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

[Serge K. <ser...@gm...>]

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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>> 
>> 
> 
>