[INFO] 2017-03-20 13:39:17,165 [root main 269] Starting smrtpipe.py : v1.87.139483 [INFO] 2017-03-20 13:39:17,165 [root main 270] Using Python : v2.7.3 [INFO] 2017-03-20 13:39:17,203 [root main 271] Platform info Linux-2.6.32-573.8.1.el6.x86_64-x86_64-with-centos-6.8-Final [INFO] 2017-03-20 13:39:17,204 [root main 272] Running on e114.grid.gs.washington.edu [INFO] 2017-03-20 13:39:17,204 [root main 273] Process id 11331 [INFO] 2017-03-20 13:39:17,204 [SMRTpipe.pbpy.io.SecondaryConfig _loadFromFile 25] Loading SecondaryConfig from /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/etc/config.xml [INFO] 2017-03-20 13:39:17,243 [SMRTpipe.SmrtPipeConfig __autoLoad 113] Loading configuration from /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/analysis/etc/smrtpipe.rc [INFO] 2017-03-20 13:39:17,271 [SMRTpipe.SmrtPipeConfig __setAlgorithmParametersPath 212] ALGO_PARAMS key not found in smrtpipe.rc - using latest bundle: /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/analysis/etc/algorithm_parameters/2015-11 [INFO] 2017-03-20 13:39:17,273 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/Analysis_Results/m170301_225711_42134_c101174162550000001823269408211763_s1_p0.2.bax.h5 5686050669 bytes [INFO] 2017-03-20 13:39:17,273 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/Analysis_Results/m170301_225711_42134_c101174162550000001823269408211763_s1_p0.1.bax.h5 5909199642 bytes [INFO] 2017-03-20 13:39:17,274 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/Analysis_Results/m170301_225711_42134_c101174162550000001823269408211763_s1_p0.3.bax.h5 6420221767 bytes [INFO] 2017-03-20 13:39:17,274 [smrtpipe.status _sanityCheck 804] Successfully found 3 files in xml:input.xml [INFO] 2017-03-20 13:39:17,274 [SMRTpipe.pbpy.io.SecondaryConfig _loadFromFile 25] Loading SecondaryConfig from /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/etc/config.xml [INFO] 2017-03-20 13:39:17,275 [SMRTpipe.SmrtPipeConfig __autoLoad 113] Loading configuration from /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/analysis/etc/smrtpipe.rc [INFO] 2017-03-20 13:39:17,276 [SMRTpipe.SmrtPipeConfig __setAlgorithmParametersPath 212] ALGO_PARAMS key not found in smrtpipe.rc - using latest bundle: /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/analysis/etc/algorithm_parameters/2015-11 [INFO] 2017-03-20 13:39:17,276 [SMRTpipe.SmrtPipeContext __init__ 98] SmrtPipeConfig Summary: TMP = /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/tmpdir PROGRESS_URL = CLUSTER_MANAGER = SGE HOST_PORT = 8080 NCHUNKS = 64 ALGO_PARAMS_PATH = /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/analysis/etc/algorithm_parameters/2015-11 MAX_SLOTS = 256 ca_distribute.hgap = useGrid:0, scriptOnGrid:1, frgCorrOnGrid:1, ovlCorrOnGrid:1 CLOUD_LARGE_FILE_CUTOFF = 10MB SMRTANALYSIS_VERSION = 2.3.0 INPUT_HDF5_EXT = bas.h5 SMRTPIPE_VERSION = 2.3.0.139497 HOST_NAME = pacbio.gs.washington.edu DENOVO_READ_SCOPES = small: 0.15, large:15, huge:1700 NPROC = 4 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 = 4 HEARTBEAT_FREQ = 60 VIS_HOST = pacbio.gs.washington.edu VIS_PORT = 8080 SHARED_DIR = /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/install/smrtanalysis_2.3.0.140936/common/userdata/shared_dir DEBUG = False ca_distribute.pb2ca = useGrid:1, scriptOnGrid:1, frgCorrOnGrid:1, ovlCorrOnGrid:1 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 = /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/analysis DATA_ROOT = /mnt VIS_NAMESPACE = IPY = ipy -X:ColorfulConsole TOC_HTML_NAME = index.html [INFO] 2017-03-20 13:39:17,456 [SMRTpipe.SmrtPipeMain run 465] Successfully found or created TMP dir '/net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/tmpdir' [INFO] 2017-03-20 13:39:17,586 [SMRTpipe.SmrtPipeContext initializeContext 235] SmrtPipeSettings Summary: settings loaded from file /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/filter global.fetch = common/protocols/preprocessing/Fetch.1.xml p_filter.minLength = 50 global.Control Filtering = common/protocols/control/RemoveControlReads.1.xml p_filter.moduleName = P_Filter global.version = 1 global.control = /net/eichler/vol24/projects/sequencing/pacbio/nobackups/smrt_userdata/references/2kb_control global.name = RS_Subreads p_control.pbalign_opts = --algorithmOptions=" -maxScore -1000 -sdpTupleSize 8 " --minAccuracy 0.01 --minLength=50 --maxHits=1 p_fetch.description = Sets up inputs p_filter.minSubReadLength = 50 p_filterreports.moduleName = P_FilterReports p_filter.description = This module filters reads based on a minimum subread length, polymerase read quality and polymerase read length. p_fetch.moduleName = P_Fetch global.barcode = common/protocols/barcode/NoBarcode.1.xml global.description = Filter subreads based on read length and quality, optionally splitting by barcode. Output FASTA and bas.h5 file of subreads. global.state = active global.filtering = common/protocols/filtering/SFilter.1.xml p_filter.readScore = 75 p_controlreports.moduleName = P_ControlReports p_control.moduleName = P_Control [INFO] 2017-03-20 13:39:17,587 [SMRTpipe.SmrtDataService setupOutputDirectories 132] Creating /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/filter/data [INFO] 2017-03-20 13:39:17,588 [SMRTpipe.SmrtDataService setupOutputDirectories 132] Creating /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/filter/results [INFO] 2017-03-20 13:39:17,589 [SMRTpipe.SmrtDataService setupOutputDirectories 136] Completed setting up DataServices in /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/filter [INFO] 2017-03-20 13:39:17,589 [SMRTpipe.SmrtPipeContext initializeContext 257] Input data is [ run/0000000-0002, run/0000000-0000, run/0000000-0001 ] [INFO] 2017-03-20 13:39:17,646 [SMRTpipe.cluster.ClusterJMS __init__ 197] cluster engine: SGE template root: /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/analysis/etc/cluster temporary dir: /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/install/smrtanalysis_2.3.0.140936/common/userdata/shared_dir/tmpDhnDGa [INFO] 2017-03-20 13:39:17,679 [SMRTpipe.SmrtPipeContext movieFiles 371] Pulling data from tags: * [INFO] 2017-03-20 13:39:17,679 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/Analysis_Results/m170301_225711_42134_c101174162550000001823269408211763_s1_p0.2.bax.h5 (5686050669 bytes) [INFO] 2017-03-20 13:39:17,680 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/Analysis_Results/m170301_225711_42134_c101174162550000001823269408211763_s1_p0.1.bax.h5 (5909199642 bytes) [INFO] 2017-03-20 13:39:17,680 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/Analysis_Results/m170301_225711_42134_c101174162550000001823269408211763_s1_p0.3.bax.h5 (6420221767 bytes) [INFO] 2017-03-20 13:39:17,752 [SMRTpipe.SmrtPipeMain _getBasVersions 413] Detected basH5 versions set(['-v2.3.0']) [INFO] 2017-03-20 13:39:20,090 [smrtpipe.status run 503] smrtpipe.py running on e114.grid.gs.washington.edu [INFO] 2017-03-20 13:39:20,090 [SMRTpipe.SmrtPipeMain run 506] using Distributed mode with 4 nproc [INFO] 2017-03-20 13:39:20,090 [smrtpipe.status run 519] SMRT Analysis 2.3.0 / SMRTpipe 1.87.139483 [INFO] 2017-03-20 13:39:20,090 [SMRTpipe.SmrtPipeMain run 522] Starting smrtpipe version 1.87.139483 [INFO] 2017-03-20 13:39:20,830 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Fetch module [INFO] 2017-03-20 13:39:20,831 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Fetch v2.4.139483 and validated settings. [INFO] 2017-03-20 13:39:20,894 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Filter module [INFO] 2017-03-20 13:39:20,899 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Filter v1.7.139483 and validated settings. [INFO] 2017-03-20 13:39:20,902 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_FilterReports module [INFO] 2017-03-20 13:39:20,902 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_FilterReports v1.21.139483 and validated settings. [INFO] 2017-03-20 13:39:20,908 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Control module [INFO] 2017-03-20 13:39:20,921 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Control v2.1.139483 and validated settings. [INFO] 2017-03-20 13:39:20,937 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_ControlReports module [INFO] 2017-03-20 13:39:20,937 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_ControlReports v2.2.139483 and validated settings. [INFO] 2017-03-20 13:39:20,939 [SMRTpipe.SmrtDataService writeTo 424] Writing 6 items to DataStore in {'smrt.data.xmlparam': , 'smrt.output.log': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/filter/log', 'smrt.data.cmdline': , 'smrt.output.root': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/filter', 'smrt.output.results': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/filter/results', 'smrt.output.data': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/filter/data'} [INFO] 2017-03-20 13:39:20,942 [SMRTpipe.SmrtPipeMain _runTasks 281] Skipping PreWorkflow as it contains zero tasks [INFO] 2017-03-20 13:39:20,944 [SMRTpipe.SmrtPipeMain _runTasks 284] Loading 14 tasks into Workflow [INFO] 2017-03-20 13:39:22,334 [SMRTpipe.SmrtPipeMain _runTasks 298] Executing workflow Workflow [INFO] 2017-03-20 13:39:22,334 [smrtpipe.status execute 620] Process id 11331 [INFO] 2017-03-20 13:39:28,314 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Fetch/toFofn [INFO] 2017-03-20 13:39:28,315 [smrtpipe.status refreshTargets 407] task P_Fetch.toFofn successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 0 slots. [INFO] 2017-03-20 13:39:28,315 [smrtpipe.status refreshTargets 409] Workflow Completion Status 1/29 in ( 3%) tasks completed. [INFO] 2017-03-20 13:39:33,325 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Fetch/adapterRpt [INFO] 2017-03-20 13:39:33,326 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads.plsFofn.Scatter [INFO] 2017-03-20 13:39:33,326 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Fetch/overviewRpt [INFO] 2017-03-20 13:39:33,329 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.plsFofn.Scatter successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 2 slots. [INFO] 2017-03-20 13:39:33,329 [smrtpipe.status refreshTargets 409] Workflow Completion Status 2/29 in ( 6%) tasks completed. [INFO] 2017-03-20 13:39:38,336 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter_003of003 [INFO] 2017-03-20 13:39:38,339 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter_002of003 [INFO] 2017-03-20 13:39:39,420 [smrtpipe.status refreshTargets 407] task P_Fetch.overviewRpt successfully completed (4.00 sec (0.07 min)). freed 1 slots, using 5 slots. [INFO] 2017-03-20 13:39:39,420 [smrtpipe.status refreshTargets 409] Workflow Completion Status 3/29 in ( . 10%) tasks completed. [INFO] 2017-03-20 13:39:44,427 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter_001of003 [INFO] 2017-03-20 13:40:14,460 [smrtpipe.status refreshTargets 407] task P_Filter.filter_003of003 successfully completed (34.00 sec (0.57 min)). freed 2 slots, using 5 slots. [INFO] 2017-03-20 13:40:14,460 [smrtpipe.status refreshTargets 409] Workflow Completion Status 4/29 in ( . 13%) tasks completed. [INFO] 2017-03-20 13:40:15,542 [smrtpipe.status refreshTargets 407] task P_Fetch.adapterRpt successfully completed (40.00 sec (0.67 min)). freed 1 slots, using 4 slots. [INFO] 2017-03-20 13:40:15,542 [smrtpipe.status refreshTargets 409] Workflow Completion Status 5/29 in ( . 17%) tasks completed. [INFO] 2017-03-20 13:40:15,545 [smrtpipe.status refreshTargets 407] task P_Filter.filter_002of003 successfully completed (35.00 sec (0.58 min)). freed 2 slots, using 2 slots. [INFO] 2017-03-20 13:40:15,545 [smrtpipe.status refreshTargets 409] Workflow Completion Status 6/29 in ( .. 20%) tasks completed. [INFO] 2017-03-20 13:40:20,552 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads_003of003 [INFO] 2017-03-20 13:40:20,553 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align_003of003 [INFO] 2017-03-20 13:40:20,554 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align_002of003 [INFO] 2017-03-20 13:40:20,557 [smrtpipe.status refreshTargets 407] task P_Filter.filter_001of003 successfully completed (34.00 sec (0.57 min)). freed 2 slots, using 9 slots. [INFO] 2017-03-20 13:40:20,557 [smrtpipe.status refreshTargets 409] Workflow Completion Status 7/29 in ( .. 24%) tasks completed. [INFO] 2017-03-20 13:40:25,565 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads_002of003 [INFO] 2017-03-20 13:44:57,117 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_003of003 successfully completed (270.00 sec (4.50 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 13:44:57,117 [smrtpipe.status refreshTargets 409] Workflow Completion Status 8/29 in ( .. 27%) tasks completed. [INFO] 2017-03-20 13:45:02,128 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter.summary.Gather [INFO] 2017-03-20 13:45:08,271 [smrtpipe.status refreshTargets 407] task P_Filter.filter.summary.Gather successfully completed (1.00 sec (0.02 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 13:45:08,272 [smrtpipe.status refreshTargets 409] Workflow Completion Status 9/29 in ( ... 31%) tasks completed. [INFO] 2017-03-20 13:45:13,279 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_FilterReports/loadingRpt [INFO] 2017-03-20 13:45:24,413 [smrtpipe.status refreshTargets 407] task P_FilterReports.loadingRpt successfully completed (7.00 sec (0.12 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 13:45:24,413 [smrtpipe.status refreshTargets 409] Workflow Completion Status 10/29 in ( ... 34%) tasks completed. [INFO] 2017-03-20 13:45:29,420 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_FilterReports/statsRpt [INFO] 2017-03-20 13:45:29,427 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_002of003 successfully completed (298.00 sec (4.97 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 13:45:29,427 [smrtpipe.status refreshTargets 409] Workflow Completion Status 11/29 in ( ... 37%) tasks completed. [INFO] 2017-03-20 13:45:34,434 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align_001of003 [INFO] 2017-03-20 13:45:51,211 [smrtpipe.status refreshTargets 407] task P_FilterReports.statsRpt successfully completed (16.00 sec (0.27 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 13:45:51,214 [smrtpipe.status refreshTargets 409] Workflow Completion Status 12/29 in ( .... 41%) tasks completed. [INFO] 2017-03-20 13:45:56,218 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads_001of003 [INFO] 2017-03-20 13:49:24,174 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_001of003 successfully completed (206.00 sec (3.43 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 13:49:24,175 [smrtpipe.status refreshTargets 409] Workflow Completion Status 13/29 in ( .... 44%) tasks completed. [INFO] 2017-03-20 13:49:29,187 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads.subreadFastq.Gather [INFO] 2017-03-20 13:51:07,571 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreadFastq.Gather successfully completed (94.00 sec (1.57 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 13:51:07,572 [smrtpipe.status refreshTargets 409] Workflow Completion Status 14/29 in ( .... 48%) tasks completed. [INFO] 2017-03-20 13:51:12,580 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads.subreads.Gather [INFO] 2017-03-20 13:52:19,804 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreads.Gather successfully completed (62.00 sec (1.03 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 13:52:19,806 [smrtpipe.status refreshTargets 409] Workflow Completion Status 15/29 in ( ..... 51%) tasks completed. [INFO] 2017-03-20 13:52:24,812 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter.rgnFofn.Gather [INFO] 2017-03-20 13:52:24,822 [smrtpipe.status refreshTargets 407] task P_Filter.filter.rgnFofn.Gather successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 13:52:24,823 [smrtpipe.status refreshTargets 409] Workflow Completion Status 16/29 in ( ..... 55%) tasks completed. [INFO] 2017-03-20 13:52:29,830 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreadSummary [INFO] 2017-03-20 13:53:57,150 [smrtpipe.status refreshTargets 407] task P_Filter.subreadSummary successfully completed (83.00 sec (1.38 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 13:53:57,151 [smrtpipe.status refreshTargets 409] Workflow Completion Status 17/29 in ( ..... 58%) tasks completed. [INFO] 2017-03-20 13:54:02,157 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_FilterReports/subreadRpt [INFO] 2017-03-20 13:54:23,311 [smrtpipe.status refreshTargets 407] task P_FilterReports.subreadRpt successfully completed (16.00 sec (0.27 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 13:54:23,311 [smrtpipe.status refreshTargets 409] Workflow Completion Status 18/29 in ( ...... 62%) tasks completed. [INFO] 2017-03-20 13:57:05,022 [smrtpipe.status refreshTargets 407] task P_Control.align_003of003 successfully completed (1003.00 sec (16.72 min)). freed 4 slots, using 8 slots. [INFO] 2017-03-20 13:57:05,023 [smrtpipe.status refreshTargets 409] Workflow Completion Status 19/29 in ( ...... 65%) tasks completed. [INFO] 2017-03-20 13:57:10,029 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn_003of003 [INFO] 2017-03-20 13:57:20,042 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn_003of003 successfully completed (5.00 sec (0.08 min)). freed 1 slots, using 8 slots. [INFO] 2017-03-20 13:57:20,043 [smrtpipe.status refreshTargets 409] Workflow Completion Status 20/29 in ( ...... 68%) tasks completed. [INFO] 2017-03-20 13:59:16,188 [smrtpipe.status refreshTargets 407] task P_Control.align_002of003 successfully completed (1132.00 sec (18.87 min)). freed 4 slots, using 4 slots. [INFO] 2017-03-20 13:59:16,189 [smrtpipe.status refreshTargets 409] Workflow Completion Status 21/29 in ( ....... 72%) tasks completed. [INFO] 2017-03-20 13:59:21,196 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn_002of003 [INFO] 2017-03-20 13:59:31,212 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn_002of003 successfully completed (5.00 sec (0.08 min)). freed 1 slots, using 4 slots. [INFO] 2017-03-20 13:59:31,213 [smrtpipe.status refreshTargets 409] Workflow Completion Status 22/29 in ( ....... 75%) tasks completed. [INFO] 2017-03-20 14:04:44,047 [smrtpipe.status refreshTargets 407] task P_Control.align_001of003 successfully completed (1143.00 sec (19.05 min)). freed 4 slots, using 0 slots. [INFO] 2017-03-20 14:04:44,048 [smrtpipe.status refreshTargets 409] Workflow Completion Status 23/29 in ( ....... 79%) tasks completed. [INFO] 2017-03-20 14:04:49,056 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn_001of003 [INFO] 2017-03-20 14:04:49,057 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align.cmpH5.Gather [INFO] 2017-03-20 14:05:00,673 [smrtpipe.status refreshTargets 407] task P_Control.align.cmpH5.Gather successfully completed (4.00 sec (0.07 min)). freed 1 slots, using 1 slots. [INFO] 2017-03-20 14:05:00,673 [smrtpipe.status refreshTargets 409] Workflow Completion Status 24/29 in ( ........ 82%) tasks completed. [INFO] 2017-03-20 14:05:00,673 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn_001of003 successfully completed (6.00 sec (0.10 min)). freed 1 slots, using 0 slots. [INFO] 2017-03-20 14:05:00,673 [smrtpipe.status refreshTargets 409] Workflow Completion Status 25/29 in ( ........ 86%) tasks completed. [INFO] 2017-03-20 14:05:05,681 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn.noCtrlFofn.Gather [INFO] 2017-03-20 14:05:05,682 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/summaryCSV [INFO] 2017-03-20 14:05:05,682 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_ControlReports/statsJsonReport [INFO] 2017-03-20 14:05:05,685 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn.noCtrlFofn.Gather successfully completed (1.00 sec (0.02 min)). freed 1 slots, using 2 slots. [INFO] 2017-03-20 14:05:05,685 [smrtpipe.status refreshTargets 409] Workflow Completion Status 26/29 in ( ........ 89%) tasks completed. [INFO] 2017-03-20 14:05:10,693 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/noControlSubreads [INFO] 2017-03-20 14:05:16,848 [smrtpipe.status refreshTargets 407] task P_ControlReports.statsJsonReport successfully completed (7.00 sec (0.12 min)). freed 1 slots, using 2 slots. [INFO] 2017-03-20 14:05:16,848 [smrtpipe.status refreshTargets 409] Workflow Completion Status 27/29 in ( ......... 93%) tasks completed. [INFO] 2017-03-20 14:05:17,937 [smrtpipe.status refreshTargets 407] task P_Control.summaryCSV successfully completed (8.00 sec (0.13 min)). freed 1 slots, using 1 slots. [INFO] 2017-03-20 14:05:17,937 [smrtpipe.status refreshTargets 409] Workflow Completion Status 28/29 in ( ......... 96%) tasks completed. [INFO] 2017-03-20 14:07:30,207 [smrtpipe.status refreshTargets 407] task P_Control.noControlSubreads successfully completed (132.00 sec (2.20 min)). freed 1 slots, using 0 slots. [INFO] 2017-03-20 14:07:30,208 [smrtpipe.status refreshTargets 409] Workflow Completion Status 29/29 in (..........100%) tasks completed. [INFO] 2017-03-20 14:07:30,954 [smrtpipe.status _runTasks 301] Completed workflow Workflow execution. [INFO] 2017-03-20 14:07:30,960 [SMRTpipe.SmrtPipeMain _runTasks 281] Skipping PostWorkflow as it contains zero tasks [INFO] 2017-03-20 14:07:30,960 [SMRTpipe.SmrtPipeMain _runTasks 333] exiting _runTask in 1690.02 sec (28.17 min) [INFO] 2017-03-20 14:07:30,960 [SMRTpipe.SmrtPipeMain run 572] Completed execution of 5 P_* modules. [WARNING] 2017-03-20 14:07:31,583 [SMRTpipe.SmrtDataService writeTo 402] Found slots NOT in DataService ['smrt.reentrant.complete'] [INFO] 2017-03-20 14:07:31,583 [SMRTpipe.SmrtDataService writeTo 424] Writing 7 items to DataStore in {'smrt.data.xmlparam': , 'smrt.output.log': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/filter/log', 'smrt.data.cmdline': , 'smrt.cells.completed': ['m170301_225711_42134_c101174162550000001823269408211763', 'm170301_225711_42134_c101174162550000001823269408211763', 'm170301_225711_42134_c101174162550000001823269408211763'], 'smrt.output.root': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/filter', 'smrt.output.results': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/filter/results', 'smrt.output.data': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170228_PCB-CC_AL_20kb_P6v2_E01_1/filter/data'} [INFO] 2017-03-20 14:07:31,591 [SMRTpipe.SmrtPipeMain shutdown 716] beginning Shutdown Process [INFO] 2017-03-20 14:07:31,592 [SMRTpipe.SmrtPipeMain _generate_final_report 651] Writing final TOC page [INFO] 2017-03-20 14:07:32,142 [SMRTpipe.SmrtPipeMain shutdown 752] Completed shutdown gracefully [INFO] 2017-03-20 14:07:32,154 [SMRTpipe.SmrtPipeMain run 641] completed SmrtPipeMain.run with exit code 0 [INFO] 2017-03-20 14:07:32,154 [root main 335] Successfully exiting smrtpipe version v1.87.139483 with exit code 0 in 1694.88 seconds (28.25 minutes)