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Old 08-12-2014, 12:05 PM   #1
AeonJeffJ
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Location: San Diego, CA

Join Date: Aug 2014
Posts: 2
Default 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
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Old 08-12-2014, 04:37 PM   #2
AeonJeffJ
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Default

Turns out you shouldn't run Masurca from the asme directory where it is installed. Thanks to a pointer from UMD.
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Old 06-05-2018, 11:41 PM   #3
aylazander
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thanks for sharing
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