[maker-devel] Fewer genes in MAKER 2.31.3

[Carson Holt]

Nothing in the scoring or gene selection has changed.

Changes are:
Fix trnascan naming so codon is included in name
Fix fgenesh parsing when used with correct_est_fusion
Fix final ID bug when '/' character used in GFF3 input ID.
Fix a start codon issue that could come up under when the right set of
parameters were used (primarily correct_est_fusion and protein2genome).


If you can provide both gff3 outputs form comparison, I could probably tell
you why.  Set up both runs to make sure that settings are indeed identical.

--Carson

From:  Shaun Jackman <sjackman at gmail.com>
Reply-To:  Shaun Jackman <sjackman at gmail.com>
Date:  Monday, May 5, 2014 at 6:09 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Fewer genes in MAKER 2.31.3

Hi, Carson. I’m annotating a 6 Mbp plant mitochondrial genome using GenBank
coding nucleotide and protein sequences from related species. I’m seeing 50
genes annotated using MAKER 2.31, and 37 genes annotated using MAKER 2.31.3.
The missing genes look good based on the evidence. I see protein_match
evidence in the 2.31.3 GFF file, but no resulting gene and mRNA.

Is there a ChangeLog indicating the changes from 2.31 to 2.31.3? Do you know
of a change that might cause this? What information can I give you that
would help debug this? My maker_opts.ctl file follows.

Cheers,
Shaun
#-----Genome (these are always required)
genome=pg29mt-concat.fa #genome sequence (fasta file or fasta embeded in
GFF3 file)
organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic

#-----EST Evidence (for best results provide a file for at least one)
est=cds_na.fa #set of ESTs or assembled mRNA-seq in fasta format

#-----Protein Homology Evidence (for best results provide a file for at
least one)
protein=cds_aa.fa #protein sequence file in fasta format (i.e. from mutiple
oransisms)

#-----Repeat Masking (leave values blank to skip repeat masking)
model_org=picea #select a model organism for RepBase masking in RepeatMasker
rmlib=rmlib.fa #provide an organism specific repeat library in fasta format
for RepeatMasker
repeat_protein=/usr/local/opt/maker/libexec/data/te_proteins.fasta #provide
a fasta file of transposable element proteins for RepeatRunner

#-----Gene Prediction
est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no

protein2genome=1 #infer predictions from protein homology, 1 = yes, 0 = no
trna=1 #find tRNAs with tRNAscan, 1 = yes, 0 = no

#-----External Application Behavior Options
cpus=4 #max number of cpus to use in BLAST and RepeatMasker (not for MPI,
leave 1 when using MPI)

#-----MAKER Behavior Options
est_forward=1 #map names and attributes forward from EST evidence, 1 = yes,
0 = no
single_exon=1 #consider single exon EST evidence when generating
annotations, 1 = yes, 0 = no
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