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

[Anja F. <fri...@ho...>]

Hi Mitch, 

thanks for the reply.
My reference sequence is lemna minor, I have it in gbk, fasta or gff format. 

Anja

Date: Wed, 29 Sep 2010 11:29:02 -0700
From: mit...@be...
To: fri...@ho...
CC: gmo...@li...
Subject: Re: [Gmod-ajax] error by runing prepare-refseqs.pl



  


    
    E-Mail-Text
  
  
    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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