[maker-devel] MAKER output concerns

[Jennifer Liberto]

To whom this may concern,
 
I am brand new to MAKER and I am concerned about the output
files that I am receiving.  My
partner and I were able to run the dpp test with no errors, all the files and
directories were accounted for.  However, when we tried to run it on our own small dataset of 5 genes,
and a surfperch genome, we were missing 2 files in the output of every contig:
 
Snig2_XXXXXXX.maker.proteins.fasta
Snig2_XXXXXXX.maker.transcripts.fasta
 
When I look at the run log for each of the contigs, I see that
blastx, blastn, tblastx, augustus, snap, and repeatrunner were called but not
exonerate; I have attached a sample run log with this post. Also, our gff files
contain only short 52 bp repeat sequences (I have attached one of these here as
well in a .txt format) and looks nothing like the gff file we received in out
dpp test.  If you could give any
pointers or hints as to why we are not receiving the two files, why exonerate
is not being called, and why our gff files contain only uniformly small repeat
sequences, the help would be greatly appreciated.  
 
Thank you for your time,
Jennifer Liberto
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