berbtab2bsml

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berbtab2bsml

Aaron Buechlein
Hello,
We recently upgraded to the newest version of ergatis, but now I am
having a problem with ber specifically with the berbtab2bsml step.
During this step I receive the following error cases:

    Error executing script exit value: 255set best mvalue for
    Sampel_Ecoli_Genome.CDS.51954528.1 to 59 from best mvalue was 59 Use
    of uninitialized value in hash element at
    /research/projects/ergatis/ergatis-v2r12-cgbr1/lib/perl5//BSML/BsmlDoc.pm
    line 372, line 1. Use of uninitialized value in hash element at
    /research/projects/ergatis/ergatis-v2r12-cgbr1/lib/perl5//BSML/BsmlDoc.pm
    line 372. Can't call method "addBsmlFeatureGroup" on an undefined
    value at
    /research/projects/ergatis/ergatis-v2r12-cgbr1/lib/perl5//BSML/BsmlBuilder.pm
    line 935.

This sequence runs fine if I use the ber component from the
ergatis-v2r11b1 release.  Any thoughts?

I should also note that due to an issue I had previously, that I copied
berbtab2bsml.pl from trunk in svn and am using that version.
Thanks,

Aaron Buechlein

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Re: berbtab2bsml

Joshua Orvis
Aaron -

Could you e-mail me (not necessarily the entire user list) the BTAB file you're trying to convert as well as the execution string shown by Ergatis?

JO

On Mon, Jun 14, 2010 at 10:06 AM, Aaron Buechlein <[hidden email]> wrote:
Hello,
We recently upgraded to the newest version of ergatis, but now I am
having a problem with ber specifically with the berbtab2bsml step.
During this step I receive the following error cases:

   Error executing script exit value: 255set best mvalue for
   Sampel_Ecoli_Genome.CDS.51954528.1 to 59 from best mvalue was 59 Use
   of uninitialized value in hash element at
   /research/projects/ergatis/ergatis-v2r12-cgbr1/lib/perl5//BSML/BsmlDoc.pm
   line 372, line 1. Use of uninitialized value in hash element at
   /research/projects/ergatis/ergatis-v2r12-cgbr1/lib/perl5//BSML/BsmlDoc.pm
   line 372. Can't call method "addBsmlFeatureGroup" on an undefined
   value at
   /research/projects/ergatis/ergatis-v2r12-cgbr1/lib/perl5//BSML/BsmlBuilder.pm
   line 935.

This sequence runs fine if I use the ber component from the
ergatis-v2r11b1 release.  Any thoughts?

I should also note that due to an issue I had previously, that I copied
berbtab2bsml.pl from trunk in svn and am using that version.
Thanks,

Aaron Buechlein

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users


------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users