[INFO] 2016-08-16 18:15:02,459 [root main 269] Starting smrtpipe.py : v1.87.139483
[INFO] 2016-08-16 18:15:02,460 [root main 270] Using Python         : v2.7.3
[INFO] 2016-08-16 18:15:02,476 [root main 271] Platform info Linux-2.6.32-431.29.2.el6.x86_64-x86_64-with-redhat-6.5-Santiago
[INFO] 2016-08-16 18:15:02,477 [root main 272] Running on rgs11.research.partners.org
[INFO] 2016-08-16 18:15:02,477 [root main 273] Process id 34938
[INFO] 2016-08-16 18:15:02,478 [SMRTpipe.pbpy.io.SecondaryConfig _loadFromFile 25] Loading SecondaryConfig from /PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/etc/config.xml
[INFO] 2016-08-16 18:15:02,479 [SMRTpipe.SmrtPipeConfig __autoLoad 113] Loading configuration from /PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/etc/smrtpipe.rc
[INFO] 2016-08-16 18:15:02,479 [SMRTpipe.SmrtPipeConfig __setAlgorithmParametersPath 212] ALGO_PARAMS key not found in smrtpipe.rc - using latest bundle: /PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/etc/algorithm_parameters/2015-11
[INFO] 2016-08-16 18:15:02,480 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /data/talkowski/Samples/XDP/PacBioBAC/AEX253-14/part 2/pacbio_ds2/1-2016-04-07-20k-4cell_509/C04_1/Analysis_Results/m160407_185746_42181_c100997922550000001823223708031671_s1_p0.1.bax.h5 2773281062 bytes
[INFO] 2016-08-16 18:15:02,481 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /data/talkowski/Samples/XDP/PacBioBAC/AEX253-14/part 2/pacbio_ds2/1-2016-04-07-20k-4cell_509/C04_1/Analysis_Results/m160407_185746_42181_c100997922550000001823223708031671_s1_p0.2.bax.h5 2578833271 bytes
[INFO] 2016-08-16 18:15:02,481 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /data/talkowski/Samples/XDP/PacBioBAC/AEX253-14/part 2/pacbio_ds2/1-2016-04-07-20k-4cell_509/C04_1/Analysis_Results/m160407_185746_42181_c100997922550000001823223708031671_s1_p0.3.bax.h5 2871262163 bytes
[INFO] 2016-08-16 18:15:02,481 [smrtpipe.status _sanityCheck 804] Successfully found 3 files in xml:/PHShome/ry077/bin/smrtanalysis/userdata/jobs/016/016450/input.xml
[INFO] 2016-08-16 18:15:02,483 [SMRTpipe.pbpy.io.SecondaryConfig _loadFromFile 25] Loading SecondaryConfig from /PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/etc/config.xml
[INFO] 2016-08-16 18:15:02,484 [SMRTpipe.SmrtPipeConfig __autoLoad 113] Loading configuration from /PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/etc/smrtpipe.rc
[INFO] 2016-08-16 18:15:02,484 [SMRTpipe.SmrtPipeConfig __setAlgorithmParametersPath 212] ALGO_PARAMS key not found in smrtpipe.rc - using latest bundle: /PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/etc/algorithm_parameters/2015-11
[INFO] 2016-08-16 18:15:02,484 [SMRTpipe.SmrtPipeContext __init__ 98] SmrtPipeConfig Summary:
                         TMP = /PHShome/ry077/bin/smrtanalysis/tmpdir                                                                     
                PROGRESS_URL = http://rgs11.research.partners.org:8080/smrtportal/api                                                     
             CLUSTER_MANAGER = LSF                                                                                                        
                   HOST_PORT = 8080                                                                                                       
                     NCHUNKS = 64                                                                                                         
            ALGO_PARAMS_PATH = /PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/etc/algorithm_parameters/2015-11
                   MAX_SLOTS = 256                                                                                                        
          ca_distribute.hgap = useGrid:0, scriptOnGrid:0, frgCorrOnGrid:0, ovlCorrOnGrid:0                                                
     CLOUD_LARGE_FILE_CUTOFF = 10MB                                                                                                       
        SMRTANALYSIS_VERSION = 2.3.0                                                                                                      
              INPUT_HDF5_EXT = bas.h5                                                                                                     
            SMRTPIPE_VERSION = 2.3.0.139497                                                                                               
                   HOST_NAME = rgs11.research.partners.org                                                                                
          DENOVO_READ_SCOPES = small: 0.15, large:15, huge:1700                                                                           
                       NPROC = 8                                                                                                          
        DENOVO_GENOME_SCOPES = small:100, large:1000, huge:40000                                                                          
                       NJOBS = 64                                                                                                         
                       CLOUD = False                                                                                                      
            REFERENCE_SCOPES = small:10, large:1000, veryLarge:100000, huge:10000000                                                      
                 MAX_THREADS = 8                                                                                                          
              HEARTBEAT_FREQ = 60                                                                                                         
                    VIS_HOST = rgs11.research.partners.org                                                                                
                    VIS_PORT = 8080                                                                                                       
                  SHARED_DIR = /PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/common/userdata/shared_dir               
                       DEBUG = False                                                                                                      
         ca_distribute.pb2ca = useGrid:0, scriptOnGrid:0, frgCorrOnGrid:0, ovlCorrOnGrid:0                                                
               SETTINGS_PATH = .                                                                                                          
             EXIT_ON_FAILURE = True                                                                                                       
       CLOUD_CHUNKS_PER_PROC = 2                                                                                                          
                 READ_SCOPES = small:3.6, large:100, veryLarge:10000, huge:1000000                                                        
                  MAX_CHUNKS = 64                                                                                                         
               ASSEMBLY_HOME = /PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis                                 
                   DATA_ROOT = /mnt                                                                                                       
               VIS_NAMESPACE =                                                                                                            
                         IPY = ipy -X:ColorfulConsole                                                                                     
               TOC_HTML_NAME = index.html                                                                                                 
[INFO] 2016-08-16 18:15:02,485 [SMRTpipe.SmrtPipeMain run 465] Successfully found or created TMP dir '/PHShome/ry077/bin/smrtanalysis/tmpdir'
[WARNING] 2016-08-16 18:15:02,493 [SMRTpipe.SmrtPipeSettings _importSettings 254] Parameter p_assembleunitig.specInRunCA is missing a value
[WARNING] 2016-08-16 18:15:02,493 [SMRTpipe.SmrtPipeSettings _importSettings 254] Parameter p_referenceuploader.organism is missing a value
[WARNING] 2016-08-16 18:15:02,493 [SMRTpipe.SmrtPipeSettings _importSettings 254] Parameter p_referenceuploader.ploidy is missing a value
[WARNING] 2016-08-16 18:15:02,493 [SMRTpipe.SmrtPipeSettings _importSettings 254] Parameter p_referenceuploader.user is missing a value
[INFO] 2016-08-16 18:15:02,494 [SMRTpipe.SmrtPipeContext initializeContext 235] SmrtPipeSettings Summary:
settings loaded from file /PHShome/ry077/bin/smrtanalysis
                            p_mapping.maxHits = 10                                                                                                                                                                                                                                                                                                                                                                                                                
                          p_filter.moduleName = P_Filter                                                                                                                                                                                                                                                                                                                                                                                                          
                     p_assembleunitig.merSize = 14                                                                                                                                                                                                                                                                                                                                                                                                                
                               global.version = 3                                                                                                                                                                                                                                                                                                                                                                                                                 
                                 global.fetch = common/protocols/preprocessing/Fetch.1.xml                                                                                                                                                                                                                                                                                                                                                                        
                      p_mapping.maxDivergence = 30                                                                                                                                                                                                                                                                                                                                                                                                                
               p_referenceuploader.moduleName = P_ReferenceUploader                                                                                                                                                                                                                                                                                                                                                                                               
                           p_fetch.moduleName = P_Fetch                                                                                                                                                                                                                                                                                                                                                                                                           
                                 global.state = active                                                                                                                                                                                                                                                                                                                                                                                                            
            p_assembleunitig.defaultFrgMinLen = 500                                                                                                                                                                                                                                                                                                                                                                                                               
                  p_mappingreports.moduleName = P_MappingReports                                                                                                                                                                                                                                                                                                                                                                                                  
       p_preassemblerdagcon.minLongReadLength = 6000                                                                                                                                                                                                                                                                                                                                                                                                              
                  p_assembleunitig.moduleName = P_AssembleUnitig                                                                                                                                                                                                                                                                                                                                                                                                  
              p_mapping.pbalign_advanced_opts =                                                                                                                                                                                                                                                                                                                                                                                                                   
                     global.Control Filtering = common/protocols/control/KeepControlReads.1.xml                                                                                                                                                                                                                                                                                                                                                                   
                               global.control = /PHShome/ry077/bin/smrtanalysis/userdata/references/2kb_control                                                                                                                                                                                                                                                                                                                                                   
              p_preassemblerdagcon.totalBestn = 24                                                                                                                                                                                                                                                                                                                                                                                                                
               p_preassemblerdagcon.minCorCov = 6                                                                                                                                                                                                                                                                                                                                                                                                                 
                   p_assembleunitig.ovlMinLen = 40                                                                                                                                                                                                                                                                                                                                                                                                                
                    p_filter.minSubReadLength = 500                                                                                                                                                                                                                                                                                                                                                                                                               
                 p_assembleunitig.libraryName = pacbioReads                                                                                                                                                                                                                                                                                                                                                                                                       
               p_assemblypolishing.moduleName = P_AssemblyPolishing                                                                                                                                                                                                                                                                                                                                                                                               
                       p_mapping.pulseMetrics = DeletionQV,IPD,InsertionQV,PulseWidth,QualityValue,MergeQV,SubstitutionQV,DeletionTag                                                                                                                                                                                                                                                                                                                             
                              global.assembly = common/protocols/assembly/PreAssemblerHGAP.3.xml                                                                                                                                                                                                                                                                                                                                                                  
                    p_assembleunitig.specTmpl = analysis/etc/celeraAssembler/unitig.spec                                                                                                                                                                                                                                                                                                                                                                          
                             global.consensus = common/protocols/consensus/AssemblyPolishing.1.xml                                                                                                                                                                                                                                                                                                                                                                
                           global.description = HGAP version 3. PacBio de novo assembler optimized for speed.                                                                                                                                                                                                                                                                                                                                                     
        p_referenceuploader.runUploaderUnitig = True                                                                                                                                                                                                                                                                                                                                                                                                              
                         p_filter.description = Filter reads for use in the pre-assembly step of HGAP, the hierarchical genome assembly process.                                                                                                                                                                                                                                                                                                                  
              p_preassemblerdagcon.moduleName = P_PreAssemblerDagcon                                                                                                                                                                                                                                                                                                                                                                                              
                 p_assembleunitig.description = This module runs Celera Assembler v8.1 to the unitig step, then finishes with our custom unitig consensus caller                                                                                                                                                                                                                                                                                                  
              p_assemblypolishing.description = Polish a pure-PacBio assembly for maximum accuracy using the Quiver algorithm.                                                                                                                                                                                                                                                                                                                                    
          p_referenceuploader.runUploaderHgap = False                                                                                                                                                                                                                                                                                                                                                                                                             
                  p_assembleunitig.genomeSize = 5000000                                                                                                                                                                                                                                                                                                                                                                                                           
                 p_referenceuploader.sawriter = sawriter -blt 8 -welter                                                                                                                                                                                                                                                                                                                                                                                           
                           p_filter.minLength = 100                                                                                                                                                                                                                                                                                                                                                                                                               
                       p_mapping.pbalign_opts = --seed=1 --minAccuracy=0.75 --minLength=50 --concordant --algorithmOptions="-useQuality"                                                                                                                                                                                                                                                                                                                          
                             p_mapping.samBam = True                                                                                                                                                                                                                                                                                                                                                                                                              
                         p_mapping.moduleName = P_Mapping                                                                                                                                                                                                                                                                                                                                                                                                         
                p_assembleunitig.ovlErrorRate = 0.06                                                                                                                                                                                                                                                                                                                                                                                                              
              p_preassemblerdagcon.splitBestn = 10                                                                                                                                                                                                                                                                                                                                                                                                                
            p_preassemblerdagcon.targetChunks = 6                                                                                                                                                                                                                                                                                                                                                                                                                 
                   p_assembleunitig.xCoverage = 25                                                                                                                                                                                                                                                                                                                                                                                                                
                      p_mapping.minAnchorSize = 12                                                                                                                                                                                                                                                                                                                                                                                                                
                             global.filtering = common/protocols/filtering/PreAssemblerSFilter.1.xml                                                                                                                                                                                                                                                                                                                                                              
              p_referenceuploader.runUploader = False                                                                                                                                                                                                                                                                                                                                                                                                             
     p_preassemblerdagcon.computeLengthCutoff = True                                                                                                                                                                                                                                                                                                                                                                                                              
                           p_filter.readScore = 0.80                                                                                                                                                                                                                                                                                                                                                                                                              
                        p_mapping.description = BLASR maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. The first set of alignments is found by querying an index of the reference genome, and then refining until only high scoring alignments are retained.  Additional pulse metrics are loaded into the resulting cmp.h5 file to enable downstream use of the Quiver algorithm.
                     p_mapping.loadPulsesOpts = bymetric                                                                                                                                                                                                                                                                                                                                                                                                          
                               global.mapping = common/protocols/mapping/BLASR_Resequencing.1.xml                                                                                                                                                                                                                                                                                                                                                                 
                          global.otfReference = reference                                                                                                                                                                                                                                                                                                                                                                                                         
                     global.referenceUploader = common/protocols/referenceuploader/ReferenceUploaderUnitig.1.xml                                                                                                                                                                                                                                                                                                                                                  
                            p_mapping.gff2Bed = True                                                                                                                                                                                                                                                                                                                                                                                                              
               p_mapping.placeRepeatsRandomly = True                                                                                                                                                                                                                                                                                                                                                                                                              
                         global.deferRefCheck = True                                                                                                                                                                                                                                                                                                                                                                                                              
                                  global.name = RS_HGAP_Assembly                                                                                                                                                                                                                                                                                                                                                                                                  
               p_preassemblerdagcon.blasrOpts = -noSplitSubreads -minReadLength 200 -maxScore -1000 -maxLCPLength 16                                                                                                                                                                                                                                                                                                                                              
                   p_referenceuploader.samIdx = samtools faidx                                                                                                                                                                                                                                                                                                                                                                                                    
                          p_fetch.description = Sets up inputs                                                                                                                                                                                                                                                                                                                                                                                                    
                 p_assembleunitig.maxSlotPerc = 1                                                                                                                                                                                                                                                                                                                                                                                                                 
        p_assemblypolishing.enableMapQVFilter = True                                                                                                                                                                                                                                                                                                                                                                                                              
                   p_preassemblerdagcon.title = Using DAG-based consensus algorithm, pre-assemble long reads as the first step of the Hierarchical Genome Assembly process (HGAP). Version 2 is a stepping stone for scaling to much larger genomes.                                                                                                                                                                                                              
                   p_filterreports.moduleName = P_FilterReports                                                                                                                                                                                                                                                                                                                                                                                                   
                     p_referenceuploader.name = reference                                                                                                                                                                                                                                                                                                                                                                                                         
[INFO] 2016-08-16 18:15:02,495 [SMRTpipe.SmrtDataService setupOutputDirectories 132] Creating /PHShome/ry077/bin/smrtanalysis/userdata/jobs/016/016450/data
[INFO] 2016-08-16 18:15:02,498 [SMRTpipe.SmrtDataService setupOutputDirectories 132] Creating /PHShome/ry077/bin/smrtanalysis/userdata/jobs/016/016450/results
[INFO] 2016-08-16 18:15:02,502 [SMRTpipe.SmrtDataService setupOutputDirectories 136] Completed setting up DataServices in /PHShome/ry077/bin/smrtanalysis/userdata/jobs/016/016450
[INFO] 2016-08-16 18:15:02,502 [SMRTpipe.SmrtPipeContext initializeContext 257] Input data is [ file//data/talkowski/Samples/XDP/PacBioBAC/AEX253-14/part 2/pacbio_ds2/1-2016-04-07-20k-4cell_509/C04_1 ]
[INFO] 2016-08-16 18:15:02,502 [SMRTpipe.SmrtPipeContext initializeContext 261] Configuration override for PROGRESS_URL: Old:  --> New: http://rgs11.research.partners.org:8080/smrtportal/api
[INFO] 2016-08-16 18:15:02,502 [SMRTpipe.SmrtPipeContext initializeContext 274] Changing working directory to /PHShome/ry077/bin/smrtanalysis/tmpdir/tmpc8MrYJ
[INFO] 2016-08-16 18:15:02,506 [SMRTpipe.cluster.ClusterJMS __init__ 197] cluster engine: LSF
 template root: /PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/etc/cluster
 temporary dir: /PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/common/userdata/shared_dir/tmpsDAcg5
[INFO] 2016-08-16 18:15:02,540 [SMRTpipe.SmrtPipeContext movieFiles 371] Pulling data from tags: *
[INFO] 2016-08-16 18:15:02,540 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /data/talkowski/Samples/XDP/PacBioBAC/AEX253-14/part 2/pacbio_ds2/1-2016-04-07-20k-4cell_509/C04_1/Analysis_Results/m160407_185746_42181_c100997922550000001823223708031671_s1_p0.1.bax.h5 (2773281062 bytes)
[INFO] 2016-08-16 18:15:02,541 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /data/talkowski/Samples/XDP/PacBioBAC/AEX253-14/part 2/pacbio_ds2/1-2016-04-07-20k-4cell_509/C04_1/Analysis_Results/m160407_185746_42181_c100997922550000001823223708031671_s1_p0.2.bax.h5 (2578833271 bytes)
[INFO] 2016-08-16 18:15:02,541 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /data/talkowski/Samples/XDP/PacBioBAC/AEX253-14/part 2/pacbio_ds2/1-2016-04-07-20k-4cell_509/C04_1/Analysis_Results/m160407_185746_42181_c100997922550000001823223708031671_s1_p0.3.bax.h5 (2871262163 bytes)
[INFO] 2016-08-16 18:15:02,619 [SMRTpipe.SmrtPipeMain _getBasVersions 413] Detected basH5 versions set(['-v2.3.0'])
[INFO] 2016-08-16 18:15:03,420 [smrtpipe.status run 503] smrtpipe.py running on rgs11.research.partners.org
[INFO] 2016-08-16 18:15:03,420 [SMRTpipe.SmrtPipeMain run 506] using Distributed mode with 8 nproc
[INFO] 2016-08-16 18:15:03,420 [smrtpipe.status run 519] SMRT Analysis 2.3.0 / SMRTpipe 1.87.139483
[INFO] 2016-08-16 18:15:03,421 [SMRTpipe.SmrtPipeMain run 522] Starting smrtpipe version 1.87.139483
[INFO] 2016-08-16 18:15:04,179 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Fetch module
[INFO] 2016-08-16 18:15:04,180 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Fetch v2.4.139483 and validated settings.
[INFO] 2016-08-16 18:15:04,190 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Filter module
[INFO] 2016-08-16 18:15:04,193 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Filter v1.7.139483 and validated settings.
[INFO] 2016-08-16 18:15:04,198 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_FilterReports module
[INFO] 2016-08-16 18:15:04,199 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_FilterReports v1.21.139483 and validated settings.
[INFO] 2016-08-16 18:15:04,205 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_PreAssemblerDagcon module
[INFO] 2016-08-16 18:15:04,208 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_PreAssemblerDagcon v2.1.124285 and validated settings.
[INFO] 2016-08-16 18:15:04,210 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_AssembleUnitig module
[INFO] 2016-08-16 18:15:04,213 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_AssembleUnitig v2.2.UnknownVersion and validated settings.
[INFO] 2016-08-16 18:15:04,221 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_ReferenceUploader module
[INFO] 2016-08-16 18:15:04,223 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_ReferenceUploader v1.2.139483 and validated settings.
[INFO] 2016-08-16 18:15:04,227 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Mapping module
[INFO] 2016-08-16 18:15:04,234 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Mapping v1.33.141997 and validated settings.
[INFO] 2016-08-16 18:15:04,249 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_MappingReports module
[INFO] 2016-08-16 18:15:04,251 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_MappingReports v1.7.140023 and validated settings.
[INFO] 2016-08-16 18:15:04,256 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_AssemblyPolishing module
[INFO] 2016-08-16 18:15:04,258 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_AssemblyPolishing v1.36.139483 and validated settings.
[INFO] 2016-08-16 18:15:04,260 [SMRTpipe.SmrtDataService writeTo 424] Writing 6 items to DataStore in {'smrt.data.xmlparam': <InputDataUrl ref:/PHShome/ry077/bin/smrtanalysis/userdata/jobs/016/016450/settings.xml >, 'smrt.output.log': '/PHShome/ry077/bin/smrtanalysis/userdata/jobs/016/016450/log', 'smrt.data.cmdline': <CompositeInputData url:xml:/PHShome/ry077/bin/smrtanalysis/userdata/jobs/016/016450/input.xml job:<JobInfo id:016450 name:HAP_seqAns > >, 'smrt.output.root': '/PHShome/ry077/bin/smrtanalysis/userdata/jobs/016/016450', 'smrt.output.results': '/PHShome/ry077/bin/smrtanalysis/userdata/jobs/016/016450/results', 'smrt.output.data': '/PHShome/ry077/bin/smrtanalysis/userdata/jobs/016/016450/data'}
[INFO] 2016-08-16 18:15:04,268 [SMRTpipe.SmrtPipeMain _runTasks 281] Skipping PreWorkflow as it contains zero tasks
[INFO] 2016-08-16 18:15:04,271 [SMRTpipe.SmrtPipeMain _runTasks 284] Loading 35 tasks into Workflow
[INFO] 2016-08-16 18:15:06,325 [SMRTpipe.SmrtPipeMain _runTasks 298] Executing workflow Workflow
[INFO] 2016-08-16 18:15:06,325 [smrtpipe.status execute 620] Process id 34938
[INFO] 2016-08-16 18:15:13,228 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Fetch/toFofn
[INFO] 2016-08-16 18:15:13,247 [smrtpipe.status refreshTargets 407] task P_Fetch.toFofn successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 0 slots.
[INFO] 2016-08-16 18:15:13,248 [smrtpipe.status refreshTargets 409] Workflow Completion Status 1/74 in (            1%) tasks completed.
[INFO] 2016-08-16 18:15:18,255 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Fetch/overviewRpt
[INFO] 2016-08-16 18:15:18,255 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Filter/filter.plsFofn.Scatter
[INFO] 2016-08-16 18:15:18,255 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Fetch/adapterRpt
[INFO] 2016-08-16 18:15:18,274 [smrtpipe.status refreshTargets 407] task P_Filter.filter.plsFofn.Scatter successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 2 slots.
[INFO] 2016-08-16 18:15:18,275 [smrtpipe.status refreshTargets 409] Workflow Completion Status 2/74 in (            2%) tasks completed.
[INFO] 2016-08-16 18:15:23,286 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Filter/filter_002of003
[INFO] 2016-08-16 18:15:23,286 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Filter/filter_001of003
[INFO] 2016-08-16 18:15:23,287 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Filter/filter_003of003
[INFO] 2016-08-16 18:15:49,485 [smrtpipe.status refreshTargets 407] task P_Fetch.overviewRpt successfully completed (12.00 sec (0.20 min)). freed 1 slots, using 7 slots.
[INFO] 2016-08-16 18:15:49,486 [smrtpipe.status refreshTargets 409] Workflow Completion Status 3/74 in (            4%) tasks completed.
[INFO] 2016-08-16 18:16:10,670 [smrtpipe.status refreshTargets 407] task P_Fetch.adapterRpt successfully completed (36.00 sec (0.60 min)). freed 1 slots, using 6 slots.
[INFO] 2016-08-16 18:16:10,671 [smrtpipe.status refreshTargets 409] Workflow Completion Status 4/74 in (            5%) tasks completed.
[INFO] 2016-08-16 18:17:38,341 [smrtpipe.status refreshTargets 407] task P_Filter.filter_002of003 successfully completed (57.00 sec (0.95 min)). freed 2 slots, using 4 slots.
[INFO] 2016-08-16 18:17:38,341 [smrtpipe.status refreshTargets 409] Workflow Completion Status 5/74 in (            6%) tasks completed.
[INFO] 2016-08-16 18:17:43,348 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Filter/subreads_002of003
[INFO] 2016-08-16 18:18:24,784 [smrtpipe.status refreshTargets 407] task P_Filter.filter_001of003 successfully completed (38.00 sec (0.63 min)). freed 2 slots, using 3 slots.
[INFO] 2016-08-16 18:18:24,784 [smrtpipe.status refreshTargets 409] Workflow Completion Status 6/74 in (            8%) tasks completed.
[INFO] 2016-08-16 18:18:29,791 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Filter/subreads_001of003
[INFO] 2016-08-16 18:19:09,840 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_002of003 successfully completed (75.00 sec (1.25 min)). freed 1 slots, using 3 slots.
[INFO] 2016-08-16 18:19:09,841 [smrtpipe.status refreshTargets 409] Workflow Completion Status 7/74 in (            9%) tasks completed.
[INFO] 2016-08-16 18:19:26,255 [smrtpipe.status refreshTargets 407] task P_Filter.filter_003of003 successfully completed (129.00 sec (2.15 min)). freed 2 slots, using 1 slots.
[INFO] 2016-08-16 18:19:26,255 [smrtpipe.status refreshTargets 409] Workflow Completion Status 8/74 in (         . 10%) tasks completed.
[INFO] 2016-08-16 18:19:31,264 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Filter/filter.summary.Gather
[INFO] 2016-08-16 18:19:31,264 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Filter/subreads_003of003
[INFO] 2016-08-16 18:19:31,265 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Filter/filter.rgnFofn.Gather
[INFO] 2016-08-16 18:19:31,285 [smrtpipe.status refreshTargets 407] task P_Filter.filter.rgnFofn.Gather successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 3 slots.
[INFO] 2016-08-16 18:19:31,285 [smrtpipe.status refreshTargets 409] Workflow Completion Status 9/74 in (         . 12%) tasks completed.
[INFO] 2016-08-16 18:19:36,292 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Filter/subreadSummary
[INFO] 2016-08-16 18:19:37,463 [smrtpipe.status refreshTargets 407] task P_Filter.filter.summary.Gather successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 3 slots.
[INFO] 2016-08-16 18:19:37,464 [smrtpipe.status refreshTargets 409] Workflow Completion Status 10/74 in (         . 13%) tasks completed.
[INFO] 2016-08-16 18:19:42,468 [smrtpipe.status refreshTargets 419] Starting task://016450/P_FilterReports/statsRpt
[INFO] 2016-08-16 18:19:42,468 [smrtpipe.status refreshTargets 419] Starting task://016450/P_FilterReports/loadingRpt
[INFO] 2016-08-16 18:20:12,508 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_001of003 successfully completed (83.00 sec (1.38 min)). freed 1 slots, using 4 slots.
[INFO] 2016-08-16 18:20:12,508 [smrtpipe.status refreshTargets 409] Workflow Completion Status 11/74 in (         . 14%) tasks completed.
[INFO] 2016-08-16 18:20:55,198 [smrtpipe.status refreshTargets 407] task P_FilterReports.loadingRpt successfully completed (10.00 sec (0.17 min)). freed 1 slots, using 3 slots.
[INFO] 2016-08-16 18:20:55,198 [smrtpipe.status refreshTargets 409] Workflow Completion Status 12/74 in (         . 16%) tasks completed.
[INFO] 2016-08-16 18:21:38,054 [smrtpipe.status refreshTargets 407] task P_Filter.subreadSummary successfully completed (58.00 sec (0.97 min)). freed 1 slots, using 2 slots.
[INFO] 2016-08-16 18:21:38,054 [smrtpipe.status refreshTargets 409] Workflow Completion Status 13/74 in (         . 17%) tasks completed.
[INFO] 2016-08-16 18:21:43,062 [smrtpipe.status refreshTargets 419] Starting task://016450/P_FilterReports/subreadRpt
[INFO] 2016-08-16 18:21:59,259 [smrtpipe.status refreshTargets 407] task P_FilterReports.statsRpt successfully completed (14.00 sec (0.23 min)). freed 1 slots, using 2 slots.
[INFO] 2016-08-16 18:21:59,259 [smrtpipe.status refreshTargets 409] Workflow Completion Status 14/74 in (         . 18%) tasks completed.
[INFO] 2016-08-16 18:22:00,412 [smrtpipe.status refreshTargets 407] task P_FilterReports.subreadRpt successfully completed (9.00 sec (0.15 min)). freed 1 slots, using 1 slots.
[INFO] 2016-08-16 18:22:00,412 [smrtpipe.status refreshTargets 409] Workflow Completion Status 15/74 in (        .. 20%) tasks completed.
[INFO] 2016-08-16 18:22:46,911 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_003of003 successfully completed (130.00 sec (2.17 min)). freed 1 slots, using 0 slots.
[INFO] 2016-08-16 18:22:46,911 [smrtpipe.status refreshTargets 409] Workflow Completion Status 16/74 in (        .. 21%) tasks completed.
[INFO] 2016-08-16 18:22:51,918 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Filter/subreads.subreadFastq.Gather
[INFO] 2016-08-16 18:22:51,918 [smrtpipe.status refreshTargets 419] Starting task://016450/P_Filter/subreads.subreads.Gather
[INFO] 2016-08-16 18:23:03,253 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreads.Gather successfully completed (2.00 sec (0.03 min)). freed 1 slots, using 1 slots.
[INFO] 2016-08-16 18:23:03,253 [smrtpipe.status refreshTargets 409] Workflow Completion Status 17/74 in (        .. 22%) tasks completed.
[INFO] 2016-08-16 18:23:08,261 [smrtpipe.status refreshTargets 419] Starting task://016450/P_PreAssemblerDagcon/filterLongReadsByLength
[INFO] 2016-08-16 18:23:14,471 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreadFastq.Gather successfully completed (5.00 sec (0.08 min)). freed 1 slots, using 1 slots.
[INFO] 2016-08-16 18:23:14,471 [smrtpipe.status refreshTargets 409] Workflow Completion Status 18/74 in (        .. 24%) tasks completed.
[INFO] 2016-08-16 18:23:24,501 [smrtpipe.status refreshTargets 407] task P_PreAssemblerDagcon.filterLongReadsByLength successfully completed (10.00 sec (0.17 min)). freed 1 slots, using 0 slots.
[INFO] 2016-08-16 18:23:24,501 [smrtpipe.status refreshTargets 409] Workflow Completion Status 19/74 in (        .. 25%) tasks completed.
[INFO] 2016-08-16 18:23:29,504 [smrtpipe.status refreshTargets 419] Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection.target.Scatter
[INFO] 2016-08-16 18:23:40,953 [smrtpipe.status refreshTargets 407] task P_PreAssemblerDagcon.hgapAlignForCorrection.target.Scatter successfully completed (3.00 sec (0.05 min)). freed 1 slots, using 0 slots.
[INFO] 2016-08-16 18:23:40,954 [smrtpipe.status refreshTargets 409] Workflow Completion Status 20/74 in (        .. 27%) tasks completed.
[INFO] 2016-08-16 18:23:45,967 [smrtpipe.status refreshTargets 419] Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006
[INFO] 2016-08-16 18:23:45,968 [smrtpipe.status refreshTargets 419] Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006
[INFO] 2016-08-16 18:23:45,968 [smrtpipe.status refreshTargets 419] Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006
[INFO] 2016-08-16 18:23:45,969 [smrtpipe.status refreshTargets 419] Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006
[INFO] 2016-08-16 18:23:45,969 [smrtpipe.status refreshTargets 419] Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006
[INFO] 2016-08-16 18:23:45,969 [smrtpipe.status refreshTargets 419] Starting task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006
[ERROR] 2016-08-16 18:23:45,970 [smrtpipe.status refreshTargets 413] *** Failed task task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006
[ERROR] 2016-08-16 18:23:45,970 [smrtpipe.status refreshTargets 413] *** Failed task task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006
[ERROR] 2016-08-16 18:23:45,971 [smrtpipe.status refreshTargets 413] *** Failed task task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006
[ERROR] 2016-08-16 18:23:45,971 [smrtpipe.status refreshTargets 413] *** Failed task task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006
[ERROR] 2016-08-16 18:23:45,971 [smrtpipe.status refreshTargets 413] *** Failed task task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006
[ERROR] 2016-08-16 18:23:45,972 [smrtpipe.status refreshTargets 413] *** Failed task task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006
[INFO] 2016-08-16 18:23:45,973 [smrtpipe.status execute 627] Found 6 failed tasks.
[INFO] 2016-08-16 18:23:45,974 [smrtpipe.status execute 629] task hgapAlignForCorrection_002of006 FAILED 
[INFO] 2016-08-16 18:23:45,974 [smrtpipe.status execute 629] task hgapAlignForCorrection_003of006 FAILED 
[INFO] 2016-08-16 18:23:45,975 [smrtpipe.status execute 629] task hgapAlignForCorrection_005of006 FAILED 
[INFO] 2016-08-16 18:23:45,975 [smrtpipe.status execute 629] task hgapAlignForCorrection_004of006 FAILED 
[INFO] 2016-08-16 18:23:45,976 [smrtpipe.status execute 629] task hgapAlignForCorrection_006of006 FAILED 
[INFO] 2016-08-16 18:23:45,976 [smrtpipe.status execute 629] task hgapAlignForCorrection_001of006 FAILED 
[ERROR] 2016-08-16 18:23:47,497 [SMRTpipe.SmrtPipeMain run 608] SmrtExit task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006 Failed
Traceback (most recent call last):
  File "/PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/SmrtPipeMain.py", line 571, in run
    self._runTasks(pModules)
  File "/PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/SmrtPipeMain.py", line 300, in _runTasks
    workflow.execute()
  File "/PHShome/ry077/bin/smrtanalysis/install/smrtanalysis_2.3.0.140936/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/engine/SmrtPipeWorkflow.py", line 640, in execute
    raise SmrtExit(str(e))
SmrtExit: SmrtExit task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006 Failed
[ERROR] 2016-08-16 18:23:47,498 [SMRTpipe.SmrtPipeMain exit 690] SmrtExit task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006 Failed
[INFO] 2016-08-16 18:23:47,498 [SMRTpipe.SmrtPipeMain exit 692] Beginning exit process
[INFO] 2016-08-16 18:23:47,498 [SMRTpipe.SmrtPipeMain shutdown 716] beginning Shutdown Process
[INFO] 2016-08-16 18:23:47,498 [SMRTpipe.SmrtPipeMain _generate_final_report 651] Writing final TOC page with error message : SmrtExit task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006 Failed
[INFO] 2016-08-16 18:23:48,071 [SMRTpipe.SmrtPipeMain shutdown 752] Completed shutdown gracefully
[INFO] 2016-08-16 18:23:48,071 [SMRTpipe.SmrtPipeMain exit 702] Sending message Exiting smrtpipe last error: SmrtExit task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006 Failed
[INFO] 2016-08-16 18:23:48,072 [smrtpipe.status failed 104] Sending Job 016450 failed message 'Exiting smrtpipe last error: SmrtExit task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_002of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_003of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_005of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_004of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_006of006 Failed task://016450/P_PreAssemblerDagcon/hgapAlignForCorrection_001of006 Failed' to url http://rgs11.research.partners.org:8080/smrtportal/api/jobs/016450/status
[INFO] 2016-08-16 18:23:48,097 [SMRTpipe.SmrtPipeMain run 641] completed SmrtPipeMain.run with exit code -1
[INFO] 2016-08-16 18:23:48,097 [root main 335] Failed smrtpipe version v1.87.139483 with exit code -1 in 525.62 seconds (8.76 minutes)
