Tuesday, July 1, 2014

Things to do today:
[1] Fill out the CDC form for Peru COMPLETE
[2] Fix the .spec file for assembly COMPLETE
I am trying this now (.spec file):

# original asm settings
utgErrorRate = 0.05
utgErrorLimit = 4.5

#defaults from the manual
cnsErrorRate = 0.06
cgwErrorRate = 0.10
ovlErrorRate = 0.06

merSize=14

merylMemory = 128000
merylThreads = 16

ovlStoreMemory = 8192

# grid info
useGrid = 0
scriptOnGrid = 0
frgCorrOnGrid = 0
ovlCorrOnGrid = 0

sge = -A assembly
sgeScript = -pe threads 16
sgeConsensus = -pe threads 1
sgeOverlap = -pe threads 2
sgeFragmentCorrection = -pe threads 2
sgeOverlapCorrection = -pe threads 1

#ovlMemory=8GB --hashload 0.7
ovlHashBits = 25
ovlThreads = 2
ovlHashBlockLength = 20000000
ovlRefBlockSize = 50000000

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

frgCorrThreads = 2
frgCorrBatchSize = 100000

ovlCorrBatchSize = 100000

# non-Grid settings, if you set useGrid to 0 above these will be used
merylMemory = 128000
merylThreads = 4

ovlStoreMemory = 8192

ovlConcurrency = 8

cnsConcurrency = 8

merOverlapperThreads = 3
merOverlapperSeedConcurrency = 3
merOverlapperExtendConcurrency = 3

frgCorrConcurrency = 2
ovlCorrConcurrency = 4
cnsConcurrency = 4

I took out the "stopAfter=overlapper"...because that interrupted. Not sure why we would want to do that.

[3] Write syllabus for high school student COMPLETE [7/2/2014]
[4] Look at Trpc2 data big Mac broken :[
[5] Enter grades into blackboard COMPLETE
[6] submit conservation paper COMPLETE [7/2/1/2014]
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