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  • Masurca error - assembler deleted prior to being run

    Greetings,

    I have installed Masurca-2.2.1 following the installation process documented on the UMD Masurca website.

    During a run initiated by the generated assembler.sh the CA subdirectory is recursively deleted prior to the script calling runCA:

    assembler.sh:
    Line 124: log 'Celera Assembler'
    Line 125: rm -rf CA
    ...
    Line 137: runCA ovlMerThreshold=$ovlMerThreshold gkpFixInsertSizes=0
    ovlMerSize=30 cgwErrorRate=0.25 ovlMemory=4GB jellyfishHashSize=$JF_SIZE
    ovlRefBlockSize=$ovlRefBlockSize ovlHashBlockSize=$ovlHashBlockSize
    ovlCorrBatchSize=$ovlCorrBatchSize stopAfter=consensusAfterUnitigger
    unitigger=bog -p genome -d CA merylThreads=16 frgCorrThreads=1
    frgCorrConcurrency=16 cnsConcurrency=16 ovlCorrConcurrency=16 ovlCon
    currency=16 ovlThreads=1 doFragmentCorrection=0 doOverlapBasedTrimming=0
    doExtendClearRanges=0 ovlMerSize=30 superReadSequences_shr.frg 1>
    runCA1.out 2>&1

    Is runCA and the rest of CA/Linux-amd64/bin supposed to be installed
    somewhere else?

    Thanks

  • #2
    Turns out you shouldn't run Masurca from the asme directory where it is installed. Thanks to a pointer from UMD.

    Comment


    • #3
      thanks for sharing
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