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

[Timothy Stitt (TGAC)]

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/


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/

p: +44 1603 450378
e: timothy.stitt at tgac.ac.uk<mailto:timothy.stitt at tgac.ac.uk>
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