[maker-devel] cluster error running maker

[Carson Holt]

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.lo
g

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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