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

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

Alright, thanks for your help!

Best regards,
Johan Wikander

On Mon, Sep 8, 2014 at 6:48 PM, Serge Koren <ser...@gm...> wrote:

> The mer overlapper can be used to assemble the corrected PacBio data. It
> just cannot be specified for the correction step of the pipeline. The
> pipeline will assemble the corrected data with default parameters. You can
> then run any assembly parameters you prefer on the generated frg file after
> correction.
>
> Sergey
>
> On Sep 6, 2014, at 1:15 AM, Johan Wikander <ka...@gm...> wrote:
>
> Looks like that was the problem, I reran the pipeline with ovl as
> overlappar and it finished. Thanks for your help!
>
> It would be great if you added that feature to PBcR, we have hade som
> really good assemblies with mer as overlapper! Is it possible to use any of
> the output from a successful PBcR run and do a assembly with mer?
>
> Best regards,
> Johan Wikander
>
>
> On Fri, Sep 5, 2014 at 9:59 PM, Serge Koren <ser...@gm...> wrote:
>
>> The 1-overlapper directory should not contained either seeds or olaps as
>> those are not generated by PBcR (they only get generated when you're
>> assembling already corrected data using the mer overlapper which is not the
>> default and not commonly used). Looking through your output, it seems that
>> your spec file sets:
>> overlapper              =       mer
>> This option should not be set for PBcR and I think is the cause of the
>> problem. I would suggest removing that option from your spec file, removing
>> the temporary directory and trying again. I'll update the code to make this
>> option invalid for PBcR.
>>
>> Sergey
>>
>> On Sep 5, 2014, at 4:52 AM, Johan Wikander <ka...@gm...> wrote:
>>
>> 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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>>
>>
>
>