Re: [AMOS-help] Celera .asm -> toAmos fails

[Adam P. <aph...@gm...>]

Hi Tom,
It does need the frg file. That explains the first error.

As for the second error, I think toAmos can only handle a single frg file as
input. You'll have to find a way to generate a single file. You should be
able to dump one from the CA gatekeeper store. I don't think simply
concatenating them together would work.

Best,
-Adam


On Sun, Apr 12, 2009 at 4:29 PM, Tom Doak <tg...@gm...> wrote:

>
> Hi,
>
> The archive seems to be down, so let me ask this question,perhaps not
> for the first time.
>
> I have used the Celera assembler to generate an assembly, and that gives
> the appearance of running fine.  However, I get the following error
> using Amos:
>
> % toAmos -a *.asm -o V5
> Have not seen sequence with id FDHZ8WC02JHQI7 at
> /usr/local/amos-2.0.8/bin/toAmos line 1073, <IN> line 3282569.
>
> I get the same error if I also provide the .frg files.
>
> % toAmos -a hol_celera-v5/9-terminator/*.asm -f *.frg -o V5
> Have not seen sequence with id FDHZ8WC02JHQI7 at
> /usr/local/amos-2.0.8/bin/toAmos line 1073, <IN> line 3282569.
>
> So..  ..  ..  ..what am I doing wrong? [I've been having a hard time
> moving old Newbler assemblies into Amos, so I decided to generate a nice
> vanilla Celera assembly.)
>
> Thanks, as always,
> Tom
>
> --
> Thomas G. Doak
> Department of Biology, Indiana University
> 1001 East Third Street
> Bloomington, IN  47405
> 812-856-0115
> http://www.indiana.edu/~lynchlab/Thomas_Doak.htm<http://www.indiana.edu/%7Elynchlab/Thomas_Doak.htm>
>
>
>
>
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