PASS
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 390634 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Generating thumbnail images
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391179 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>57 name=>DESIGN_ID value=>577051
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391179 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>58 name=>DESIGN_ID1_A01 value=>577051
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391179 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>59 name=>DESIGN_ID2_A01 value=>577051
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391180 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>60 name=>SAMPLE_TRACKING value=>None
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391180 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>61 name=>control:sample_tracking:A_A01 value=>None
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391181 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>62 name=>control:sample_tracking:B_A01 value=>None
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391181 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>63 name=>MAGIC_ALIGNMENT value=>6581857
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391182 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>64 name=>MAGIC_ALIGNMENT1_A01 value=>6581857
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391182 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>65 name=>MAGIC_ALIGNMENT2_A01 value=>6581857
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391182 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>66 name=>MAGIC_ALIGNMENT3_A01 value=>6581857
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391184 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>67 name=>MAGIC_ALIGNMENT4_A01 value=>6581857
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391184 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>68 name=>CHIP_ID value=>546409
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391185 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>69 name=>CHIP_ID1_A01 value=>546409
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391188 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>6 id=>70 name=>CHIP_ID2_A01 value=>546409
2014-02-13 11:55:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391291 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy3] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:55:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391401 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - alignment file for labeled sample[3] dye[Cy3]:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321258623_157141311.tif.properties is stored as Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321299325_563950235.properties
2014-02-13 11:55:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391516 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Finished aligning array for 546409 arrayA01 dye:Cy3
2014-02-13 11:55:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391618 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy3] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:55:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391619 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:auto align tiff files for labeled sample:3.[COMPLETED] was removed from submitted tasks.
2014-02-13 11:55:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391747 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Aligning sample for 546409 array:A02 dye:Cy3.
2014-02-13 11:55:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391784 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:55:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 391784 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:55:21,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Looking for fiducial corners...
2014-02-13 11:55:22,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperLeft
2014-02-13 11:55:22,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperRight
2014-02-13 11:55:22,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerLeft
2014-02-13 11:55:22,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerRight
2014-02-13 11:55:22,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Fine tuning...
2014-02-13 11:55:22,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:55:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 405174 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Evaluating accuracy of autoalignment
2014-02-13 11:55:35,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 415764 [pool-1-thread-1] INFO com.nimblegen.common.jobservice.jobs.AlignmentCheckUtil - finished confirming alignment for 546409:A02:Cy3. matches [UR,LR,LL,UL]: [[2, 1, 3, 2]] confirmed: true
2014-02-13 11:55:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 415876 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Outcome of auto-alignment confirmation: PASS
2014-02-13 11:55:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 415987 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Generating thumbnail images
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416595 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>71 name=>DESIGN_ID value=>577051
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416596 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>72 name=>DESIGN_ID1_A01 value=>577051
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416596 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>73 name=>DESIGN_ID2_A01 value=>577051
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416596 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>74 name=>SAMPLE_TRACKING value=>None
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416597 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>75 name=>control:sample_tracking:A_A01 value=>None
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416598 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>76 name=>control:sample_tracking:B_A01 value=>None
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416598 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>77 name=>MAGIC_ALIGNMENT value=>6581857
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416599 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>78 name=>MAGIC_ALIGNMENT1_A01 value=>6581857
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416599 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>79 name=>MAGIC_ALIGNMENT2_A01 value=>6581857
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416600 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>80 name=>MAGIC_ALIGNMENT3_A01 value=>6581857
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416601 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>81 name=>MAGIC_ALIGNMENT4_A01 value=>6581857
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416601 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>82 name=>CHIP_ID value=>546409
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416601 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>83 name=>CHIP_ID1_A01 value=>546409
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416605 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>5 id=>84 name=>CHIP_ID2_A01 value=>546409
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416708 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy3] was saved from [BURSTED] to [COMPLETE].
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416818 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - alignment file for labeled sample[1] dye[Cy3]:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321256918_680220543.tif.properties is stored as Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321324914_1520929864.properties
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 416942 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Finished aligning array for 546409 arrayA02 dye:Cy3
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 417045 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[1] dye[Cy3] was saved from [COMPLETE] to [COMPLETE].
2014-02-13 11:55:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 417045 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:auto align tiff files for labeled sample:1.[COMPLETED] was removed from submitted tasks.
2014-02-13 11:55:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 417979 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:start analysis workflow[COMPLETED] was removed from submitted tasks.
2014-02-13 11:55:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 419040 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:start analysis workflow[COMPLETED] was removed from submitted tasks.
2014-02-13 11:55:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 420140 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:start analysis workflow[COMPLETED] was removed from submitted tasks.
2014-02-13 11:55:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 420142 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 11:55:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 420162 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 11:55:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 420162 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:Importing Image for slide barcode 546409 dye:Cy3[COMPLETED] was removed from job service submissions.
2014-02-13 11:55:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 420409 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing slide for barcode: 558216 dye: Cy3.
2014-02-13 11:55:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 420415 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - No NDF provided. Bursting does not require NDF file. Using NCD as NDF file.
2014-02-13 11:55:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 420419 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:55:45,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321122821A03_1822169514.tif
2014-02-13 11:55:49,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321122821A02_1822169514.tif
2014-02-13 11:55:51,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321122821A01_1822169514.tif
2014-02-13 11:55:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 437045 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy3] was saved from [IMAGE_FOUND] to [IMAGE_FOUND].
2014-02-13 11:55:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 438511 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy3] was saved from [IMAGE_FOUND] to [IMAGE_FOUND].
2014-02-13 11:55:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 440227 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy3] was saved from [IMAGE_FOUND] to [BURSTED].
2014-02-13 11:56:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 440321 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy3] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:56:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 440430 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done bursting slide into array image(s) for barcode: 558216 dye: Cy3
2014-02-13 11:56:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 440430 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:burst slide tiff[558216] dye[Cy3].[COMPLETED] was removed from submitted tasks.
2014-02-13 11:56:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 440571 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Aligning sample for 558216 array:A03 dye:Cy3.
2014-02-13 11:56:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 440586 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:56:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 440586 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:56:11,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Looking for fiducial corners...
2014-02-13 11:56:11,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperLeft
2014-02-13 11:56:11,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperRight
2014-02-13 11:56:11,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerLeft
2014-02-13 11:56:11,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerRight
2014-02-13 11:56:12,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Fine tuning...
2014-02-13 11:56:12,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:56:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 454189 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Evaluating accuracy of autoalignment
2014-02-13 11:56:23,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 464236 [pool-1-thread-1] INFO com.nimblegen.common.jobservice.jobs.AlignmentCheckUtil - finished confirming alignment for 558216:A03:Cy3. matches [UR,LR,LL,UL]: [[2, 1, 3, 2]] confirmed: true
2014-02-13 11:56:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 464984 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Outcome of auto-alignment confirmation: PASS
2014-02-13 11:56:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465093 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Generating thumbnail images
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465671 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>85 name=>DESIGN_ID value=>577051
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>86 name=>DESIGN_ID1_A01 value=>577051
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>87 name=>DESIGN_ID2_A01 value=>577051
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>88 name=>SAMPLE_TRACKING value=>None
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>89 name=>control:sample_tracking:A_A01 value=>None
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>90 name=>control:sample_tracking:B_A01 value=>None
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>91 name=>MAGIC_ALIGNMENT value=>6581857
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>92 name=>MAGIC_ALIGNMENT1_A01 value=>6581857
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>93 name=>MAGIC_ALIGNMENT2_A01 value=>6581857
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>94 name=>MAGIC_ALIGNMENT3_A01 value=>6581857
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>95 name=>MAGIC_ALIGNMENT4_A01 value=>6581857
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>96 name=>CHIP_ID value=>558216
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>97 name=>CHIP_ID1_A01 value=>558216
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465686 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>7 id=>98 name=>CHIP_ID2_A01 value=>558216
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465795 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy3] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 465936 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - alignment file for labeled sample[11] dye[Cy3]:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321355760_1552122293.tif.properties is stored as Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321373934_1918509251.properties
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 466045 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Finished aligning array for 558216 arrayA03 dye:Cy3
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 466154 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy3] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 466154 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:auto align tiff files for labeled sample:11.[COMPLETED] was removed from submitted tasks.
2014-02-13 11:56:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 466295 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Aligning sample for 558216 array:A01 dye:Cy3.
2014-02-13 11:56:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 466326 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:56:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 466326 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:56:36,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Looking for fiducial corners...
2014-02-13 11:56:36,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperLeft
2014-02-13 11:56:36,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperRight
2014-02-13 11:56:36,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerLeft
2014-02-13 11:56:37,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerRight
2014-02-13 11:56:37,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Fine tuning...
2014-02-13 11:56:37,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:56:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 479180 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Evaluating accuracy of autoalignment
2014-02-13 11:56:49,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490116 [pool-1-thread-1] INFO com.nimblegen.common.jobservice.jobs.AlignmentCheckUtil - finished confirming alignment for 558216:A01:Cy3. matches [UR,LR,LL,UL]: [[2, 1, 3, 2]] confirmed: true
2014-02-13 11:56:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490225 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Outcome of auto-alignment confirmation: PASS
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490334 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Generating thumbnail images
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>99 name=>DESIGN_ID value=>577051
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>100 name=>DESIGN_ID1_A01 value=>577051
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>101 name=>DESIGN_ID2_A01 value=>577051
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>102 name=>SAMPLE_TRACKING value=>None
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>103 name=>control:sample_tracking:A_A01 value=>None
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>104 name=>control:sample_tracking:B_A01 value=>None
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>105 name=>MAGIC_ALIGNMENT value=>6581857
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>106 name=>MAGIC_ALIGNMENT1_A01 value=>6581857
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>107 name=>MAGIC_ALIGNMENT2_A01 value=>6581857
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>108 name=>MAGIC_ALIGNMENT3_A01 value=>6581857
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>109 name=>MAGIC_ALIGNMENT4_A01 value=>6581857
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>110 name=>CHIP_ID value=>558216
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>111 name=>CHIP_ID1_A01 value=>558216
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 490942 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>9 id=>112 name=>CHIP_ID2_A01 value=>558216
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 491052 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy3] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 491161 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - alignment file for labeled sample[9] dye[Cy3]:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321358724_217219257.tif.properties is stored as Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321398909_27321455.properties
2014-02-13 11:56:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 491270 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Finished aligning array for 558216 arrayA01 dye:Cy3
2014-02-13 11:56:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 491364 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy3] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:56:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 491364 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:auto align tiff files for labeled sample:9.[COMPLETED] was removed from submitted tasks.
2014-02-13 11:56:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 491566 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Analysis attempted for labeled sample id[11], but stopped because experiment alignment is not set.
2014-02-13 11:56:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 491566 [pool-1-thread-1] DEBUG com.nimblegen.common.jobservice.jobs.RunDefaultAnalysisWorkflowForLabeledSampleJob - Analysis attempted for labeled sample id[11], but stopped because experiment alignment is not set.
2014-02-13 11:56:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 492097 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:start analysis workflow[COMPLETED] was removed from submitted tasks.
2014-02-13 11:56:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 492268 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Aligning sample for 558216 array:A02 dye:Cy3.
2014-02-13 11:56:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 492300 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:56:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 492300 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:57:01,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Looking for fiducial corners...
2014-02-13 11:57:02,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperLeft
2014-02-13 11:57:02,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperRight
2014-02-13 11:57:02,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerLeft
2014-02-13 11:57:02,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerRight
2014-02-13 11:57:02,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Fine tuning...
2014-02-13 11:57:03,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:57:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 505419 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Evaluating accuracy of autoalignment
2014-02-13 11:57:15,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 515699 [pool-1-thread-1] INFO com.nimblegen.common.jobservice.jobs.AlignmentCheckUtil - finished confirming alignment for 558216:A02:Cy3. matches [UR,LR,LL,UL]: [[2, 1, 3, 2]] confirmed: true
2014-02-13 11:57:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 515808 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Outcome of auto-alignment confirmation: PASS
2014-02-13 11:57:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 515918 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Generating thumbnail images
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516448 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>113 name=>DESIGN_ID value=>577051
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516448 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>114 name=>DESIGN_ID1_A01 value=>577051
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516448 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>115 name=>DESIGN_ID2_A01 value=>577051
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516448 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>116 name=>SAMPLE_TRACKING value=>None
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516464 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>117 name=>control:sample_tracking:A_A01 value=>None
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516464 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>118 name=>control:sample_tracking:B_A01 value=>None
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516464 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>119 name=>MAGIC_ALIGNMENT value=>6581857
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516464 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>120 name=>MAGIC_ALIGNMENT1_A01 value=>6581857
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516464 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>121 name=>MAGIC_ALIGNMENT2_A01 value=>6581857
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516464 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>122 name=>MAGIC_ALIGNMENT3_A01 value=>6581857
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516464 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>123 name=>MAGIC_ALIGNMENT4_A01 value=>6581857
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516464 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>124 name=>CHIP_ID value=>558216
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516464 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>125 name=>CHIP_ID1_A01 value=>558216
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516464 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>8 id=>126 name=>CHIP_ID2_A01 value=>558216
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516573 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy3] was saved from [BURSTED] to [COMPLETE].
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516682 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - alignment file for labeled sample[7] dye[Cy3]:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321357227_535216215.tif.properties is stored as Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321425148_1406178292.properties
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516791 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Finished aligning array for 558216 arrayA02 dye:Cy3
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516900 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy3] was saved from [COMPLETE] to [COMPLETE].
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 516900 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:auto align tiff files for labeled sample:7.[COMPLETED] was removed from submitted tasks.
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 517088 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Analysis attempted for labeled sample id[9], but stopped because experiment alignment is not set.
2014-02-13 11:57:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 517088 [pool-1-thread-1] DEBUG com.nimblegen.common.jobservice.jobs.RunDefaultAnalysisWorkflowForLabeledSampleJob - Analysis attempted for labeled sample id[9], but stopped because experiment alignment is not set.
2014-02-13 11:57:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 517618 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:start analysis workflow[COMPLETED] was removed from submitted tasks.
2014-02-13 11:57:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 517805 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Analysis attempted for labeled sample id[7], but stopped because experiment alignment is not set.
2014-02-13 11:57:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 517805 [pool-1-thread-1] DEBUG com.nimblegen.common.jobservice.jobs.RunDefaultAnalysisWorkflowForLabeledSampleJob - Analysis attempted for labeled sample id[7], but stopped because experiment alignment is not set.
2014-02-13 11:57:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 518460 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:start analysis workflow[COMPLETED] was removed from submitted tasks.
2014-02-13 11:57:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 518460 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 11:57:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 518476 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 11:57:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 518476 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:Importing Image for slide barcode 558216 dye:Cy3[COMPLETED] was removed from job service submissions.
2014-02-13 11:57:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 518741 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing slide for barcode: 558216 dye: Cy5.
2014-02-13 11:57:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 518741 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - No NDF provided. Bursting does not require NDF file. Using NCD as NDF file.
2014-02-13 11:57:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 518741 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:57:24,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321130309A03_2143614679.tif
2014-02-13 11:57:27,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321130309A02_2143614679.tif
2014-02-13 11:57:30,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321130309A01_2143614679.tif
2014-02-13 11:57:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 536353 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy5] was saved from [IMAGE_FOUND] to [IMAGE_FOUND].
2014-02-13 11:57:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 537991 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy5] was saved from [IMAGE_FOUND] to [IMAGE_FOUND].
2014-02-13 11:57:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 539473 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy5] was saved from [IMAGE_FOUND] to [BURSTED].
2014-02-13 11:57:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 539583 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy5] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:57:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 539692 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done bursting slide into array image(s) for barcode: 558216 dye: Cy5
2014-02-13 11:57:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 539692 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:burst slide tiff[558216] dye[Cy5].[COMPLETED] was removed from submitted tasks.
2014-02-13 11:57:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 539832 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Aligning sample for 558216 array:A02 dye:Cy5.
2014-02-13 11:57:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 539848 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:57:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 539848 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:57:50,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Looking for fiducial corners...
2014-02-13 11:57:50,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperLeft
2014-02-13 11:57:50,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperRight
2014-02-13 11:57:51,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerLeft
2014-02-13 11:57:51,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerRight
2014-02-13 11:57:51,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Fine tuning...
2014-02-13 11:57:51,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:57:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 553451 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Evaluating accuracy of autoalignment
2014-02-13 11:58:03,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 563466 [pool-1-thread-1] INFO com.nimblegen.common.jobservice.jobs.AlignmentCheckUtil - finished confirming alignment for 558216:A02:Cy5. matches [UR,LR,LL,UL]: [[2, 1, 3, 2]] confirmed: true
2014-02-13 11:58:03,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 563575 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Outcome of auto-alignment confirmation: PASS
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564324 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Generating thumbnail images
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>127 name=>DESIGN_ID value=>577051
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>128 name=>DESIGN_ID1_A01 value=>577051
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>129 name=>DESIGN_ID2_A01 value=>577051
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>130 name=>SAMPLE_TRACKING value=>None
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>131 name=>control:sample_tracking:A_A01 value=>None
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>132 name=>control:sample_tracking:B_A01 value=>None
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>133 name=>MAGIC_ALIGNMENT value=>6581857
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>134 name=>MAGIC_ALIGNMENT1_A01 value=>6581857
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>135 name=>MAGIC_ALIGNMENT2_A01 value=>6581857
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>136 name=>MAGIC_ALIGNMENT3_A01 value=>6581857
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>137 name=>MAGIC_ALIGNMENT4_A01 value=>6581857
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>138 name=>CHIP_ID value=>558216
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>139 name=>CHIP_ID1_A01 value=>558216
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564854 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>11 id=>140 name=>CHIP_ID2_A01 value=>558216
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 564963 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy5] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 565073 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - alignment file for labeled sample[8] dye[Cy5]:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321456519_379867819.tif.properties is stored as Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321473180_679392472.properties
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 565182 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Finished aligning array for 558216 arrayA02 dye:Cy5
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 565291 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy5] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:58:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 565291 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:auto align tiff files for labeled sample:8.[COMPLETED] was removed from submitted tasks.
2014-02-13 11:58:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 565416 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Aligning sample for 558216 array:A01 dye:Cy5.
2014-02-13 11:58:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 565447 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:58:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 565447 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:58:15,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Looking for fiducial corners...
2014-02-13 11:58:15,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperLeft
2014-02-13 11:58:15,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperRight
2014-02-13 11:58:16,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerLeft
2014-02-13 11:58:16,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerRight
2014-02-13 11:58:16,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Fine tuning...
2014-02-13 11:58:16,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:58:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 578208 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Evaluating accuracy of autoalignment
2014-02-13 11:58:28,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589096 [pool-1-thread-1] INFO com.nimblegen.common.jobservice.jobs.AlignmentCheckUtil - finished confirming alignment for 558216:A01:Cy5. matches [UR,LR,LL,UL]: [[2, 1, 3, 2]] confirmed: true
2014-02-13 11:58:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589221 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Outcome of auto-alignment confirmation: PASS
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589330 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Generating thumbnail images
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589907 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>141 name=>DESIGN_ID value=>577051
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589907 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>142 name=>DESIGN_ID1_A01 value=>577051
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589907 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>143 name=>DESIGN_ID2_A01 value=>577051
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589907 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>144 name=>SAMPLE_TRACKING value=>None
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589907 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>145 name=>control:sample_tracking:A_A01 value=>None
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589907 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>146 name=>control:sample_tracking:B_A01 value=>None
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589907 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>147 name=>MAGIC_ALIGNMENT value=>6581857
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589923 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>148 name=>MAGIC_ALIGNMENT1_A01 value=>6581857
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589923 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>149 name=>MAGIC_ALIGNMENT2_A01 value=>6581857
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589923 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>150 name=>MAGIC_ALIGNMENT3_A01 value=>6581857
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589923 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>151 name=>MAGIC_ALIGNMENT4_A01 value=>6581857
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589923 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>152 name=>CHIP_ID value=>558216
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589923 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>153 name=>CHIP_ID1_A01 value=>558216
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 589923 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>12 id=>154 name=>CHIP_ID2_A01 value=>558216
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 590032 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy5] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 590141 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - alignment file for labeled sample[10] dye[Cy5]:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321458189_2028694249.tif.properties is stored as Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321497937_1622562292.properties
2014-02-13 11:58:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 590266 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Finished aligning array for 558216 arrayA01 dye:Cy5
2014-02-13 11:58:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 590375 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy5] was saved from [BURSTED] to [BURSTED].
2014-02-13 11:58:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 590375 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:auto align tiff files for labeled sample:10.[COMPLETED] was removed from submitted tasks.
2014-02-13 11:58:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 590516 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Aligning sample for 558216 array:A03 dye:Cy5.
2014-02-13 11:58:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 590547 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:58:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 590547 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:58:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Looking for fiducial corners...
2014-02-13 11:58:40,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperLeft
2014-02-13 11:58:41,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential UpperRight
2014-02-13 11:58:41,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerLeft
2014-02-13 11:58:41,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Found potential LowerRight
2014-02-13 11:58:41,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Fine tuning...
2014-02-13 11:58:41,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker,
2014-02-13 11:58:43,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 604096 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Evaluating accuracy of autoalignment
2014-02-13 11:58:54,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 614937 [pool-1-thread-1] INFO com.nimblegen.common.jobservice.jobs.AlignmentCheckUtil - finished confirming alignment for 558216:A03:Cy5. matches [UR,LR,LL,UL]: [[2, 1, 3, 2]] confirmed: true
2014-02-13 11:58:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615047 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Outcome of auto-alignment confirmation: PASS
2014-02-13 11:58:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615156 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Generating thumbnail images
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>155 name=>DESIGN_ID value=>577051
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>156 name=>DESIGN_ID1_A01 value=>577051
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>157 name=>DESIGN_ID2_A01 value=>577051
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>158 name=>SAMPLE_TRACKING value=>None
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>159 name=>control:sample_tracking:A_A01 value=>None
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>160 name=>control:sample_tracking:B_A01 value=>None
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>161 name=>MAGIC_ALIGNMENT value=>6581857
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>162 name=>MAGIC_ALIGNMENT1_A01 value=>6581857
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>163 name=>MAGIC_ALIGNMENT2_A01 value=>6581857
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>164 name=>MAGIC_ALIGNMENT3_A01 value=>6581857
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>165 name=>MAGIC_ALIGNMENT4_A01 value=>6581857
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>166 name=>CHIP_ID value=>558216
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>167 name=>CHIP_ID1_A01 value=>558216
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615811 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - created decoded number record: arrayTiffId=>10 id=>168 name=>CHIP_ID2_A01 value=>558216
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 615983 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy5] was saved from [BURSTED] to [COMPLETE].
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 616107 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - alignment file for labeled sample[12] dye[Cy5]:Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321454991_1409981611.tif.properties is stored as Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321523887_1643493455.properties
2014-02-13 11:58:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 616232 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Finished aligning array for 558216 arrayA03 dye:Cy5
2014-02-13 11:58:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 616451 [pool-1-thread-1] DEBUG com.nimblegen.common.services.model.impl.SlideService - status for slide result[2] dye[Cy5] was saved from [COMPLETE] to [COMPLETE].
2014-02-13 11:58:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 616451 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:auto align tiff files for labeled sample:12.[COMPLETED] was removed from submitted tasks.
2014-02-13 11:58:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 617621 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:start analysis workflow[COMPLETED] was removed from submitted tasks.
2014-02-13 11:58:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 618666 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:start analysis workflow[COMPLETED] was removed from submitted tasks.
2014-02-13 11:58:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 619711 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:start analysis workflow[COMPLETED] was removed from submitted tasks.
2014-02-13 11:58:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 619711 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 11:58:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 619742 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 11:58:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 619742 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:Importing Image for slide barcode 558216 dye:Cy5[COMPLETED] was removed from job service submissions.
2014-02-13 11:58:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620257 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620382 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620382 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:16 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620382 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:17 dataclass:class java.lang.Long]] is being set.
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620382 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620382 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620382 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 141ms
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620397 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620397 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620444 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Pair report
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620460 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620475 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620491 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620600 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Output directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620600 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Outputing report for Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321151487_1842096315.tif
2014-02-13 11:59:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 620631 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - TempFile : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A03_ClaireOlson_1_2_3\tmp.1392321540314_342864280\546409A03_ClaireOlson_1_2_3_635.tif
2014-02-13 11:59:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 621864 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:59:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 621864 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:59:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 656090 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A03_ClaireOlson_1_2_3\tmp.1392321540314_342864280\546409A03_ClaireOlson_1_2_3_635.pair
2014-02-13 11:59:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 656090 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - fixing design name
2014-02-13 11:59:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 656183 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A03_ClaireOlson_1_2_3\tmp.1392321540314_342864280\546409A03_ClaireOlson_1_2_3_635.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 11:59:12 PST 2014 border=0 ul_x=88.605 ul_y=182.118 ur_x=2945.681 ur_y=158.220 lr_x=2978.512 lr_y=3974.562 ll_x=120.955 ll_y=3998.470 qcscore=0.292 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.' = # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A03_ClaireOlson_1_2_3\tmp.1392321540314_342864280\546409A03_ClaireOlson_1_2_3_635.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 11:59:12 PST 2014 border=0 ul_x=88.605 ul_y=182.118 ur_x=2945.681 ur_y=158.220 lr_x=2978.512 lr_y=3974.562 ll_x=120.955 ll_y=3998.470 qcscore=0.292 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.'
2014-02-13 11:59:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668047 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A03_ClaireOlson_1_2_3\546409A03_ClaireOlson_1_2_3_2014-02-13T115947_635.pair
2014-02-13 11:59:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668140 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Pair submitted
2014-02-13 11:59:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668140 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 11:59:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668296 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 11:59:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668296 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 11:59:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668328 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 11:59:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668328 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A03_ClaireOlson_1_2_3(Cy5) Pair Report Workflow 2014-02-13 11:53:55[COMPLETED] was removed from job service submissions.
2014-02-13 11:59:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668406 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 11:59:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668515 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 11:59:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668530 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 11:59:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668546 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 11:59:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668546 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 546409A03_ClaireOlson_1_2_3
2014-02-13 11:59:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668593 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 11:59:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668624 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 11:59:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668624 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 11:59:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 668655 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 11:59:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 680106 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 11:59:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 680121 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 11:59:59,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321151487_1842096315.xys...
2014-02-13 12:00:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 684676 [SwingWorker-pool-5-thread-8] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:00:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 684676 [SwingWorker-pool-5-thread-8] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:00:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 689887 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:00:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 689887 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:00:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 689918 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:00:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 689949 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:00:14,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 695269 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:00:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 699480 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:00:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 703201 [AWT-EventQueue-0] DEBUG com.nimblegen.deva.app.mainpanel.scan.FullScreenDualmagePanel$1 - Component Resized
2014-02-13 12:00:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 703201 [AWT-EventQueue-0] DEBUG com.nimblegen.deva.app.mainpanel.scan.FullScreenDualmagePanel$1 - Component Moved
2014-02-13 12:00:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 709815 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710424 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710439 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710455 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710471 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710471 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:22 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710471 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:23 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710471 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710471 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710471 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 42081ms
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710486 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710486 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710517 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710533 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710549 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710549 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:00:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 710564 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 727755 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF report complete
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 727771 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF submitted
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 727771 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 727927 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 727927 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 727958 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 727958 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A03_ClaireOlson_1_2_3(Cy5) GFF Report Workflow 2014-02-13 11:53:56[COMPLETED] was removed from job service submissions.
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728020 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728145 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728145 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:39 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728145 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:40 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728145 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728145 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728145 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 140ms
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728161 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728161 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728208 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Pair report
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728223 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728223 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:00:47,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728239 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:00:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728317 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Output directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson
2014-02-13 12:00:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728317 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Outputing report for Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321154837_774399534.tif
2014-02-13 12:00:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 728348 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - TempFile : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A01_ClaireOlson_1_2_3\tmp.1392321648046_1145681697\546409A01_ClaireOlson_1_2_3_635.tif
2014-02-13 12:00:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 729237 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:00:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 729237 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:01:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 762246 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A01_ClaireOlson_1_2_3\tmp.1392321648046_1145681697\546409A01_ClaireOlson_1_2_3_635.pair
2014-02-13 12:01:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 762246 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - fixing design name
2014-02-13 12:01:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 762340 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A01_ClaireOlson_1_2_3\tmp.1392321648046_1145681697\546409A01_ClaireOlson_1_2_3_635.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:00:59 PST 2014 border=0 ul_x=99.215 ul_y=189.687 ur_x=2956.693 ur_y=165.860 lr_x=2987.898 lr_y=3981.984 ll_x=130.544 ll_y=4005.175 qcscore=0.262 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.' = # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A01_ClaireOlson_1_2_3\tmp.1392321648046_1145681697\546409A01_ClaireOlson_1_2_3_635.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:00:59 PST 2014 border=0 ul_x=99.215 ul_y=189.687 ur_x=2956.693 ur_y=165.860 lr_x=2987.898 lr_y=3981.984 ll_x=130.544 ll_y=4005.175 qcscore=0.262 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.'
2014-02-13 12:01:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 774882 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A01_ClaireOlson_1_2_3\546409A01_ClaireOlson_1_2_3_2014-02-13T120134_635.pair
2014-02-13 12:01:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 774960 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Pair submitted
2014-02-13 12:01:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 774960 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:01:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 775116 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:01:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 775116 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:01:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 775147 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:01:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 775147 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A01_ClaireOlson_1_2_3(Cy5) Pair Report Workflow 2014-02-13 11:53:56[COMPLETED] was removed from job service submissions.
2014-02-13 12:01:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 775210 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:01:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 775319 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:01:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 775335 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:01:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 775335 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:01:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 775350 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 546409A01_ClaireOlson_1_2_3
2014-02-13 12:01:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 775397 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:01:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 775413 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:01:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 775413 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:01:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 775444 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:01:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 786442 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:01:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 786457 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:01:46,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321154837_774399534.xys...
2014-02-13 12:01:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 793399 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:01:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 793399 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:01:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 793415 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:01:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 793430 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:01:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 797361 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:02:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 801090 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812306 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812571 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812587 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812602 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812618 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812618 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:45 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812618 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:46 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812618 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812618 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812618 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 37424ms
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812618 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812618 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812665 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812680 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812680 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812696 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:02:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 812712 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 828826 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF report complete
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 828842 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF submitted
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 828842 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 828982 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 828982 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 828998 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 828998 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A01_ClaireOlson_1_2_3(Cy5) GFF Report Workflow 2014-02-13 11:53:57[COMPLETED] was removed from job service submissions.
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829060 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829185 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829185 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:62 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829185 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:63 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829185 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829185 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829185 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 140ms
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829185 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829185 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829247 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Pair report
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829263 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829263 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:02:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829279 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:02:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829372 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Output directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson
2014-02-13 12:02:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829372 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Outputing report for Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321153073_1131389620.tif
2014-02-13 12:02:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 829403 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - TempFile : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A02_ClaireOlson_1_2_3\tmp.1392321749086_1464768790\546409A02_ClaireOlson_1_2_3_635.tif
2014-02-13 12:02:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 830589 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:02:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 830589 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:03:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 863255 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A02_ClaireOlson_1_2_3\tmp.1392321749086_1464768790\546409A02_ClaireOlson_1_2_3_635.pair
2014-02-13 12:03:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 863255 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - fixing design name
2014-02-13 12:03:03,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 863349 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A02_ClaireOlson_1_2_3\tmp.1392321749086_1464768790\546409A02_ClaireOlson_1_2_3_635.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:02:41 PST 2014 border=0 ul_x=94.267 ul_y=186.289 ur_x=2951.570 ur_y=162.265 lr_x=2983.661 lr_y=3978.223 ll_x=126.053 ll_y=4002.376 qcscore=0.277 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.' = # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A02_ClaireOlson_1_2_3\tmp.1392321749086_1464768790\546409A02_ClaireOlson_1_2_3_635.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:02:41 PST 2014 border=0 ul_x=94.267 ul_y=186.289 ur_x=2951.570 ur_y=162.265 lr_x=2983.661 lr_y=3978.223 ll_x=126.053 ll_y=4002.376 qcscore=0.277 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.'
2014-02-13 12:03:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876125 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A02_ClaireOlson_1_2_3\546409A02_ClaireOlson_1_2_3_2014-02-13T120315_635.pair
2014-02-13 12:03:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876203 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Pair submitted
2014-02-13 12:03:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876203 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:03:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876374 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:03:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876374 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:03:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876390 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:03:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876406 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A02_ClaireOlson_1_2_3(Cy5) Pair Report Workflow 2014-02-13 11:53:57[COMPLETED] was removed from job service submissions.
2014-02-13 12:03:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876452 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:03:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876562 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:03:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876577 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:03:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876593 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:03:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876593 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 546409A02_ClaireOlson_1_2_3
2014-02-13 12:03:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876640 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:03:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876671 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:03:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876671 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:03:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 876702 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:03:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 887559 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:03:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 887591 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:03:27,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321153073_1131389620.xys...
2014-02-13 12:03:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 896857 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:03:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 896873 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:03:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 896873 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:03:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 896888 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:03:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 900570 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:03:43,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 904111 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:03:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915109 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915670 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915686 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915686 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915702 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915702 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:68 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915702 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:69 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915702 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915702 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915702 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39265ms
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915717 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915717 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915748 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915764 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915780 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915780 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:03:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 915795 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:04:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932003 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF report complete
2014-02-13 12:04:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932003 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF submitted
2014-02-13 12:04:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932019 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:04:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932175 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:04:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932175 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:04:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932191 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:04:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932206 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A02_ClaireOlson_1_2_3(Cy5) GFF Report Workflow 2014-02-13 11:53:58[COMPLETED] was removed from job service submissions.
2014-02-13 12:04:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932269 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:04:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932534 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:04:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932549 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:04:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932565 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:04:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932580 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 546409A03_ClaireOlson_1_2_3
2014-02-13 12:04:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932643 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:04:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932658 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:04:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932658 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:04:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 932690 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:04:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 943298 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:04:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 943313 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:04:23,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321255435_1709097168.xys...
2014-02-13 12:04:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 953188 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:04:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 953188 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:04:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 953203 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:04:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 953219 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:04:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 956729 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:04:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 960208 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:04:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971237 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971767 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971783 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971783 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971798 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971798 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:109 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971798 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:110 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971798 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971798 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971798 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39545ms
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971814 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971814 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971845 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 971986 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 972001 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 972001 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 972017 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 546409A03_ClaireOlson_1_2_3
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 972064 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 972095 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 972095 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:04:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 972142 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:05:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 982203 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:05:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 982219 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:05:02,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321151487_1842096315.xys...
2014-02-13 12:05:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 992453 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:05:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 992468 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:05:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 992468 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:05:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 992484 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:05:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 996134 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:05:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 999956 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011453 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011734 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011749 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011765 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011765 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011765 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:113 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011765 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:1 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011765 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011765 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011765 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39920ms
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011781 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011781 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011812 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:116 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011812 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run loess.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011859 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:111 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011859 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run loess.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011890 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:114 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011890 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Probe Uniqueness Filter.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011905 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:108 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011905 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Probe Uniqueness Filter.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:05:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1011952 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting calculating ratio.
2014-02-13 12:05:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1015244 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:112 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:05:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1015259 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed calculating ratio.
2014-02-13 12:05:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1015259 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run ratio.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:05:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1015790 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Biweight Mean Centering.
2014-02-13 12:05:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1015805 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Biweight mean value: -0.5559
2014-02-13 12:05:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1016336 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Biweight Mean Centering.
2014-02-13 12:05:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1016336 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:117 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:05:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1016336 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run biweight normalization.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:05:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1016367 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Merge Data operation.
2014-02-13 12:05:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1016398 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting averaging replicate data.
2014-02-13 12:05:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1016929 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed averaging replicate data.
2014-02-13 12:05:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1016929 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:115 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:05:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1016944 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Merge Data operation complete.
2014-02-13 12:05:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1016944 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Merge container data.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:05:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1016991 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for Merge Data.
2014-02-13 12:05:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1017007 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:16
2014-02-13 12:05:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1019066 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:2075
2014-02-13 12:05:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1019861 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:2870
2014-02-13 12:05:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1019877 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done saving analysis data for Merge Data.
2014-02-13 12:05:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1019877 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:output analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:05:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1019908 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF Report.
2014-02-13 12:06:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1040578 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed GFF Report.
2014-02-13 12:06:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1040578 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate GFF report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:06:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1040609 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Peak Identification
2014-02-13 12:08:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1199727 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:118 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:08:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1199743 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Peak Identification complete
2014-02-13 12:08:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1199743 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Peak Identification[COMPLETED] was removed from submitted tasks.
2014-02-13 12:08:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1199805 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF Report.
2014-02-13 12:08:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1200741 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed GFF Report.
2014-02-13 12:08:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1200741 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate GFF report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:08:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1200772 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for Peak Identification.
2014-02-13 12:08:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1200772 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:0
2014-02-13 12:08:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1200881 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:109
2014-02-13 12:08:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201162 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:390
2014-02-13 12:08:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201178 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done saving analysis data for Peak Identification.
2014-02-13 12:08:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201178 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:output analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201381 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201381 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201396 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201396 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A03_ClaireOlson_1_2_3(Cy5/Cy3) ChIP-chip Workflow 2014-02-13 11:55:36[COMPLETED] was removed from job service submissions.
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201537 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201724 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201724 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:123 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201724 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:124 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201724 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201724 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201724 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 187ms
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201739 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201739 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201771 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Pair report
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201786 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201802 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201802 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201895 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Output directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201895 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Outputing report for Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321255435_1709097168.tif
2014-02-13 12:08:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1201927 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - TempFile : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A03_ClaireOlson_1_2_3\tmp.1392322121609_1718985683\546409A03_ClaireOlson_1_2_3_532.tif
2014-02-13 12:08:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1202800 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:08:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1202800 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:09:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1235747 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A03_ClaireOlson_1_2_3\tmp.1392322121609_1718985683\546409A03_ClaireOlson_1_2_3_532.pair
2014-02-13 12:09:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1235747 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - fixing design name
2014-02-13 12:09:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1235841 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A03_ClaireOlson_1_2_3\tmp.1392322121609_1718985683\546409A03_ClaireOlson_1_2_3_532.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:08:53 PST 2014 border=0 ul_x=88.519 ul_y=181.776 ur_x=2945.838 ur_y=157.199 lr_x=2978.385 lr_y=3974.172 ll_x=121.183 ll_y=3998.385 qcscore=0.313 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.' = # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A03_ClaireOlson_1_2_3\tmp.1392322121609_1718985683\546409A03_ClaireOlson_1_2_3_532.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:08:53 PST 2014 border=0 ul_x=88.519 ul_y=181.776 ur_x=2945.838 ur_y=157.199 lr_x=2978.385 lr_y=3974.172 ll_x=121.183 ll_y=3998.385 qcscore=0.313 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.'
2014-02-13 12:09:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250224 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A03_ClaireOlson_1_2_3\546409A03_ClaireOlson_1_2_3_2014-02-13T120929_532.pair
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250302 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Pair submitted
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250302 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250458 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250458 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250489 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250489 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A03_ClaireOlson_1_2_3(Cy3) Pair Report Workflow 2014-02-13 11:55:37[COMPLETED] was removed from job service submissions.
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250536 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250692 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250707 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250707 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250723 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 546409A03_ClaireOlson_1_2_3
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250770 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250785 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250785 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:09:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1250816 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:09:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1261112 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:09:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1261128 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:09:41,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321255435_1709097168.xys...
2014-02-13 12:09:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1271127 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:09:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1271127 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:09:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1271143 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:09:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1271159 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:09:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1274715 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:09:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1278334 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:10:08,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289301 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289863 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289878 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289894 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289910 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289910 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:129 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289910 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:130 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289910 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289910 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289910 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39374ms
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289925 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289925 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289956 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289972 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289972 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1289988 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:10:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1290003 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:10:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306258 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF report complete
2014-02-13 12:10:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306258 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF submitted
2014-02-13 12:10:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306258 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:10:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306414 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:10:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306414 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:10:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306445 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:10:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306445 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A03_ClaireOlson_1_2_3(Cy3) GFF Report Workflow 2014-02-13 11:55:37[COMPLETED] was removed from job service submissions.
2014-02-13 12:10:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306492 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:10:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306617 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:10:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306633 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:10:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306648 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:10:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306648 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 546409A01_ClaireOlson_1_2_3
2014-02-13 12:10:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306695 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:10:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306726 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:10:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306726 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:10:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1306757 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:10:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1317412 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:10:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1317428 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:10:37,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321258623_157141311.xys...
2014-02-13 12:10:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1327255 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:10:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1327255 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:10:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1327255 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:10:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1327271 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:10:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1330828 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:10:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1334338 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1345367 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1345913 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1345913 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1345928 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1345944 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1345944 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:170 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1345944 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:171 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1345944 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1345944 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1345944 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39467ms
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1345960 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1345960 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1345991 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1346131 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1346131 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1346147 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1346162 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 546409A01_ClaireOlson_1_2_3
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1346209 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1346240 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1346240 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:11:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1346272 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:11:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1356396 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:11:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1356411 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:11:16,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321154837_774399534.xys...
2014-02-13 12:11:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1366349 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:11:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1366349 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:11:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1366411 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:11:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1366427 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:11:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1370061 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:11:33,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1373540 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:11:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1384959 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385302 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385318 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385333 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385365 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385365 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:174 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385365 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:1 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385365 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385365 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385365 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39390ms
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385380 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385411 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385443 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:177 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385443 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run loess.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385489 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:172 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385489 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run loess.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385521 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:175 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385521 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Probe Uniqueness Filter.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385536 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:169 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385536 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Probe Uniqueness Filter.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:11:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1385567 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting calculating ratio.
2014-02-13 12:11:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1388687 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:173 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:11:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1388687 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed calculating ratio.
2014-02-13 12:11:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1388687 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run ratio.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:11:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1389218 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Biweight Mean Centering.
2014-02-13 12:11:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1389218 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Biweight mean value: -0.8872
2014-02-13 12:11:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1389670 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Biweight Mean Centering.
2014-02-13 12:11:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1389670 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:178 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:11:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1389670 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run biweight normalization.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:11:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1389701 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Merge Data operation.
2014-02-13 12:11:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1389733 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting averaging replicate data.
2014-02-13 12:11:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1390169 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed averaging replicate data.
2014-02-13 12:11:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1390169 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:176 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:11:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1390185 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Merge Data operation complete.
2014-02-13 12:11:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1390185 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Merge container data.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:11:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1390232 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF Report.
2014-02-13 12:12:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1410496 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed GFF Report.
2014-02-13 12:12:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1410496 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate GFF report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:12:10,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1410527 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Peak Identification
2014-02-13 12:14:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1568818 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:179 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:14:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1568834 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Peak Identification complete
2014-02-13 12:14:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1568834 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Peak Identification[COMPLETED] was removed from submitted tasks.
2014-02-13 12:14:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1568865 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for Merge Data.
2014-02-13 12:14:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1568881 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:16
2014-02-13 12:14:50,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1570737 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:1872
2014-02-13 12:14:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1571517 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:2652
2014-02-13 12:14:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1571517 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done saving analysis data for Merge Data.
2014-02-13 12:14:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1571517 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:output analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:14:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1571548 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF Report.
2014-02-13 12:14:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1572203 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed GFF Report.
2014-02-13 12:14:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1572203 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate GFF report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:14:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1572235 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for Peak Identification.
2014-02-13 12:14:51,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1572235 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:0
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1572328 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:93
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1572640 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:405
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1572656 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done saving analysis data for Peak Identification.
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1572656 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:output analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1572905 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1572921 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1572937 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1572937 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A01_ClaireOlson_1_2_3(Cy5/Cy3) ChIP-chip Workflow 2014-02-13 11:55:37[COMPLETED] was removed from job service submissions.
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573015 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573155 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573155 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:184 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573155 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:185 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573155 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573155 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573155 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 156ms
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573155 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573155 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573186 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Pair report
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573202 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573202 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573217 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573295 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Output directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson
2014-02-13 12:14:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573295 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Outputing report for Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321258623_157141311.tif
2014-02-13 12:14:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1573327 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - TempFile : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A01_ClaireOlson_1_2_3\tmp.1392322493025_1167874577\546409A01_ClaireOlson_1_2_3_532.tif
2014-02-13 12:14:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1574185 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:14:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1574185 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:15:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1606710 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A01_ClaireOlson_1_2_3\tmp.1392322493025_1167874577\546409A01_ClaireOlson_1_2_3_532.pair
2014-02-13 12:15:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1606710 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - fixing design name
2014-02-13 12:15:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1606788 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A01_ClaireOlson_1_2_3\tmp.1392322493025_1167874577\546409A01_ClaireOlson_1_2_3_532.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:15:04 PST 2014 border=0 ul_x=99.507 ul_y=189.746 ur_x=2956.872 ur_y=165.575 lr_x=2988.208 lr_y=3981.419 ll_x=130.731 ll_y=4005.568 qcscore=0.273 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.' = # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A01_ClaireOlson_1_2_3\tmp.1392322493025_1167874577\546409A01_ClaireOlson_1_2_3_532.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:15:04 PST 2014 border=0 ul_x=99.507 ul_y=189.746 ur_x=2956.872 ur_y=165.575 lr_x=2988.208 lr_y=3981.419 ll_x=130.731 ll_y=4005.568 qcscore=0.273 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.'
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619408 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A01_ClaireOlson_1_2_3\546409A01_ClaireOlson_1_2_3_2014-02-13T121539_532.pair
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619486 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Pair submitted
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619486 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619642 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619642 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619674 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619674 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A01_ClaireOlson_1_2_3(Cy3) Pair Report Workflow 2014-02-13 11:55:38[COMPLETED] was removed from job service submissions.
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619720 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619845 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619861 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619861 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619876 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 546409A01_ClaireOlson_1_2_3
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619923 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619939 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619939 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:15:39,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1619970 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:15:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1630094 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:15:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1630110 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:15:50,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321258623_157141311.xys...
2014-02-13 12:15:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1640156 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:15:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1640156 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:15:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1640172 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:15:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1640187 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:16:03,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1643760 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:16:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1647551 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:16:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1658845 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659422 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659438 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659438 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659453 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659453 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:190 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659453 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:191 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659453 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659453 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659453 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39748ms
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659469 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659469 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659500 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659500 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659516 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659531 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:16:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1659531 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1675599 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF report complete
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1675599 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF submitted
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1675599 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1675755 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1675755 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1675771 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1675771 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A01_ClaireOlson_1_2_3(Cy3) GFF Report Workflow 2014-02-13 11:55:38[COMPLETED] was removed from job service submissions.
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1675833 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1676020 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1676036 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1676036 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1676051 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 546409A02_ClaireOlson_1_2_3
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1676098 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1676114 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1676129 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:16:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1676145 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:16:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1686862 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:16:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1686878 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:16:46,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321256918_680220543.xys...
2014-02-13 12:16:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1697392 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:16:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1697392 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:16:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1697407 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:16:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1697423 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:17:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1700980 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:17:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1704630 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:17:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716190 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716736 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716736 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716751 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716767 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716767 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:231 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716767 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:232 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716767 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716767 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716767 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 40950ms
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716782 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716782 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716798 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716938 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716954 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716954 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1716970 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 546409A02_ClaireOlson_1_2_3
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1717016 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1717048 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1717048 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:17:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1717079 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:17:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1727250 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:17:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1727266 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:17:27,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321153073_1131389620.xys...
2014-02-13 12:17:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1737249 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:17:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1737249 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:17:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1737265 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:17:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1737281 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:17:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1740791 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:17:43,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1744176 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755501 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755782 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755782 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755798 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755813 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755813 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:235 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755813 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:1 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755813 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755813 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755813 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39015ms
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755813 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755813 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755844 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:238 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755844 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run loess.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755876 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:233 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755876 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run loess.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755891 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:236 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755891 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Probe Uniqueness Filter.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755907 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:230 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755907 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Probe Uniqueness Filter.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:17:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1755938 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting calculating ratio.
2014-02-13 12:17:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1759089 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:234 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:17:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1759105 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed calculating ratio.
2014-02-13 12:17:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1759105 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run ratio.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:17:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1759604 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Biweight Mean Centering.
2014-02-13 12:17:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1759604 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Biweight mean value: -1.0474
2014-02-13 12:17:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1760056 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Biweight Mean Centering.
2014-02-13 12:17:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1760056 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:239 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:17:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1760056 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run biweight normalization.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:17:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1760087 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Merge Data operation.
2014-02-13 12:17:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1760103 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting averaging replicate data.
2014-02-13 12:18:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1760555 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed averaging replicate data.
2014-02-13 12:18:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1760555 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:237 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:18:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1760555 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Merge Data operation complete.
2014-02-13 12:18:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1760555 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Merge container data.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:18:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1760618 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for Merge Data.
2014-02-13 12:18:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1760633 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:15
2014-02-13 12:18:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1762459 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:1841
2014-02-13 12:18:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1763207 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:2589
2014-02-13 12:18:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1763207 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done saving analysis data for Merge Data.
2014-02-13 12:18:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1763207 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:output analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:18:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1763239 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF Report.
2014-02-13 12:18:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1783378 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed GFF Report.
2014-02-13 12:18:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1783378 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate GFF report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:18:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1783394 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Peak Identification
2014-02-13 12:21:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1941388 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:240 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:21:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1941404 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Peak Identification complete
2014-02-13 12:21:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1941404 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Peak Identification[COMPLETED] was removed from submitted tasks.
2014-02-13 12:21:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1941451 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF Report.
2014-02-13 12:21:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942090 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed GFF Report.
2014-02-13 12:21:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942090 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate GFF report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:21:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942106 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for Peak Identification.
2014-02-13 12:21:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942122 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:16
2014-02-13 12:21:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942246 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:140
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942480 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:374
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942496 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done saving analysis data for Peak Identification.
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942496 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:output analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942652 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942652 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942683 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942683 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A02_ClaireOlson_1_2_3(Cy5/Cy3) ChIP-chip Workflow 2014-02-13 11:55:38[COMPLETED] was removed from job service submissions.
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942730 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942886 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942886 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:245 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942886 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:246 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942886 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942886 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942886 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 172ms
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942902 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942902 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942933 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Pair report
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942948 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942948 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1942964 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1943042 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Output directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1943042 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Outputing report for Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321256918_680220543.tif
2014-02-13 12:21:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1943073 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - TempFile : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A02_ClaireOlson_1_2_3\tmp.1392322862771_761423084\546409A02_ClaireOlson_1_2_3_532.tif
2014-02-13 12:21:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1944618 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:21:04,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1944618 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:21:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1976862 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A02_ClaireOlson_1_2_3\tmp.1392322862771_761423084\546409A02_ClaireOlson_1_2_3_532.pair
2014-02-13 12:21:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1976862 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - fixing design name
2014-02-13 12:21:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1976956 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A02_ClaireOlson_1_2_3\tmp.1392322862771_761423084\546409A02_ClaireOlson_1_2_3_532.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:21:14 PST 2014 border=0 ul_x=94.375 ul_y=186.085 ur_x=2951.847 ur_y=161.782 lr_x=2983.734 lr_y=3978.439 ll_x=126.530 ll_y=4002.524 qcscore=0.308 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.' = # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A02_ClaireOlson_1_2_3\tmp.1392322862771_761423084\546409A02_ClaireOlson_1_2_3_532.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:21:14 PST 2014 border=0 ul_x=94.375 ul_y=186.085 ur_x=2951.847 ur_y=161.782 lr_x=2983.734 lr_y=3978.439 ll_x=126.530 ll_y=4002.524 qcscore=0.308 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.'
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989420 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\546409_ClaireOlson_1_2_3\546409A02_ClaireOlson_1_2_3\546409A02_ClaireOlson_1_2_3_2014-02-13T122149_532.pair
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989498 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Pair submitted
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989498 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989639 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989639 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989654 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989654 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A02_ClaireOlson_1_2_3(Cy3) Pair Report Workflow 2014-02-13 11:55:39[COMPLETED] was removed from job service submissions.
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989701 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989857 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989857 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989873 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989873 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 546409A02_ClaireOlson_1_2_3
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989966 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989982 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1989982 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:21:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 1990013 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:21:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2000168 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:21:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2000200 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:22:00,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321256918_680220543.xys...
2014-02-13 12:22:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2009778 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:22:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2009778 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:22:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2009793 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:22:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2009793 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:22:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2013335 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:22:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2017578 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028326 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028872 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028888 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028903 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028903 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028903 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:251 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028903 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:252 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028919 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028919 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028919 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39218ms
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028919 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028919 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028950 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028966 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028981 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028981 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:22:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2028997 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:22:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045080 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF report complete
2014-02-13 12:22:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045096 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF submitted
2014-02-13 12:22:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045096 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:22:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045236 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:22:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045236 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:22:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045252 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:22:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045252 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:546409A02_ClaireOlson_1_2_3(Cy3) GFF Report Workflow 2014-02-13 11:55:39[COMPLETED] was removed from job service submissions.
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045314 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045470 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045470 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:268 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045470 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:269 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045470 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045470 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045470 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 171ms
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045486 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045486 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045517 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Pair report
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045533 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045548 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045564 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045657 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Output directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045657 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Outputing report for Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321355760_1552122293.tif
2014-02-13 12:22:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2045673 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - TempFile : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A03_ClaireOlson_4_5_6\tmp.1392322965371_1354217676\558216A03_ClaireOlson_4_5_6_532.tif
2014-02-13 12:22:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2046827 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:22:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2046827 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:23:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2080336 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A03_ClaireOlson_4_5_6\tmp.1392322965371_1354217676\558216A03_ClaireOlson_4_5_6_532.pair
2014-02-13 12:23:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2080336 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - fixing design name
2014-02-13 12:23:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2080461 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A03_ClaireOlson_4_5_6\tmp.1392322965371_1354217676\558216A03_ClaireOlson_4_5_6_532.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:22:57 PST 2014 border=0 ul_x=97.272 ul_y=189.612 ur_x=2955.288 ur_y=179.165 lr_x=2968.723 lr_y=3996.197 ll_x=111.208 ll_y=4006.068 qcscore=0.320 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.' = # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A03_ClaireOlson_4_5_6\tmp.1392322965371_1354217676\558216A03_ClaireOlson_4_5_6_532.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:22:57 PST 2014 border=0 ul_x=97.272 ul_y=189.612 ur_x=2955.288 ur_y=179.165 lr_x=2968.723 lr_y=3996.197 ll_x=111.208 ll_y=4006.068 qcscore=0.320 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.'
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2092597 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A03_ClaireOlson_4_5_6\558216A03_ClaireOlson_4_5_6_2014-02-13T122332_532.pair
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2092675 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Pair submitted
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2092675 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2092987 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2092987 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2093003 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2093003 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A03_ClaireOlson_4_5_6(Cy3) Pair Report Workflow 2014-02-13 11:56:51[COMPLETED] was removed from job service submissions.
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2093050 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2093206 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2093206 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2093221 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2093221 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 558216A03_ClaireOlson_4_5_6
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2093268 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2093299 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:23:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2093299 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:23:33,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2093330 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:23:43,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2104266 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:23:43,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2104281 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:23:44,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321355760_1552122293.xys...
2014-02-13 12:23:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2114078 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:23:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2114078 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:23:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2114094 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:23:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2114109 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:23:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2117713 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:24:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2121441 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132595 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132860 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132876 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132892 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132907 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132907 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:274 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132907 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:275 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132907 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132907 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132907 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39857ms
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132907 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132907 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132938 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132954 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132954 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132970 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:24:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2132985 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:24:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149100 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF report complete
2014-02-13 12:24:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149115 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF submitted
2014-02-13 12:24:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149115 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:24:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149256 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:24:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149256 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:24:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149271 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:24:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149271 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A03_ClaireOlson_4_5_6(Cy3) GFF Report Workflow 2014-02-13 11:56:51[COMPLETED] was removed from job service submissions.
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149318 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149474 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149474 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:291 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149474 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:292 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149474 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149474 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149474 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 156ms
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149490 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149490 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149521 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Pair report
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149536 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149536 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149568 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149630 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Output directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149630 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Outputing report for Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321358724_217219257.tif
2014-02-13 12:24:29,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2149661 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - TempFile : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A01_ClaireOlson_4_5_6\tmp.1392323069359_1981015150\558216A01_ClaireOlson_4_5_6_532.tif
2014-02-13 12:24:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2150878 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:24:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2150878 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:25:03,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2183372 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A01_ClaireOlson_4_5_6\tmp.1392323069359_1981015150\558216A01_ClaireOlson_4_5_6_532.pair
2014-02-13 12:25:03,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2183372 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - fixing design name
2014-02-13 12:25:03,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2183466 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A01_ClaireOlson_4_5_6\tmp.1392323069359_1981015150\558216A01_ClaireOlson_4_5_6_532.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:24:41 PST 2014 border=0 ul_x=111.600 ul_y=197.610 ur_x=2969.285 ur_y=187.880 lr_x=2981.247 lr_y=4003.650 ll_x=123.055 ll_y=4012.758 qcscore=0.292 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.' = # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A01_ClaireOlson_4_5_6\tmp.1392323069359_1981015150\558216A01_ClaireOlson_4_5_6_532.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:24:41 PST 2014 border=0 ul_x=111.600 ul_y=197.610 ur_x=2969.285 ur_y=187.880 lr_x=2981.247 lr_y=4003.650 ll_x=123.055 ll_y=4012.758 qcscore=0.292 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.'
2014-02-13 12:25:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2195962 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A01_ClaireOlson_4_5_6\558216A01_ClaireOlson_4_5_6_2014-02-13T122515_532.pair
2014-02-13 12:25:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196040 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Pair submitted
2014-02-13 12:25:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196040 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:25:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196195 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:25:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196195 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:25:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196211 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:25:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196211 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A01_ClaireOlson_4_5_6(Cy3) Pair Report Workflow 2014-02-13 11:57:16[COMPLETED] was removed from job service submissions.
2014-02-13 12:25:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196258 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:25:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196383 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:25:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196445 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:25:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196461 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:25:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196461 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 558216A01_ClaireOlson_4_5_6
2014-02-13 12:25:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196507 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:25:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196539 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:25:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196539 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:25:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2196554 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:25:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2207474 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:25:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2207490 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:25:27,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321358724_217219257.xys...
2014-02-13 12:25:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2216881 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:25:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2216881 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:25:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2216896 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:25:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2216912 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:25:40,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2220469 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:25:43,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2223979 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:25:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2234727 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235304 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235304 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235320 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235335 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235335 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:297 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235335 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:298 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235335 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235335 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235335 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39093ms
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235351 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235351 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235367 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235382 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235382 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235398 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:25:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2235413 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251372 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF report complete
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251388 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF submitted
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251388 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251528 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251528 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251544 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251544 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A01_ClaireOlson_4_5_6(Cy3) GFF Report Workflow 2014-02-13 11:57:17[COMPLETED] was removed from job service submissions.
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251668 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251793 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251793 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:314 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251793 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:315 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251793 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251793 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251793 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 203ms
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251809 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251809 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251824 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Pair report
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251840 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251856 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251856 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251934 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Output directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251934 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Outputing report for Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321357227_535216215.tif
2014-02-13 12:26:11,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2251965 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - TempFile : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A02_ClaireOlson_4_5_6\tmp.1392323171663_15562647\558216A02_ClaireOlson_4_5_6_532.tif
2014-02-13 12:26:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2253010 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:26:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2253010 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:26:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2284974 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A02_ClaireOlson_4_5_6\tmp.1392323171663_15562647\558216A02_ClaireOlson_4_5_6_532.pair
2014-02-13 12:26:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2284974 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - fixing design name
2014-02-13 12:26:44,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2285068 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A02_ClaireOlson_4_5_6\tmp.1392323171663_15562647\558216A02_ClaireOlson_4_5_6_532.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:26:23 PST 2014 border=0 ul_x=105.105 ul_y=193.980 ur_x=2962.680 ur_y=183.883 lr_x=2975.552 lr_y=4000.412 ll_x=117.944 ll_y=4010.020 qcscore=0.299 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.' = # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A02_ClaireOlson_4_5_6\tmp.1392323171663_15562647\558216A02_ClaireOlson_4_5_6_532.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:26:23 PST 2014 border=0 ul_x=105.105 ul_y=193.980 ur_x=2962.680 ur_y=183.883 lr_x=2975.552 lr_y=4000.412 ll_x=117.944 ll_y=4010.020 qcscore=0.299 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.'
2014-02-13 12:26:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2296783 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A02_ClaireOlson_4_5_6\558216A02_ClaireOlson_4_5_6_2014-02-13T122656_532.pair
2014-02-13 12:26:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2296877 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Pair submitted
2014-02-13 12:26:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2296877 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:26:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2297017 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:26:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2297017 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:26:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2297033 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:26:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2297033 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A02_ClaireOlson_4_5_6(Cy3) Pair Report Workflow 2014-02-13 11:57:17[COMPLETED] was removed from job service submissions.
2014-02-13 12:26:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2297079 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:26:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2297204 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:26:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2297267 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:26:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2297282 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:26:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2297282 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 558216A02_ClaireOlson_4_5_6
2014-02-13 12:26:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2297329 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:26:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2297345 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:26:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2297345 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:26:57,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2297376 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:27:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2308171 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:27:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2308186 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:27:07,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321357227_535216215.xys...
2014-02-13 12:27:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2317687 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:27:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2317687 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:27:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2317687 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:27:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2317702 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:27:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2321321 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:27:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2325175 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337311 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337592 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337608 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337623 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337639 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337639 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:320 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337639 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:321 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337639 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337639 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337639 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 40560ms
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337639 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337654 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337670 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337686 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337686 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337701 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:27:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2337717 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:27:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355033 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF report complete
2014-02-13 12:27:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355033 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF submitted
2014-02-13 12:27:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355033 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:27:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355189 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:27:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355204 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:27:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355220 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:27:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355220 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A02_ClaireOlson_4_5_6(Cy3) GFF Report Workflow 2014-02-13 11:57:17[COMPLETED] was removed from job service submissions.
2014-02-13 12:27:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355282 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:27:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355438 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:27:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355454 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:27:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355469 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:27:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355485 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 558216A02_ClaireOlson_4_5_6
2014-02-13 12:27:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355532 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:27:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355547 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:27:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355547 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:27:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2355579 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:28:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2365921 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:28:05,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2365937 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:28:05,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321357227_535216215.xys...
2014-02-13 12:28:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2376264 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:28:15,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2376264 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:28:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2376373 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:28:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2376389 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:28:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2379946 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:28:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2383393 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2394547 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2394828 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2394828 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2394843 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2394859 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2394859 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:361 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2394859 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:362 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2394859 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2394859 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2394859 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39592ms
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2394875 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2394875 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2394890 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2395015 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2395031 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2395031 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2395046 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 558216A02_ClaireOlson_4_5_6
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2395109 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2395155 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2395155 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:28:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2395202 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:28:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2405326 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:28:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2405342 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:28:45,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321456519_379867819.xys...
2014-02-13 12:28:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2415373 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:28:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2415373 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:28:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2415388 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:28:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2415404 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:28:58,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2418914 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:29:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2422330 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2433718 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2433999 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434014 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434014 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434030 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434030 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:365 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434030 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:1 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434030 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434030 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434030 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39155ms
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434046 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434046 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434061 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:368 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434061 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run loess.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434092 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:363 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434092 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run loess.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434108 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:366 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434108 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Probe Uniqueness Filter.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434108 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:360 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434108 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Probe Uniqueness Filter.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:29:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2434124 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting calculating ratio.
2014-02-13 12:29:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2437290 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:364 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:29:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2437290 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed calculating ratio.
2014-02-13 12:29:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2437290 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run ratio.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:29:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2437805 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Biweight Mean Centering.
2014-02-13 12:29:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2437805 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Biweight mean value: -0.3584
2014-02-13 12:29:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2438226 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Biweight Mean Centering.
2014-02-13 12:29:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2438226 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:369 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:29:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2438226 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run biweight normalization.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:29:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2438258 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Merge Data operation.
2014-02-13 12:29:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2438273 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting averaging replicate data.
2014-02-13 12:29:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2438726 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed averaging replicate data.
2014-02-13 12:29:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2438726 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:367 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:29:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2438726 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Merge Data operation complete.
2014-02-13 12:29:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2438726 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Merge container data.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:29:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2438757 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Peak Identification
2014-02-13 12:31:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2596954 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:370 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:31:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2596970 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Peak Identification complete
2014-02-13 12:31:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2596970 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Peak Identification[COMPLETED] was removed from submitted tasks.
2014-02-13 12:31:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2596986 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF Report.
2014-02-13 12:32:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2617390 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed GFF Report.
2014-02-13 12:32:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2617390 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate GFF report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:32:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2617406 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for Merge Data.
2014-02-13 12:32:17,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2617421 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:15
2014-02-13 12:32:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2619387 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:1981
2014-02-13 12:32:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2620416 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:3010
2014-02-13 12:32:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2620416 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done saving analysis data for Merge Data.
2014-02-13 12:32:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2620416 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:output analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:32:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2620448 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF Report.
2014-02-13 12:32:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621103 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed GFF Report.
2014-02-13 12:32:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621103 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate GFF report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:32:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621118 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for Peak Identification.
2014-02-13 12:32:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621118 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:0
2014-02-13 12:32:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621212 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:94
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621508 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:390
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621524 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done saving analysis data for Peak Identification.
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621524 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:output analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621680 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621680 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621696 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621696 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A02_ClaireOlson_4_5_6(Cy5/Cy3) ChIP-chip Workflow 2014-02-13 11:58:56[COMPLETED] was removed from job service submissions.
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621742 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621914 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621914 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:375 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621914 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:376 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621914 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621914 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621914 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 187ms
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621930 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621930 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621945 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Pair report
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621961 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621961 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2621976 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2622054 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Output directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2622054 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Outputing report for Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321456519_379867819.tif
2014-02-13 12:32:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2622070 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - TempFile : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A02_ClaireOlson_4_5_6\tmp.1392323541768_1079867662\558216A02_ClaireOlson_4_5_6_635.tif
2014-02-13 12:32:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2623053 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:32:22,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2623053 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:32:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2655224 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A02_ClaireOlson_4_5_6\tmp.1392323541768_1079867662\558216A02_ClaireOlson_4_5_6_635.pair
2014-02-13 12:32:54,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2655224 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - fixing design name
2014-02-13 12:32:55,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2655310 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A02_ClaireOlson_4_5_6\tmp.1392323541768_1079867662\558216A02_ClaireOlson_4_5_6_635.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:32:33 PST 2014 border=0 ul_x=105.130 ul_y=193.839 ur_x=2962.585 ur_y=184.189 lr_x=2975.504 lr_y=4000.542 ll_x=117.540 ll_y=4009.758 qcscore=0.276 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.' = # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A02_ClaireOlson_4_5_6\tmp.1392323541768_1079867662\558216A02_ClaireOlson_4_5_6_635.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:32:33 PST 2014 border=0 ul_x=105.130 ul_y=193.839 ur_x=2962.585 ur_y=184.189 lr_x=2975.504 lr_y=4000.542 ll_x=117.540 ll_y=4009.758 qcscore=0.276 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.'
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667380 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A02_ClaireOlson_4_5_6\558216A02_ClaireOlson_4_5_6_2014-02-13T123307_635.pair
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667464 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Pair submitted
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667465 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667601 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667602 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667620 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667621 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A02_ClaireOlson_4_5_6(Cy5) Pair Report Workflow 2014-02-13 11:58:56[COMPLETED] was removed from job service submissions.
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667659 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667793 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667804 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667814 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667825 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 558216A02_ClaireOlson_4_5_6
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667869 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667894 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667894 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:33:07,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2667922 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:33:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2678735 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:33:18,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2678752 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:33:18,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321456519_379867819.xys...
2014-02-13 12:33:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2688140 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:33:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2688142 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:33:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2688194 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:33:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2688205 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:33:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2691751 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:33:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2695284 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:33:45,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706022 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706508 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706519 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706528 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706538 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706538 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:381 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706538 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:382 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706538 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706539 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706539 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 38890ms
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706548 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706548 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706599 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706609 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706618 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706628 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:33:46,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2706638 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2722710 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF report complete
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2722720 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF submitted
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2722721 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2722847 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2722848 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2722865 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2722866 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A02_ClaireOlson_4_5_6(Cy5) GFF Report Workflow 2014-02-13 11:58:56[COMPLETED] was removed from job service submissions.
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2722908 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2723051 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2723061 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2723071 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2723081 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 558216A01_ClaireOlson_4_5_6
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2723124 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2723146 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2723146 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:34:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2723174 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:34:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2733752 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:34:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2733767 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:34:13,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321358724_217219257.xys...
2014-02-13 12:34:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2743997 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:34:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2743999 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:34:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2744008 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:34:23,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2744018 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:34:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2747568 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:34:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2751015 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:34:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762137 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762412 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762423 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762433 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762445 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762446 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:422 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762446 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:423 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762446 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762446 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762446 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39548ms
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762456 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762456 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762473 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762616 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762626 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762639 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762649 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 558216A01_ClaireOlson_4_5_6
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762692 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762724 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762724 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:34:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2762751 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:34:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2772903 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:34:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2772922 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:34:52,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321458189_2028694249.xys...
2014-02-13 12:35:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2782896 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:35:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2782898 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:35:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2782907 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:35:02,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2782917 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:35:06,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2786429 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:35:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2789839 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:35:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801098 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801383 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801394 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801407 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801418 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801418 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:426 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801418 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:1 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801418 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801419 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801419 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 38955ms
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801428 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801429 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801449 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:429 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801449 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run loess.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801471 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:424 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801471 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run loess.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801478 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:427 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801478 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Probe Uniqueness Filter.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801482 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:421 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801483 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Probe Uniqueness Filter.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:35:21,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2801499 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting calculating ratio.
2014-02-13 12:35:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2804691 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:425 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:35:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2804703 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed calculating ratio.
2014-02-13 12:35:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2804703 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run ratio.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:35:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2805208 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Biweight Mean Centering.
2014-02-13 12:35:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2805219 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Biweight mean value: -0.2523
2014-02-13 12:35:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2805648 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Biweight Mean Centering.
2014-02-13 12:35:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2805649 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:430 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:35:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2805649 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run biweight normalization.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:35:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2805667 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Merge Data operation.
2014-02-13 12:35:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2805690 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting averaging replicate data.
2014-02-13 12:35:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2806131 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed averaging replicate data.
2014-02-13 12:35:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2806131 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:428 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:35:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2806141 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Merge Data operation complete.
2014-02-13 12:35:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2806142 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Merge container data.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:35:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2806161 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for Merge Data.
2014-02-13 12:35:25,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2806175 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:13
2014-02-13 12:35:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2808008 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:1846
2014-02-13 12:35:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2808735 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:2573
2014-02-13 12:35:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2808746 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done saving analysis data for Merge Data.
2014-02-13 12:35:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2808747 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:output analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:35:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2808762 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF Report.
2014-02-13 12:35:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2829480 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed GFF Report.
2014-02-13 12:35:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2829481 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate GFF report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:35:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2829497 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Peak Identification
2014-02-13 12:38:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2986544 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:431 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:38:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2986560 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Peak Identification complete
2014-02-13 12:38:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2986560 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Peak Identification[COMPLETED] was removed from submitted tasks.
2014-02-13 12:38:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2986576 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF Report.
2014-02-13 12:38:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2987246 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed GFF Report.
2014-02-13 12:38:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2987246 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate GFF report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:38:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2987262 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for Peak Identification.
2014-02-13 12:38:26,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2987262 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:0
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2987356 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:94
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2987590 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:328
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2987590 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done saving analysis data for Peak Identification.
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2987590 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:output analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2987761 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2987761 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2987777 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2987777 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A01_ClaireOlson_4_5_6(Cy5/Cy3) ChIP-chip Workflow 2014-02-13 11:58:57[COMPLETED] was removed from job service submissions.
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2987824 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988042 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988042 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:436 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988042 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:437 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988042 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988042 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988042 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 234ms
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988058 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988058 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988073 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Pair report
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988073 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988089 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988104 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988182 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Output directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988182 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Outputing report for Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321458189_2028694249.tif
2014-02-13 12:38:27,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2988214 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - TempFile : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A01_ClaireOlson_4_5_6\tmp.1392323907912_22543965\558216A01_ClaireOlson_4_5_6_635.tif
2014-02-13 12:38:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2989103 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:38:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 2989103 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:39:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3021285 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A01_ClaireOlson_4_5_6\tmp.1392323907912_22543965\558216A01_ClaireOlson_4_5_6_635.pair
2014-02-13 12:39:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3021285 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - fixing design name
2014-02-13 12:39:01,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3021379 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A01_ClaireOlson_4_5_6\tmp.1392323907912_22543965\558216A01_ClaireOlson_4_5_6_635.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:38:38 PST 2014 border=0 ul_x=111.483 ul_y=197.478 ur_x=2969.104 ur_y=188.324 lr_x=2981.206 lr_y=4004.011 ll_x=123.386 ll_y=4012.794 qcscore=0.292 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.' = # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A01_ClaireOlson_4_5_6\tmp.1392323907912_22543965\558216A01_ClaireOlson_4_5_6_635.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:38:38 PST 2014 border=0 ul_x=111.483 ul_y=197.478 ur_x=2969.104 ur_y=188.324 lr_x=2981.206 lr_y=4004.011 ll_x=123.386 ll_y=4012.794 qcscore=0.292 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.'
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3033500 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A01_ClaireOlson_4_5_6\558216A01_ClaireOlson_4_5_6_2014-02-13T123913_635.pair
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3033578 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Pair submitted
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3033578 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3033718 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3033718 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3033734 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3033734 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A01_ClaireOlson_4_5_6(Cy5) Pair Report Workflow 2014-02-13 11:58:57[COMPLETED] was removed from job service submissions.
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3033781 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3033937 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3033937 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3033952 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3033968 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 558216A01_ClaireOlson_4_5_6
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3033999 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3034030 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3034030 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:39:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3034061 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:39:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3044841 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:39:24,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3044856 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:39:24,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321458189_2028694249.xys...
2014-02-13 12:39:33,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3054263 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:39:33,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3054279 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:39:33,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3054279 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:39:33,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3054294 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:39:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3058241 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:39:41,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3061938 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:39:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3072967 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:39:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073248 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:39:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073264 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:39:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073264 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:39:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073279 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:39:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073279 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:442 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:39:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073279 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:443 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:39:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073279 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:39:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073279 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:39:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073279 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39514ms
2014-02-13 12:39:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073295 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:39:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073295 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:39:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073311 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:39:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073311 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:39:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073326 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:39:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073326 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:39:53,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3073342 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3089534 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF report complete
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3089534 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF submitted
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3089534 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3089659 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3089675 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3089690 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3089690 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A01_ClaireOlson_4_5_6(Cy5) GFF Report Workflow 2014-02-13 11:58:58[COMPLETED] was removed from job service submissions.
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3089722 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3089924 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3089940 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3089956 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3089956 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 558216A03_ClaireOlson_4_5_6
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3090002 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3090018 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3090018 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:40:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3090049 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:40:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3100610 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:40:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3100626 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:40:20,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321454991_1409981611.xys...
2014-02-13 12:40:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3110937 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:40:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3110937 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:40:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3110953 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:40:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3110968 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:40:34,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3114525 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:40:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3117973 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:40:48,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129064 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129361 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129361 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129376 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129392 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129392 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:487 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129392 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:1 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129392 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129392 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129392 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39670ms
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129407 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129407 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129407 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129563 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129563 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129595 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129595 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 558216A03_ClaireOlson_4_5_6
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129641 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129673 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129673 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:40:49,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3129704 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:40:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3139812 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:40:59,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3139828 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:40:59,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321355760_1552122293.xys...
2014-02-13 12:41:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3149812 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:41:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3149812 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:41:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3149828 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:41:09,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3149828 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:41:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3153384 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:41:16,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3156785 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168563 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168859 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168859 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168875 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168890 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168890 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:483 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168890 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:484 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168890 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168890 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168890 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 39483ms
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168906 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168906 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168922 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:485 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168922 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run loess.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168937 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:490 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168937 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run loess.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168937 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:482 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168937 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Probe Uniqueness Filter.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168937 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:488 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168937 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Probe Uniqueness Filter.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:41:28,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3168953 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting calculating ratio.
2014-02-13 12:41:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3172166 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:486 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:41:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3172166 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed calculating ratio.
2014-02-13 12:41:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3172166 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run ratio.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:41:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3172666 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Biweight Mean Centering.
2014-02-13 12:41:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3172681 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Biweight mean value: -0.2324
2014-02-13 12:41:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3173134 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Biweight Mean Centering.
2014-02-13 12:41:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3173134 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:491 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:41:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3173134 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run biweight normalization.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:41:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3173149 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Merge Data operation.
2014-02-13 12:41:32,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3173165 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting averaging replicate data.
2014-02-13 12:41:33,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3173617 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed averaging replicate data.
2014-02-13 12:41:33,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3173617 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:489 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:41:33,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3173633 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Merge Data operation complete.
2014-02-13 12:41:33,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3173633 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Merge container data.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:41:33,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3173648 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for Merge Data.
2014-02-13 12:41:33,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3173648 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:0
2014-02-13 12:41:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3175505 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:1857
2014-02-13 12:41:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3176316 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:2668
2014-02-13 12:41:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3176316 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done saving analysis data for Merge Data.
2014-02-13 12:41:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3176332 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:output analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:41:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3176332 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF Report.
2014-02-13 12:41:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3196580 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed GFF Report.
2014-02-13 12:41:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3196580 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate GFF report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:41:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3196596 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Peak Identification
2014-02-13 12:44:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3356228 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:492 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:44:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3356244 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Peak Identification complete
2014-02-13 12:44:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3356244 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Run Peak Identification[COMPLETED] was removed from submitted tasks.
2014-02-13 12:44:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3356260 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for Peak Identification.
2014-02-13 12:44:35,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3356275 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at file write start:15
2014-02-13 12:44:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3356416 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - Time at finished file write:156
2014-02-13 12:44:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3356681 [pool-1-thread-1] DEBUG com.nimblegen.common.pio.dataio.write.GenomeDatasetWriteAdapter - total write time:421
2014-02-13 12:44:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3356696 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Done saving analysis data for Peak Identification.
2014-02-13 12:44:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3356696 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:output analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:44:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3356696 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF Report.
2014-02-13 12:44:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357258 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed GFF Report.
2014-02-13 12:44:36,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357258 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate GFF report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357383 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357383 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357414 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357414 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A03_ClaireOlson_4_5_6(Cy5/Cy3) ChIP-chip Workflow 2014-02-13 11:58:58[COMPLETED] was removed from job service submissions.
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357445 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357742 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357742 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:497 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357742 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:498 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357742 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357757 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357757 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 327ms
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357757 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357757 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357773 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Pair report
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357788 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357804 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357820 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357882 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Output directory: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357882 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - Outputing report for Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321454991_1409981611.tif
2014-02-13 12:44:37,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3357913 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - TempFile : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A03_ClaireOlson_4_5_6\tmp.1392324277611_1336206301\558216A03_ClaireOlson_4_5_6_635.tif
2014-02-13 12:44:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3359161 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:44:38,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3359161 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:45:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3400234 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A03_ClaireOlson_4_5_6\tmp.1392324277611_1336206301\558216A03_ClaireOlson_4_5_6_635.pair
2014-02-13 12:45:19,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3400235 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - fixing design name
2014-02-13 12:45:20,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3400320 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A03_ClaireOlson_4_5_6\tmp.1392324277611_1336206301\558216A03_ClaireOlson_4_5_6_635.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:44:50 PST 2014 border=0 ul_x=97.350 ul_y=189.733 ur_x=2955.105 ur_y=180.170 lr_x=2968.249 lr_y=3996.343 ll_x=110.737 ll_y=4005.864 qcscore=0.314 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.' = # software=DEVA version=1.2.1 imagefile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A03_ClaireOlson_4_5_6\tmp.1392324277611_1336206301\558216A03_ClaireOlson_4_5_6_635.tif designfile=Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf designname=1392321089619_1901547662 designid=577051 date=Thu Feb 13 12:44:50 PST 2014 border=0 ul_x=97.350 ul_y=189.733 ur_x=2955.105 ur_y=180.170 lr_x=2968.249 lr_y=3996.343 ll_x=110.737 ll_y=4005.864 qcscore=0.314 locallyaligned=no correctAstig=no Knots= auto=no company_name='Roche NimbleGen, Inc.' intended_use='For Life Science Research only. Not for use in diagnostic procedures.'
2014-02-13 12:45:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3410905 [pool-1-thread-1] DEBUG com.nimblegen.common.services.infrastructure.ExportService - PAIR file : Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\558216_ClaireOlson_4_5_6\558216A03_ClaireOlson_4_5_6\558216A03_ClaireOlson_4_5_6_2014-02-13T124530_635.pair
2014-02-13 12:45:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3410995 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Pair submitted
2014-02-13 12:45:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3410996 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:45:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3411130 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:45:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3411131 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:45:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3411152 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:45:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3411152 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A03_ClaireOlson_4_5_6(Cy5) Pair Report Workflow 2014-02-13 11:58:58[COMPLETED] was removed from job service submissions.
2014-02-13 12:45:30,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3411189 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting Analysis Data Input
2014-02-13 12:45:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3411305 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:45:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3411316 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:45:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3411327 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:45:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3411337 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing array: 558216A03_ClaireOlson_4_5_6
2014-02-13 12:45:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3411380 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning extract of XYS File.
2014-02-13 12:45:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3411401 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NCD file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089446_1917447781.ncd
2014-02-13 12:45:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3411402 [pool-1-thread-1] DEBUG com.nimblegen.common.nimblescanfacade.NimbleScanScannedTiffProcessor - Using NDF file: Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\data\filestore\2014\2\13\11\1392321089619_1901547662.ndf
2014-02-13 12:45:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3411434 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - loading alignment settings
2014-02-13 12:45:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3422541 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating XYS report
2014-02-13 12:45:42,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3422565 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - generating signal report
2014-02-13 12:45:42,INFO,com.nimblegen.deva.projectmanager.launcher.StreamWorker, Generating X,Y and Signal Report to Z:\users\c\csather\TO_BE_REVIEWED_SCANS\02132014\ClaireOlson\DEVA\temporary_working_files\temp_files\1392321454991_1409981611.xys...
2014-02-13 12:45:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3432340 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - completed XYS reporting
2014-02-13 12:45:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3432343 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Tile Cache was flushed.
2014-02-13 12:45:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3432356 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed extract of XYS File.
2014-02-13 12:45:52,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3432375 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Beginning merge data process.
2014-02-13 12:45:56,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3436319 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed XYS file
2014-02-13 12:46:00,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3440514 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed POS file
2014-02-13 12:46:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3452513 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Parsed NDF file
2014-02-13 12:46:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453244 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Writing genome data set
2014-02-13 12:46:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453260 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed merge data process.
2014-02-13 12:46:12,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453279 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Saving analysis data for connected operations.
2014-02-13 12:46:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453313 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Processing output data.
2014-02-13 12:46:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453314 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:503 dataclass:class com.nimblegen.deva.common.domain.data.impl.GenomeDataset]] is being set.
2014-02-13 12:46:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453314 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.DockBuffer - data for port buffer[[port buffer--id:504 dataclass:class java.lang.Long]] is being set.
2014-02-13 12:46:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453314 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:2 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:46:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453326 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.analysisworkflow.AbstractOperation - Data not set. A dock buffer does not exist for operation:analysis data input port:3 (this could be normal usage where nothing is connected to the port so the data are not needed downstream.)
2014-02-13 12:46:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453326 [pool-1-thread-1] DEBUG com.nimblegen.common.analysis.OperationAnalysisDataInput$InputAnalysisData - Total time for input: 42147ms
2014-02-13 12:46:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453338 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Completed Analysis Data Input
2014-02-13 12:46:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453350 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:input analysis data[COMPLETED] was removed from submitted tasks.
2014-02-13 12:46:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453393 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:46:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453408 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Use extraction settings based on slide format
2014-02-13 12:46:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453428 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Border width setting: 0
2014-02-13 12:46:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453440 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Not using local alignment
2014-02-13 12:46:13,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3453454 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - Starting GFF report
2014-02-13 12:46:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3471457 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF report complete
2014-02-13 12:46:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3471467 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - GFF submitted
2014-02-13 12:46:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3471468 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:Generate report[COMPLETED] was removed from submitted tasks.
2014-02-13 12:46:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3471600 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - subtask:complete job.[COMPLETED] was removed from submitted tasks.
2014-02-13 12:46:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3471601 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Attempting deletion of 1 filetokens.
2014-02-13 12:46:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3471621 [pool-1-thread-1] DEBUG com.nimblegen.common.services.pioservices.impl.FilePioService$TransactionalFileDeleter - Successfully deleted 1/1 file tokens.
2014-02-13 12:46:31,DEBUG,com.nimblegen.deva.projectmanager.launcher.StreamWorker, 3471621 [pool-1-thread-1] DEBUG com.nimblegen.deva.common.jobservice.JobService - task:558216A03_ClaireOlson_4_5_6(Cy5) GFF Report Workflow 2014-02-13 11:58:59[COMPLETED] was removed from job service submissions.