[wgs-assembler-users] PBcR hybrid assembly overlap failure

[Johan W. <ka...@gm...>]

Hi!
The last couple of days I have struggled to complete a correction and
hybrid assembly with PacBio Long Reads, Illumina and 454 data using PBcR.

The overlapper runs for approx. 30 hrs, finishes all the overlap jobs, but
afterwards the pipeline suddenly crashes. At first I thought I had the
wrong version of java, but after trying different versions I assume that
the problem is resource exhaustion. I have tried to tweak the settings too
make the assembly less demanding, but it still crashes.

Any help or suggestions are greatly appreciated!

The system is a Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00GHz with 128GB of RAM.

I run it from the command line using the following options:
PBcR -pbCNS -length 500 -partitions 200 -l bug3-PBcR-Ill454PB9 -s
pacbio.spec -fastq ../seq/pb_051_3-filtered_subreads.fastq
genomeSize=7900000

The spec-file:
useGrid=0
scriptOnGrid=0

ovlMemory = 96
ovlStoreMemory= 96000
merylMemory = 96000


frgMinLen=65
ovlMinLen=55
overlapper=mer
merOverlapperThreads=20
batThreads=20
gkpFixInsertSizes=1
ovlHashBits=29
ovlHashBlockLength=4000000
unitigger=bogart
doChimeraDetection=normal
bogBadMateDepth=5
createACE=1
cleanup=aggressive
doToggle=1

../bug3-ShortIllumina_30X.frg
../bug3-LongIllumina_20X.frg
../bug3-454.frg

The last 10 lines of *.err: http://pastebin.com/Mi4Hhi6Y
The output from PBcR: http://pastebin.com/dH2UPqLr

Best regards,
Johan Wikander