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

[Waldbieser, G. <Geo...@AR...>]

I apologize but I accidentally overwrote that data when restarting a new assembly with wgs 7. I will recompile 8.0 with AS_READ_NORMAL_LEN_BITS = 15 and retry. This is the setting I have used successfully with wgs7 versions, and is likely the source of my problem. Thanks!

Geoff

From: ti...@gm... [mailto:ti...@gm...] On Behalf Of Ole Kristian Tørresen
Sent: Monday, November 18, 2013 1:47 PM
To: Walenz, Brian
Cc: Waldbieser, Geoff; wgs...@li...
Subject: Re: [wgs-assembler-users] consensus failures in wgs-8.0

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...<mailto: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





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