[maker-devel] MAKER output concerns

[Carson Holt]

Hi Jennifer,

The contig you ran with was only 52 bp in length and contained only
repetitive sequence.  Exonerate only runs if there are BLAST results that
need polishing, which there weren't.
The Snig2_XXXXXXX.maker.proteins.fasta and
Snig2_XXXXXXX.maker.transcripts.fasta were not produced because there were
no proteins or transcripts to report.

In general running on sequence shorter than 10,000 bp isn't useful.  This is
because programs like SNAP and Augustus need sequence flanking the actual
gene to make their calls, and with intron/exon structure you are unlikely to
fully capture a gene (end to end) at random in under 10kb for many
eukaryotic organisms.

If you are trying to use raw reads, you will need to assemble them first
before running MAKER.  Let us know specifically what you are trying to do,
and we can give you pointers on how to proceed.

Thanks,
Carson



From:  Jennifer Liberto <jrliberto at yahoo.com>
Reply-To:  Jennifer Liberto <jrliberto at yahoo.com>
Date:  Wednesday, 6 June, 2012 2:22 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] MAKER output concerns

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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