Re: [Gmod-ajax] error by runing prepare-refseqs.pl

[Mitch S. <mit...@be...>]

  Hi,

prepare-refseqs.pl is trying to get a reference sequence (chromosome, 
contig, scaffold, or whatever you have) out of the database.  But it's 
not getting back what it expected to get.

I randomly chose "1" as the name of the reference sequence in the 
example I sent you; I don't know how your reference sequences are 
named.  Are they chromosomes, or scaffolds, or something else?  And how 
are they named?  Is there a reference sequence called "1"?

The intended usage of prepare-refseqs.pl is for you to put a list of 
reference sequence names on the command line, as the values of the 
"--refs" argument.  For example,  if you have 3 scaffolds named scaf1, 
scaf2, and scaf3, your prepare-refseqs.pl command would look like this:

bin/prepare-refseqs.pl --conf taro.json --refs scaf1,scaf2,scaf3

In order for that to work, those sequences should already have been 
loaded into your database.

Hope this helps,
Mitch

On 09/29/2010 07:51 AM, Anja Friedrich wrote:
>
>
> ------------------------------------------------------------------------
> From: fri...@ho...
> To: gmo...@li...
> Subject: error by runing prepare-refseqs.pl
> Date: Wed, 29 Sep 2010 16:32:22 +0200
>
> Hi all,
>
> I tried to run:
>
> >bin/prepare-refseqs.pl --conf taro.json --refs 1
>
> but I get:
>
> Can't call method "name" on an undefined value at 
> bin/prepare-refseqs.pl line 72.
>
> Any idea?
>
> Cheers,
> Anja
>
>
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