View Single Post
Old 08-12-2014, 01:05 PM   #1
Junior Member
Location: San Diego, CA

Join Date: Aug 2014
Posts: 2
Default Masurca error - assembler deleted prior to being run


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

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

AeonJeffJ is offline   Reply With Quote