[porklock] [arguments]  (get --user sr320 --source /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff --config /condor01/scratch/sr320/Sff2Fastq_PiuraChilensis_Coquimbo-2014-12-06-16-53-21.873/logs/irods-config -m ipc-execution-id,0115e113-1d11-44c3-a78a-3c98146c91d8,UUID -m ipc-analysis-id,D26F5774-6A95-4095-BC65-614D454AC42E,UUID)
[porklock] [options]  {:user sr320, :source /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff, :destination ., :config /condor01/scratch/sr320/Sff2Fastq_PiuraChilensis_Coquimbo-2014-12-06-16-53-21.873/logs/irods-config, :meta [(ipc-execution-id 0115e113-1d11-44c3-a78a-3c98146c91d8 UUID) (ipc-analysis-id D26F5774-6A95-4095-BC65-614D454AC42E 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@1b0324a3
[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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
   dataId:208963586
   specColType:NORMAL
   objectType:DATA_OBJECT
   collectionPath:
   objectPath:
   checksum:b76154596e72b48ab0da9e2b85879377
   ownerName:sr320
   ownerZone:iplant
  objSize:2452941716
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:56 MST 2014
   modifiedAt:Sat Dec 06 16:50:56 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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
   dataId:208963586
   specColType:NORMAL
   objectType:DATA_OBJECT
   collectionPath:
   objectPath:
   checksum:b76154596e72b48ab0da9e2b85879377
   ownerName:sr320
   ownerZone:iplant
  objSize:2452941716
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:56 MST 2014
   modifiedAt:Sat Dec 06 16:50:56 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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6' and DATA_NAME = '2012_01_05_PilarHaye_LB1_SFF.sff' 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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6' and DATA_NAME = '2012_01_05_PilarHaye_LB1_SFF.sff' 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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff  are   ((ipc-execution-id 0115e113-1d11-44c3-a78a-3c98146c91d8 UUID) (ipc-analysis-id D26F5774-6A95-4095-BC65-614D454AC42E UUID))
[porklock]  Size of tuple  (ipc-execution-id 0115e113-1d11-44c3-a78a-3c98146c91d8 UUID)  is  3
[porklock]  Might be adding metadata to  /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff   (ipc-execution-id 0115e113-1d11-44c3-a78a-3c98146c91d8 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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
   dataId:208963586
   specColType:NORMAL
   objectType:DATA_OBJECT
   collectionPath:
   objectPath:
   checksum:b76154596e72b48ab0da9e2b85879377
   ownerName:sr320
   ownerZone:iplant
  objSize:2452941716
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:56 MST 2014
   modifiedAt:Sat Dec 06 16:50:56 MST 2014
[main] INFO  pub.DataObjectAOImpl  - findMetadataValuesForDataObject: /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  io.IRODSFileImpl  - setting file name, given path = 2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  io.IRODSFileImpl  - detected local separator = /
[main] INFO  io.IRODSFileImpl  - file name was set as: 2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  pub.FileCatalogObjectAOImpl  - retrieveObjStat()
[main] INFO  pub.FileCatalogObjectAOImpl  - irodsAbsolutePath:/iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
   dataId:208963586
   specColType:NORMAL
   objectType:DATA_OBJECT
   collectionPath:
   objectPath:
   checksum:b76154596e72b48ab0da9e2b85879377
   ownerName:sr320
   ownerZone:iplant
  objSize:2452941716
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:56 MST 2014
   modifiedAt:Sat Dec 06 16:50:56 MST 2014
[main] INFO  io.IRODSFileImpl  - setting file name, given path = /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  io.IRODSFileImpl  - detected local separator = /
[main] INFO  io.IRODSFileImpl  - file name was set as: 2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  pub.IRODSGenQueryExecutorImpl  - executeIRODSQueryAndCloseResultInZone()
[main] INFO  pub.IRODSGenQueryExecutorImpl  - query: org.irods.jargon.core.query.IRODSGenQueryFromBuilder@7655ff39
[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: 3
[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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff ()
[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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
   dataId:208963586
   specColType:NORMAL
   objectType:DATA_OBJECT
   collectionPath:
   objectPath:
   checksum:b76154596e72b48ab0da9e2b85879377
   ownerName:sr320
   ownerZone:iplant
  objSize:2452941716
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:56 MST 2014
   modifiedAt:Sat Dec 06 16:50:56 MST 2014
[main] INFO  pub.DataObjectAOImpl  - findMetadataValuesForDataObject: /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  io.IRODSFileImpl  - setting file name, given path = 2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  io.IRODSFileImpl  - detected local separator = /
[main] INFO  io.IRODSFileImpl  - file name was set as: 2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  pub.FileCatalogObjectAOImpl  - retrieveObjStat()
[main] INFO  pub.FileCatalogObjectAOImpl  - irodsAbsolutePath:/iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
   dataId:208963586
   specColType:NORMAL
   objectType:DATA_OBJECT
   collectionPath:
   objectPath:
   checksum:b76154596e72b48ab0da9e2b85879377
   ownerName:sr320
   ownerZone:iplant
  objSize:2452941716
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:56 MST 2014
   modifiedAt:Sat Dec 06 16:50:56 MST 2014
[main] INFO  io.IRODSFileImpl  - setting file name, given path = /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  io.IRODSFileImpl  - detected local separator = /
[main] INFO  io.IRODSFileImpl  - file name was set as: 2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  pub.IRODSGenQueryExecutorImpl  - executeIRODSQueryAndCloseResultInZone()
[main] INFO  pub.IRODSGenQueryExecutorImpl  - query: org.irods.jargon.core.query.IRODSGenQueryFromBuilder@2296ff51
[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: 3
[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   0115e113-1d11-44c3-a78a-3c98146c91d8   /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
   dataId:208963586
   specColType:NORMAL
   objectType:DATA_OBJECT
   collectionPath:
   objectPath:
   checksum:b76154596e72b48ab0da9e2b85879377
   ownerName:sr320
   ownerZone:iplant
  objSize:2452941716
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:56 MST 2014
   modifiedAt:Sat Dec 06 16:50:56 MST 2014
[main] INFO  pub.DataObjectAOImpl  - adding avu metadata to data object: avu data:
   attrib:ipc-execution-id
   value:0115e113-1d11-44c3-a78a-3c98146c91d8
   units:UUID
[main] INFO  pub.DataObjectAOImpl  - absolute path: /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  pub.FileCatalogObjectAOImpl  - resoveAbsolutePathViaObjStat()
[main] INFO  pub.FileCatalogObjectAOImpl  - retrieveObjStat()
[main] INFO  pub.FileCatalogObjectAOImpl  - irodsAbsolutePath:/iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6
[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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6
   dataId:208963583
   specColType:NORMAL
   objectType:COLLECTION
   collectionPath:
   objectPath:
   checksum:
   ownerName:de-irods
   ownerZone:iplant
  objSize:0
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:55 MST 2014
   modifiedAt:Sat Dec 06 16:50:55 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 D26F5774-6A95-4095-BC65-614D454AC42E UUID)  is  3
[porklock]  Might be adding metadata to  /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff   (ipc-analysis-id D26F5774-6A95-4095-BC65-614D454AC42E 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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
   dataId:208963586
   specColType:NORMAL
   objectType:DATA_OBJECT
   collectionPath:
   objectPath:
   checksum:b76154596e72b48ab0da9e2b85879377
   ownerName:sr320
   ownerZone:iplant
  objSize:2452941716
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:56 MST 2014
   modifiedAt:Sat Dec 06 16:50:56 MST 2014
[main] INFO  pub.DataObjectAOImpl  - findMetadataValuesForDataObject: /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  io.IRODSFileImpl  - setting file name, given path = 2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  io.IRODSFileImpl  - detected local separator = /
[main] INFO  io.IRODSFileImpl  - file name was set as: 2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  pub.FileCatalogObjectAOImpl  - retrieveObjStat()
[main] INFO  pub.FileCatalogObjectAOImpl  - irodsAbsolutePath:/iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
   dataId:208963586
   specColType:NORMAL
   objectType:DATA_OBJECT
   collectionPath:
   objectPath:
   checksum:b76154596e72b48ab0da9e2b85879377
   ownerName:sr320
   ownerZone:iplant
  objSize:2452941716
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:56 MST 2014
   modifiedAt:Sat Dec 06 16:50:56 MST 2014
[main] INFO  io.IRODSFileImpl  - setting file name, given path = /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  io.IRODSFileImpl  - detected local separator = /
[main] INFO  io.IRODSFileImpl  - file name was set as: 2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  pub.IRODSGenQueryExecutorImpl  - executeIRODSQueryAndCloseResultInZone()
[main] INFO  pub.IRODSGenQueryExecutorImpl  - query: org.irods.jargon.core.query.IRODSGenQueryFromBuilder@27dad48d
[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: 4
[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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff ()
[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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
   dataId:208963586
   specColType:NORMAL
   objectType:DATA_OBJECT
   collectionPath:
   objectPath:
   checksum:b76154596e72b48ab0da9e2b85879377
   ownerName:sr320
   ownerZone:iplant
  objSize:2452941716
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:56 MST 2014
   modifiedAt:Sat Dec 06 16:50:56 MST 2014
[main] INFO  pub.DataObjectAOImpl  - findMetadataValuesForDataObject: /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  io.IRODSFileImpl  - setting file name, given path = 2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  io.IRODSFileImpl  - detected local separator = /
[main] INFO  io.IRODSFileImpl  - file name was set as: 2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  pub.FileCatalogObjectAOImpl  - retrieveObjStat()
[main] INFO  pub.FileCatalogObjectAOImpl  - irodsAbsolutePath:/iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
   dataId:208963586
   specColType:NORMAL
   objectType:DATA_OBJECT
   collectionPath:
   objectPath:
   checksum:b76154596e72b48ab0da9e2b85879377
   ownerName:sr320
   ownerZone:iplant
  objSize:2452941716
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:56 MST 2014
   modifiedAt:Sat Dec 06 16:50:56 MST 2014
[main] INFO  io.IRODSFileImpl  - setting file name, given path = /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  io.IRODSFileImpl  - detected local separator = /
[main] INFO  io.IRODSFileImpl  - file name was set as: 2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  pub.IRODSGenQueryExecutorImpl  - executeIRODSQueryAndCloseResultInZone()
[main] INFO  pub.IRODSGenQueryExecutorImpl  - query: org.irods.jargon.core.query.IRODSGenQueryFromBuilder@fb8896c
[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: 4
[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-analysis-id   D26F5774-6A95-4095-BC65-614D454AC42E   /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
   dataId:208963586
   specColType:NORMAL
   objectType:DATA_OBJECT
   collectionPath:
   objectPath:
   checksum:b76154596e72b48ab0da9e2b85879377
   ownerName:sr320
   ownerZone:iplant
  objSize:2452941716
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:56 MST 2014
   modifiedAt:Sat Dec 06 16:50:56 MST 2014
[main] INFO  pub.DataObjectAOImpl  - adding avu metadata to data object: avu data:
   attrib:ipc-analysis-id
   value:D26F5774-6A95-4095-BC65-614D454AC42E
   units:UUID
[main] INFO  pub.DataObjectAOImpl  - absolute path: /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff
[main] INFO  pub.FileCatalogObjectAOImpl  - resoveAbsolutePathViaObjStat()
[main] INFO  pub.FileCatalogObjectAOImpl  - retrieveObjStat()
[main] INFO  pub.FileCatalogObjectAOImpl  - irodsAbsolutePath:/iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6
[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/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6
   dataId:208963583
   specColType:NORMAL
   objectType:COLLECTION
   collectionPath:
   objectPath:
   checksum:
   ownerName:de-irods
   ownerZone:iplant
  objSize:0
   cacheDir:
   cacheDirty:false
   createdAt:replNumber:0Sat Dec 06 16:50:55 MST 2014
   modifiedAt:Sat Dec 06 16:50:55 MST 2014
[main] INFO  connection.IRODSCommands  - calling irods function with byte array
[main] INFO  connection.IRODSCommands  - reading message from irods
================================================================================ 
env: 
{"clientUserName" "sr320",
 "irodsAuthFileName" "./.irods/.irodsA",
 "irodsEnvFile" "./.irods/.irodsEnv"}
 
command:
/usr/local2/icommands/iget -f -P /iplant/home/sr320/austral/PK_Unzip_PiuraChilensis_Coquimbo-2014-12-06-23-49-58.6/2012_01_05_PilarHaye_LB1_SFF.sff ./
 
stdout: 
0/1 -  0.00% of files done   0.000/2339.254 MB -  0.00% of file sizes done
Processing 2012_01_05_PilarHaye_LB1_SFF.sff - 2339.254 MB   2014-12-06.16:53:29
2012_01_05_PilarHaye_LB1_SFF.sff - 199.995/2339.254 MB -  8.55% done   2014-12-06.16:53:35
2012_01_05_PilarHaye_LB1_SFF.sff - 719.984/2339.254 MB - 30.78% done   2014-12-06.16:53:40
2012_01_05_PilarHaye_LB1_SFF.sff - 1359.969/2339.254 MB - 58.14% done   2014-12-06.16:53:47
2012_01_05_PilarHaye_LB1_SFF.sff - 1586.170/2339.254 MB - 67.81% done   2014-12-06.16:53:49
2012_01_05_PilarHaye_LB1_SFF.sff - 2339.254/2339.254 MB - 100.00% done   2014-12-06.16:53:53

[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/1417910008976
[main] INFO  connection.IRODSConnection  - now disconnected