[INFO] 2017-03-20 17:01:43,111 [root main 269] Starting smrtpipe.py : v1.87.139483 [INFO] 2017-03-20 17:01:43,111 [root main 270] Using Python : v2.7.3 [INFO] 2017-03-20 17:01:43,166 [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 17:01:43,167 [root main 272] Running on e210.grid.gs.washington.edu [INFO] 2017-03-20 17:01:43,167 [root main 273] Process id 28484 [INFO] 2017-03-20 17:01:43,168 [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 17:01:43,182 [SMRTpipe.SmrtPipeConfig __autoLoad 113] Loading configuration from /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/analysis/etc/smrtpipe.rc [INFO] 2017-03-20 17:01:43,196 [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 17:01:43,198 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A02_1/Analysis_Results/m170315_063041_42134_c101169382550000001823273008151700_s1_p0.2.bax.h5 3998770836 bytes [INFO] 2017-03-20 17:01:43,199 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A02_1/Analysis_Results/m170315_063041_42134_c101169382550000001823273008151700_s1_p0.1.bax.h5 4198241825 bytes [INFO] 2017-03-20 17:01:43,199 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A02_1/Analysis_Results/m170315_063041_42134_c101169382550000001823273008151700_s1_p0.3.bax.h5 4274881528 bytes [INFO] 2017-03-20 17:01:43,199 [smrtpipe.status _sanityCheck 804] Successfully found 3 files in xml:input.xml [INFO] 2017-03-20 17:01:43,200 [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 17:01:43,201 [SMRTpipe.SmrtPipeConfig __autoLoad 113] Loading configuration from /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/analysis/etc/smrtpipe.rc [INFO] 2017-03-20 17:01:43,202 [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 17:01:43,202 [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 17:01:43,318 [SMRTpipe.SmrtPipeMain run 465] Successfully found or created TMP dir '/net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/tmpdir' [INFO] 2017-03-20 17:01:43,428 [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_A02_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 17:01:43,431 [SMRTpipe.SmrtDataService setupOutputDirectories 132] Creating /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A02_1/filter/data [INFO] 2017-03-20 17:01:43,431 [SMRTpipe.SmrtDataService setupOutputDirectories 132] Creating /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A02_1/filter/results [INFO] 2017-03-20 17:01:43,432 [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_A02_1/filter [INFO] 2017-03-20 17:01:43,433 [SMRTpipe.SmrtPipeContext initializeContext 257] Input data is [ run/0000000-0002, run/0000000-0000, run/0000000-0001 ] [INFO] 2017-03-20 17:01:43,465 [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/tmpmGQbLk [INFO] 2017-03-20 17:01:43,514 [SMRTpipe.SmrtPipeContext movieFiles 371] Pulling data from tags: * [INFO] 2017-03-20 17:01:43,514 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A02_1/Analysis_Results/m170315_063041_42134_c101169382550000001823273008151700_s1_p0.2.bax.h5 (3998770836 bytes) [INFO] 2017-03-20 17:01:43,515 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A02_1/Analysis_Results/m170315_063041_42134_c101169382550000001823273008151700_s1_p0.1.bax.h5 (4198241825 bytes) [INFO] 2017-03-20 17:01:43,515 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A02_1/Analysis_Results/m170315_063041_42134_c101169382550000001823273008151700_s1_p0.3.bax.h5 (4274881528 bytes) [INFO] 2017-03-20 17:01:43,553 [SMRTpipe.SmrtPipeMain _getBasVersions 413] Detected basH5 versions set(['-v2.3.0']) [INFO] 2017-03-20 17:01:46,120 [smrtpipe.status run 503] smrtpipe.py running on e210.grid.gs.washington.edu [INFO] 2017-03-20 17:01:46,121 [SMRTpipe.SmrtPipeMain run 506] using Distributed mode with 4 nproc [INFO] 2017-03-20 17:01:46,121 [smrtpipe.status run 519] SMRT Analysis 2.3.0 / SMRTpipe 1.87.139483 [INFO] 2017-03-20 17:01:46,121 [SMRTpipe.SmrtPipeMain run 522] Starting smrtpipe version 1.87.139483 [INFO] 2017-03-20 17:01:47,267 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Fetch module [INFO] 2017-03-20 17:01:47,269 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Fetch v2.4.139483 and validated settings. [INFO] 2017-03-20 17:01:47,291 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Filter module [INFO] 2017-03-20 17:01:47,296 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Filter v1.7.139483 and validated settings. [INFO] 2017-03-20 17:01:47,299 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_FilterReports module [INFO] 2017-03-20 17:01:47,301 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_FilterReports v1.21.139483 and validated settings. [INFO] 2017-03-20 17:01:47,308 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Control module [INFO] 2017-03-20 17:01:47,317 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Control v2.1.139483 and validated settings. [INFO] 2017-03-20 17:01:47,319 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_ControlReports module [INFO] 2017-03-20 17:01:47,320 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_ControlReports v2.2.139483 and validated settings. [INFO] 2017-03-20 17:01:47,322 [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_A02_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_A02_1/filter', 'smrt.output.results': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A02_1/filter/results', 'smrt.output.data': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A02_1/filter/data'} [INFO] 2017-03-20 17:01:47,328 [SMRTpipe.SmrtPipeMain _runTasks 281] Skipping PreWorkflow as it contains zero tasks [INFO] 2017-03-20 17:01:47,332 [SMRTpipe.SmrtPipeMain _runTasks 284] Loading 14 tasks into Workflow [INFO] 2017-03-20 17:01:48,208 [SMRTpipe.SmrtPipeMain _runTasks 298] Executing workflow Workflow [INFO] 2017-03-20 17:01:48,208 [smrtpipe.status execute 620] Process id 28484 [INFO] 2017-03-20 17:01:54,705 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Fetch/toFofn [INFO] 2017-03-20 17:01:54,707 [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 17:01:54,707 [smrtpipe.status refreshTargets 409] Workflow Completion Status 1/29 in ( 3%) tasks completed. [INFO] 2017-03-20 17:01:59,713 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads.plsFofn.Scatter [INFO] 2017-03-20 17:01:59,714 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Fetch/overviewRpt [INFO] 2017-03-20 17:01:59,714 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Fetch/adapterRpt [INFO] 2017-03-20 17:01:59,717 [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 17:01:59,717 [smrtpipe.status refreshTargets 409] Workflow Completion Status 2/29 in ( 6%) tasks completed. [INFO] 2017-03-20 17:02:04,725 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter_001of003 [INFO] 2017-03-20 17:02:04,726 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter_003of003 [INFO] 2017-03-20 17:02:11,362 [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 17:02:11,363 [smrtpipe.status refreshTargets 409] Workflow Completion Status 3/29 in ( . 10%) tasks completed. [INFO] 2017-03-20 17:02:16,370 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter_002of003 [INFO] 2017-03-20 17:02:41,402 [smrtpipe.status refreshTargets 407] task P_Filter.filter_001of003 successfully completed (34.00 sec (0.57 min)). freed 2 slots, using 5 slots. [INFO] 2017-03-20 17:02:41,402 [smrtpipe.status refreshTargets 409] Workflow Completion Status 4/29 in ( . 13%) tasks completed. [INFO] 2017-03-20 17:02:41,405 [smrtpipe.status refreshTargets 407] task P_Filter.filter_003of003 successfully completed (34.00 sec (0.57 min)). freed 2 slots, using 3 slots. [INFO] 2017-03-20 17:02:41,405 [smrtpipe.status refreshTargets 409] Workflow Completion Status 5/29 in ( . 17%) tasks completed. [INFO] 2017-03-20 17:02:46,413 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads_001of003 [INFO] 2017-03-20 17:02:46,415 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align_001of003 [INFO] 2017-03-20 17:02:47,943 [smrtpipe.status refreshTargets 407] task P_Fetch.adapterRpt successfully completed (43.00 sec (0.72 min)). freed 1 slots, using 7 slots. [INFO] 2017-03-20 17:02:47,943 [smrtpipe.status refreshTargets 409] Workflow Completion Status 6/29 in ( .. 20%) tasks completed. [INFO] 2017-03-20 17:02:52,950 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads_003of003 [INFO] 2017-03-20 17:02:52,966 [smrtpipe.status refreshTargets 407] task P_Filter.filter_002of003 successfully completed (33.00 sec (0.55 min)). freed 2 slots, using 6 slots. [INFO] 2017-03-20 17:02:52,966 [smrtpipe.status refreshTargets 409] Workflow Completion Status 7/29 in ( .. 24%) tasks completed. [INFO] 2017-03-20 17:02:58,870 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align_003of003 [INFO] 2017-03-20 17:05:56,397 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_003of003 successfully completed (182.00 sec (3.03 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 17:05:56,400 [smrtpipe.status refreshTargets 409] Workflow Completion Status 8/29 in ( .. 27%) tasks completed. [INFO] 2017-03-20 17:06:02,820 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads_002of003 [INFO] 2017-03-20 17:06:32,894 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_001of003 successfully completed (221.00 sec (3.68 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 17:06:32,904 [smrtpipe.status refreshTargets 409] Workflow Completion Status 9/29 in ( ... 31%) tasks completed. [INFO] 2017-03-20 17:06:37,911 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter.rgnFofn.Gather [INFO] 2017-03-20 17:06:37,922 [smrtpipe.status refreshTargets 407] task P_Filter.filter.rgnFofn.Gather successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 17:06:37,922 [smrtpipe.status refreshTargets 409] Workflow Completion Status 10/29 in ( ... 34%) tasks completed. [INFO] 2017-03-20 17:06:42,929 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreadSummary [INFO] 2017-03-20 17:08:11,878 [smrtpipe.status refreshTargets 407] task P_Filter.subreadSummary successfully completed (84.00 sec (1.40 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 17:08:11,892 [smrtpipe.status refreshTargets 409] Workflow Completion Status 11/29 in ( ... 37%) tasks completed. [INFO] 2017-03-20 17:08:16,900 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_FilterReports/subreadRpt [INFO] 2017-03-20 17:08:33,953 [smrtpipe.status refreshTargets 407] task P_FilterReports.subreadRpt successfully completed (13.00 sec (0.22 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 17:08:33,953 [smrtpipe.status refreshTargets 409] Workflow Completion Status 12/29 in ( .... 41%) tasks completed. [INFO] 2017-03-20 17:08:38,964 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align_002of003 [INFO] 2017-03-20 17:08:53,994 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_002of003 successfully completed (171.00 sec (2.85 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 17:08:53,995 [smrtpipe.status refreshTargets 409] Workflow Completion Status 13/29 in ( .... 44%) tasks completed. [INFO] 2017-03-20 17:08:59,004 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads.subreads.Gather [INFO] 2017-03-20 17:09:57,467 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreads.Gather successfully completed (54.00 sec (0.90 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 17:09:57,469 [smrtpipe.status refreshTargets 409] Workflow Completion Status 14/29 in ( .... 48%) tasks completed. [INFO] 2017-03-20 17:10:02,478 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads.subreadFastq.Gather [INFO] 2017-03-20 17:11:31,623 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreadFastq.Gather successfully completed (79.00 sec (1.32 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 17:11:31,625 [smrtpipe.status refreshTargets 409] Workflow Completion Status 15/29 in ( ..... 51%) tasks completed. [INFO] 2017-03-20 17:11:36,633 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter.summary.Gather [INFO] 2017-03-20 17:11:43,241 [smrtpipe.status refreshTargets 407] task P_Filter.filter.summary.Gather successfully completed (2.00 sec (0.03 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 17:11:43,241 [smrtpipe.status refreshTargets 409] Workflow Completion Status 16/29 in ( ..... 55%) tasks completed. [INFO] 2017-03-20 17:11:48,251 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_FilterReports/loadingRpt [INFO] 2017-03-20 17:11:59,796 [smrtpipe.status refreshTargets 407] task P_FilterReports.loadingRpt successfully completed (7.00 sec (0.12 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 17:11:59,796 [smrtpipe.status refreshTargets 409] Workflow Completion Status 17/29 in ( ..... 58%) tasks completed. [INFO] 2017-03-20 17:12:04,807 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_FilterReports/statsRpt [INFO] 2017-03-20 17:12:27,218 [smrtpipe.status refreshTargets 407] task P_FilterReports.statsRpt successfully completed (18.00 sec (0.30 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 17:12:27,221 [smrtpipe.status refreshTargets 409] Workflow Completion Status 18/29 in ( ...... 62%) tasks completed. [INFO] 2017-03-20 17:13:22,999 [smrtpipe.status refreshTargets 407] task P_Control.align_001of003 successfully completed (634.00 sec (10.57 min)). freed 4 slots, using 8 slots. [INFO] 2017-03-20 17:13:23,000 [smrtpipe.status refreshTargets 409] Workflow Completion Status 19/29 in ( ...... 65%) tasks completed. [INFO] 2017-03-20 17:13:28,007 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn_001of003 [INFO] 2017-03-20 17:13:33,020 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn_001of003 successfully completed (4.00 sec (0.07 min)). freed 1 slots, using 8 slots. [INFO] 2017-03-20 17:13:33,020 [smrtpipe.status refreshTargets 409] Workflow Completion Status 20/29 in ( ...... 68%) tasks completed. [INFO] 2017-03-20 17:13:38,029 [smrtpipe.status refreshTargets 407] task P_Control.align_003of003 successfully completed (634.00 sec (10.57 min)). freed 4 slots, using 4 slots. [INFO] 2017-03-20 17:13:38,030 [smrtpipe.status refreshTargets 409] Workflow Completion Status 21/29 in ( ....... 72%) tasks completed. [INFO] 2017-03-20 17:13:43,038 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn_003of003 [INFO] 2017-03-20 17:13:53,061 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn_003of003 successfully completed (6.00 sec (0.10 min)). freed 1 slots, using 4 slots. [INFO] 2017-03-20 17:13:53,063 [smrtpipe.status refreshTargets 409] Workflow Completion Status 22/29 in ( ....... 75%) tasks completed. [INFO] 2017-03-20 17:19:42,926 [smrtpipe.status refreshTargets 407] task P_Control.align_002of003 successfully completed (661.00 sec (11.02 min)). freed 4 slots, using 0 slots. [INFO] 2017-03-20 17:19:42,927 [smrtpipe.status refreshTargets 409] Workflow Completion Status 23/29 in ( ....... 79%) tasks completed. [INFO] 2017-03-20 17:19:47,934 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn_002of003 [INFO] 2017-03-20 17:19:47,935 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align.cmpH5.Gather [INFO] 2017-03-20 17:19:54,928 [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 17:19:54,929 [smrtpipe.status refreshTargets 409] Workflow Completion Status 24/29 in ( ........ 82%) tasks completed. [INFO] 2017-03-20 17:19:54,932 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn_002of003 successfully completed (4.00 sec (0.07 min)). freed 1 slots, using 0 slots. [INFO] 2017-03-20 17:19:54,932 [smrtpipe.status refreshTargets 409] Workflow Completion Status 25/29 in ( ........ 86%) tasks completed. [INFO] 2017-03-20 17:19:59,940 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn.noCtrlFofn.Gather [INFO] 2017-03-20 17:19:59,941 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/summaryCSV [INFO] 2017-03-20 17:19:59,941 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_ControlReports/statsJsonReport [INFO] 2017-03-20 17:19:59,944 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn.noCtrlFofn.Gather successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 2 slots. [INFO] 2017-03-20 17:19:59,944 [smrtpipe.status refreshTargets 409] Workflow Completion Status 26/29 in ( ........ 89%) tasks completed. [INFO] 2017-03-20 17:20:04,951 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/noControlSubreads [INFO] 2017-03-20 17:20:11,896 [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 17:20:11,897 [smrtpipe.status refreshTargets 409] Workflow Completion Status 27/29 in ( ......... 93%) tasks completed. [INFO] 2017-03-20 17:20:18,333 [smrtpipe.status refreshTargets 407] task P_Control.summaryCSV successfully completed (14.00 sec (0.23 min)). freed 1 slots, using 1 slots. [INFO] 2017-03-20 17:20:18,334 [smrtpipe.status refreshTargets 409] Workflow Completion Status 28/29 in ( ......... 96%) tasks completed. [INFO] 2017-03-20 17:21:41,457 [smrtpipe.status refreshTargets 407] task P_Control.noControlSubreads successfully completed (94.00 sec (1.57 min)). freed 1 slots, using 0 slots. [INFO] 2017-03-20 17:21:41,457 [smrtpipe.status refreshTargets 409] Workflow Completion Status 29/29 in (..........100%) tasks completed. [INFO] 2017-03-20 17:21:42,438 [smrtpipe.status _runTasks 301] Completed workflow Workflow execution. [INFO] 2017-03-20 17:21:42,444 [SMRTpipe.SmrtPipeMain _runTasks 281] Skipping PostWorkflow as it contains zero tasks [INFO] 2017-03-20 17:21:42,444 [SMRTpipe.SmrtPipeMain _runTasks 333] exiting _runTask in 1195.12 sec (19.92 min) [INFO] 2017-03-20 17:21:42,444 [SMRTpipe.SmrtPipeMain run 572] Completed execution of 5 P_* modules. [WARNING] 2017-03-20 17:21:43,537 [SMRTpipe.SmrtDataService writeTo 402] Found slots NOT in DataService ['smrt.reentrant.complete'] [INFO] 2017-03-20 17:21:43,537 [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_A02_1/filter/log', 'smrt.data.cmdline': , 'smrt.cells.completed': ['m170315_063041_42134_c101169382550000001823273008151700', 'm170315_063041_42134_c101169382550000001823273008151700', 'm170315_063041_42134_c101169382550000001823273008151700'], 'smrt.output.root': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A02_1/filter', 'smrt.output.results': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A02_1/filter/results', 'smrt.output.data': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A02_1/filter/data'} [INFO] 2017-03-20 17:21:43,553 [SMRTpipe.SmrtPipeMain shutdown 716] beginning Shutdown Process [INFO] 2017-03-20 17:21:43,553 [SMRTpipe.SmrtPipeMain _generate_final_report 651] Writing final TOC page [INFO] 2017-03-20 17:21:44,446 [SMRTpipe.SmrtPipeMain shutdown 752] Completed shutdown gracefully [INFO] 2017-03-20 17:21:44,449 [SMRTpipe.SmrtPipeMain run 641] completed SmrtPipeMain.run with exit code 0 [INFO] 2017-03-20 17:21:44,450 [root main 335] Successfully exiting smrtpipe version v1.87.139483 with exit code 0 in 1201.25 seconds (20.02 minutes)