From: Florent A. <flo...@gm...> - 2011-05-13 00:09:00
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Hi Chris, Did you try to visualize this file with the AMOS visualization tool, Hawkeye? Does it error with Hawkeye or otherwise misplace reads? Florent On 13/05/11 03:01, Chris Munk wrote: > Hello, > > I am having trouble opening an ace file with consed. > > Using Velvet version 1.102, I tried using the options to generate > asm.afg files (-read_trkg yes -amos_file yes ), then running amos2ace > to make an ace file. When I try opening the ace file with consed, I > get an error message like: > >> exception thrown: ace file error detected from source file >> parseAceFile.cpp at 2036 >> Error in file vlv65_shortPaired_4_asm.ace at line 2871277. Line: >> BS -10 -10 165322629 >> >> Should be BS<start #> <end #> <readname> but<start #> wasn't numeric >> >> ace file: vlv65_shortPaired_4_asm.ace >> Version 20.70 (beta) (110506) >> ace file error detected from source file parseAceFile.cpp at 2036 >> Error in file vlv65_shortPaired_4_asm.ace at line 2871277. Line: >> BS -10 -10 165322629 >> >> Should be BS<start #> <end #> <readname> but<start #> wasn't numeric >> ace file = vlv65_shortPaired_4_asm.ace >> ace file error detected from source file parseAceFile.cpp at 2036 >> Error in file vlv65_shortPaired_4_asm.ace at line 2871277. Line: >> BS -10 -10 165322629 >> >> Should be BS<start #> <end #> <readname> but<start #> wasn't numeric >> ace file = vlv65_shortPaired_4_asm.ace >> Version 20.70 (beta) (110506) > consed seems to be having trouble with the negative coordinates. > > > Is this a problem with amos2ace? > > Is there a better way to make an ace file from a Velvet assembly? > > Thank you. > > Chris Munk > > ***** > A. Christine Munk > JGI-LANL sequence finisher > Los Alamos National Laboratory > Genome Science (B-6) > phone: 505-667-0779 > > ------------------------------------------------------------------------------ > Achieve unprecedented app performance and reliability > What every C/C++ and Fortran developer should know. > Learn how Intel has extended the reach of its next-generation tools > to help boost performance applications - inlcuding clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > AMOS-help mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-help |