dispersed_repeat features on rm_gff GFF3 file

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dispersed_repeat features on rm_gff GFF3 file

Santiago Revale-2
Dear Maker developers,

Can Maker deal with a "dispersed_repeat" one-level features GFF3 file provided to the rm_gff option in the control file?

We're trying to annotate a genome of a non-model Drosophila species using a previously generated GFF3 file with repeats for this species. Some months ago, Carson Holt replied to a post (https://groups.google.com/g/maker-devel/c/BhBMTF8dze8/m/y-QwJYRFAQAJ) saying that "They (repeat models) must be match/match_part two level feature for rm_gff". However, all features on our GFF3 file are 'dispersed_repeat' one-level features.

Here is how our file looks like (extract of the file for a scaffold attached as well, repeats.gff3):

##sequence-region scaffold1062|size32755 1 32755
scaffold1062|size32755  RepeatMasker    dispersed_repeat        1       47      271     -       .       Target=DNAREP1_DM 26 73;ID=2740
scaffold1062|size32755  RepeatMasker    dispersed_repeat        48      83      263     +       .       Target=Dbuz_kz3_5_36225 704 739;ID=2741
scaffold1062|size32755  RepeatMasker    dispersed_repeat        340     386     299     -       .       Target=rnd-1_family-30 19 65;ID=2742
scaffold1062|size32755  RepeatMasker    dispersed_repeat        349     387     247     +       .       Target=rnd-1_family-29 1 71;ID=2743
scaffold1062|size32755  RepeatMasker    dispersed_repeat        388     430     240     +       .       Target=rnd-5_family-3333_TIR_P 3669 3713;ID=2744
scaffold1062|size32755  RepeatMasker    dispersed_repeat        446     555     408     -       .       Target=rnd-1_family-15 16 138;ID=2745


I'm attaching both the log file and the CTL file for what it's worth (Dtest.log / maker_opts.ctl).

I wonder whether Maker handled right our rm_gff file, whether the generated output is reliable. If not, do you think modifying the GFF3 file manually duplicating each row and changing the third column to 'match/match_part' could do the trick?

Thank you very much in advance.

Best regards,
Santiago


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Dtest.log (53K) Download Attachment
maker_opts.ctl (6K) Download Attachment
repeats.gff3 (1K) Download Attachment