[INFO] 2017-03-20 09:27:24,053 [root main 269] Starting smrtpipe.py : v1.87.139483 [INFO] 2017-03-20 09:27:24,053 [root main 270] Using Python : v2.7.3 [INFO] 2017-03-20 09:27:24,069 [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 09:27:24,070 [root main 272] Running on e109.grid.gs.washington.edu [INFO] 2017-03-20 09:27:24,070 [root main 273] Process id 507 [INFO] 2017-03-20 09:27:24,070 [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 09:27:24,071 [SMRTpipe.SmrtPipeConfig __autoLoad 113] Loading configuration from /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/analysis/etc/smrtpipe.rc [INFO] 2017-03-20 09:27:24,072 [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 09:27:24,075 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/Analysis_Results/m170315_190851_42134_c101169382550000001823273008151702_s1_p0.1.bax.h5 4168518035 bytes [INFO] 2017-03-20 09:27:24,075 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/Analysis_Results/m170315_190851_42134_c101169382550000001823273008151702_s1_p0.3.bax.h5 4105486858 bytes [INFO] 2017-03-20 09:27:24,075 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/Analysis_Results/m170315_190851_42134_c101169382550000001823273008151702_s1_p0.2.bax.h5 3952281915 bytes [INFO] 2017-03-20 09:27:24,075 [smrtpipe.status _sanityCheck 804] Successfully found 3 files in xml:input.xml [INFO] 2017-03-20 09:27:24,076 [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 09:27:24,077 [SMRTpipe.SmrtPipeConfig __autoLoad 113] Loading configuration from /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/analysis/etc/smrtpipe.rc [INFO] 2017-03-20 09:27:24,077 [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 09:27:24,078 [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 09:27:24,095 [SMRTpipe.SmrtPipeMain run 465] Successfully found or created TMP dir '/net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/tmpdir' [INFO] 2017-03-20 09:27:24,361 [SMRTpipe.SmrtPipeContext initializeContext 235] SmrtPipeSettings Summary: settings loaded from file /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_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 09:27:24,363 [SMRTpipe.SmrtDataService setupOutputDirectories 132] Creating /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/filter/data [INFO] 2017-03-20 09:27:24,364 [SMRTpipe.SmrtDataService setupOutputDirectories 132] Creating /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/filter/results [INFO] 2017-03-20 09:27:24,364 [SMRTpipe.SmrtDataService setupOutputDirectories 136] Completed setting up DataServices in /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/filter [INFO] 2017-03-20 09:27:24,365 [SMRTpipe.SmrtPipeContext initializeContext 257] Input data is [ run/0000000-0002, run/0000000-0000, run/0000000-0001 ] [INFO] 2017-03-20 09:27:24,405 [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/tmp6DrN60 [INFO] 2017-03-20 09:27:24,442 [SMRTpipe.SmrtPipeContext movieFiles 371] Pulling data from tags: * [INFO] 2017-03-20 09:27:24,443 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/Analysis_Results/m170315_190851_42134_c101169382550000001823273008151702_s1_p0.1.bax.h5 (4168518035 bytes) [INFO] 2017-03-20 09:27:24,443 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/Analysis_Results/m170315_190851_42134_c101169382550000001823273008151702_s1_p0.3.bax.h5 (4105486858 bytes) [INFO] 2017-03-20 09:27:24,443 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/Analysis_Results/m170315_190851_42134_c101169382550000001823273008151702_s1_p0.2.bax.h5 (3952281915 bytes) [INFO] 2017-03-20 09:27:24,486 [SMRTpipe.SmrtPipeMain _getBasVersions 413] Detected basH5 versions set(['-v2.3.0']) [INFO] 2017-03-20 09:27:25,137 [smrtpipe.status run 503] smrtpipe.py running on e109.grid.gs.washington.edu [INFO] 2017-03-20 09:27:25,137 [SMRTpipe.SmrtPipeMain run 506] using Distributed mode with 4 nproc [INFO] 2017-03-20 09:27:25,137 [smrtpipe.status run 519] SMRT Analysis 2.3.0 / SMRTpipe 1.87.139483 [INFO] 2017-03-20 09:27:25,138 [SMRTpipe.SmrtPipeMain run 522] Starting smrtpipe version 1.87.139483 [INFO] 2017-03-20 09:27:25,675 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Fetch module [INFO] 2017-03-20 09:27:25,676 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Fetch v2.4.139483 and validated settings. [INFO] 2017-03-20 09:27:25,692 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Filter module [INFO] 2017-03-20 09:27:25,697 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Filter v1.7.139483 and validated settings. [INFO] 2017-03-20 09:27:25,699 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_FilterReports module [INFO] 2017-03-20 09:27:25,700 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_FilterReports v1.21.139483 and validated settings. [INFO] 2017-03-20 09:27:25,703 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Control module [INFO] 2017-03-20 09:27:25,707 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Control v2.1.139483 and validated settings. [INFO] 2017-03-20 09:27:25,708 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_ControlReports module [INFO] 2017-03-20 09:27:25,709 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_ControlReports v2.2.139483 and validated settings. [INFO] 2017-03-20 09:27:25,710 [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/170314_PCB-CC_20kb_P6v2_A04_1/filter/log', 'smrt.data.cmdline': , 'smrt.output.root': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/filter', 'smrt.output.results': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/filter/results', 'smrt.output.data': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/filter/data'} [INFO] 2017-03-20 09:27:25,714 [SMRTpipe.SmrtPipeMain _runTasks 281] Skipping PreWorkflow as it contains zero tasks [INFO] 2017-03-20 09:27:25,716 [SMRTpipe.SmrtPipeMain _runTasks 284] Loading 14 tasks into Workflow [INFO] 2017-03-20 09:27:26,224 [SMRTpipe.SmrtPipeMain _runTasks 298] Executing workflow Workflow [INFO] 2017-03-20 09:27:26,225 [smrtpipe.status execute 620] Process id 507 [INFO] 2017-03-20 09:27:31,952 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Fetch/toFofn [INFO] 2017-03-20 09:27:31,954 [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 09:27:31,954 [smrtpipe.status refreshTargets 409] Workflow Completion Status 1/29 in ( 3%) tasks completed. [INFO] 2017-03-20 09:27:36,963 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align.plsFofn.Scatter [INFO] 2017-03-20 09:27:36,964 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Fetch/overviewRpt [INFO] 2017-03-20 09:27:36,965 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Fetch/adapterRpt [INFO] 2017-03-20 09:27:36,967 [smrtpipe.status refreshTargets 407] task P_Control.align.plsFofn.Scatter successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 2 slots. [INFO] 2017-03-20 09:27:36,968 [smrtpipe.status refreshTargets 409] Workflow Completion Status 2/29 in ( 6%) tasks completed. [INFO] 2017-03-20 09:27:41,975 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter_001of003 [INFO] 2017-03-20 09:27:41,976 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter_002of003 [INFO] 2017-03-20 09:27:43,067 [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 09:27:43,067 [smrtpipe.status refreshTargets 409] Workflow Completion Status 3/29 in ( . 10%) tasks completed. [INFO] 2017-03-20 09:27:48,074 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter_003of003 [INFO] 2017-03-20 09:28:14,475 [smrtpipe.status refreshTargets 407] task P_Fetch.adapterRpt successfully completed (32.00 sec (0.53 min)). freed 1 slots, using 6 slots. [INFO] 2017-03-20 09:28:14,476 [smrtpipe.status refreshTargets 409] Workflow Completion Status 4/29 in ( . 13%) tasks completed. [INFO] 2017-03-20 09:28:19,485 [smrtpipe.status refreshTargets 407] task P_Filter.filter_001of003 successfully completed (33.00 sec (0.55 min)). freed 2 slots, using 4 slots. [INFO] 2017-03-20 09:28:19,485 [smrtpipe.status refreshTargets 409] Workflow Completion Status 5/29 in ( . 17%) tasks completed. [INFO] 2017-03-20 09:28:19,488 [smrtpipe.status refreshTargets 407] task P_Filter.filter_002of003 successfully completed (34.00 sec (0.57 min)). freed 2 slots, using 2 slots. [INFO] 2017-03-20 09:28:19,489 [smrtpipe.status refreshTargets 409] Workflow Completion Status 6/29 in ( .. 20%) tasks completed. [INFO] 2017-03-20 09:28:24,496 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads_001of003 [INFO] 2017-03-20 09:28:24,497 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align_001of003 [INFO] 2017-03-20 09:28:24,498 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads_002of003 [INFO] 2017-03-20 09:28:24,502 [smrtpipe.status refreshTargets 407] task P_Filter.filter_003of003 successfully completed (33.00 sec (0.55 min)). freed 2 slots, using 6 slots. [INFO] 2017-03-20 09:28:24,502 [smrtpipe.status refreshTargets 409] Workflow Completion Status 7/29 in ( .. 24%) tasks completed. [INFO] 2017-03-20 09:28:29,511 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align_002of003 [INFO] 2017-03-20 09:30:05,697 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_002of003 successfully completed (99.00 sec (1.65 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 09:30:05,698 [smrtpipe.status refreshTargets 409] Workflow Completion Status 8/29 in ( .. 27%) tasks completed. [INFO] 2017-03-20 09:30:10,705 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter.summary.Gather [INFO] 2017-03-20 09:30:10,708 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_001of003 successfully completed (101.00 sec (1.68 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 09:30:10,708 [smrtpipe.status refreshTargets 409] Workflow Completion Status 9/29 in ( ... 31%) tasks completed. [INFO] 2017-03-20 09:30:15,714 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads_003of003 [INFO] 2017-03-20 09:30:16,859 [smrtpipe.status refreshTargets 407] task P_Filter.filter.summary.Gather successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 09:30:16,859 [smrtpipe.status refreshTargets 409] Workflow Completion Status 10/29 in ( ... 34%) tasks completed. [INFO] 2017-03-20 09:30:21,865 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_FilterReports/statsRpt [INFO] 2017-03-20 09:30:48,587 [smrtpipe.status refreshTargets 407] task P_FilterReports.statsRpt successfully completed (19.00 sec (0.32 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 09:30:48,587 [smrtpipe.status refreshTargets 409] Workflow Completion Status 11/29 in ( ... 37%) tasks completed. [INFO] 2017-03-20 09:30:53,594 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_FilterReports/loadingRpt [INFO] 2017-03-20 09:31:04,744 [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 09:31:04,744 [smrtpipe.status refreshTargets 409] Workflow Completion Status 12/29 in ( .... 41%) tasks completed. [INFO] 2017-03-20 09:31:09,752 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align_003of003 [INFO] 2017-03-20 09:31:45,374 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_003of003 successfully completed (87.00 sec (1.45 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 09:31:45,375 [smrtpipe.status refreshTargets 409] Workflow Completion Status 13/29 in ( .... 44%) tasks completed. [INFO] 2017-03-20 09:31:50,383 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads.subreads.Gather [INFO] 2017-03-20 09:32:11,526 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreads.Gather successfully completed (18.00 sec (0.30 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 09:32:11,527 [smrtpipe.status refreshTargets 409] Workflow Completion Status 14/29 in ( .... 48%) tasks completed. [INFO] 2017-03-20 09:32:16,530 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads.subreadFastq.Gather [INFO] 2017-03-20 09:32:53,278 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreadFastq.Gather successfully completed (33.00 sec (0.55 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 09:32:53,279 [smrtpipe.status refreshTargets 409] Workflow Completion Status 15/29 in ( ..... 51%) tasks completed. [INFO] 2017-03-20 09:32:58,285 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter.rgnFofn.Gather [INFO] 2017-03-20 09:32:58,288 [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 09:32:58,288 [smrtpipe.status refreshTargets 409] Workflow Completion Status 16/29 in ( ..... 55%) tasks completed. [INFO] 2017-03-20 09:33:03,295 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreadSummary [INFO] 2017-03-20 09:34:20,008 [smrtpipe.status refreshTargets 407] task P_Filter.subreadSummary successfully completed (70.00 sec (1.17 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 09:34:20,009 [smrtpipe.status refreshTargets 409] Workflow Completion Status 17/29 in ( ..... 58%) tasks completed. [INFO] 2017-03-20 09:34:25,015 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_FilterReports/subreadRpt [INFO] 2017-03-20 09:34:46,663 [smrtpipe.status refreshTargets 407] task P_FilterReports.subreadRpt successfully completed (15.00 sec (0.25 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 09:34:46,663 [smrtpipe.status refreshTargets 409] Workflow Completion Status 18/29 in ( ...... 62%) tasks completed. [INFO] 2017-03-20 09:39:43,890 [smrtpipe.status refreshTargets 407] task P_Control.align_001of003 successfully completed (673.00 sec (11.22 min)). freed 4 slots, using 8 slots. [INFO] 2017-03-20 09:39:43,891 [smrtpipe.status refreshTargets 409] Workflow Completion Status 19/29 in ( ...... 65%) tasks completed. [INFO] 2017-03-20 09:39:43,893 [smrtpipe.status refreshTargets 407] task P_Control.align_002of003 successfully completed (669.00 sec (11.15 min)). freed 4 slots, using 4 slots. [INFO] 2017-03-20 09:39:43,893 [smrtpipe.status refreshTargets 409] Workflow Completion Status 20/29 in ( ...... 68%) tasks completed. [INFO] 2017-03-20 09:39:49,349 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn_001of003 [INFO] 2017-03-20 09:39:49,350 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn_002of003 [INFO] 2017-03-20 09:39:59,363 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn_002of003 successfully completed (5.00 sec (0.08 min)). freed 1 slots, using 5 slots. [INFO] 2017-03-20 09:39:59,363 [smrtpipe.status refreshTargets 409] Workflow Completion Status 21/29 in ( ....... 72%) tasks completed. [INFO] 2017-03-20 09:39:59,365 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn_001of003 successfully completed (5.00 sec (0.08 min)). freed 1 slots, using 4 slots. [INFO] 2017-03-20 09:39:59,366 [smrtpipe.status refreshTargets 409] Workflow Completion Status 22/29 in ( ....... 75%) tasks completed. [INFO] 2017-03-20 09:41:39,973 [smrtpipe.status refreshTargets 407] task P_Control.align_003of003 successfully completed (629.00 sec (10.48 min)). freed 4 slots, using 0 slots. [INFO] 2017-03-20 09:41:39,974 [smrtpipe.status refreshTargets 409] Workflow Completion Status 23/29 in ( ....... 79%) tasks completed. [INFO] 2017-03-20 09:41:44,982 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align.cmpH5.Gather [INFO] 2017-03-20 09:41:44,983 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn_003of003 [INFO] 2017-03-20 09:41:51,587 [smrtpipe.status refreshTargets 407] task P_Control.align.cmpH5.Gather successfully completed (3.00 sec (0.05 min)). freed 1 slots, using 1 slots. [INFO] 2017-03-20 09:41:51,587 [smrtpipe.status refreshTargets 409] Workflow Completion Status 24/29 in ( ........ 82%) tasks completed. [INFO] 2017-03-20 09:41:51,587 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn_003of003 successfully completed (4.00 sec (0.07 min)). freed 1 slots, using 0 slots. [INFO] 2017-03-20 09:41:51,587 [smrtpipe.status refreshTargets 409] Workflow Completion Status 25/29 in ( ........ 86%) tasks completed. [INFO] 2017-03-20 09:41:56,595 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/summaryCSV [INFO] 2017-03-20 09:41:56,596 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_ControlReports/statsJsonReport [INFO] 2017-03-20 09:41:56,596 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn.noCtrlFofn.Gather [INFO] 2017-03-20 09:41:56,599 [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 09:41:56,599 [smrtpipe.status refreshTargets 409] Workflow Completion Status 26/29 in ( ........ 89%) tasks completed. [INFO] 2017-03-20 09:42:01,606 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/noControlSubreads [INFO] 2017-03-20 09:42:12,785 [smrtpipe.status refreshTargets 407] task P_ControlReports.statsJsonReport successfully completed (11.00 sec (0.18 min)). freed 1 slots, using 2 slots. [INFO] 2017-03-20 09:42:12,786 [smrtpipe.status refreshTargets 409] Workflow Completion Status 27/29 in ( ......... 93%) tasks completed. [INFO] 2017-03-20 09:42:18,955 [smrtpipe.status refreshTargets 407] task P_Control.summaryCSV successfully completed (16.00 sec (0.27 min)). freed 1 slots, using 1 slots. [INFO] 2017-03-20 09:42:18,956 [smrtpipe.status refreshTargets 409] Workflow Completion Status 28/29 in ( ......... 96%) tasks completed. [INFO] 2017-03-20 09:43:30,713 [smrtpipe.status refreshTargets 407] task P_Control.noControlSubreads successfully completed (83.00 sec (1.38 min)). freed 1 slots, using 0 slots. [INFO] 2017-03-20 09:43:30,713 [smrtpipe.status refreshTargets 409] Workflow Completion Status 29/29 in (..........100%) tasks completed. [INFO] 2017-03-20 09:43:31,628 [smrtpipe.status _runTasks 301] Completed workflow Workflow execution. [INFO] 2017-03-20 09:43:31,634 [SMRTpipe.SmrtPipeMain _runTasks 281] Skipping PostWorkflow as it contains zero tasks [INFO] 2017-03-20 09:43:31,634 [SMRTpipe.SmrtPipeMain _runTasks 333] exiting _runTask in 965.92 sec (16.10 min) [INFO] 2017-03-20 09:43:31,635 [SMRTpipe.SmrtPipeMain run 572] Completed execution of 5 P_* modules. [WARNING] 2017-03-20 09:43:32,230 [SMRTpipe.SmrtDataService writeTo 402] Found slots NOT in DataService ['smrt.reentrant.complete'] [INFO] 2017-03-20 09:43:32,230 [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/170314_PCB-CC_20kb_P6v2_A04_1/filter/log', 'smrt.data.cmdline': , 'smrt.cells.completed': ['m170315_190851_42134_c101169382550000001823273008151702', 'm170315_190851_42134_c101169382550000001823273008151702', 'm170315_190851_42134_c101169382550000001823273008151702'], 'smrt.output.root': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/filter', 'smrt.output.results': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/filter/results', 'smrt.output.data': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A04_1/filter/data'} [INFO] 2017-03-20 09:43:32,232 [SMRTpipe.SmrtPipeMain shutdown 716] beginning Shutdown Process [INFO] 2017-03-20 09:43:32,232 [SMRTpipe.SmrtPipeMain _generate_final_report 651] Writing final TOC page [INFO] 2017-03-20 09:43:32,783 [SMRTpipe.SmrtPipeMain shutdown 752] Completed shutdown gracefully [INFO] 2017-03-20 09:43:32,786 [SMRTpipe.SmrtPipeMain run 641] completed SmrtPipeMain.run with exit code 0 [INFO] 2017-03-20 09:43:32,786 [root main 335] Successfully exiting smrtpipe version v1.87.139483 with exit code 0 in 968.71 seconds (16.15 minutes)