[porklock] [arguments] (get --user sr320 --source /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq --config /condor01/scratch/sr320/FASTX_trimmer_PiuraChilensis_Valdivia-2014-12-07-09-02-54.839/logs/irods-config -m ipc-execution-id,404a69f9-5d45-438e-96d2-223a258ce0e8,UUID -m ipc-analysis-id,3DDC9FEA-3242-464D-A9E4-C4498DCD22C9,UUID) [porklock] [options] {:user sr320, :source /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq, :destination ., :config /condor01/scratch/sr320/FASTX_trimmer_PiuraChilensis_Valdivia-2014-12-07-09-02-54.839/logs/irods-config, :meta [(ipc-execution-id 404a69f9-5d45-438e-96d2-223a258ce0e8 UUID) (ipc-analysis-id 3DDC9FEA-3242-464D-A9E4-C4498DCD22C9 UUID)], :help false} [porklock] [remnants] [] [main] INFO clojure-commons.config - CONFIG: porklock.irods-home = /iplant/home [main] INFO clojure-commons.config - CONFIG: porklock.irods-host = data.iplantcollaborative.org [main] INFO clojure-commons.config - CONFIG: porklock.irods-pass = ******** [main] INFO clojure-commons.config - CONFIG: porklock.irods-port = 1247 [main] INFO clojure-commons.config - CONFIG: porklock.irods-resc = [main] INFO clojure-commons.config - CONFIG: porklock.irods-user = ******** [main] INFO clojure-commons.config - CONFIG: porklock.irods-zone = iplant ================================================================================ env: {"irodsAuthFileName" "./.irods/.irodsA", "irodsEnvFile" "./.irods/.irodsEnv"} command: /usr/local2/icommands/iinit stdout: Enter your current iRODS password: [main] INFO connection.IRODSSimpleProtocolManager - creating simple protocol manager [main] INFO connection.IRODSSession - IRODS Session creation, loading default properties, these may be overridden... [main] INFO pub.IRODSFileSystem - IRODSfileSystem is initialized [main] INFO connection.AuthenticationFactoryImpl - instanceAuthMechanism() [main] INFO connection.AuthenticationFactoryImpl - authScheme:STANDARD [main] INFO connection.AuthenticationFactoryImpl - using standard auth [main] INFO connection.IRODSConnection - pipeline configuration:PipelineConfiguration irodsSocketTimeout:0 irodsParallelSocketTimeout:120 internalInputStreamBufferSize:0 internalOutputStreamBufferSize:0 internalCacheBufferSize:-1 localFileOutputStreamBufferSize:0 localFileInputStreamBufferSize:0 defaultEncoding:UTF-8 inputToOutputCopyBufferByteSize:8192 instrument:false reconnect:false reconnect time in millis:600000 [main] INFO connection.IRODSConnection - opening irods socket [main] INFO connection.IRODSConnection - connect() [main] INFO connection.IRODSConnection - connecting socket to agent [main] INFO connection.IRODSConnection - normal iRODS connection [main] INFO connection.IRODSConnection - connection to socket made... [main] INFO connection.IRODSConnection - default buffer on input stream [main] INFO connection.IRODSConnection - default buffer on input stream [main] INFO connection.IRODSConnection - socket opened successfully [main] INFO connection.IRODSCommands - reading message from irods [main] INFO connection.AuthMechanism - startup response:StartupResponseData: status:0 relVersion:rods3.3.1 apiVersion:d reconnPort:0 reconnAddr: cookie:0 [main] INFO connection.StandardIRODSAuth - authenticate [main] INFO connection.StandardIRODSAuth - sending standard irods password [main] INFO connection.IRODSCommands - reading message from irods [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO connection.StandardIRODSAuth - auth was successful [main] INFO connection.StandardIRODSAuth - auth response was:org.irods.jargon.core.connection.auth.AuthResponse@781205b8 [main] INFO connection.EnvironmentalInfoAccessor - getting irods server properties [main] INFO connection.DiscoveredServerPropertiesCache - now retriving server properties from cache with zone:iplant [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO connection.EnvironmentalInfoAccessor - server response obtained [main] INFO connection.IRODSCommands - IRODS server properties icat enabled?:ICAT_ENABLED Server boot time:1414533460 Rel version:rods3.3.1 API version:d zone:iplant [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO pub.CollectionAndDataObjectListAndSearchAOImpl - objStat: absolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq dataId:208964000 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:24a3e37c674b81a85dbedef6bf620c4a ownerName:sr320 ownerZone:iplant objSize:740033686 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Dec 06 16:55:13 MST 2014 modifiedAt:Sat Dec 06 16:57:53 MST 2014 [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO pub.CollectionAndDataObjectListAndSearchAOImpl - objStat: absolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq dataId:208964000 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:24a3e37c674b81a85dbedef6bf620c4a ownerName:sr320 ownerZone:iplant objSize:740033686 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Dec 06 16:55:13 MST 2014 modifiedAt:Sat Dec 06 16:57:53 MST 2014 [main] INFO pub.UserGroupAOImpl - find user group with user name: sr320 [main] INFO pub.UserGroupAOImpl - query string: SELECT USER_GROUP_NAME,USER_GROUP_ID WHERE USER_NAME = 'sr320' [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResult() [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone() [main] INFO pub.IRODSGenQueryExecutorImpl - query: IRODSQuery: queryString:SELECT USER_GROUP_NAME,USER_GROUP_ID WHERE USER_NAME = 'sr320' numberOfResultsDesired:500 [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO query.GenQueryProcessor - continuation value: 0 [main] INFO query.GenQueryProcessor - total records:0 [main] INFO query.QueryResultProcessingUtils - rows returned from iRODS query: 2 [main] INFO query.GenQueryProcessor - auto closing result set [main] INFO query.GenQueryProcessor - getting more results for query [main] INFO query.GenQueryProcessor - no results to close, ignore [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResult() [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone() [main] INFO pub.IRODSGenQueryExecutorImpl - query: IRODSQuery: queryString:select USER_ID where USER_NAME = 'public' numberOfResultsDesired:50000 [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO query.GenQueryProcessor - continuation value: 0 [main] INFO query.GenQueryProcessor - total records:0 [main] INFO query.QueryResultProcessingUtils - rows returned from iRODS query: 1 [main] INFO query.GenQueryProcessor - auto closing result set [main] INFO query.GenQueryProcessor - getting more results for query [main] INFO query.GenQueryProcessor - no results to close, ignore [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResult() [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone() [main] INFO pub.IRODSGenQueryExecutorImpl - query: IRODSQuery: queryString:select DATA_ACCESS_TYPE where COLL_NAME = '/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5' and DATA_NAME = 'PiuraChilensis_Valdivia.fastq' and DATA_ACCESS_USER_ID = '10004' numberOfResultsDesired:50000 [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO query.GenQueryProcessor - response from IRODS call indicates no rows found [main] INFO query.GenQueryProcessor - auto closing result set [main] INFO query.GenQueryProcessor - getting more results for query [main] INFO query.GenQueryProcessor - no results to close, ignore [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResult() [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone() [main] INFO pub.IRODSGenQueryExecutorImpl - query: IRODSQuery: queryString:select USER_ID where USER_NAME = 'sr320' numberOfResultsDesired:50000 [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO query.GenQueryProcessor - continuation value: 0 [main] INFO query.GenQueryProcessor - total records:0 [main] INFO query.QueryResultProcessingUtils - rows returned from iRODS query: 1 [main] INFO query.GenQueryProcessor - auto closing result set [main] INFO query.GenQueryProcessor - getting more results for query [main] INFO query.GenQueryProcessor - no results to close, ignore [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResult() [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone() [main] INFO pub.IRODSGenQueryExecutorImpl - query: IRODSQuery: queryString:select DATA_ACCESS_TYPE where COLL_NAME = '/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5' and DATA_NAME = 'PiuraChilensis_Valdivia.fastq' and DATA_ACCESS_USER_ID = '73068066' numberOfResultsDesired:50000 [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO query.GenQueryProcessor - continuation value: 0 [main] INFO query.GenQueryProcessor - total records:0 [main] INFO query.QueryResultProcessingUtils - rows returned from iRODS query: 1 [main] INFO query.GenQueryProcessor - auto closing result set [main] INFO query.GenQueryProcessor - getting more results for query [main] INFO query.GenQueryProcessor - no results to close, ignore [porklock] Metadata tuples for /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq are ((ipc-execution-id 404a69f9-5d45-438e-96d2-223a258ce0e8 UUID) (ipc-analysis-id 3DDC9FEA-3242-464D-A9E4-C4498DCD22C9 UUID)) [porklock] Size of tuple (ipc-execution-id 404a69f9-5d45-438e-96d2-223a258ce0e8 UUID) is 3 [porklock] Might be adding metadata to /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq (ipc-execution-id 404a69f9-5d45-438e-96d2-223a258ce0e8 UUID) [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO pub.CollectionAndDataObjectListAndSearchAOImpl - objStat: absolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq dataId:208964000 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:24a3e37c674b81a85dbedef6bf620c4a ownerName:sr320 ownerZone:iplant objSize:740033686 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Dec 06 16:55:13 MST 2014 modifiedAt:Sat Dec 06 16:57:53 MST 2014 [main] INFO pub.DataObjectAOImpl - findMetadataValuesForDataObject: /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO io.IRODSFileImpl - setting file name, given path = PiuraChilensis_Valdivia.fastq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: PiuraChilensis_Valdivia.fastq [main] INFO pub.FileCatalogObjectAOImpl - retrieveObjStat() [main] INFO pub.FileCatalogObjectAOImpl - irodsAbsolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO pub.CollectionAndDataObjectListAndSearchAOImpl - objStat: absolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq dataId:208964000 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:24a3e37c674b81a85dbedef6bf620c4a ownerName:sr320 ownerZone:iplant objSize:740033686 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Dec 06 16:55:13 MST 2014 modifiedAt:Sat Dec 06 16:57:53 MST 2014 [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: PiuraChilensis_Valdivia.fastq [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone() [main] INFO pub.IRODSGenQueryExecutorImpl - query: org.irods.jargon.core.query.IRODSGenQueryFromBuilder@5bfefcd4 [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO query.GenQueryProcessor - continuation value: 0 [main] INFO query.GenQueryProcessor - total records:0 [main] INFO query.QueryResultProcessingUtils - rows returned from iRODS query: 8 [main] INFO query.GenQueryProcessor - auto closing result set [main] INFO query.GenQueryProcessor - getting more results for query [main] INFO query.GenQueryProcessor - no results to close, ignore [porklock] AVU? /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq () [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO pub.CollectionAndDataObjectListAndSearchAOImpl - objStat: absolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq dataId:208964000 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:24a3e37c674b81a85dbedef6bf620c4a ownerName:sr320 ownerZone:iplant objSize:740033686 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Dec 06 16:55:13 MST 2014 modifiedAt:Sat Dec 06 16:57:53 MST 2014 [main] INFO pub.DataObjectAOImpl - findMetadataValuesForDataObject: /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO io.IRODSFileImpl - setting file name, given path = PiuraChilensis_Valdivia.fastq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: PiuraChilensis_Valdivia.fastq [main] INFO pub.FileCatalogObjectAOImpl - retrieveObjStat() [main] INFO pub.FileCatalogObjectAOImpl - irodsAbsolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO pub.CollectionAndDataObjectListAndSearchAOImpl - objStat: absolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq dataId:208964000 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:24a3e37c674b81a85dbedef6bf620c4a ownerName:sr320 ownerZone:iplant objSize:740033686 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Dec 06 16:55:13 MST 2014 modifiedAt:Sat Dec 06 16:57:53 MST 2014 [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: PiuraChilensis_Valdivia.fastq [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone() [main] INFO pub.IRODSGenQueryExecutorImpl - query: org.irods.jargon.core.query.IRODSGenQueryFromBuilder@4841798b [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO query.GenQueryProcessor - continuation value: 0 [main] INFO query.GenQueryProcessor - total records:0 [main] INFO query.QueryResultProcessingUtils - rows returned from iRODS query: 8 [main] INFO query.GenQueryProcessor - auto closing result set [main] INFO query.GenQueryProcessor - getting more results for query [main] INFO query.GenQueryProcessor - no results to close, ignore [porklock] Adding metadata ipc-execution-id 404a69f9-5d45-438e-96d2-223a258ce0e8 /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO pub.CollectionAndDataObjectListAndSearchAOImpl - objStat: absolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq dataId:208964000 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:24a3e37c674b81a85dbedef6bf620c4a ownerName:sr320 ownerZone:iplant objSize:740033686 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Dec 06 16:55:13 MST 2014 modifiedAt:Sat Dec 06 16:57:53 MST 2014 [main] INFO pub.DataObjectAOImpl - adding avu metadata to data object: avu data: attrib:ipc-execution-id value:404a69f9-5d45-438e-96d2-223a258ce0e8 units:UUID [main] INFO pub.DataObjectAOImpl - absolute path: /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO pub.FileCatalogObjectAOImpl - resoveAbsolutePathViaObjStat() [main] INFO pub.FileCatalogObjectAOImpl - retrieveObjStat() [main] INFO pub.FileCatalogObjectAOImpl - irodsAbsolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5 [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO pub.CollectionAndDataObjectListAndSearchAOImpl - objStat: absolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5 dataId:208963964 specColType:NORMAL objectType:COLLECTION collectionPath: objectPath: checksum: ownerName:de-irods ownerZone:iplant objSize:0 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Dec 06 16:55:03 MST 2014 modifiedAt:Sat Dec 06 16:57:53 MST 2014 [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [porklock] Size of tuple (ipc-analysis-id 3DDC9FEA-3242-464D-A9E4-C4498DCD22C9 UUID) is 3 [porklock] Might be adding metadata to /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq (ipc-analysis-id 3DDC9FEA-3242-464D-A9E4-C4498DCD22C9 UUID) [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO pub.CollectionAndDataObjectListAndSearchAOImpl - objStat: absolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq dataId:208964000 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:24a3e37c674b81a85dbedef6bf620c4a ownerName:sr320 ownerZone:iplant objSize:740033686 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Dec 06 16:55:13 MST 2014 modifiedAt:Sat Dec 06 16:57:53 MST 2014 [main] INFO pub.DataObjectAOImpl - findMetadataValuesForDataObject: /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO io.IRODSFileImpl - setting file name, given path = PiuraChilensis_Valdivia.fastq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: PiuraChilensis_Valdivia.fastq [main] INFO pub.FileCatalogObjectAOImpl - retrieveObjStat() [main] INFO pub.FileCatalogObjectAOImpl - irodsAbsolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO pub.CollectionAndDataObjectListAndSearchAOImpl - objStat: absolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq dataId:208964000 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:24a3e37c674b81a85dbedef6bf620c4a ownerName:sr320 ownerZone:iplant objSize:740033686 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Dec 06 16:55:13 MST 2014 modifiedAt:Sat Dec 06 16:57:53 MST 2014 [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: PiuraChilensis_Valdivia.fastq [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone() [main] INFO pub.IRODSGenQueryExecutorImpl - query: org.irods.jargon.core.query.IRODSGenQueryFromBuilder@57c73051 [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO query.GenQueryProcessor - continuation value: 0 [main] INFO query.GenQueryProcessor - total records:0 [main] INFO query.QueryResultProcessingUtils - rows returned from iRODS query: 9 [main] INFO query.GenQueryProcessor - auto closing result set [main] INFO query.GenQueryProcessor - getting more results for query [main] INFO query.GenQueryProcessor - no results to close, ignore [porklock] AVU? /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq ({:unit UUID, :value 3DDC9FEA-3242-464D-A9E4-C4498DCD22C9, :attr ipc-analysis-id}) [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO pub.CollectionAndDataObjectListAndSearchAOImpl - objStat: absolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq dataId:208964000 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:24a3e37c674b81a85dbedef6bf620c4a ownerName:sr320 ownerZone:iplant objSize:740033686 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Dec 06 16:55:13 MST 2014 modifiedAt:Sat Dec 06 16:57:53 MST 2014 [main] INFO pub.DataObjectAOImpl - findMetadataValuesForDataObject: /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO io.IRODSFileImpl - setting file name, given path = PiuraChilensis_Valdivia.fastq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: PiuraChilensis_Valdivia.fastq [main] INFO pub.FileCatalogObjectAOImpl - retrieveObjStat() [main] INFO pub.FileCatalogObjectAOImpl - irodsAbsolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO pub.CollectionAndDataObjectListAndSearchAOImpl - objStat: absolutePath:/iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq dataId:208964000 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:24a3e37c674b81a85dbedef6bf620c4a ownerName:sr320 ownerZone:iplant objSize:740033686 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Dec 06 16:55:13 MST 2014 modifiedAt:Sat Dec 06 16:57:53 MST 2014 [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: PiuraChilensis_Valdivia.fastq [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone() [main] INFO pub.IRODSGenQueryExecutorImpl - query: org.irods.jargon.core.query.IRODSGenQueryFromBuilder@563542dc [main] INFO connection.IRODSCommands - calling irods function with byte array [main] INFO connection.IRODSCommands - reading message from irods [main] INFO query.GenQueryProcessor - continuation value: 0 [main] INFO query.GenQueryProcessor - total records:0 [main] INFO query.QueryResultProcessingUtils - rows returned from iRODS query: 9 [main] INFO query.GenQueryProcessor - auto closing result set [main] INFO query.GenQueryProcessor - getting more results for query [main] INFO query.GenQueryProcessor - no results to close, ignore ================================================================================ env: {"clientUserName" "sr320", "irodsAuthFileName" "./.irods/.irodsA", "irodsEnvFile" "./.irods/.irodsEnv"} command: /usr/local2/icommands/iget -f -P /iplant/home/sr320/austral/Sff2Fastq_PiuraChilensis_Valdivia-2014-12-06-23-54-12.5/PiuraChilensis_Valdivia.fastq ./ stdout: 0/1 - 0.00% of files done 0.000/705.735 MB - 0.00% of file sizes done Processing PiuraChilensis_Valdivia.fastq - 705.735 MB 2014-12-07.09:03:03 PiuraChilensis_Valdivia.fastq - 39.999/705.735 MB - 5.67% done 2014-12-07.09:03:08 PiuraChilensis_Valdivia.fastq - 124.107/705.735 MB - 17.59% done 2014-12-07.09:03:08 PiuraChilensis_Valdivia.fastq - 705.735/705.735 MB - 100.00% done 2014-12-07.09:03:18 [main] INFO connection.IRODSSession - closing all irods sessions [main] INFO connection.IRODSCommands - closing connection [main] INFO connection.IRODSCommands - shutdown()...check if executor service is running for reconnect [main] INFO connection.IRODSCommands - shutting down, need to send disconnect to irods [main] INFO connection.IRODSCommands - sending disconnect message [main] INFO connection.IRODSConnection - shutting down connection: true [main] INFO connection.IRODSConnection - is connected for : irodsSimpleConnection/main/1417968182781 [main] INFO connection.IRODSConnection - now disconnected