Re: [AMOS-help] ace file won't open with consed

[Florent A. <flo...@gm...>]

Hi Chris,

Please keep the messages on the AMOS mailing list.

Actually, I should have told you to try to open your AFG file with 
Hawkeye, not your ACE file. Maybe try this.

But could you also look at your AFG file with a text editor and tell me 
whether it has 'RED' entries in it?

Thanks,

Florent


On 14/05/11 01:37, Chris Munk wrote:
> Hi Florent,
>
> Hawkeye doesn't seem to work either, I get this error:
>
> Opening vlv65_shortPaired_4_asm.ace... ERROR in openBank():
> WHAT: Could not open bank file, vlv65_shortPaired_4_asm.ace/RED.ifo, 
> Not a directory
> LINE: 1037
> FILE: Bank_AMOS.cc
>
> Perhaps I needed more information for amos2ace?  The only input I gave 
> was the asm.afg file.  Does it also need a data file?
>
> I apologize, I don't know very much about what I am trying to do.
>
> Thanks,
>
> Chris
>
>
>
>> 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
>>>
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