[main] INFO zookeeper.ZooKeeper - Client environment:zookeeper.version=3.3.2-1031432, built on 11/05/2010 05:32 GMT [main] INFO zookeeper.ZooKeeper - Client environment:host.name=cnode1.iplantcollaborative.org [main] INFO zookeeper.ZooKeeper - Client environment:java.version=1.6.0_27 [main] INFO zookeeper.ZooKeeper - Client environment:java.vendor=Sun Microsystems Inc. [main] INFO zookeeper.ZooKeeper - Client environment:java.home=/usr/java/jdk1.6.0_27/jre [main] INFO zookeeper.ZooKeeper - Client environment:java.class.path=/usr/local/lib/porklock/porklock-1.2.1-SNAPSHOT-standalone.jar [main] INFO zookeeper.ZooKeeper - Client environment:java.library.path=/usr/java/jdk1.6.0_27/jre/lib/amd64/server:/usr/java/jdk1.6.0_27/jre/lib/amd64:/usr/java/jdk1.6.0_27/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib [main] INFO zookeeper.ZooKeeper - Client environment:java.io.tmpdir=/tmp [main] INFO zookeeper.ZooKeeper - Client environment:java.compiler= [main] INFO zookeeper.ZooKeeper - Client environment:os.name=Linux [main] INFO zookeeper.ZooKeeper - Client environment:os.arch=amd64 [main] INFO zookeeper.ZooKeeper - Client environment:os.version=2.6.18-348.18.1.el5 [main] INFO zookeeper.ZooKeeper - Client environment:user.name=condor [main] INFO zookeeper.ZooKeeper - Client environment:user.home=/var/lib/condor [main] INFO zookeeper.ZooKeeper - Client environment:user.dir=/var/lib/condor/iplant-de-jobs/sr320/E474C503-5AC6-47CA-A151-25478E5D074B [porklock] [arguments] (get --user sr320 --source /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq --config /condor01/scratch/sr320/RNAseq2bedgraph_E-2014-03-08-07-36-07.971/logs/irods-config -m ipc-execution-id,E474C503-5AC6-47CA-A151-25478E5D074B,UUID -m ipc-analysis-id,EA5B9AC6-3526-4100-88DD-0E961B678D71,UUID) [porklock] [options] {:user sr320, :source /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq, :destination ., :config /condor01/scratch/sr320/RNAseq2bedgraph_E-2014-03-08-07-36-07.971/logs/irods-config, :meta [(ipc-execution-id E474C503-5AC6-47CA-A151-25478E5D074B UUID) (ipc-analysis-id EA5B9AC6-3526-4100-88DD-0E961B678D71 UUID)], :help false} [porklock] [remnants] [] [main] WARN clojure-commons.config - CONFIG: porklock.irods-home = /iplant/home [main] WARN clojure-commons.config - CONFIG: porklock.irods-host = data.iplantcollaborative.org [main] WARN clojure-commons.config - CONFIG: porklock.irods-pass = ******** [main] WARN clojure-commons.config - CONFIG: porklock.irods-port = 1247 [main] WARN clojure-commons.config - CONFIG: porklock.irods-resc = [main] WARN clojure-commons.config - CONFIG: porklock.irods-user = ******** [main] WARN 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:-1 internalCacheBufferSize:65535 localFileOutputStreamBufferSize:0 localFileInputStreamBufferSize:0 defaultEncoding:UTF-8 inputToOutputCopyBufferByteSize:8192 instrument:false reconnect:false reconnect time in millis:600000 [main] INFO connection.IRODSConnection - using internal cache buffer of size:65535 [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 - no buffer on output 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 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@6c97d3f0 [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:1391616767 Rel version:rods3.3 API version:d zone:iplant [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO io.IRODSFileImpl - isDirectory() for path:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - looking up objStat, not cached in file [main] INFO pub.IRODSFileSystemAOImpl - getObjStat(final String irodsAbsolutePath) [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq dataId:103195231 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:b490a030319d7e477a3a52fcae3b6e09 ownerName:sr320 ownerZone:iplant objSize:1487132340 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:26:08 MST 2014 modifiedAt:Sat Mar 08 07:26:08 MST 2014 [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO io.IRODSFileImpl - isFile() for path:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - looking up objStat, not cached in file [main] INFO pub.IRODSFileSystemAOImpl - getObjStat(final String irodsAbsolutePath) [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq dataId:103195231 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:b490a030319d7e477a3a52fcae3b6e09 ownerName:sr320 ownerZone:iplant objSize:1487132340 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:26:08 MST 2014 modifiedAt:Sat Mar 08 07:26:08 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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437' and DATA_NAME = 'E.fq' 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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437' and DATA_NAME = 'E.fq' 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 [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO io.IRODSFileImpl - isDirectory() for path:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - looking up objStat, not cached in file [main] INFO pub.IRODSFileSystemAOImpl - getObjStat(final String irodsAbsolutePath) [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq dataId:103195231 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:b490a030319d7e477a3a52fcae3b6e09 ownerName:sr320 ownerZone:iplant objSize:1487132340 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:26:08 MST 2014 modifiedAt:Sat Mar 08 07:26:08 MST 2014 [porklock] Metadata tuples for /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq are ((ipc-execution-id E474C503-5AC6-47CA-A151-25478E5D074B UUID) (ipc-analysis-id EA5B9AC6-3526-4100-88DD-0E961B678D71 UUID)) [porklock] Size of tuple (ipc-execution-id E474C503-5AC6-47CA-A151-25478E5D074B UUID) is 3 [porklock] Might be adding metadata to /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq (ipc-execution-id E474C503-5AC6-47CA-A151-25478E5D074B UUID) [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO io.IRODSFileImpl - isDirectory() for path:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - looking up objStat, not cached in file [main] INFO pub.IRODSFileSystemAOImpl - getObjStat(final String irodsAbsolutePath) [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq dataId:103195231 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:b490a030319d7e477a3a52fcae3b6e09 ownerName:sr320 ownerZone:iplant objSize:1487132340 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:26:08 MST 2014 modifiedAt:Sat Mar 08 07:26:08 MST 2014 [main] INFO pub.DataObjectAOImpl - findMetadataValuesForDataObject: /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - setting file name, given path = E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO pub.FileCatalogObjectAOImpl - retrieveObjStat() [main] INFO pub.FileCatalogObjectAOImpl - irodsAbsolutePath:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq dataId:103195231 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:b490a030319d7e477a3a52fcae3b6e09 ownerName:sr320 ownerZone:iplant objSize:1487132340 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:26:08 MST 2014 modifiedAt:Sat Mar 08 07:26:08 MST 2014 [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone() [main] INFO pub.IRODSGenQueryExecutorImpl - query: org.irods.jargon.core.query.IRODSGenQueryFromBuilder@919db9e [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq () [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO io.IRODSFileImpl - isDirectory() for path:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - looking up objStat, not cached in file [main] INFO pub.IRODSFileSystemAOImpl - getObjStat(final String irodsAbsolutePath) [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq dataId:103195231 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:b490a030319d7e477a3a52fcae3b6e09 ownerName:sr320 ownerZone:iplant objSize:1487132340 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:26:08 MST 2014 modifiedAt:Sat Mar 08 07:26:08 MST 2014 [main] INFO pub.DataObjectAOImpl - findMetadataValuesForDataObject: /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - setting file name, given path = E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO pub.FileCatalogObjectAOImpl - retrieveObjStat() [main] INFO pub.FileCatalogObjectAOImpl - irodsAbsolutePath:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq dataId:103195231 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:b490a030319d7e477a3a52fcae3b6e09 ownerName:sr320 ownerZone:iplant objSize:1487132340 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:26:08 MST 2014 modifiedAt:Sat Mar 08 07:26:08 MST 2014 [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone() [main] INFO pub.IRODSGenQueryExecutorImpl - query: org.irods.jargon.core.query.IRODSGenQueryFromBuilder@4268cc6 [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 E474C503-5AC6-47CA-A151-25478E5D074B /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO io.IRODSFileImpl - isDirectory() for path:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - looking up objStat, not cached in file [main] INFO pub.IRODSFileSystemAOImpl - getObjStat(final String irodsAbsolutePath) [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq dataId:103195231 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:b490a030319d7e477a3a52fcae3b6e09 ownerName:sr320 ownerZone:iplant objSize:1487132340 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:26:08 MST 2014 modifiedAt:Sat Mar 08 07:26:08 MST 2014 [main] INFO pub.DataObjectAOImpl - adding avu metadata to data object: avu data: attrib:ipc-execution-id value:E474C503-5AC6-47CA-A151-25478E5D074B units:UUID [main] INFO pub.DataObjectAOImpl - absolute path: /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO pub.FileCatalogObjectAOImpl - resoveAbsolutePathViaObjStat() [main] INFO pub.FileCatalogObjectAOImpl - retrieveObjStat() [main] INFO pub.FileCatalogObjectAOImpl - irodsAbsolutePath:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437 [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437 dataId:103195228 specColType:NORMAL objectType:COLLECTION collectionPath: objectPath: checksum: ownerName:de-irods ownerZone:iplant objSize:0 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:24:52 MST 2014 modifiedAt:Sat Mar 08 07:24:52 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 EA5B9AC6-3526-4100-88DD-0E961B678D71 UUID) is 3 [porklock] Might be adding metadata to /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq (ipc-analysis-id EA5B9AC6-3526-4100-88DD-0E961B678D71 UUID) [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO io.IRODSFileImpl - isDirectory() for path:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - looking up objStat, not cached in file [main] INFO pub.IRODSFileSystemAOImpl - getObjStat(final String irodsAbsolutePath) [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq dataId:103195231 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:b490a030319d7e477a3a52fcae3b6e09 ownerName:sr320 ownerZone:iplant objSize:1487132340 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:26:08 MST 2014 modifiedAt:Sat Mar 08 07:26:08 MST 2014 [main] INFO pub.DataObjectAOImpl - findMetadataValuesForDataObject: /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - setting file name, given path = E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO pub.FileCatalogObjectAOImpl - retrieveObjStat() [main] INFO pub.FileCatalogObjectAOImpl - irodsAbsolutePath:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq dataId:103195231 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:b490a030319d7e477a3a52fcae3b6e09 ownerName:sr320 ownerZone:iplant objSize:1487132340 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:26:08 MST 2014 modifiedAt:Sat Mar 08 07:26:08 MST 2014 [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone() [main] INFO pub.IRODSGenQueryExecutorImpl - query: org.irods.jargon.core.query.IRODSGenQueryFromBuilder@36511e0a [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq () [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO io.IRODSFileImpl - isDirectory() for path:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - looking up objStat, not cached in file [main] INFO pub.IRODSFileSystemAOImpl - getObjStat(final String irodsAbsolutePath) [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq dataId:103195231 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:b490a030319d7e477a3a52fcae3b6e09 ownerName:sr320 ownerZone:iplant objSize:1487132340 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:26:08 MST 2014 modifiedAt:Sat Mar 08 07:26:08 MST 2014 [main] INFO pub.DataObjectAOImpl - findMetadataValuesForDataObject: /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - setting file name, given path = E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO pub.FileCatalogObjectAOImpl - retrieveObjStat() [main] INFO pub.FileCatalogObjectAOImpl - irodsAbsolutePath:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq dataId:103195231 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:b490a030319d7e477a3a52fcae3b6e09 ownerName:sr320 ownerZone:iplant objSize:1487132340 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:26:08 MST 2014 modifiedAt:Sat Mar 08 07:26:08 MST 2014 [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone() [main] INFO pub.IRODSGenQueryExecutorImpl - query: org.irods.jargon.core.query.IRODSGenQueryFromBuilder@78b3e62 [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 EA5B9AC6-3526-4100-88DD-0E961B678D71 /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - setting file name, given path = /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - detected local separator = / [main] INFO io.IRODSFileImpl - file name was set as: E.fq [main] INFO io.IRODSFileImpl - isDirectory() for path:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO io.IRODSFileImpl - looking up objStat, not cached in file [main] INFO pub.IRODSFileSystemAOImpl - getObjStat(final String irodsAbsolutePath) [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq dataId:103195231 specColType:NORMAL objectType:DATA_OBJECT collectionPath: objectPath: checksum:b490a030319d7e477a3a52fcae3b6e09 ownerName:sr320 ownerZone:iplant objSize:1487132340 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:26:08 MST 2014 modifiedAt:Sat Mar 08 07:26:08 MST 2014 [main] INFO pub.DataObjectAOImpl - adding avu metadata to data object: avu data: attrib:ipc-analysis-id value:EA5B9AC6-3526-4100-88DD-0E961B678D71 units:UUID [main] INFO pub.DataObjectAOImpl - absolute path: /iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq [main] INFO pub.FileCatalogObjectAOImpl - resoveAbsolutePathViaObjStat() [main] INFO pub.FileCatalogObjectAOImpl - retrieveObjStat() [main] INFO pub.FileCatalogObjectAOImpl - irodsAbsolutePath:/iplant/home/sr320/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437 [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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437 dataId:103195228 specColType:NORMAL objectType:COLLECTION collectionPath: objectPath: checksum: ownerName:de-irods ownerZone:iplant objSize:0 cacheDir: cacheDirty:false createdAt:replNumber:0Sat Mar 08 07:24:52 MST 2014 modifiedAt:Sat Mar 08 07:24:52 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/Cgigas_v9/Zhang/fastq/E-2014-03-08-07-24-12.437/E.fq ./ stdout: 0/1 - 0.00% of files done 0.000/1418.207 MB - 0.00% of file sizes done Processing E.fq - 1418.207 MB 2014-03-08.07:36:12 E.fq - 439.990/1418.207 MB - 31.02% done 2014-03-08.07:36:24 E.fq - 945.898/1418.207 MB - 66.70% done 2014-03-08.07:36:37 E.fq - 1114.534/1418.207 MB - 78.59% done 2014-03-08.07:36:38 E.fq - 1418.207/1418.207 MB - 100.00% done 2014-03-08.07:36:39 [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/1394289372231 [main] INFO connection.IRODSConnection - now disconnected