[maker-devel] New assembly annotation

[andrei.kiselev at lrsv.ups-tlse.fr]

Hello.
I'have recently got a new genome assembly using PacBio of oomycete Aphanomyces. 
I used MAKER in the manner as described here https://groups.google.com/forum/#!searchin/maker-devel/new$20assembly%7Csort:date/maker-devel/Xo5YbWgNwFw/KstkmXYYAgAJ (https://groups.google.com/forum/#!searchin/maker-devel/new%2420assembly%7Csort:date/maker-devel/Xo5YbWgNwFw/KstkmXYYAgAJ)

After first run I got the number of transcripts slightly higher than were in gff file of previous version of genome. Then I run the second MAKER with new gff file in option pred_gff + augustus trained for my species. As a result I got only half of the transcripts from initial gff.

Is there something that I could overlook running MAKER? Attached is control file of the last run.

Thank you in advance.
Andrei
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