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

[Carson Holt]

Actually that is not a GFF3 file. It appears to be GTF which is structured different from GFF3. You would need to convert to GFF3.

You can try the sequence ontology converter here —> http://www.sequenceontology.org/cgi-bin/converter.cgi <http://www.sequenceontology.org/cgi-bin/converter.cgi>

Unfortunately it will not likely be a painless process as GTF files vary so much between sources that one GTF file might not actually be compatible with another GTF file, so you may have to spend some time editing the file for the converter to work.

—Carson




> On Nov 10, 2014, at 6:59 AM, Timothy Stitt (TGAC) <Timothy.Stitt at tgac.ac.uk> wrote:
> 
> Thanks Carson.
> 
> I checked the *.gff files for ' and " symbols. I only observed a bunch of " in one of the files as follows:
> 
> scaffold16677 exonerate:protein2genome:local
> gene 128238
> 128710 339
> - .
> gene_id 0 ; sequence Lus10000040|PACid:23139618 ; gene_orientation +
> scaffold16677 exonerate:protein2genome:local
> cds 128645
> 128710 .
> - .
> scaffold16677 exonerate:protein2genome:local
> exon 128645
> 128710 .
> - .
> insertions 0 ; deletions 0
> scaffold16677 exonerate:protein2genome:local
> splice5 128643
> 128644 .
> - .
> intron_id 1 ; splice_site "GT"
> scaffold16677 exonerate:protein2genome:local
> intron 128552
> 128644 .
> - .
> intron_id 1
> scaffold16677 exonerate:protein2genome:local
> splice3 128552
> 128553 .
> - .
> intron_id 0 ; splice_site "AG"
> scaffold16677 exonerate:protein2genome:local
> cds 128442
> 128551 .
> - .
> scaffold16677 exonerate:protein2genome:local
> exon 128442
> 128551 .
> - .
> insertions 0 ; deletions 0
> scaffold16677 exonerate:protein2genome:local
> splice5 128440
> 128441 .
> - .
> intron_id 2 ; splice_site "GT"
> scaffold16677 exonerate:protein2genome:local
> intron 128362
> 128441 .
> - .
> intron_id 2
> scaffold16677 exonerate:protein2genome:local
> splice3 128362
> 128363 .
> - .
> intron_id 1 ; splice_site "AG"
> 
> Would these "GT", "AG" etc. strings cause the problem? If so, how should I change them to be correct?
> 
> Thanks,
> 
> 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>
> 
> From: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Date: Sunday, 9 November 2014 00:13
> To: Timothy Stitt <timothy.stitt at tgac.ac.uk <mailto:timothy.stitt at tgac.ac.uk>>
> Cc: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: Re: [maker-devel] DBD::SQLite::db do failed errors
> 
> It’s caused by one of the characters in your GFF3 file.  For example characters NOT in the set [a-zA-Z0-9.:^*$@!+_?-|] must be escaped in GFF3 with exceptions outlined in the format spec.  You mayhave either a ‘ or a “ that must be escaped.
> 
> —Carson
> 
> 
> 
> 
>> On Nov 8, 2014, at 6:58 AM, Timothy Stitt (TGAC) <Timothy.Stitt at tgac.ac.uk <mailto:Timothy.Stitt at tgac.ac.uk>> wrote:
>> 
>> Dear Maker Support,
>> 
>> I'm running Maker v2.31.7 and I'm receiving lots of the following warnings/errors during the run. The errors don't seem to prevent the calculation from completing so I was just wondering how I can avoid getting them?
>> 
>> <snip>
>> STATUS: Setting up database for any GFF3 input...
>> DBD::SQLite::db do failed: near ",": syntax error at /usr/users/TGAC_ga007/stittt/Software/MAKER/UV/2.31.7/bin/../lib/GFFDB.pm line 496, <$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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> 

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