[maker-devel] Maker, no fasta files in output

[Ansie Yssel]

Dear Carson

I am subscribed to the Maker list, but for some reason I cannot post a new
topic when I view the Forum page. I hope it is OK if I email you directly?

I am trying to annotate a newly sequenced genome.
I have RNAseq data, a species specific repeat library that was generated
with REPET, the unmasked genome, and proteins from a "closley" related
species (actually not that close, but my species is the only one in its
genus, so I took proteins from another genus in the same family).

I started by following Support Protocol 1, on page 10 of the article
"Genome annotation and Curation using MAKER and MAKER-P" published in Curr
Protoc Bioinformatics 48.

The input that I used for generating the gene models (before training SNAP)
was:
the est data, my genome and the protein data. I also set est2genome=1 and
protein2genome=1. I also used Repeat masking and included my species
specific repeat library.
softmasking was set to 1
That output was used to train snap.

Then I ran maker in "Gene prediction mode" as outlined on page 11 using the
hmm file as input (and setting est2genome=0 and protein2genome=0). Repeat
masking was enabled, again using my species specific library.

I trained snap for a second time.
That output was used as input for Basic Protocol 1 on page 3 of the
aforementioned article.
Input for Basic Protocol 1 was:
The snap hmm file
my unmasked genome
the species specific repeat library
RNAseq evidence
the protein evidence from a close relative
softmasking was set to 1
est2genome=0
protein2genome=0

I collected the results as outlined on page 5 of the article.
However I noticed that there were no Fasta files.
Do you have any idea what could have gone wrong?
Can I send my log files to you? Thanks in advance for any assistance.

Kind Regards
Anna Yssel

On 12 April 2018 at 10:16, Ansie Yssel <aejysselansie at gmail.com> wrote:

> Dear Carson
>
> I am subscribed to the Maker list, but for some reason I cannot post a new
> topic when I view the Forum page. I hope it is OK if I email you directly?
>
> I am trying to annotate a newly sequenced genome.
> I have RNAseq data, a species specific repeat library that was generated
> with REPET, the unmasked genome, and proteins from a "closley" related
> species (actually not that close, but my species is the only one in its
> genus, so I took proteins from another genus in the same family).
>
> I started by following Support Protocol 1, on page 10 of the article
> "Genome annotation and Curation using MAKER and MAKER-P" published in Curr
> Protoc Bioinformatics 48.
>
> The input that I used for generating the gene models (before training
> SNAP) was:
> the est data, my genome and the protein data. I also set est2genome=1 and
> protein2genome=1. I also used Repeat masking and included my species
> specific repeat library.
> softmasking was set to 1
> That output was used to train snap.
>
> Then I ran maker in "Gene prediction mode" as outlined on page 11 using
> the hmm file as input (and setting est2genome=0 and protein2genome=0).
> Repeat masking was enabled, again using my species specific library.
>
> I trained snap for a second time.
> That output was used as input for Basic Protocol 1 on page 3 of the
> aforementioned article.
> Input for Basic Protocol 1 was:
> The snap hmm file
> my unmasked genome
> the species specific repeat library
> RNAseq evidence
> the protein evidence from a close relative
> softmasking was set to 1
> est2genome=0
> protein2genome=0
>
> I collected the results as outlined on page 5 of the article.
> However I noticed that there were no Fasta files.
> Do you have any idea what could have gone wrong?
> Can I send my log files to you? Thanks in advance for any assistance.
>
> Kind Regards
> Anna Yssel
>
>
>
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-- 
Kind Regards
A Yssel

Centre of Microbial and Plant Genetics
KU Leuven
Faculteit Bio-ingenieurswetenschappen
Kasteelpark Arenberg 20, bus 2460
B-3001 Heverlee
Belgium
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