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  • #1

    Help: de novo assembly using SMRT portal and hgap.3

    Problem: Extremely new to assembly and attempting to execute de novo assembly using hgap.3 in SMRT portal using 9 SMRTcells. lambda example data provided runs fine so I assume that there isn't a problem with the actual process and instead just with what I am doing.

    Error I get is P_PreAssemblerDagcon/hgapCorrection Failed. Not sure why.

    Additionally it could be a problem with my server but being that none of the memory fills up during the process I feel like I am missing something.

    Any help would be amazing and let me know if i can post anything that would be helpful for a solution.

    Thanks
    Tags: pacbio, pacbio correction, smrt analysis, smrt portal, smrtanalysis
  • #2
    There isn't enough information here to figure out what is going on. Have you looked at the "View Log" button output for the job that failed on the SMRTportal? If you don't feel comfortable posting the log information on the forum you could email PacBio tech support and include that output.

    Comment

    • #3
      Here is the view log output for the failed job.

      [INFO] 2016-02-28 18:48:54,219 [root main 270] Starting smrtpipe.py : v1.85.133289
      [INFO] 2016-02-28 18:48:54,220 [root main 271] Using Python : v2.7.3
      [INFO] 2016-02-28 18:48:54,230 [root main 272] Platform info Linux-3.16.0-57-generic-x86_64-with-Ubuntu-14.04-trusty
      [INFO] 2016-02-28 18:48:54,230 [root main 273] Running on friesen-lab-computer
      [INFO] 2016-02-28 18:48:54,231 [root main 274] Process id 62594
      [INFO] 2016-02-28 18:48:54,231 [SMRTpipe.pbpy.io.SecondaryConfig _loadFromFile 25] Loading SecondaryConfig from /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/etc/config.xml
      [INFO] 2016-02-28 18:48:54,240 [SMRTpipe.SmrtPipeConfig __autoLoad 113] Loading configuration from /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/analysis/etc/smrtpipe.rc
      [INFO] 2016-02-28 18:48:54,250 [SMRTpipe.SmrtPipeConfig __setAlgorithmParametersPath 212] ALGO_PARAMS key not found in smrtpipe.rc - using latest bundle: /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/analysis/etc/algorithm_parameters/2014-03
      [INFO] 2016-02-28 18:48:54,253 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/A01_1/Analysis_Results/m160205_202924_42151_c100937642550000001823216806101630_s1_p0.1.bax.h5 3118293624 bytes
      [INFO] 2016-02-28 18:48:54,254 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/A01_1/Analysis_Results/m160205_202924_42151_c100937642550000001823216806101630_s1_p0.2.bax.h5 3096524303 bytes
      [INFO] 2016-02-28 18:48:54,256 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/A01_1/Analysis_Results/m160205_202924_42151_c100937642550000001823216806101630_s1_p0.3.bax.h5 3131515636 bytes
      [INFO] 2016-02-28 18:48:54,256 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/F03_1/Analysis_Results/m160209_222609_42151_c100937642550000001823216806101636_s1_p0.1.bax.h5 9826113063 bytes
      [INFO] 2016-02-28 18:48:54,257 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/F03_1/Analysis_Results/m160209_222609_42151_c100937642550000001823216806101636_s1_p0.2.bax.h5 8847536745 bytes
      [INFO] 2016-02-28 18:48:54,258 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/F03_1/Analysis_Results/m160209_222609_42151_c100937642550000001823216806101636_s1_p0.3.bax.h5 8660106571 bytes
      [INFO] 2016-02-28 18:48:54,260 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/G03_1/Analysis_Results/m160210_044522_42151_c100937642550000001823216806101637_s1_p0.1.bax.h5 10397206632 bytes
      [INFO] 2016-02-28 18:48:54,261 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/G03_1/Analysis_Results/m160210_044522_42151_c100937642550000001823216806101637_s1_p0.2.bax.h5 8896807724 bytes
      [INFO] 2016-02-28 18:48:54,262 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/G03_1/Analysis_Results/m160210_044522_42151_c100937642550000001823216806101637_s1_p0.3.bax.h5 8770450475 bytes
      [INFO] 2016-02-28 18:48:54,262 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/A03_1/Analysis_Results/m160208_211005_42151_c100937642550000001823216806101632_s1_p0.1.bax.h5 4262061828 bytes
      [INFO] 2016-02-28 18:48:54,262 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/A03_1/Analysis_Results/m160208_211005_42151_c100937642550000001823216806101632_s1_p0.2.bax.h5 4444715980 bytes
      [INFO] 2016-02-28 18:48:54,264 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/A03_1/Analysis_Results/m160208_211005_42151_c100937642550000001823216806101632_s1_p0.3.bax.h5 5001249228 bytes
      [INFO] 2016-02-28 18:48:54,265 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/D03_1/Analysis_Results/m160209_094743_42151_c100937642550000001823216806101634_s1_p0.1.bax.h5 9588943418 bytes
      [INFO] 2016-02-28 18:48:54,265 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/D03_1/Analysis_Results/m160209_094743_42151_c100937642550000001823216806101634_s1_p0.2.bax.h5 8973091617 bytes
      [INFO] 2016-02-28 18:48:54,266 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/D03_1/Analysis_Results/m160209_094743_42151_c100937642550000001823216806101634_s1_p0.3.bax.h5 8496818708 bytes
      [INFO] 2016-02-28 18:48:54,266 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/E03_1/Analysis_Results/m160209_160656_42151_c100937642550000001823216806101635_s1_p0.1.bax.h5 10082235080 bytes
      [INFO] 2016-02-28 18:48:54,266 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/E03_1/Analysis_Results/m160209_160656_42151_c100937642550000001823216806101635_s1_p0.2.bax.h5 9148614091 bytes
      [INFO] 2016-02-28 18:48:54,267 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/E03_1/Analysis_Results/m160209_160656_42151_c100937642550000001823216806101635_s1_p0.3.bax.h5 8917808086 bytes
      [INFO] 2016-02-28 18:48:54,267 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/H03_1/Analysis_Results/m160210_110935_42151_c100937372550000001823216806101690_s1_p0.1.bax.h5 8475423219 bytes
      [INFO] 2016-02-28 18:48:54,268 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/H03_1/Analysis_Results/m160210_110935_42151_c100937372550000001823216806101690_s1_p0.2.bax.h5 7687682307 bytes
      [INFO] 2016-02-28 18:48:54,268 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/H03_1/Analysis_Results/m160210_110935_42151_c100937372550000001823216806101690_s1_p0.3.bax.h5 7324602593 bytes
      [INFO] 2016-02-28 18:48:54,269 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/C03_1/Analysis_Results/m160209_032830_42151_c100937642550000001823216806101633_s1_p0.1.bax.h5 8528912415 bytes
      [INFO] 2016-02-28 18:48:54,269 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/C03_1/Analysis_Results/m160209_032830_42151_c100937642550000001823216806101633_s1_p0.2.bax.h5 8586867196 bytes
      [INFO] 2016-02-28 18:48:54,269 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/C03_1/Analysis_Results/m160209_032830_42151_c100937642550000001823216806101633_s1_p0.3.bax.h5 9113034259 bytes
      [INFO] 2016-02-28 18:48:54,301 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/B01_1/Analysis_Results/m160206_024804_42151_c100937642550000001823216806101631_s1_p0.1.bax.h5 3573475555 bytes
      [INFO] 2016-02-28 18:48:54,302 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/B01_1/Analysis_Results/m160206_024804_42151_c100937642550000001823216806101631_s1_p0.2.bax.h5 3611434136 bytes
      [INFO] 2016-02-28 18:48:54,302 [SMRTpipe.SmrtPipeMain _sanityCheck 796] Found file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/B01_1/Analysis_Results/m160206_024804_42151_c100937642550000001823216806101631_s1_p0.3.bax.h5 3575852392 bytes
      [INFO] 2016-02-28 18:48:54,302 [smrtpipe.status _sanityCheck 804] Successfully found 27 files in xml:/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/input.xml
      [INFO] 2016-02-28 18:48:54,303 [SMRTpipe.pbpy.io.SecondaryConfig _loadFromFile 25] Loading SecondaryConfig from /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/etc/config.xml
      [INFO] 2016-02-28 18:48:54,304 [SMRTpipe.SmrtPipeConfig __autoLoad 113] Loading configuration from /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/analysis/etc/smrtpipe.rc
      [INFO] 2016-02-28 18:48:54,304 [SMRTpipe.SmrtPipeConfig __setAlgorithmParametersPath 212] ALGO_PARAMS key not found in smrtpipe.rc - using latest bundle: /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/analysis/etc/algorithm_parameters/2014-03
      [INFO] 2016-02-28 18:48:54,305 [SMRTpipe.SmrtPipeContext __init__ 98] SmrtPipeConfig Summary:
      TMP = /media/friesen_lab/2TB/download/smrtanalysis/tmpdir
      PROGRESS_URL = http://134.129.124.234:8080/smrtportal/api
      CLUSTER_MANAGER = BASH
      HOST_PORT = 8080
      NCHUNKS = 64
      ALGO_PARAMS_PATH = /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/analysis/etc/algorithm_parameters/2014-03
      MAX_SLOTS = 256
      ca_distribute.hgap = useGrid:0, scriptOnGrid:1, frgCorrOnGrid:1, ovlCorrOnGrid:1
      CLOUD_LARGE_FILE_CUTOFF = 10MB
      SMRTANALYSIS_VERSION = v2.2.0
      INPUT_HDF5_EXT = bas.h5
      SMRTPIPE_VERSION = v2.2.0.132739
      HOST_NAME = 134.129.124.234
      DENOVO_READ_SCOPES = small: 0.15, large:15, huge:1700
      NPROC = 11
      DENOVO_GENOME_SCOPES = small:100, large:1000, huge:40000
      NJOBS = 64
      CLOUD = False
      REFERENCE_SCOPES = small:10, large:1000, veryLarge:100000, huge:10000000
      MAX_THREADS = 8
      HEARTBEAT_FREQ = 60
      VIS_HOST = 134.129.124.234
      VIS_PORT = 8080
      SHARED_DIR = /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/userdata/shared_dir
      DEBUG = False
      ca_distribute.pb2ca = useGrid:1, scriptOnGrid:1, frgCorrOnGrid:1, ovlCorrOnGrid:1
      SETTINGS_PATH = .
      EXIT_ON_FAILURE = False
      CLOUD_CHUNKS_PER_PROC = 2
      READ_SCOPES = small:3.6, large:100, veryLarge:10000, huge:1000000
      MAX_CHUNKS = 64
      ASSEMBLY_HOME = /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/analysis
      DATA_ROOT = /mnt
      VIS_NAMESPACE =
      IPY = ipy -X:ColorfulConsole
      TOC_HTML_NAME = index.html
      [INFO] 2016-02-28 18:48:54,306 [SMRTpipe.SmrtPipeMain run 465] Successfully found or created TMP dir '/media/friesen_lab/2TB/download/smrtanalysis/tmpdir'
      [WARNING] 2016-02-28 18:48:54,326 [SMRTpipe.SmrtPipeSettings _importSettings 195] Parameter global.control is missing a value
      [WARNING] 2016-02-28 18:48:54,326 [SMRTpipe.SmrtPipeSettings _importSettings 254] Parameter p_assembleunitig.specInRunCA is missing a value
      [WARNING] 2016-02-28 18:48:54,327 [SMRTpipe.SmrtPipeSettings _importSettings 254] Parameter p_referenceuploader.organism is missing a value
      [WARNING] 2016-02-28 18:48:54,327 [SMRTpipe.SmrtPipeSettings _importSettings 254] Parameter p_referenceuploader.ploidy is missing a value
      [WARNING] 2016-02-28 18:48:54,327 [SMRTpipe.SmrtPipeSettings _importSettings 254] Parameter p_referenceuploader.user is missing a value
      [INFO] 2016-02-28 18:48:54,328 [SMRTpipe.SmrtPipeContext initializeContext 235] SmrtPipeSettings Summary:
      settings loaded from file /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/admin/bin
      p_mapping.maxHits = 10
      p_filter.moduleName = P_Filter
      p_assembleunitig.merSize = 14
      global.version = 3
      global.fetch = common/protocols/preprocessing/Fetch.1.xml
      p_mapping.maxDivergence = 30
      p_referenceuploader.moduleName = P_ReferenceUploader
      p_fetch.moduleName = P_Fetch
      global.state = active
      p_assembleunitig.defaultFrgMinLen = 500
      p_mappingreports.moduleName = P_MappingReports
      p_preassemblerdagcon.minLongReadLength = 6000
      p_assembleunitig.moduleName = P_AssembleUnitig
      p_assemblypolishing.moduleName = P_AssemblyPolishing
      global.Control Filtering = common/protocols/control/KeepControlReads.1.xml
      p_mapping.placeRepeatsRandomly = True
      p_preassemblerdagcon.totalBestn = 24
      p_preassemblerdagcon.minCorCov = 6
      p_assembleunitig.ovlMinLen = 40
      p_filter.minSubReadLength = 500
      p_assembleunitig.libraryName = pacbioReads
      p_mapping.pulseMetrics = DeletionQV,IPD,InsertionQV,PulseWidth,QualityValue,MergeQV,SubstitutionQV,DeletionTag
      global.assembly = common/protocols/assembly/PreAssemblerHGAP.3.xml
      p_assembleunitig.specTmpl = analysis/etc/celeraAssembler/unitig.spec
      global.consensus = common/protocols/consensus/AssemblyPolishing.1.xml
      global.description = (BETA) HGAP version 3. PacBio de novo assembler optimized for speed.
      p_referenceuploader.runUploaderUnitig = True
      p_filter.description = Filter reads for use in the pre-assembly step of HGAP, the hierarchical genome assembly process.
      p_preassemblerdagcon.moduleName = P_PreAssemblerDagcon
      p_assembleunitig.description = This module runs Celera Assembler v8.1 to the unitig step, then finishes with our custom unitig consensus caller
      p_assemblypolishing.description = Polish a pure-PacBio assembly for maximum accuracy using the Quiver algorithm.
      p_referenceuploader.runUploaderHgap = False
      p_assembleunitig.genomeSize = 45000000
      p_referenceuploader.sawriter = sawriter -blt 8 -welter
      p_filter.minLength = 100
      p_mapping.pbalign_opts = --seed=1 --minAccuracy=0.75 --minLength=50 --algorithmOptions="-useQuality"
      p_mapping.samBam = True
      p_mapping.moduleName = P_Mapping
      p_assembleunitig.ovlErrorRate = 0.06
      p_preassemblerdagcon.splitBestn = 10
      p_preassemblerdagcon.targetChunks = 10
      p_assembleunitig.xCoverage = 25
      p_mapping.minAnchorSize = 12
      global.filtering = common/protocols/filtering/PreAssemblerSFilter.1.xml
      p_referenceuploader.runUploader = False
      p_preassemblerdagcon.computeLengthCutoff = True
      p_filter.readScore = 0.80
      p_mapping.description = BLASR maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. The first set of alignments is found by querying an index of the reference genome, and then refining until only high scoring alignments are retained. Additional pulse metrics are loaded into the resulting cmp.h5 file to enable downstream use of the Quiver algorithm.
      p_mapping.loadPulsesOpts = bymetric
      global.mapping = common/protocols/mapping/BLASR.1.xml
      global.otfReference = reference
      global.referenceUploader = common/protocols/referenceuploader/ReferenceUploaderUnitig.1.xml
      p_mapping.gff2Bed = True
      global.deferRefCheck = True
      global.name = RS_HGAP_Assembly_3
      p_preassemblerdagcon.blasrOpts = -noSplitSubreads -minReadLength 200 -maxScore -1000 -maxLCPLength 16
      p_referenceuploader.samIdx = samtools faidx
      p_fetch.description = Sets up inputs
      p_assembleunitig.maxSlotPerc = 1
      p_assemblypolishing.enableMapQVFilter = True
      p_preassemblerdagcon.title = Using DAG-based consensus algorithm, pre-assemble long reads as the first step of the Hierarchical Genome Assembly process (HGAP). Version 2 is a stepping stone for scaling to much larger genomes.
      p_filterreports.moduleName = P_FilterReports
      p_referenceuploader.name = reference
      [INFO] 2016-02-28 18:48:54,331 [SMRTpipe.SmrtDataService setupOutputDirectories 132] Creating /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/data
      [INFO] 2016-02-28 18:48:54,332 [SMRTpipe.SmrtDataService setupOutputDirectories 132] Creating /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/results
      [INFO] 2016-02-28 18:48:54,332 [SMRTpipe.SmrtDataService setupOutputDirectories 136] Completed setting up DataServices in /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441
      [INFO] 2016-02-28 18:48:54,332 [SMRTpipe.SmrtPipeContext initializeContext 257] Input data is [ file//media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/A01_1, file//media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/F03_1, file//media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/G03_1, file//media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/A03_1, file//media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/D03_1, file//media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/E03_1, file//media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/H03_1, file//media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/C03_1, file//media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/B01_1 ]
      [INFO] 2016-02-28 18:48:54,332 [SMRTpipe.SmrtPipeContext initializeContext 261] Configuration override for PROGRESS_URL: Old: --> New: http://134.129.124.234:8080/smrtportal/api
      [INFO] 2016-02-28 18:48:54,333 [SMRTpipe.SmrtPipeContext initializeContext 274] Changing working directory to /media/friesen_lab/2TB/download/smrtanalysis/tmpdir/tmp2O9wQI
      [INFO] 2016-02-28 18:48:54,345 [SMRTpipe.SmrtPipeContext movieFiles 371] Pulling data from tags: primaryAnalysisProtocol=['Analysis_Results']
      [INFO] 2016-02-28 18:48:54,346 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/A01_1/Analysis_Results/m160205_202924_42151_c100937642550000001823216806101630_s1_p0.1.bax.h5 (3118293624 bytes)
      [INFO] 2016-02-28 18:48:54,347 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/A01_1/Analysis_Results/m160205_202924_42151_c100937642550000001823216806101630_s1_p0.2.bax.h5 (3096524303 bytes)
      [INFO] 2016-02-28 18:48:54,348 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/A01_1/Analysis_Results/m160205_202924_42151_c100937642550000001823216806101630_s1_p0.3.bax.h5 (3131515636 bytes)
      [INFO] 2016-02-28 18:48:54,349 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/F03_1/Analysis_Results/m160209_222609_42151_c100937642550000001823216806101636_s1_p0.1.bax.h5 (9826113063 bytes)
      [INFO] 2016-02-28 18:48:54,350 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/F03_1/Analysis_Results/m160209_222609_42151_c100937642550000001823216806101636_s1_p0.2.bax.h5 (8847536745 bytes)
      [INFO] 2016-02-28 18:48:54,350 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/F03_1/Analysis_Results/m160209_222609_42151_c100937642550000001823216806101636_s1_p0.3.bax.h5 (8660106571 bytes)
      [INFO] 2016-02-28 18:48:54,351 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/G03_1/Analysis_Results/m160210_044522_42151_c100937642550000001823216806101637_s1_p0.1.bax.h5 (10397206632 bytes)
      [INFO] 2016-02-28 18:48:54,352 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/G03_1/Analysis_Results/m160210_044522_42151_c100937642550000001823216806101637_s1_p0.2.bax.h5 (8896807724 bytes)
      [INFO] 2016-02-28 18:48:54,352 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/G03_1/Analysis_Results/m160210_044522_42151_c100937642550000001823216806101637_s1_p0.3.bax.h5 (8770450475 bytes)
      [INFO] 2016-02-28 18:48:54,353 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/A03_1/Analysis_Results/m160208_211005_42151_c100937642550000001823216806101632_s1_p0.1.bax.h5 (4262061828 bytes)
      [INFO] 2016-02-28 18:48:54,353 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/A03_1/Analysis_Results/m160208_211005_42151_c100937642550000001823216806101632_s1_p0.2.bax.h5 (4444715980 bytes)
      [INFO] 2016-02-28 18:48:54,354 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/A03_1/Analysis_Results/m160208_211005_42151_c100937642550000001823216806101632_s1_p0.3.bax.h5 (5001249228 bytes)
      [INFO] 2016-02-28 18:48:54,355 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/D03_1/Analysis_Results/m160209_094743_42151_c100937642550000001823216806101634_s1_p0.1.bax.h5 (9588943418 bytes)
      [INFO] 2016-02-28 18:48:54,355 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/D03_1/Analysis_Results/m160209_094743_42151_c100937642550000001823216806101634_s1_p0.2.bax.h5 (8973091617 bytes)
      [INFO] 2016-02-28 18:48:54,356 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/D03_1/Analysis_Results/m160209_094743_42151_c100937642550000001823216806101634_s1_p0.3.bax.h5 (8496818708 bytes)
      [INFO] 2016-02-28 18:48:54,356 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/E03_1/Analysis_Results/m160209_160656_42151_c100937642550000001823216806101635_s1_p0.1.bax.h5 (10082235080 bytes)
      [INFO] 2016-02-28 18:48:54,357 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/E03_1/Analysis_Results/m160209_160656_42151_c100937642550000001823216806101635_s1_p0.2.bax.h5 (9148614091 bytes)
      [INFO] 2016-02-28 18:48:54,358 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/E03_1/Analysis_Results/m160209_160656_42151_c100937642550000001823216806101635_s1_p0.3.bax.h5 (8917808086 bytes)
      [INFO] 2016-02-28 18:48:54,359 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/H03_1/Analysis_Results/m160210_110935_42151_c100937372550000001823216806101690_s1_p0.1.bax.h5 (8475423219 bytes)
      [INFO] 2016-02-28 18:48:54,361 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/H03_1/Analysis_Results/m160210_110935_42151_c100937372550000001823216806101690_s1_p0.2.bax.h5 (7687682307 bytes)
      [INFO] 2016-02-28 18:48:54,362 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/H03_1/Analysis_Results/m160210_110935_42151_c100937372550000001823216806101690_s1_p0.3.bax.h5 (7324602593 bytes)
      [INFO] 2016-02-28 18:48:54,364 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/C03_1/Analysis_Results/m160209_032830_42151_c100937642550000001823216806101633_s1_p0.1.bax.h5 (8528912415 bytes)
      [INFO] 2016-02-28 18:48:54,365 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/C03_1/Analysis_Results/m160209_032830_42151_c100937642550000001823216806101633_s1_p0.2.bax.h5 (8586867196 bytes)
      [INFO] 2016-02-28 18:48:54,366 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160208_Wyatt_Friesen_USDA_MagBeads_269/C03_1/Analysis_Results/m160209_032830_42151_c100937642550000001823216806101633_s1_p0.3.bax.h5 (9113034259 bytes)
      [INFO] 2016-02-28 18:48:54,366 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/B01_1/Analysis_Results/m160206_024804_42151_c100937642550000001823216806101631_s1_p0.1.bax.h5 (3573475555 bytes)
      [INFO] 2016-02-28 18:48:54,368 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/B01_1/Analysis_Results/m160206_024804_42151_c100937642550000001823216806101631_s1_p0.2.bax.h5 (3611434136 bytes)
      [INFO] 2016-02-28 18:48:54,369 [SMRTpipe.SmrtPipeContext movieFiles 391] Found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/inputs_dropbox/Link to 15A_pacbiodata/20160205__Wyatt_Friesen_USDA_MagBeads_268/B01_1/Analysis_Results/m160206_024804_42151_c100937642550000001823216806101631_s1_p0.3.bax.h5 (3575852392 bytes)
      [INFO] 2016-02-28 18:48:54,751 [SMRTpipe.SmrtPipeMain _getBasVersions 413] Detected basH5 versions set(['-v2.3.0'])
      [INFO] 2016-02-28 18:48:56,430 [smrtpipe.status run 503] smrtpipe.py running on friesen-lab-computer
      [INFO] 2016-02-28 18:48:56,431 [smrtpipe.status run 519] SMRT Analysis v2.2.0 / SMRTpipe 1.85.133289
      [INFO] 2016-02-28 18:48:56,431 [SMRTpipe.SmrtPipeMain run 522] Starting smrtpipe version 1.85.133289
      [INFO] 2016-02-28 18:48:57,707 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Fetch module
      [INFO] 2016-02-28 18:48:57,712 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Fetch v2.4.132105 and validated settings.
      [INFO] 2016-02-28 18:48:57,730 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Filter module
      [INFO] 2016-02-28 18:48:57,734 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Filter v1.7.133178 and validated settings.
      [INFO] 2016-02-28 18:48:57,737 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_FilterReports module
      [INFO] 2016-02-28 18:48:57,738 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_FilterReports v1.21.132105 and validated settings.
      [INFO] 2016-02-28 18:48:57,753 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_PreAssemblerDagcon module
      [INFO] 2016-02-28 18:48:57,757 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_PreAssemblerDagcon v2.1.124285 and validated settings.
      [INFO] 2016-02-28 18:48:57,764 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_AssembleUnitig module
      [INFO] 2016-02-28 18:48:57,768 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_AssembleUnitig v2.2.UnknownVersion and validated settings.
      [INFO] 2016-02-28 18:48:57,794 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_ReferenceUploader module
      [INFO] 2016-02-28 18:48:57,796 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_ReferenceUploader v1.2.132105 and validated settings.
      [INFO] 2016-02-28 18:48:57,806 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_Mapping module
      [INFO] 2016-02-28 18:48:57,817 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_Mapping v1.33.132536 and validated settings.
      [INFO] 2016-02-28 18:48:57,831 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_MappingReports module
      [INFO] 2016-02-28 18:48:57,832 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_MappingReports v1.7.132536 and validated settings.
      [INFO] 2016-02-28 18:48:57,837 [SMRTpipe.SmrtPipeMain _dynamicallyLoadModule 846] Dynamically Loaded P_AssemblyPolishing module
      [INFO] 2016-02-28 18:48:57,840 [SMRTpipe.SmrtPipeMain _loadModules 212] Loaded module P_AssemblyPolishing v1.36.132576 and validated settings.
      [INFO] 2016-02-28 18:48:57,842 [SMRTpipe.SmrtDataService writeTo 424] Writing 6 items to DataStore in {'smrt.data.xmlparam': , 'smrt.output.log': '/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/log', 'smrt.data.cmdline': >, 'smrt.output.root': '/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441', 'smrt.output.results': '/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/results', 'smrt.output.data': '/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/data'}
      [INFO] 2016-02-28 18:48:57,847 [SMRTpipe.SmrtPipeMain _runTasks 281] Skipping PreWorkflow as it contains zero tasks
      [INFO] 2016-02-28 18:48:57,851 [SMRTpipe.SmrtPipeMain _runTasks 284] Loading 37 tasks into Workflow
      [INFO] 2016-02-28 18:48:59,045 [SMRTpipe.SmrtPipeMain _runTasks 298] Executing workflow Workflow
      [INFO] 2016-02-28 18:48:59,046 [smrtpipe.status execute 620] Process id 62594
      [INFO] 2016-02-28 18:49:05,901 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Fetch/toFofn
      [INFO] 2016-02-28 18:49:05,923 [smrtpipe.status refreshTargets 407] task P_Fetch.toFofn successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 0 slots.
      [INFO] 2016-02-28 18:49:05,923 [smrtpipe.status refreshTargets 409] Workflow Completion Status 1/62 in ( 1%) tasks completed.
      [INFO] 2016-02-28 18:49:10,932 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Fetch/adapterRpt
      [INFO] 2016-02-28 18:49:10,932 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter.plsFofn.Scatter
      [INFO] 2016-02-28 18:49:10,933 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Fetch/overviewRpt
      [INFO] 2016-02-28 18:49:10,933 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Fetch/getChemistry
      [INFO] 2016-02-28 18:49:10,959 [smrtpipe.status refreshTargets 407] task P_Filter.filter.plsFofn.Scatter successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 3 slots.
      [INFO] 2016-02-28 18:49:10,959 [smrtpipe.status refreshTargets 409] Workflow Completion Status 2/62 in ( 3%) tasks completed.
      [INFO] 2016-02-28 18:49:13,850 [smrtpipe.status refreshTargets 407] task P_Fetch.getChemistry successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 2 slots.
      [INFO] 2016-02-28 18:49:13,850 [smrtpipe.status refreshTargets 409] Workflow Completion Status 3/62 in ( 4%) tasks completed.
      [INFO] 2016-02-28 18:49:16,502 [smrtpipe.status refreshTargets 407] task P_Fetch.overviewRpt successfully completed (3.00 sec (0.05 min)). freed 1 slots, using 1 slots.
      [INFO] 2016-02-28 18:49:16,502 [smrtpipe.status refreshTargets 409] Workflow Completion Status 4/62 in ( 6%) tasks completed.
      [INFO] 2016-02-28 18:49:21,532 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter_004of011
      [INFO] 2016-02-28 18:49:21,533 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter_011of011
      [INFO] 2016-02-28 18:49:21,533 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter_002of011
      [INFO] 2016-02-28 18:49:21,534 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter_010of011
      [INFO] 2016-02-28 18:49:21,534 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter_005of011
      [INFO] 2016-02-28 18:49:21,534 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter_007of011
      [INFO] 2016-02-28 18:49:21,535 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter_006of011
      [INFO] 2016-02-28 18:51:14,006 [smrtpipe.status refreshTargets 407] task P_Filter.filter_007of011 successfully completed (114.00 sec (1.90 min)). freed 2 slots, using 13 slots.
      [INFO] 2016-02-28 18:51:14,007 [smrtpipe.status refreshTargets 409] Workflow Completion Status 5/62 in ( 8%) tasks completed.
      [INFO] 2016-02-28 18:51:19,013 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreads_007of011
      [INFO] 2016-02-28 18:51:19,046 [smrtpipe.status refreshTargets 407] task P_Filter.filter_011of011 successfully completed (117.00 sec (1.95 min)). freed 2 slots, using 12 slots.
      [INFO] 2016-02-28 18:51:19,047 [smrtpipe.status refreshTargets 409] Workflow Completion Status 6/62 in ( 9%) tasks completed.
      [INFO] 2016-02-28 18:51:24,055 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreads_011of011
      [INFO] 2016-02-28 18:51:24,113 [smrtpipe.status refreshTargets 407] task P_Filter.filter_010of011 successfully completed (124.00 sec (2.07 min)). freed 2 slots, using 11 slots.
      [INFO] 2016-02-28 18:51:24,114 [smrtpipe.status refreshTargets 409] Workflow Completion Status 7/62 in ( . 11%) tasks completed.
      [INFO] 2016-02-28 18:51:29,123 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreads_010of011
      [INFO] 2016-02-28 18:52:10,626 [smrtpipe.status refreshTargets 407] task P_Filter.filter_006of011 successfully completed (168.00 sec (2.80 min)). freed 2 slots, using 10 slots.
      [INFO] 2016-02-28 18:52:10,626 [smrtpipe.status refreshTargets 409] Workflow Completion Status 8/62 in ( . 12%) tasks completed.
      [INFO] 2016-02-28 18:52:15,633 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreads_006of011
      [INFO] 2016-02-28 18:52:15,670 [smrtpipe.status refreshTargets 407] task P_Filter.filter_005of011 successfully completed (175.00 sec (2.92 min)). freed 2 slots, using 9 slots.
      [INFO] 2016-02-28 18:52:15,670 [smrtpipe.status refreshTargets 409] Workflow Completion Status 9/62 in ( . 14%) tasks completed.
      [INFO] 2016-02-28 18:52:20,676 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreads_005of011
      [INFO] 2016-02-28 18:52:20,734 [smrtpipe.status refreshTargets 407] task P_Filter.filter_004of011 successfully completed (178.00 sec (2.97 min)). freed 2 slots, using 8 slots.
      [INFO] 2016-02-28 18:52:20,734 [smrtpipe.status refreshTargets 409] Workflow Completion Status 10/62 in ( . 16%) tasks completed.
      [INFO] 2016-02-28 18:52:20,795 [smrtpipe.status refreshTargets 407] task P_Filter.filter_002of011 successfully completed (179.00 sec (2.98 min)). freed 2 slots, using 6 slots.
      [INFO] 2016-02-28 18:52:20,795 [smrtpipe.status refreshTargets 409] Workflow Completion Status 11/62 in ( . 17%) tasks completed.
      [INFO] 2016-02-28 18:52:25,805 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreads_004of011
      [INFO] 2016-02-28 18:52:25,807 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreads_002of011
      [INFO] 2016-02-28 18:55:42,678 [smrtpipe.status refreshTargets 407] task P_Fetch.adapterRpt successfully completed (393.00 sec (6.55 min)). freed 1 slots, using 7 slots.
      [INFO] 2016-02-28 18:55:42,679 [smrtpipe.status refreshTargets 409] Workflow Completion Status 12/62 in ( . 19%) tasks completed.
      [INFO] 2016-02-28 18:55:47,686 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter_008of011
      [INFO] 2016-02-28 18:57:35,551 [smrtpipe.status refreshTargets 407] task P_Filter.filter_008of011 successfully completed (107.00 sec (1.78 min)). freed 2 slots, using 7 slots.
      [INFO] 2016-02-28 18:57:35,551 [smrtpipe.status refreshTargets 409] Workflow Completion Status 13/62 in ( .. 20%) tasks completed.
      [INFO] 2016-02-28 18:57:40,558 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreads_008of011
      [INFO] 2016-02-28 21:15:41,631 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_011of011 successfully completed (8658.00 sec (144.30 min)). freed 1 slots, using 7 slots.
      [INFO] 2016-02-28 21:15:41,633 [smrtpipe.status refreshTargets 409] Workflow Completion Status 14/62 in ( .. 22%) tasks completed.
      [INFO] 2016-02-28 21:15:46,645 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter_009of011
      [INFO] 2016-02-28 21:17:33,089 [smrtpipe.status refreshTargets 407] task P_Filter.filter_009of011 successfully completed (108.00 sec (1.80 min)). freed 2 slots, using 7 slots.
      [INFO] 2016-02-28 21:17:33,090 [smrtpipe.status refreshTargets 409] Workflow Completion Status 15/62 in ( .. 24%) tasks completed.
      [INFO] 2016-02-28 21:17:39,264 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreads_009of011
      [INFO] 2016-02-28 21:18:24,325 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_004of011 successfully completed (8762.00 sec (146.03 min)). freed 1 slots, using 7 slots.
      [INFO] 2016-02-28 21:18:24,325 [smrtpipe.status refreshTargets 409] Workflow Completion Status 16/62 in ( .. 25%) tasks completed.
      [INFO] 2016-02-28 21:18:29,333 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter_003of011
      [INFO] 2016-02-28 21:21:13,617 [smrtpipe.status refreshTargets 407] task P_Filter.filter_003of011 successfully completed (167.00 sec (2.78 min)). freed 2 slots, using 7 slots.
      [INFO] 2016-02-28 21:21:13,617 [smrtpipe.status refreshTargets 409] Workflow Completion Status 17/62 in ( .. 27%) tasks completed.
      [INFO] 2016-02-28 21:21:18,620 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreads_003of011
      [INFO] 2016-02-28 21:30:57,956 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_010of011 successfully completed (9568.00 sec (159.47 min)). freed 1 slots, using 7 slots.
      [INFO] 2016-02-28 21:30:57,956 [smrtpipe.status refreshTargets 409] Workflow Completion Status 18/62 in ( .. 29%) tasks completed.
      [INFO] 2016-02-28 21:31:02,963 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter_001of011
      [INFO] 2016-02-28 21:32:54,362 [smrtpipe.status refreshTargets 407] task P_Filter.filter_001of011 successfully completed (114.00 sec (1.90 min)). freed 2 slots, using 7 slots.
      [INFO] 2016-02-28 21:32:54,362 [smrtpipe.status refreshTargets 409] Workflow Completion Status 19/62 in ( ... 30%) tasks completed.
      [INFO] 2016-02-28 21:33:00,802 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter.summary.Gather
      [INFO] 2016-02-28 21:33:05,138 [smrtpipe.status refreshTargets 407] task P_Filter.filter.summary.Gather successfully completed (2.00 sec (0.03 min)). freed 1 slots, using 7 slots.
      [INFO] 2016-02-28 21:33:05,138 [smrtpipe.status refreshTargets 409] Workflow Completion Status 20/62 in ( ... 32%) tasks completed.
      [INFO] 2016-02-28 21:33:10,149 [smrtpipe.status refreshTargets 419] Starting task://016441/P_FilterReports/statsRpt
      [INFO] 2016-02-28 21:34:39,647 [smrtpipe.status refreshTargets 407] task P_FilterReports.statsRpt successfully completed (90.00 sec (1.50 min)). freed 1 slots, using 7 slots.
      [INFO] 2016-02-28 21:34:39,648 [smrtpipe.status refreshTargets 409] Workflow Completion Status 21/62 in ( ... 33%) tasks completed.
      [INFO] 2016-02-28 21:34:44,652 [smrtpipe.status refreshTargets 419] Starting task://016441/P_FilterReports/loadingRpt
      [INFO] 2016-02-28 21:35:18,719 [smrtpipe.status refreshTargets 407] task P_FilterReports.loadingRpt successfully completed (31.00 sec (0.52 min)). freed 1 slots, using 7 slots.
      [INFO] 2016-02-28 21:35:18,719 [smrtpipe.status refreshTargets 409] Workflow Completion Status 22/62 in ( ... 35%) tasks completed.
      [INFO] 2016-02-28 21:35:23,722 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/filter.rgnFofn.Gather
      [INFO] 2016-02-28 21:35:28,745 [smrtpipe.status refreshTargets 407] task P_Filter.filter.rgnFofn.Gather successfully completed (2.00 sec (0.03 min)). freed 1 slots, using 7 slots.
      [INFO] 2016-02-28 21:35:28,745 [smrtpipe.status refreshTargets 409] Workflow Completion Status 23/62 in ( ... 37%) tasks completed.
      [INFO] 2016-02-28 21:35:33,753 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreadSummary
      [INFO] 2016-02-28 21:52:56,595 [smrtpipe.status refreshTargets 407] task P_Filter.subreadSummary successfully completed (1043.00 sec (17.38 min)). freed 1 slots, using 7 slots.
      [INFO] 2016-02-28 21:52:56,595 [smrtpipe.status refreshTargets 409] Workflow Completion Status 24/62 in ( ... 38%) tasks completed.
      [INFO] 2016-02-28 21:53:01,605 [smrtpipe.status refreshTargets 419] Starting task://016441/P_FilterReports/subreadRpt
      [INFO] 2016-02-28 21:54:05,730 [smrtpipe.status refreshTargets 407] task P_FilterReports.subreadRpt successfully completed (65.00 sec (1.08 min)). freed 1 slots, using 7 slots.
      [INFO] 2016-02-28 21:54:05,730 [smrtpipe.status refreshTargets 409] Workflow Completion Status 25/62 in ( .... 40%) tasks completed.
      [INFO] 2016-02-28 21:54:10,737 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreads_001of011
      [INFO] 2016-02-28 22:06:53,139 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_008of011 successfully completed (11354.00 sec (189.23 min)). freed 1 slots, using 7 slots.
      [INFO] 2016-02-28 22:06:53,139 [smrtpipe.status refreshTargets 409] Workflow Completion Status 26/62 in ( .... 41%) tasks completed.
      [INFO] 2016-02-28 22:12:56,889 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_007of011 successfully completed (12099.00 sec (201.65 min)). freed 1 slots, using 6 slots.
      [INFO] 2016-02-28 22:12:56,889 [smrtpipe.status refreshTargets 409] Workflow Completion Status 27/62 in ( .... 43%) tasks completed.
      [INFO] 2016-02-28 22:38:14,519 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_006of011 successfully completed (13561.00 sec (226.02 min)). freed 1 slots, using 5 slots.
      [INFO] 2016-02-28 22:38:14,519 [smrtpipe.status refreshTargets 409] Workflow Completion Status 28/62 in ( .... 45%) tasks completed.
      [INFO] 2016-02-28 22:39:01,103 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_002of011 successfully completed (13599.00 sec (226.65 min)). freed 1 slots, using 4 slots.
      [INFO] 2016-02-28 22:39:01,103 [smrtpipe.status refreshTargets 409] Workflow Completion Status 29/62 in ( .... 46%) tasks completed.
      [INFO] 2016-02-28 22:40:02,642 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_005of011 successfully completed (13666.00 sec (227.77 min)). freed 1 slots, using 3 slots.
      [INFO] 2016-02-28 22:40:02,642 [smrtpipe.status refreshTargets 409] Workflow Completion Status 30/62 in ( .... 48%) tasks completed.
      [INFO] 2016-02-28 23:12:06,142 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_009of011 successfully completed (6868.00 sec (114.47 min)). freed 1 slots, using 2 slots.
      [INFO] 2016-02-28 23:12:06,142 [smrtpipe.status refreshTargets 409] Workflow Completion Status 31/62 in ( ..... 50%) tasks completed.
      [INFO] 2016-02-28 23:18:29,849 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_001of011 successfully completed (5063.00 sec (84.38 min)). freed 1 slots, using 1 slots.
      [INFO] 2016-02-28 23:18:29,849 [smrtpipe.status refreshTargets 409] Workflow Completion Status 32/62 in ( ..... 51%) tasks completed.
      [INFO] 2016-02-28 23:33:25,330 [smrtpipe.status refreshTargets 407] task P_Filter.subreads_003of011 successfully completed (7929.00 sec (132.15 min)). freed 1 slots, using 0 slots.
      [INFO] 2016-02-28 23:33:25,330 [smrtpipe.status refreshTargets 409] Workflow Completion Status 33/62 in ( ..... 53%) tasks completed.
      [INFO] 2016-02-28 23:33:30,336 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreads.subreadFastq.Gather
      [INFO] 2016-02-28 23:33:30,337 [smrtpipe.status refreshTargets 419] Starting task://016441/P_Filter/subreads.subreads.Gather
      [INFO] 2016-02-28 23:40:09,894 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreads.Gather successfully completed (398.00 sec (6.63 min)). freed 1 slots, using 1 slots.
      [INFO] 2016-02-28 23:40:09,895 [smrtpipe.status refreshTargets 409] Workflow Completion Status 34/62 in ( ..... 54%) tasks completed.
      [INFO] 2016-02-28 23:40:14,902 [smrtpipe.status refreshTargets 419] Starting task://016441/P_PreAssemblerDagcon/filterLongReadsByLength
      [INFO] 2016-02-28 23:40:52,835 [smrtpipe.status refreshTargets 407] task P_Filter.subreads.subreadFastq.Gather successfully completed (439.00 sec (7.32 min)). freed 1 slots, using 1 slots.
      [INFO] 2016-02-28 23:40:52,835 [smrtpipe.status refreshTargets 409] Workflow Completion Status 35/62 in ( ..... 56%) tasks completed.
      [INFO] 2016-02-28 23:43:32,976 [smrtpipe.status refreshTargets 407] task P_PreAssemblerDagcon.filterLongReadsByLength successfully completed (198.00 sec (3.30 min)). freed 1 slots, using 0 slots.
      [INFO] 2016-02-28 23:43:32,977 [smrtpipe.status refreshTargets 409] Workflow Completion Status 36/62 in ( ..... 58%) tasks completed.
      [INFO] 2016-02-28 23:43:37,983 [smrtpipe.status refreshTargets 419] Starting task://016441/P_PreAssemblerDagcon/hgapAlignForCorrection
      [INFO] 2016-02-29 15:25:55,617 [smrtpipe.status refreshTargets 407] task P_PreAssemblerDagcon.hgapAlignForCorrection successfully completed (56541.00 sec (942.35 min)). freed 11 slots, using 0 slots.
      [INFO] 2016-02-29 15:25:55,618 [smrtpipe.status refreshTargets 409] Workflow Completion Status 37/62 in ( ..... 59%) tasks completed.
      [INFO] 2016-02-29 15:26:00,624 [smrtpipe.status refreshTargets 419] Starting task://016441/P_PreAssemblerDagcon/hgapFilterM4
      [INFO] 2016-02-29 15:27:22,110 [smrtpipe.status refreshTargets 407] task P_PreAssemblerDagcon.hgapFilterM4 successfully completed (83.00 sec (1.38 min)). freed 1 slots, using 0 slots.
      [INFO] 2016-02-29 15:27:22,110 [smrtpipe.status refreshTargets 409] Workflow Completion Status 38/62 in ( ...... 61%) tasks completed.
      [INFO] 2016-02-29 15:27:27,113 [smrtpipe.status refreshTargets 419] Starting task://016441/P_PreAssemblerDagcon/hgapCorrection
      [ERROR] 2016-02-29 16:46:10,095 [smrtpipe.status refreshTargets 413] *** Failed task task://016441/P_PreAssemblerDagcon/hgapCorrection
      [INFO] 2016-02-29 16:46:10,103 [smrtpipe.status execute 627] Found 1 failed tasks.
      [INFO] 2016-02-29 16:46:10,103 [smrtpipe.status execute 629] task hgapCorrection FAILED
      [ERROR] 2016-02-29 16:46:16,437 [SMRTpipe.SmrtPipeMain run 608] SmrtExit task://016441/P_PreAssemblerDagcon/hgapCorrection Failed
      Traceback (most recent call last):
      File "/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/SmrtPipeMain.py", line 571, in run
      self._runTasks(pModules)
      File "/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/SmrtPipeMain.py", line 300, in _runTasks
      workflow.execute()
      File "/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/engine/SmrtPipeWorkflow.py", line 640, in execute
      raise SmrtExit(str(e))
      SmrtExit: SmrtExit task://016441/P_PreAssemblerDagcon/hgapCorrection Failed
      [ERROR] 2016-02-29 16:46:16,438 [SMRTpipe.SmrtPipeMain exit 690] SmrtExit task://016441/P_PreAssemblerDagcon/hgapCorrection Failed
      [INFO] 2016-02-29 16:46:16,438 [SMRTpipe.SmrtPipeMain exit 692] Beginning exit process
      [INFO] 2016-02-29 16:46:16,438 [SMRTpipe.SmrtPipeMain shutdown 716] beginning Shutdown Process
      [INFO] 2016-02-29 16:46:16,438 [SMRTpipe.SmrtPipeMain _generate_final_report 651] Writing final TOC page with error message : SmrtExit task://016441/P_PreAssemblerDagcon/hgapCorrection Failed
      [INFO] 2016-02-29 16:46:17,929 [SMRTpipe.SmrtPipeMain shutdown 752] Completed shutdown gracefully
      [INFO] 2016-02-29 16:46:17,929 [SMRTpipe.SmrtPipeMain exit 702] Sending message Exiting smrtpipe last error: SmrtExit task://016441/P_PreAssemblerDagcon/hgapCorrection Failed
      [INFO] 2016-02-29 16:46:17,929 [smrtpipe.status failed 104] Sending Job 016441 failed message 'Exiting smrtpipe last error: SmrtExit task://016441/P_PreAssemblerDagcon/hgapCorrection Failed' to url http://134.129.124.234:8080/smrtport.../016441/status
      [INFO] 2016-02-29 16:46:17,985 [SMRTpipe.SmrtPipeMain run 641] completed SmrtPipeMain.run with exit code -1
      [INFO] 2016-02-29 16:46:17,985 [root main 336] Failed smrtpipe version v1.85.133289 with exit code -1 in 79043.68 seconds (1317.39 minutes)

      Comment

      • #4
        hgapCorrection is not running as a multipart task, my guess is that the single job breaks the 4gb file size limit for blasr. You can confirm this from the specific log file for the hgapCorrection task, .<job dir>/log/P_PreAssemblerDagcon/hgapCorrection.log, if you don't have access to the file system the file is available in the techsupport download on the main job page. How is SMRT Analysis installed, are you running on a single machine?

        Comment

        • #5
          rhall

          Thanks for the advice. I'll post the log below. I am running on a single machine which I was told could manage this process but I’m not entirely sure that is true (still pretty new to this).

          #!/bin/bash
          # Setting up SMRTpipe environment
          echo "Setting up ENV on $(uname -n)" for task hgapCorrection
          if [ -z $SEYMOUR_HOME ]; then
          SEYMOUR_HOME=/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377
          fi

          source $SEYMOUR_HOME/etc/setup.sh

          # Create the local TMP dir if it doesn't exist
          tmp_dir=$(readlink -m "/media/friesen_lab/2TB/download/smrtanalysis/tmpdir")
          if [ ! -e "$tmp_dir" ]; then
          stat=0
          mkdir -p $tmp_dir || stat=$?
          if [[ $stat -ne 0 ]]; then
          echo "SMRTpipe Unable to create TMP dir '/media/friesen_lab/2TB/download/smrtanalysis/tmpdir' on $(uname -n)" 1>&2
          exit 1
          else
          echo "successfully created or found TMP dir '/media/friesen_lab/2TB/download/smrtanalysis/tmpdir'"
          fi
          elif [[ ! -d "$tmp_dir" ]]; then
          echo "SMRTpipe TMP /media/friesen_lab/2TB/download/smrtanalysis/tmpdir must be a directory on $(uname -n)" 1>&2
          exit 1
          fi

          ########### TASK metadata #############
          # Task : hgapCorrection
          # Module : P_PreAssemblerDagcon
          # Module Version : 2.1.124285
          # TaskType : None
          # URL : task://016441/P_PreAssemblerDagcon/hgapCorrection
          # createdAt : 2016-02-28 18:48:59.033653
          # createdAt (UTC) : 2016-02-29 00:48:59.033665
          # ncmds : 1
          # LogPath : /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/log/P_PreAssemblerDagcon/hgapCorrection.log
          # Script Path : /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/workflow/P_PreAssemblerDagcon/hgapCorrection.sh

          # Input : /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/.seeds.m4.filter
          # Input : /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/data/filtered_subreads.fasta
          # Input : /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4
          # Input : /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4.fofn
          # Output : /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/data/corrected.fastq
          # Output : /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/data/corrected.fasta
          #
          ########### END TASK metadata #############

          # Writing to log file
          cat /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/workflow/P_PreAssemblerDagcon/hgapCorrection.sh >> /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/log/P_PreAssemblerDagcon/hgapCorrection.log;



          echo "Running task://016441/P_PreAssemblerDagcon/hgapCorrection on $(uname -a)"

          echo "Started on $(date -u)"
          echo 'Validating existence of Input Files'
          if [ -e /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/.seeds.m4.filter ]
          then
          echo 'Successfully found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/.seeds.m4.filter'
          else
          echo 'WARNING: Unable to find necessary input file, or dir /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/.seeds.m4.filter.'
          fi
          if [ -e /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/data/filtered_subreads.fasta ]
          then
          echo 'Successfully found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/data/filtered_subreads.fasta'
          else
          echo 'WARNING: Unable to find necessary input file, or dir /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/data/filtered_subreads.fasta.'
          fi
          if [ -e /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4 ]
          then
          echo 'Successfully found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4'
          else
          echo 'WARNING: Unable to find necessary input file, or dir /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4.'
          fi
          if [ -e /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4.fofn ]
          then
          echo 'Successfully found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4.fofn'
          else
          echo 'WARNING: Unable to find necessary input file, or dir /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4.fofn.'
          fi
          echo 'Successfully validated input files'

          # Task hgapCorrection commands:


          # Completed writing Task hgapCorrection commands


          # Task 1
          tmp=$(mktemp -d -p /media/friesen_lab/2TB/download/smrtanalysis/tmpdir);mym4=/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4 allm4=/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4.fofn subreads=/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/data/filtered_subreads.fasta bestn=24 nproc=11 fasta=/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/data/corrected.fasta fastq=/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/data/corrected.fastq cov=6 tmp=$tmp pbdagcon_wf.sh; rmdir $tmp || exit $?
          echo "Task 1 completed at $(date)"



          rcode=$?
          echo "Finished on $(date -u)"
          echo "Task hgapCorrection with nproc 11 with exit code ${rcode}."
          exit ${rcode}# Writing stdout and stderr from Popen:
          Setting up ENV on friesen-lab-computer for task hgapCorrection
          Running task://016441/P_PreAssemblerDagcon/hgapCorrection on Linux friesen-lab-computer 3.16.0-57-generic #77~14.04.1-Ubuntu SMP Thu Dec 17 23:20:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
          Started on Mon Feb 29 21:27:22 UTC 2016
          Validating existence of Input Files
          Successfully found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/.seeds.m4.filter
          Successfully found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/data/filtered_subreads.fasta
          Successfully found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4
          Successfully found /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4.fofn
          Successfully validated input files
          Generating pre-alignments
          m4topre.py /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4 /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/seeds.m4.fofn /media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/common/jobs/016/016441/data/filtered_subreads.fasta 24 > /media/friesen_lab/2TB/download/smrtanalysis/tmpdir/tmp.biV2OMIj5Y/aln.104683.pre
          Traceback (most recent call last):
          File "/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/analysis/bin/m4topre.py", line 208, in <module>
          sys.exit(main())
          File "/media/friesen_lab/2TB/download/smrtanalysis/install/smrtanalysis-2.2.0.133377/analysis/bin/m4topre.py", line 205, in main
          rec.tseqlength, str(tst), str(tnd), qseq, tseq])
          IOError: [Errno 28] No space left on device
          Task 1 completed at Mon Feb 29 16:46:07 CST 2016
          Finished on Mon Feb 29 22:46:07 UTC 2016
          Task hgapCorrection with nproc 11 with exit code 0.

          Comment

          • #6
            @scarlsen58: Can you post brief hardware specs (RAM, CPU) for this server? Are you able to complete the run if you process fewer (say 3) SMRTcells.

            As for the immediate error in that last log

            IOError: [Errno 28] No space left on device
            Looks like a storage location (perhaps temp dir) is filling up.

            Comment

            • #7
              You will need to free up space on the drive being used for tmp, or alternatively point the tmp directory somewhere else.
              I'm guessing 9 cells is to assembly ~50Mb genome? Anything bigger than a single bacteria is going to be difficult on a single machine. Although it isn't impossible, you will just have to be prepared for some trouble shooting.

              Comment

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