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

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

Hi!
Thanks for your reply! The only folders I have in 1-overlapper/ are olaps/
and seeds/, both empty. The 1.out, 2.out etc. are all located in
1-overlapper/.

Output files from partition 1: http://pastebin.com/FeJj1kF6
Output files from partition 79 (last partition):
http://pastebin.com/Hqhdi2vF

Best regards,
Johan Wikander



On Thu, Sep 4, 2014 at 6:05 PM, Serge Koren <ser...@gm...> wrote:

> Hi,
>
> When you use hybrid correction, MHAP and java are not used (these are only
> used for self-correction). In the hybrid correction case, BLASR is still
> used for the alignments. The likeliest source of your error is something
> going wrong with the BLASR run on your system.
>
> Do you have any outputs in the 1-overlapper/001/* directory? Can you send
> all the output from one overlap partition (for example 1.out, 1.hash.err,
> etc) that should help diagnose what went wrong.
>
> Sergey
>
> On Sep 4, 2014, at 8:17 AM, Johan Wikander <ka...@gm...> wrote:
>
> 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
>
>
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