Re: Maker, no fasta files in output

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Re: 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 <[hidden email]> 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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Re: Maker, no fasta files in output

Carson Holt-2
Hi Anna,

The lack of results means you either had no results from SNAP or no evidence supporting results in your run. You can check for SNAP results just by looking for snap_masked features in the GFF3. For evidence, make sure you still provided the protein= and est= files even though you tunred off est2genome/protein2genome.

—Carson

On Apr 13, 2018, at 12:35 AM, Ansie Yssel <[hidden email]> 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

On 12 April 2018 at 10:16, Ansie Yssel <[hidden email]> 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


Virus-free. www.avast.com
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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
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org