[maker-devel] <MAKER Trac Server> #28: readline() on closed filehandle GEN162 at ../est2genome.pm line 44

[Stephanie Pao]

Thanks! confirmed that /tmp filling up is the problem, this is with the
previous release of maker.

On Thu, May 7, 2009 at 5:54 PM, MAKER <maker-devel at yandell-lab.org> wrote:

> #28: readline() on closed filehandle GEN162 at ../est2genome.pm line 44
>
> -------------------------------+--------------------------------------------
>  Reporter:  sspao at ucdavis.edu  |       Owner:
>     Type:  defect             |      Status:  new
>  Priority:  major              |   Milestone:
> Component:  Code               |     Version:  0.001
>  Keywords:                     |
>
> -------------------------------+--------------------------------------------
>  Run stops with multiple readline() on closed filehandle messages and
>  finally with:
>  ------------- EXCEPTION  -------------
>  MSG: Could not open
>  /home/sspao/runvv4/theVoid.vvgrm.seq/vvgrm.seq.1.dicotvtvvEST.blastn: No
>  such file or directory
>  STACK Bio::Root::IO::_initialize_io /home/sspao/mod/Bio/Root/IO.pm:273
>  STACK Bio::Root::IO::new /home/sspao/mod/Bio/Root/IO.pm:213
>  STACK Bio::SearchIO::new /home/sspao/mod/Bio/SearchIO.pm:135
>  STACK Bio::SearchIO::new /home/sspao/mod/Bio/SearchIO.pm:167
>  STACK Widget::blastn::parse
>  /home/sspao/apps/maker/bin/../lib/Widget/blastn.pm:53
>  STACK main::blastn /home/sspao/apps/maker/bin/maker:1290
>  STACK toplevel /home/sspao/apps/maker/bin/maker:336
>
>  --------------------------------------
>
>  Other relevant information:
>  the second file (/vvgrm.seq.1.dicotvtvvEST.blastn) is not found in theVoid
>  directory.
>  this error is repeatable presently, however a previous run did not appear
>  to have this problem.
>
> --
> Ticket URL: <http://malachite.genetics.utah.edu/projects/maker/ticket/28>
> MAKER <http://www.yandell-lab.org/maker>
> MAKER annotation pipline
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