[maker-devel] cluster error running maker

[Carson Holt]

That is one I haven't seen before (including on large multi-megabase contigs
).

Right before the error, it will say the location of the file that is being
read.  It will terminate in  ".augustus".  Could you send that file to me?
Augustus seems to be producing something weird in it's output.

Thanks,
Carson



From:  Walter Eckalbar <weckalba at asu.edu>
Date:  Friday, 8 June, 2012 12:15 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] cluster error running maker

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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