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  • problem in PacBioToCA in correction of long reads

    Hello,

    I try to run PacBioToCA to correct long reads.

    But here is the error.

    ###
    ### Reading options from 'spec_file.spec'
    ###

    Warning: no frag files specified, assuming self-correction of pacbio sequences.
    Running with 8 threads and 200 partitions
    ********* Starting correction...
    CA: /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin
    AMOS:/usr/local/genome/amos/bin
    SMRTportal:/projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin (blasr 1.3.1.142244)
    Bowtie:/usr/local/genome/bin
    ******** Configuration Summary ********
    cnsErrorRate = 0.25
    gridEngineHoldOption = -hold_jid "WAIT_TAG"
    utgErrorRate = 0.15
    mhapLoadFactor = 12500
    onlyContained = 0
    gridEngineOutputOption = -j y -o
    gridOptionsOverlapCorrection = -pe threads 1
    asmObtErrorLimit = 4.5
    gridOptionsCorrection = -pe threads 16 -l mem=2GB
    gridOptionsFragmentCorrection = -pe threads 2
    ovlCorrConcurrency = 4
    submitToGrid = 0
    maxUncorrectedGap = 1500
    mhapVersion = 1.5b1
    ovlRefBlockLength = 100000000000
    blasr =
    gridEngineArraySubmitID = $TASK_ID
    ovlConcurrency = 8
    merylThreads = 8
    utgMergeErrorRate = 0.025
    gridOptionsScript = -pe threads 16
    asmCnsErrorRate = 0.1
    gridOptionsOverlap = -pe threads 2
    falconForce =
    mhapPrecompute = 1
    cleanup = 1
    shortReads =
    merCompression = 1
    doOverlapBasedTrimming = 0
    gridEngineJobID = JOB_ID
    assembleCoverage = 25
    asmMerSize = 22
    genomeSize = 4.8m
    cgwErrorRate = 0.25
    gridEngineArrayName = ARRAY_NAME
    merylMemory = 128000
    libraryname = LIB
    consensusConcurrency = 4
    utgGraphErrorRate = 0.025
    asmCgwErrorRate = 0.1
    repeats =
    useGrid = 0
    gridEngineNameToJobIDCommand =
    gridEngineSubmitCommand = qsub
    asmObtErrorRate = 0.03
    assemble = 1
    ovlMemory = 251
    ovlHashBits = 25
    frgCorrBatchSize = 100000
    frgMinLen = 64
    batOptions = -RS -NS -CS
    merOverlapperExtendBatchSize = 250000
    asmOvlErrorRate = 0.03
    longReads = 1
    utgGraphErrorLimit = 0
    specFile = spec_file.spec
    pbcns = 0
    partitions = 200
    merSize = 14
    merOverlapperSeedBatchSize = 500000
    bowtie =
    frgCorrOnGrid = 0
    scriptOnGrid = 0
    ovlErrorRate = 0.25
    gridEngineArrayOption = -t ARRAY_JOBS
    coverageCutoff = 0
    frgCorrConcurrency = 2
    ovlHashBlockLength = 20000000
    gridOptionsConsensus = -pe threads 1
    QV = 54.5
    cnsMinFrags = 1000
    merOverlapperThreads = 3
    gridEngineSyncOption = -sync y
    utgErrorLimit = 4.5
    doUnitigSplitting = 0
    cnsConcurrency = 4
    samFOFN =
    ovlStoreMemory = 8192
    gridEngineTaskID = SGE_TASK_ID
    length = 500
    unitigger = bogart
    maxCoverage = 40
    stopAfter = overlapper
    asmUtgErrorRate = 0.025
    bankPath =
    gridOptions = -A assembly
    fastqFile = /projet/maiage/save/user/Bureau/WEcoli_raw.fastq
    doFragmentCorrection = 1
    merOverlapperExtendConcurrency = 3
    merOverlapperSeedConcurrency = 3
    asmOBT = 1
    ovlCorrBatchSize = 100000
    ovlCorrOnGrid = 0
    sensitive = 0
    mhap =
    gridEngineNameOption = -cwd -N
    assembleMinCoverage = 10
    threads = 8
    falconcns = 1
    gridEnginePropagateCommand = qalter -hold_jid "WAIT_TAG"
    shell = /bin/bash
    ovlRefBlockSize = 50000000
    asmCns = pbutgcns
    gridOptionsMhap = -pe threads 2
    utgMergeErrorLimit = 0
    falconOptions = --max_n_read 200 --min_idt 0.70 --output_multi --local_match_count_threshold 2
    frgCorrThreads = 2
    ovlThreads = 8
    ****************
    ----------------------------------------START Thu Apr 20 13:47:24 2017
    mkdir tempLIB
    ----------------------------------------END Thu Apr 20 13:47:24 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:47:24 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/fastqToCA -libraryname LIB -type sanger -technology none -feature doConsensusCorrection 1 -reads /projet/maiage/save/user/Bureau/WEcoli_raw.fastq > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.frg
    ----------------------------------------END Thu Apr 20 13:47:24 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:47:24 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.spec -p asm -d tempLIB stopAfter=initialStoreBuilding /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.frg
    ENV: SGE_TASK_ID needs to be unset, done.
    ----------------------------------------START Thu Apr 20 13:47:24 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/gatekeeper -o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/asm.gkpStore.BUILDING -F /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.frg > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/asm.gkpStore.err 2>&1
    ----------------------------------------END Thu Apr 20 13:47:26 2017 (2 seconds)
    numFrags = 8451
    Stop requested after 'initialstorebuilding'.
    ----------------------------------------END Thu Apr 20 13:47:26 2017 (2 seconds)
    Will be correcting PacBio library 1 with librarie[s] 1 - 1
    ----------------------------------------START Thu Apr 20 13:47:26 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/gatekeeper -dumpfragments -invert -tabular -longestovermin 1 500 -longestlength 1 192 /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.gkpStore 2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.seedlength |awk '{if (!(match($1, "UID") != 0 && length($1) == 3)) { print "frg uid "$1" isdeleted 1"; } }' > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.toerase.uid
    ----------------------------------------END Thu Apr 20 13:47:26 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:47:26 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/gatekeeper --edit /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.toerase.uid /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.gkpStore > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.toerase.out 2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.toerase.err
    ----------------------------------------END Thu Apr 20 13:47:26 2017 (0 seconds)
    Running with 6684.375X (for genome size 4.8m) of LIB sequences (32085 bp).
    Correcting with 10887268X sequences (52258890 bp).
    Warning: enabling MHAP overlapper to align long reads to long reads.
    ----------------------------------------START Thu Apr 20 13:47:26 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/jellyfish count -m 14 -s 120000000 -t 8 -o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.mers /projet/maiage/save/user/Bureau/WEcoli_raw.fastq
    ----------------------------------------END Thu Apr 20 13:47:29 2017 (3 seconds)
    ----------------------------------------START Thu Apr 20 13:47:29 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/jellyfish histo -t 8 -f /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.mers > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.hist
    ----------------------------------------END Thu Apr 20 13:47:31 2017 (2 seconds)
    ----------------------------------------START Thu Apr 20 13:47:31 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/jellyfish dump -c -t -L 6 /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.mers |awk -v TOTAL=38698633 '{printf("%s\t%0.10f\t%d\t%d\n", $1, $2/TOTAL, $2, TOTAL)}' |sort -T . -rnk2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.ignore
    ----------------------------------------END Thu Apr 20 13:47:35 2017 (4 seconds)
    ----------------------------------------START Thu Apr 20 13:47:35 2017
    rm /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/asm.mers*
    ----------------------------------------END Thu Apr 20 13:47:35 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:47:35 2017
    mkdir /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/1-overlapper
    ----------------------------------------END Thu Apr 20 13:47:35 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:47:35 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/gatekeeper -dumpfragments -tabular asm.gkpStore |awk '{print $1"\t"$2}' > asm.eidToIID
    ----------------------------------------END Thu Apr 20 13:47:35 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:47:35 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/gatekeeper -dumpfragments -tabular asm.gkpStore |awk '{print $2"\t"$10}' > asm.iidToLen
    ----------------------------------------END Thu Apr 20 13:47:35 2017 (0 seconds)
    ----------------------------------------START CONCURRENT Thu Apr 20 13:47:35 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/1-overlapper/ovlprep.sh 1
    Scanning store to find libraries used and reads to dump.
    Added 0 reads to maintain mate relationships.
    Dumping 0 fragments from unknown library (version 1 has these)
    Dumping 8451 fragments from library IID 1
    ----------------------------------------END CONCURRENT Thu Apr 20 13:48:39 2017 (64 seconds)
    ----------------------------------------START CONCURRENT Thu Apr 20 13:48:39 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/1-overlapper/overlap.sh 1
    ----------------------------------------END CONCURRENT Thu Apr 20 13:48:46 2017 (7 seconds)
    ----------------------------------------START Thu Apr 20 13:48:46 2017
    rm -f 000001.ovls
    ----------------------------------------END Thu Apr 20 13:48:46 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:48:46 2017
    rm -f *.dat
    ----------------------------------------END Thu Apr 20 13:48:46 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:48:46 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.spec -p asm -d . ovlMerThreshold= ovlHashLibrary=1 ovlRefLibrary=1-1 ovlCheckLibrary=1 obtHashLibrary=1-1 obtRefLibrary=1-1 obtCheckLibrary=0 gridEnginePropagateHold="pBcR_asm" stopAfter=overlapper
    ENV: SGE_TASK_ID needs to be unset, done.
    ----------------------------------------START Thu Apr 20 13:48:47 2017
    find -L /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/./1-overlapper \( -name \*ovb.gz -or -name \*ovb \) -print > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/./asm.ovlStore.list
    ----------------------------------------END Thu Apr 20 13:48:47 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:48:47 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild -o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/./asm.ovlStore.BUILDING -g /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/./asm.gkpStore -M 8192 -L /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/./asm.ovlStore.list > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/tempLIB/./asm.ovlStore.err 2>&1
    ----------------------------------------END Thu Apr 20 13:48:47 2017 (0 seconds)
    Stop requested after 'overlapper'.
    ----------------------------------------END Thu Apr 20 13:48:47 2017 (1 seconds)
    ----------------------------------------START Thu Apr 20 13:48:47 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runCorrection.sh
    ----------------------------------------END Thu Apr 20 13:48:48 2017 (1 seconds)
    ----------------------------------------START Thu Apr 20 13:48:48 2017
    rm -rf asm.paired.ovlStore
    ----------------------------------------END Thu Apr 20 13:48:48 2017 (0 seconds)
    ----------------------------------------START CONCURRENT Thu Apr 20 13:48:48 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 1
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 2
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 3
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 4
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 5
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 6
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 7
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 8
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 9
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 10
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 11
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 12
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 13
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    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 89
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 90
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 91
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 92
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 93
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 94
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 95
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 96
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 97
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 98
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 99
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 100
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 101
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 102
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 103
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 104
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 105
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 106
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 107
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 108
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 109
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 110
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 111
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 112
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 113
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 114
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 115
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 116
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 117
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 118
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 119
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 120
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 121
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 122
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 123
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 124
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 125
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 126
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 127
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 128
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 129
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 130
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 131
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 132
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 133
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 134
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 135
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 136
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 137
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 138
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 139
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 140
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 141
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 142
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 143
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 144
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 145
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 146
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 147
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 148
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 149
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 150
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 151
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 152
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 153
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 154
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 155
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 156
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 157
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 158
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 159
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 160
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 161
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 162
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 163
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 164
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 165
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 166
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 167
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 168
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 169
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 170
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 171
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 172
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 173
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 174
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 175
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 176
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 177
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 178
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 179
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 180
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 181
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 182
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 183
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 184
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 185
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 186
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 187
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 188
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 189
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 190
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 191
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 192
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 193
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 194
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 195
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 196
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 197
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 198
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 199
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/runPartition.sh 200
    ----------------------------------------END CONCURRENT Thu Apr 20 13:49:44 2017 (56 seconds)
    ----------------------------------------START Thu Apr 20 13:49:44 2017
    rm -rf core.*
    ----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:44 2017
    cat `ls asm.[0-9]*.log | sort -T . -rnk1` > corrected.log
    ----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:44 2017
    cat corrected.log |awk '{print $1}' |sort -T . |uniq -c |awk '{if ($1 > 1) print $2}' > asm.split.uid
    ----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:44 2017
    cp asm.layout.err /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.correction.err
    ----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:44 2017
    cp asm.layout.hist /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.correction.hist
    ----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:44 2017
    cat `ls [0-9]*.fasta |grep trim |sort -T . -rnk1` > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.fasta
    ----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:44 2017
    cat `ls [0-9]*.qual |grep trim | sort -T . -rnk1` > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.qual
    ----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:44 2017
    cat `ls [0-9]*.fastq |grep trim | sort -T . -rnk1` > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.fastq
    ----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:44 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/fastqToCA -libraryname LIB -technology pacbio-corrected -type sanger -reads /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.fastq > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.frg
    ----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
    ls: impossible d'accéder à /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/*sge.out*: Aucun fichier ou dossier de ce type
    ******** Correction Summary ********
    ----------------------------------------START Thu Apr 20 13:49:44 2017
    rm -rf tempLIB/[0-9]*.*
    ----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:44 2017
    rm -rf tempLIB/asm.[0-9]*.log
    ----------------------------------------END Thu Apr 20 13:49:44 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:44 2017
    rm -rf tempLIB/asm.gkpStore
    ----------------------------------------END Thu Apr 20 13:49:45 2017 (1 seconds)
    ----------------------------------------START Thu Apr 20 13:49:45 2017
    rm -rf tempLIB/asm.ovlStore
    ----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:45 2017
    rm -rf tempLIB/asm.[0-9]*.lay
    ----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
    ********* Finished correcting 32085 bp (using 52258890 bp).
    ********* Assembling corrected sequences.
    Assembling with average 8437 (min frag 3000) and using ovl is 100
    ----------------------------------------START Thu Apr 20 13:49:45 2017
    ln -sf LIB.fastq LIB.u.fastq
    ----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:45 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/fastqSample -U -I LIB -O LIB.longest25 -c 25 -g 4.8m -max
    Counting the number of reads in the input.
    Found 13649 bases and 2 reads in 'LIB.u.fastq'
    Sorting by length
    Extracting 1 reads into LIB.longest25.u.fastq
    ----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:45 2017
    mv LIB.longest25.u.fastq LIB.longest25.fastq
    ----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:45 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/fastqToCA -libraryname LIB -technology pacbio-corrected -type sanger -reads /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.longest25.fastq > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//LIB.longest25.frg
    ----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:45 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.spec -p asm -d LIB ovlRefBlockLength=100000000000 ovlRefBlockSize=0 useGrid=0 scriptOnGrid=0 unitigger=bogart ovlErrorRate=0.03 utgErrorRate=0.025 cgwErrorRate=0.1 cnsErrorRate=0.1 utgGraphErrorLimit=0 utgGraphErrorRate=0.025 utgMergeErrorLimit=0 utgMergeErrorRate=0.025 frgCorrBatchSize=100000 doOverlapBasedTrimming=1 obtErrorRate=0.03 obtErrorLimit=4.5 frgMinLen=3000 ovlMinLen=100 "batOptions=-RS -NS -CS" consensus=pbutgcns merSize=22 cnsMaxCoverage=1 cnsReuseUnitigs=1 gridEnginePropagateHold="pBcR_asm" LIB.longest25.frg
    ENV: SGE_TASK_ID needs to be unset, done.
    ----------------------------------------START Thu Apr 20 13:49:45 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/gatekeeper -o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore.BUILDING -T -F /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB.longest25.frg > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore.err 2>&1
    ----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
    numFrags = 1
    ----------------------------------------START Thu Apr 20 13:49:45 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/initialTrim \
    -log /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.initialTrim.log \
    -frg /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore \
    > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.initialTrim.summary \
    2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.initialTrim.err
    ----------------------------------------END Thu Apr 20 13:49:45 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:45 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/meryl -B -C -v -m 22 -memory 128000 -threads 8 -c 0 -L 2 -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore:chain -o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm-C-ms22-cm0 > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/meryl.err 2>&1
    ----------------------------------------END Thu Apr 20 13:49:46 2017 (1 seconds)
    ----------------------------------------START Thu Apr 20 13:49:46 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/estimate-mer-threshold -m /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm-C-ms22-cm0 > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm-C-ms22-cm0.estMerThresh.out 2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm-C-ms22-cm0.estMerThresh.err
    ----------------------------------------END Thu Apr 20 13:49:46 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:46 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/meryl -Dt -n 1048576 -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm-C-ms22-cm0 > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm.nmers.obt.fasta 2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm.nmers.obt.fasta.err
    ----------------------------------------END Thu Apr 20 13:49:46 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:46 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/meryl -Dt -n 1048576 -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm-C-ms22-cm0 > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm.nmers.ovl.fasta 2> /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-mercounts/asm.nmers.ovl.fasta.err
    ----------------------------------------END Thu Apr 20 13:49:46 2017 (0 seconds)
    Reset OBT mer threshold from to 1048576.
    Reset OVL mer threshold from to 1048576.
    ----------------------------------------START Thu Apr 20 13:49:46 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/overlap_partition \
    -g /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore \
    -bl 20000000 \
    -bs 0 \
    -rs 0 \
    -rl 100000000000 \
    -o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim-overlap \
    > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim-overlap/overlap_partition.err 2>&1
    ----------------------------------------END Thu Apr 20 13:49:46 2017 (0 seconds)
    Created 0 overlap jobs. Last batch '', last job ''.
    ----------------------------------------START CONCURRENT Thu Apr 20 13:49:46 2017
    ----------------------------------------END CONCURRENT Thu Apr 20 13:49:46 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:46 2017
    find -L /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim-overlap \( -name \*ovb.gz -or -name \*ovb \) -print > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.list
    ----------------------------------------END Thu Apr 20 13:49:46 2017 (0 seconds)
    ----------------------------------------START Thu Apr 20 13:49:46 2017
    /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild -obt -o /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.BUILDING -g /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore -M 8192 -L /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.list > /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.err 2>&1
    ----------------------------------------END Thu Apr 20 13:49:46 2017 (0 seconds)
    ERROR: Failed with signal HUP (1)
    ================================================================================

    runCA failed.

    ----------------------------------------
    Stack trace:

    at /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA line 1628.
    main::caFailure("failed to build the obt store", "/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/L"...) called at /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA line 3819
    main:verlapTrim() called at /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA line 6252

    ----------------------------------------
    Last few lines of the relevant log file (/projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.err):


    ----------------------------------------
    Failure message:

    failed to build the obt store

    ----------------------------------------END Thu Apr 20 13:49:46 2017 (1 seconds)
    Failed to execute /projet/maiage/save/user/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA -s /projet/maiage/save/user/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.spec -p asm -d LIB ovlRefBlockLength=100000000000 ovlRefBlockSize=0 useGrid=0 scriptOnGrid=0 unitigger=bogart ovlErrorRate=0.03 utgErrorRate=0.025 cgwErrorRate=0.1 cnsErrorRate=0.1 utgGraphErrorLimit=0 utgGraphErrorRate=0.025 utgMergeErrorLimit=0 utgMergeErrorRate=0.025 frgCorrBatchSize=100000 doOverlapBasedTrimming=1 obtErrorRate=0.03 obtErrorLimit=4.5 frgMinLen=3000 ovlMinLen=100 "batOptions=-RS -NS -CS" consensus=pbutgcns merSize=22 cnsMaxCoverage=1 cnsReuseUnitigs=1 gridEnginePropagateHold="pBcR_asm" LIB.longest25.frg
    can you help me
    thanks
    Last edited by mido1951; 04-20-2017, 06:26 AM.

  • #2
    Problem resolved

    Comment

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