[maker-devel] Using maker with precomputed transcript / protein alignments

[Daniel Standage]

Greetings!

I have some precomputed transcript and protein alignments that I would like
to use with Maker. I have converted them into GFF3 format (see attached
examples) and provided them to their corresponding entries (est_gff,
altest_gff, protein_gff) in the maker_opts.ctl file.

Unfortunately, Maker seems to be getting caught up on processing these GFF3
files. I've tried running Maker 2.10 as well as the development version
(checked out a few months ago--svn server isn't responding so I can't give
a precise revision number), and in both cases Maker hangs while trying to
create the GFF3 database. These are the last lines I see in STDERR when *
--debug* is set.

STATUS: Setting up database for any GFF3 input...
Calling GFFDB::new at /N/u/dstandag/Mason/local/src/maker-dev/bin/maker
line 587.

I can't find any documentation specifying any explicit requirements for the
alignment-containing GFF3 input files. Maker output uses the pretty
canonical *expressed_sequence_match*, *protein_match*, and
*match_part*features for encoding alignments, and I have used this
convention with my
input (see attached examples). I have also double-checked that my examples
are valid GFF3, so my guess is that Maker has additional
constraints/expectations for certain fields in the GFF3 files (score
column? required attributes?). Is this correct, and if so would you be able
to point me toward any related documentation I may have missed?

Many thanks.

--
Daniel S. Standage
Ph.D. Candidate
Bioinformatics and Computational Biology Program
Department of Genetics, Development, and Cell Biology
Iowa State University
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130524/f7fe3c81/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: prot-example.gff3
Type: application/octet-stream
Size: 1080 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130524/f7fe3c81/attachment-0004.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: trans-example.gff3
Type: application/octet-stream
Size: 1306 bytes
Desc: not available
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20130524/f7fe3c81/attachment-0005.obj>