[maker-devel] cluster error running maker

[Walter Eckalbar]

Hi Carson,

I will try this as well to get my 2.25 version of maker running.

I have hit another error on my local machine.  This only seems to come up
with scaffolds > 5Mbp.  And am hitting this same error with version 2.10
and 2.25.

  [0] = Make
  [1] = 0
  [2] = additional
  [3] = prediction
  [4] = runs.
dead in Widget::augustus::parse_gene unknown feature type:additional
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:GL343198.1

Do you have a suggestion for this one?

Thanks for all your help,

Walter


On 8 June 2012 05:45, Carson Holt <carsonhh at gmail.com> wrote:

> Here is a patch for the Proc::ProcessTable module in Perl.  Thanks to
> Volker Brendel at Iowa State for this one.
>
> Apply in Proc-ProcessTable-0.45 directory with --> patch -np1 <
> 646785-and-handle-Hex29.patch
>
> This adds to previously posted 646785 patch.  At least on some
> systems, commands can contain "(" and ")".  See comments in the code.
>
>
> Download Proc-ProcessTable-0.45 to reinstall before applying the patch.
>
>
> I'll also send you a link in a separate e-mail to download a maker 2.26
> test version where I've replaced Proc::ProcessTable with a different module
> because of the failure on some systems.
>
> Thanks,
> Carson
>
>
>
>
> From: Walter Eckalbar <weckalba at asu.edu>
> Date: Thursday, 7 June, 2012 4:40 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] cluster error running maker
>
> Hi everyone,
>
> I have been retrying installing maker on our university cluster,
> everything seems to install correctly, but when I run maker I find the
> following error message:
>
> Ran into unknown state (hex char: 29) at
> /home/weckalba/RNAseq/maker/lib/File/..//Proc/Signal.pm line 94.
> A data structure will be created for you at:
> /scratch/weckalba/Maker/genome.maker.output/genome_datastore
>
> To access files for individual sequences use the datastore index:
>
> /scratch/weckalba/Maker/genome.maker.output/genome_master_datastore_index.log
>
> DBD::SQLite::db do failed: disk I/O error at
> /home/weckalba/RNAseq/maker/bin/../lib/GFFDB.pm line 88.
> DBD::SQLite::db selectcol_arrayref failed: disk I/O error at
> /home/weckalba/RNAseq/maker/bin/../lib/GFFDB.pm line 90.
> DBD::SQLite::db do failed: disk I/O error at
> /home/weckalba/RNAseq/maker/bin/../lib/GFFDB.pm line 92.
> DBD::SQLite::db do failed: disk I/O error at
> /home/weckalba/RNAseq/maker/bin/../lib/GFFDB.pm line 161.
>
>
> Seems to have something to do with permissions and DBD::SQLite.  I
> installed DBD::SQLite on my own home directories and routed the perl path
> to it (and other CPAN installs in the same directories).
>
> I was wondering if anyone ever encountered this before and knew a work
> around.  The admins for our cluster are unfortunately very slow to respond.
>
> Thanks
>
> Walter
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>
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