[maker-devel] DBD::SQLite::db do failed errors

[Carson Holt]

It’s caused by one of the characters in your GFF3 file.  For example characters NOT in the set [a-zA-Z0-9.:^*$@!+_?-|] must be escaped in GFF3 with exceptions outlined in the format spec.  You mayhave either a ‘ or a “ that must be escaped.

—Carson




> On Nov 8, 2014, at 6:58 AM, Timothy Stitt (TGAC) <Timothy.Stitt at tgac.ac.uk> wrote:
> 
> Dear Maker Support,
> 
> I'm running Maker v2.31.7 and I'm receiving lots of the following warnings/errors during the run. The errors don't seem to prevent the calculation from completing so I was just wondering how I can avoid getting them?
> 
> <snip>
> STATUS: Setting up database for any GFF3 input...
> DBD::SQLite::db do failed: near ",": syntax error at /usr/users/TGAC_ga007/stittt/Software/MAKER/UV/2.31.7/bin/../lib/GFFDB.pm line 496, <$IN> line 1.
> DBD::SQLite::db do failed: near ",": syntax error at /usr/users/TGAC_ga007/stittt/Software/MAKER/UV/2.31.7/bin/../lib/GFFDB.pm line 496, <$IN> line 2.
> DBD::SQLite::db do failed: near ",": syntax error at /usr/users/TGAC_ga007/stittt/Software/MAKER/UV/2.31.7/bin/../lib/GFFDB.pm line 496, <$IN> line 3.
> …
> </snip>
> 
> Thanks in advance,
> 
> Tim.
> ---
> Timothy Stitt PhD / Head of Scientific Computing
> The Genome Analysis Centre (TGAC)
> http://www.tgac.ac.uk/ <http://www.tgac.ac.uk/>
> 
> p: +44 1603 450378
> e: timothy.stitt at tgac.ac.uk <mailto:timothy.stitt at tgac.ac.uk>_______________________________________________
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