Re: [wgs-assembler-users] huge assembly with thousands of MergeScaffoldsAggressive iterations

[kuhl <ku...@mo...>]

Hello Brian,

thanks for the help. Fortunately, in step 7-4 cgw successfully finished
MergeScaffoldsAggressive after iteration 564.

Best wishes, Heiner


On Mon, 30 Jul 2012 12:44:16 -0400, "Walenz, Brian" <bw...@jc...>
wrote:
> Hi, Heiner-
> 
> Working backwards through your email:
> 
> We've also noticed the 'large scaffold gets lots of little contigs
added'
> problem.  This seems to be dominating our run time.  I'm working on this
> problem at the moment.  Our previous solution was basically what you
did:
> let it run until we get impatient, then kill it and restart from the
next
> checkpoint label.
> 
> The CVS tip has a slight improvement in cgw, committed around the 20th. 
I
> hope to have much more within the next week.
> 
> You can ignore the mates in the library, but not the reads.  To ignore
the
> mates, simply delete the mate link from gkpStore.  At the very bottom of
> the
> 'gatekeeper' page on the wiki is 'allfragsunmated' which will remove the
> mate link from all reads in a single library.  This is a destructive
> operation!  Save a backup of gkpStore/fnm and gkpStore/fpk if you want
to
> revert.  (these two files store metadata for long and short fragments
> resp.)
> 
>
http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Gatekeep
> er
> 
> FYI- The 5-consensus-insert-size directory has a plot of the insert size
> histogram for each library.  These are based on unitigs, and so the 20k
> library might not be represented well.  tigStore (the command) can also
> analyze mate pairs for contigs/unitigs in the store with -d matepair.
> 
> b
> 
> 
> On 7/26/12 5:39 PM, "kuhl" <ku...@mo...> wrote:
> 
>> Hi Brian et al.,
>> 
>> I am currently running a huge assembly with CA7 (2.5Gb 30x Illumina +
>> 454,
>> cgw takes 150-300Gb RAM). It is now in step 7-2 and I have just stopped
>> cgw
>> at MergeScaffoldsAggressive iteration 1641 and restarted it at
>> ckp08-2SM. I
>> did this also in 7-0 at iteration 2xxx. Now I am not sure, if I should
>> maybe rerun scaffolding without 20 kb mate pairs, which I think are
>> responsible for this mess. So I have two questions:
>> 
>> How can I convince cgw to ignore a certain library without doing steps
>> 0-5
>> again? 
>> 
>> Is there a rule of thumb, when MergeScaffoldsAggressive should be
>> stopped?
>> 
>> 
>> In my case it looks like cgw is only very slightly progressing with
each
>> iteration and there is one large scaffold that is growing more and
>> more...
>> 
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 32 at idx 3355 out of
>> 60498
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 19 at idx 8774 out of
>> 60498
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 55 at idx 286 out of
60500
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 32 at idx 3355 out of
>> 60500
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 16 at idx 10594 out of
>> 60500
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 7 at idx 20348 out of
>> 60500
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 55 at idx 286 out of
60489
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 32 at idx 3355 out of
>> 60489
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 19 at idx 8773 out of
>> 60489
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 9 at idx 16854 out of
>> 60489
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 55 at idx 286 out of
60486
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 32 at idx 3355 out of
>> 60486
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 16 at idx 10593 out of
>> 60486
>> ExamineUsableSEdges()- maxWeightEdge from 0 to 7 at idx 20428 out of
>> 60486
>> 
>> Regards, Heiner
>> 
>>
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-- 
---------------------------------------------------------------
Dr. Heiner Kuhl
MPI Molecular Genetics            Tel:   + 49 + 30 / 8413 1551
Next Generation Sequencing        
Ihnestrasse 73                    email: ku...@mo...
D-14195 Berlin                    http://www.molgen.mpg.de
---------------------------------------------------------------