[wgs-assembler-users] Issue with overlap prep during PBcR run

[Stephanie D'S. <sd...@bu...>]

#PBcR options
genomeSize=2100000000
maxCoverage=50
maxGap = 1500
blasr=-noRefineAlign -advanceHalf -noSplitSubreads -minMatch 10 -minPctIdentity 70 -bestn 24 -nCandidates 24

# original asm settings
merSize = 14

#merylMemory = 128000
#merylThreads = 32

# ovlStoreMemory = 8192

# grid info


ovlHashBits = 27
# ovlThreads = 32
ovlHashBlockLength = 6000000000
ovlRefBlockLength  = 1000000000
ovlRefBlockSize = 0


# for mer overlapper
merCompression = 1
merOverlapperSeedBatchSize = 500000
merOverlapperExtendBatchSize = 250000

#frgCorrThreads = 2
#frgCorrBatchSize = 100000

#ovlCorrBatchSize = 100000







#akshaya's
ovlStoreMemory=256000
ovlThreads=45
ovlCorrConcurrency=20
ovlCorrBatchSize=3000000

merylMemory=256000
merylThreads=45

frgCorrThreads=48
frgCorrBatchSize=3000000
frgCorrConcurrency=20



/archive/Steph/lane1.frg
/archive/Steph/lane2.frg
/archive/Steph/lane3.frg