[INFO] 2017-03-20 13:39:17,164 [root main 269] Starting smrtpipe.py : v1.87.139483 [INFO] 2017-03-20 13:39:17,164 [root main 270] Using Python : v2.7.3 [INFO] 2017-03-20 13:39:17,190 [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 13:39:17,192 [root main 272] Running on e122.grid.gs.washington.edu [INFO] 2017-03-20 13:39:17,192 [root main 273] Process id 14467 [INFO] 2017-03-20 13:39:17,192 [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 13:39:17,242 [SMRTpipe.SmrtPipeConfig __autoLoad 113] Loading configuration from /net/eichler/vol24/projects/sequencing/pacbio/software/smrtanalysis/current/analysis/etc/smrtpipe.rc [INFO] 2017-03-20 13:39:17,270 [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/170314_PCB-CC_20kb_P6v2_A01_1/Analysis_Results/m170315_001112_42134_c101169372550000001823273008151717_s1_p0.1.bax.h5 4152773505 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/170314_PCB-CC_20kb_P6v2_A01_1/Analysis_Results/m170315_001112_42134_c101169372550000001823273008151717_s1_p0.2.bax.h5 4701165532 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/170314_PCB-CC_20kb_P6v2_A01_1/Analysis_Results/m170315_001112_42134_c101169372550000001823273008151717_s1_p0.3.bax.h5 5398563989 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 13:39:17,275 [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 13:39:17,277 [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 13:39:17,585 [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_A01_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/170314_PCB-CC_20kb_P6v2_A01_1/filter/data [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/170314_PCB-CC_20kb_P6v2_A01_1/filter/results [INFO] 2017-03-20 13:39:17,588 [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_A01_1/filter [INFO] 2017-03-20 13:39:17,588 [SMRTpipe.SmrtPipeContext initializeContext 257] Input data is [ run/0000000-0002, run/0000000-0000, run/0000000-0001 ] [INFO] 2017-03-20 13:39:17,638 [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/tmprDfXgB [INFO] 2017-03-20 13:39:17,674 [SMRTpipe.SmrtPipeContext movieFiles 371] Pulling data from tags: * [INFO] 2017-03-20 13:39:17,674 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A01_1/Analysis_Results/m170315_001112_42134_c101169372550000001823273008151717_s1_p0.1.bax.h5 (4152773505 bytes) [INFO] 2017-03-20 13:39:17,674 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A01_1/Analysis_Results/m170315_001112_42134_c101169372550000001823273008151717_s1_p0.2.bax.h5 (4701165532 bytes) [INFO] 2017-03-20 13:39:17,675 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A01_1/Analysis_Results/m170315_001112_42134_c101169372550000001823273008151717_s1_p0.3.bax.h5 (5398563989 bytes) [INFO] 2017-03-20 13:39:17,735 [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 e122.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 13:39:20,091 [smrtpipe.status run 519] SMRT Analysis 2.3.0 / SMRTpipe 1.87.139483 [INFO] 2017-03-20 13:39:20,091 [SMRTpipe.SmrtPipeMain run 522] Starting smrtpipe version 1.87.139483 [INFO] 2017-03-20 13:39:20,829 [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 13:39:20,887 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Filter module [INFO] 2017-03-20 13:39:20,890 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Filter v1.7.139483 and validated settings. [INFO] 2017-03-20 13:39:20,901 [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 13:39:20,907 [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 13:39:20,938 [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/170314_PCB-CC_20kb_P6v2_A01_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_A01_1/filter', 'smrt.output.results': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A01_1/filter/results', 'smrt.output.data': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A01_1/filter/data'} [INFO] 2017-03-20 13:39:20,944 [SMRTpipe.SmrtPipeMain _runTasks 281] Skipping PreWorkflow as it contains zero tasks [INFO] 2017-03-20 13:39:20,947 [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 14467 [INFO] 2017-03-20 13:39:28,294 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Fetch/toFofn [INFO] 2017-03-20 13:39:28,295 [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 13:39:28,295 [smrtpipe.status refreshTargets 409] Workflow Completion Status 1/29 in ( 3%) tasks completed. [INFO] 2017-03-20 13:39:33,300 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Fetch/overviewRpt [INFO] 2017-03-20 13:39:33,301 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align.plsFofn.Scatter [INFO] 2017-03-20 13:39:33,302 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Fetch/adapterRpt [INFO] 2017-03-20 13:39:33,304 [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 13:39:33,304 [smrtpipe.status refreshTargets 409] Workflow Completion Status 2/29 in ( 6%) tasks completed. [INFO] 2017-03-20 13:39:38,308 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter_002of003 [INFO] 2017-03-20 13:39:38,309 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter_001of003 [INFO] 2017-03-20 13:39:39,371 [smrtpipe.status refreshTargets 407] task P_Fetch.overviewRpt successfully completed (3.00 sec (0.05 min)). freed 1 slots, using 5 slots. [INFO] 2017-03-20 13:39:39,371 [smrtpipe.status refreshTargets 409] Workflow Completion Status 3/29 in ( . 10%) tasks completed. [INFO] 2017-03-20 13:39:44,378 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter_003of003 [INFO] 2017-03-20 13:40:10,516 [smrtpipe.status refreshTargets 407] task P_Fetch.adapterRpt successfully completed (35.00 sec (0.58 min)). freed 1 slots, using 6 slots. [INFO] 2017-03-20 13:40:10,517 [smrtpipe.status refreshTargets 409] Workflow Completion Status 4/29 in ( . 13%) tasks completed. [INFO] 2017-03-20 13:40:15,526 [smrtpipe.status refreshTargets 407] task P_Filter.filter_002of003 successfully completed (35.00 sec (0.58 min)). freed 2 slots, using 4 slots. [INFO] 2017-03-20 13:40:15,526 [smrtpipe.status refreshTargets 409] Workflow Completion Status 5/29 in ( . 17%) tasks completed. [INFO] 2017-03-20 13:40:15,529 [smrtpipe.status refreshTargets 407] task P_Filter.filter_001of003 successfully completed (34.00 sec (0.57 min)). freed 2 slots, using 2 slots. [INFO] 2017-03-20 13:40:15,529 [smrtpipe.status refreshTargets 409] Workflow Completion Status 6/29 in ( .. 20%) tasks completed. [INFO] 2017-03-20 13:40:20,537 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align_002of003 [INFO] 2017-03-20 13:40:20,538 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads_002of003 [INFO] 2017-03-20 13:40:20,538 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads_001of003 [INFO] 2017-03-20 13:40:20,545 [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 13:40:20,545 [smrtpipe.status refreshTargets 409] Workflow Completion Status 7/29 in ( .. 24%) tasks completed. [INFO] 2017-03-20 13:40:25,552 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align_001of003 [INFO] 2017-03-20 13:43:30,123 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_001of003 successfully completed (184.00 sec (3.07 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 13:43:30,124 [smrtpipe.status refreshTargets 409] Workflow Completion Status 8/29 in ( .. 27%) tasks completed. [INFO] 2017-03-20 13:43:36,647 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter.summary.Gather [INFO] 2017-03-20 13:43:43,196 [smrtpipe.status refreshTargets 407] task P_Filter.filter.summary.Gather successfully completed (3.00 sec (0.05 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 13:43:43,196 [smrtpipe.status refreshTargets 409] Workflow Completion Status 9/29 in ( ... 31%) tasks completed. [INFO] 2017-03-20 13:43:48,205 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_FilterReports/statsRpt [INFO] 2017-03-20 13:44:14,520 [smrtpipe.status refreshTargets 407] task P_FilterReports.statsRpt successfully completed (22.00 sec (0.37 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 13:44:14,529 [smrtpipe.status refreshTargets 409] Workflow Completion Status 10/29 in ( ... 34%) tasks completed. [INFO] 2017-03-20 13:44:19,628 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_FilterReports/loadingRpt [INFO] 2017-03-20 13:44:30,866 [smrtpipe.status refreshTargets 407] task P_FilterReports.loadingRpt successfully completed (8.00 sec (0.13 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 13:44:30,866 [smrtpipe.status refreshTargets 409] Workflow Completion Status 11/29 in ( ... 37%) tasks completed. [INFO] 2017-03-20 13:44:35,873 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads_003of003 [INFO] 2017-03-20 13:44:41,715 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_002of003 successfully completed (256.00 sec (4.27 min)). freed 1 slots, using 9 slots. [INFO] 2017-03-20 13:44:41,715 [smrtpipe.status refreshTargets 409] Workflow Completion Status 12/29 in ( .... 41%) tasks completed. [INFO] 2017-03-20 13:44:46,724 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align_003of003 [INFO] 2017-03-20 13:46:58,250 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_003of003 successfully completed (138.00 sec (2.30 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 13:46:58,252 [smrtpipe.status refreshTargets 409] Workflow Completion Status 13/29 in ( .... 44%) tasks completed. [INFO] 2017-03-20 13:47:03,260 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads.subreads.Gather [INFO] 2017-03-20 13:47:45,507 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreads.Gather successfully completed (34.00 sec (0.57 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 13:47:45,508 [smrtpipe.status refreshTargets 409] Workflow Completion Status 14/29 in ( .... 48%) tasks completed. [INFO] 2017-03-20 13:47:50,517 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreads.subreadFastq.Gather [INFO] 2017-03-20 13:49:32,858 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreadFastq.Gather successfully completed (96.00 sec (1.60 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 13:49:32,859 [smrtpipe.status refreshTargets 409] Workflow Completion Status 15/29 in ( ..... 51%) tasks completed. [INFO] 2017-03-20 13:49:37,867 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/filter.rgnFofn.Gather [INFO] 2017-03-20 13:49:37,886 [smrtpipe.status refreshTargets 407] task P_Filter.filter.rgnFofn.Gather successfully completed (1.00 sec (0.02 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 13:49:37,887 [smrtpipe.status refreshTargets 409] Workflow Completion Status 16/29 in ( ..... 55%) tasks completed. [INFO] 2017-03-20 13:49:42,895 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Filter/subreadSummary [INFO] 2017-03-20 13:51:05,773 [smrtpipe.status refreshTargets 407] task P_Filter.subreadSummary successfully completed (78.00 sec (1.30 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 13:51:05,778 [smrtpipe.status refreshTargets 409] Workflow Completion Status 17/29 in ( ..... 58%) tasks completed. [INFO] 2017-03-20 13:51:10,795 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_FilterReports/subreadRpt [INFO] 2017-03-20 13:51:32,016 [smrtpipe.status refreshTargets 407] task P_FilterReports.subreadRpt successfully completed (14.00 sec (0.23 min)). freed 1 slots, using 12 slots. [INFO] 2017-03-20 13:51:32,016 [smrtpipe.status refreshTargets 409] Workflow Completion Status 18/29 in ( ...... 62%) tasks completed. [INFO] 2017-03-20 13:51:42,031 [smrtpipe.status refreshTargets 407] task P_Control.align_001of003 successfully completed (672.00 sec (11.20 min)). freed 4 slots, using 8 slots. [INFO] 2017-03-20 13:51:42,031 [smrtpipe.status refreshTargets 409] Workflow Completion Status 19/29 in ( ...... 65%) tasks completed. [INFO] 2017-03-20 13:51:47,039 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn_001of003 [INFO] 2017-03-20 13:51:53,504 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn_001of003 successfully completed (5.00 sec (0.08 min)). freed 1 slots, using 8 slots. [INFO] 2017-03-20 13:51:53,504 [smrtpipe.status refreshTargets 409] Workflow Completion Status 20/29 in ( ...... 68%) tasks completed. [INFO] 2017-03-20 13:53:55,316 [smrtpipe.status refreshTargets 407] task P_Control.align_002of003 successfully completed (812.00 sec (13.53 min)). freed 4 slots, using 4 slots. [INFO] 2017-03-20 13:53:55,316 [smrtpipe.status refreshTargets 409] Workflow Completion Status 21/29 in ( ....... 72%) tasks completed. [INFO] 2017-03-20 13:54:00,324 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn_002of003 [INFO] 2017-03-20 13:54:10,343 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn_002of003 successfully completed (6.00 sec (0.10 min)). freed 1 slots, using 4 slots. [INFO] 2017-03-20 13:54:10,343 [smrtpipe.status refreshTargets 409] Workflow Completion Status 22/29 in ( ....... 75%) tasks completed. [INFO] 2017-03-20 13:57:42,088 [smrtpipe.status refreshTargets 407] task P_Control.align_003of003 successfully completed (767.00 sec (12.78 min)). freed 4 slots, using 0 slots. [INFO] 2017-03-20 13:57:42,091 [smrtpipe.status refreshTargets 409] Workflow Completion Status 23/29 in ( ....... 79%) tasks completed. [INFO] 2017-03-20 13:57:47,099 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/align.cmpH5.Gather [INFO] 2017-03-20 13:57:47,100 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn_003of003 [INFO] 2017-03-20 13:57:58,723 [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 13:57:58,723 [smrtpipe.status refreshTargets 409] Workflow Completion Status 24/29 in ( ........ 82%) tasks completed. [INFO] 2017-03-20 13:57:58,723 [smrtpipe.status refreshTargets 407] task P_Control.updateRgn_003of003 successfully completed (5.00 sec (0.08 min)). freed 1 slots, using 0 slots. [INFO] 2017-03-20 13:57:58,723 [smrtpipe.status refreshTargets 409] Workflow Completion Status 25/29 in ( ........ 86%) tasks completed. [INFO] 2017-03-20 13:58:03,731 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/summaryCSV [INFO] 2017-03-20 13:58:03,732 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/updateRgn.noCtrlFofn.Gather [INFO] 2017-03-20 13:58:03,732 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_ControlReports/statsJsonReport [INFO] 2017-03-20 13:58:03,735 [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 13:58:03,735 [smrtpipe.status refreshTargets 409] Workflow Completion Status 26/29 in ( ........ 89%) tasks completed. [INFO] 2017-03-20 13:58:08,743 [smrtpipe.status refreshTargets 419] Starting task://Anonymous/P_Control/noControlSubreads [INFO] 2017-03-20 13:58:14,844 [smrtpipe.status refreshTargets 407] task P_ControlReports.statsJsonReport successfully completed (5.00 sec (0.08 min)). freed 1 slots, using 2 slots. [INFO] 2017-03-20 13:58:14,844 [smrtpipe.status refreshTargets 409] Workflow Completion Status 27/29 in ( ......... 93%) tasks completed. [INFO] 2017-03-20 13:58:25,973 [smrtpipe.status refreshTargets 407] task P_Control.summaryCSV successfully completed (15.00 sec (0.25 min)). freed 1 slots, using 1 slots. [INFO] 2017-03-20 13:58:25,973 [smrtpipe.status refreshTargets 409] Workflow Completion Status 28/29 in ( ......... 96%) tasks completed. [INFO] 2017-03-20 13:59:57,683 [smrtpipe.status refreshTargets 407] task P_Control.noControlSubreads successfully completed (104.00 sec (1.73 min)). freed 1 slots, using 0 slots. [INFO] 2017-03-20 13:59:57,684 [smrtpipe.status refreshTargets 409] Workflow Completion Status 29/29 in (..........100%) tasks completed. [INFO] 2017-03-20 13:59:58,242 [smrtpipe.status _runTasks 301] Completed workflow Workflow execution. [INFO] 2017-03-20 13:59:58,247 [SMRTpipe.SmrtPipeMain _runTasks 281] Skipping PostWorkflow as it contains zero tasks [INFO] 2017-03-20 13:59:58,247 [SMRTpipe.SmrtPipeMain _runTasks 333] exiting _runTask in 1237.31 sec (20.62 min) [INFO] 2017-03-20 13:59:58,248 [SMRTpipe.SmrtPipeMain run 572] Completed execution of 5 P_* modules. [WARNING] 2017-03-20 13:59:58,835 [SMRTpipe.SmrtDataService writeTo 402] Found slots NOT in DataService ['smrt.reentrant.complete'] [INFO] 2017-03-20 13:59:58,835 [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_A01_1/filter/log', 'smrt.data.cmdline': , 'smrt.cells.completed': ['m170315_001112_42134_c101169372550000001823273008151717', 'm170315_001112_42134_c101169372550000001823273008151717', 'm170315_001112_42134_c101169372550000001823273008151717'], 'smrt.output.root': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A01_1/filter', 'smrt.output.results': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A01_1/filter/results', 'smrt.output.data': '/net/eichler/pacbio/home/pacbio-aspera3/oly_genome_pacbio.SW.SS_10kb/170314_PCB-CC_20kb_P6v2_A01_1/filter/data'} [INFO] 2017-03-20 13:59:58,849 [SMRTpipe.SmrtPipeMain shutdown 716] beginning Shutdown Process [INFO] 2017-03-20 13:59:58,849 [SMRTpipe.SmrtPipeMain _generate_final_report 651] Writing final TOC page [INFO] 2017-03-20 13:59:59,387 [SMRTpipe.SmrtPipeMain shutdown 752] Completed shutdown gracefully [INFO] 2017-03-20 13:59:59,390 [SMRTpipe.SmrtPipeMain run 641] completed SmrtPipeMain.run with exit code 0 [INFO] 2017-03-20 13:59:59,390 [root main 335] Successfully exiting smrtpipe version v1.87.139483 with exit code 0 in 1242.12 seconds (20.70 minutes)