Re: [wgs-assembler-users] consensus failures in wgs-8.0

[Walenz, B. <bw...@jc...>]

I’ve occasionally had trouble with moderately deep (75x) unitigs that are long (megabases) that can come from PacBio assemblies.  Yes, the occasional very deep unitigs (> 100x) caused by repeats/contaminants are now handled well.

The utgcns *.err logging now includes the depth of the unitig and the amount of sequence in contained reads:

Working on unitig 0 (0 unitigs and 88003 fragments)
  unitig 0 detected 85431 contains (70.68x, 90.86%) 2572 dovetail (7.11x, 9.14%)
    unitig 0 removing 85431 contains; processing only 2572 reads

In this case, I changed parameters (cnsReduceUnitigs=75 5 IIRC) to use only the dovetail reads for consensus.

http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=RunCA#Consensus


On 11/18/13 2:47 PM, "Ole Kristian Tørresen" <ol...@st...> wrote:

Hi Geoff and Brian.
Couldn't this be a very deep unitig? I often have trouble with this.

But when I'm looking at the code now, you seem to have fixed this, Brian.

What is the content of the last partition's .err file, Geoff?

Ole


On 18 November 2013 20:28, Walenz, Brian <bw...@jc...> wrote:
Hi, Geoff-

I just realized that my future-proofing increase of AS_READ_MAX_NORMAL_LEN_BITS from the usual default of 11 to 16 means that utgcns now needs 16gb memory to run.  With BITS=15, it needed ‘only’ 4gb.  Hard to tell if this is your problem.

b




On 11/15/13 7:34 PM, "Waldbieser, Geoff" <Geo...@AR... <http://Geo...@AR...> > wrote:

I have set up an assembly of PacBio long reads and Illumina single reads (84bp to 4kb length) with wgs-8.0. Consensus was partitioned into 122 files. After utgcnsfix errors, I have restarted wgs 3 times (after removing the 5-consensus/consensus.sh file). Each iteration fixes more jobs, but I have finally come to the last job that will not run. This data assembled in a few hours using subversion wgs_r4437.
___________________________________
Geoffrey C. Waldbieser
Research Molecular Biologist
Warmwater Aquaculture Research Unit
Agricultural Research Service
United States Department of Agriculture
Stoneville, MS 38776
(662) 686-3593





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

------------------------------------------------------------------------------
Shape the Mobile Experience: Free Subscription
Software experts and developers: Be at the forefront of tech innovation.
Intel(R) Software Adrenaline delivers strategic insight and game-changing
conversations that shape the rapidly evolving mobile landscape. Sign up now.
http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
_______________________________________________
wgs-assembler-users mailing list
wgs...@li...
https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users