maker_map_ids issue

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maker_map_ids issue

Vining, Kelly

Hello,

I’m having an issue with the id mapping part of the maker pipeline. Specifically, when I run the map_gff_ids script, I get no error messages, the script appears to run, but there are no changes to the gff file. This is one of three genomes that I’m currently annotating, and only this one is having this particular problem. I’ve tried to find any suspect characters or anything amiss with the gff file, but can’t see anything. I’ve recreated the map file multiple times, but that doesn’t fix the problem, either.

 

Here are the commands I used to make the map file and to try to map the ids to the gff:


maker_map_ids --prefix Corav.Jeff_ --justify 5  Corav.Jeff.all.gff > Corav.Jeff.all.id.map

map_gff_ids Corav.Jeff.all.id.map Corav.Jeff.all.gff

 

I’ve attached the map file itself, as well as a subset of the gff file.

 

Any help with this is much appreciated!

 

Best,

 

Kelly Vining, Ph.D.

Assistant Professor, Department of Horticulture

4071 Agriculture and Life Sciences Bldg

Oregon State University

Corvallis, Oregon 97331

 


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Corav.Jeff.all.id.map (6M) Download Attachment
Corav.Jeff.First1000Lines.gff (262K) Download Attachment
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Re: maker_map_ids issue

Carson Holt-2
Sorry for the slow reply. Your e-mail was marked as spam for some reason by the e-mail list software, and I only review the spam folder on the list server every few weeks.

The issue is the way you named the contigs in the input assembly fasta file. Example —> scaffold_1_length=72278661

If you would have just had a name like this 'scaffold_1 length=72278661’ it would have been fine (spaces separate IDs from comments in fasta format), but the equals sign becomes part of the name when you use an ‘_’ character and it creates downstream issues. The way things are ordered it looks as if you did some intermediate processing of the file (i.e. not directly from the maker run)? The original MAKER file should have replaced the ‘=‘ sign with a URI escape sequence (string starting with a % sign) to avoid this kind of issue. But the intermediate processing step appears to have removed the URI escape and changed it back to an ‘=‘ sign which because it used to separate Key=Value in GFF3 format is an illegal character to have in GFF3 (escaping is required by the format).

There is an easy way to fix this in your files though.

Run these commands on your files —> 
perl -p -e 's/_length=\d+//g’ Corav.Jeff.First1000Lines.gff > Corav.Jeff.First1000Lines.fix.gff
perl -p -e 's/_length=\d+//g’ Corav.Jeff.all.id.map > Corav.Jeff.all.id.fix.map

Then run —> 
map_gff_ids Corav.Jeff.all.id.fix.map Corav.Jeff.all.fix.gff

—Carson


On Aug 2, 2018, at 11:24 AM, Vining, Kelly <[hidden email]> wrote:

Hello,
I’m having an issue with the id mapping part of the maker pipeline. Specifically, when I run the map_gff_ids script, I get no error messages, the script appears to run, but there are no changes to the gff file. This is one of three genomes that I’m currently annotating, and only this one is having this particular problem. I’ve tried to find any suspect characters or anything amiss with the gff file, but can’t see anything. I’ve recreated the map file multiple times, but that doesn’t fix the problem, either.
 
Here are the commands I used to make the map file and to try to map the ids to the gff:

maker_map_ids --prefix Corav.Jeff_ --justify 5  Corav.Jeff.all.gff > Corav.Jeff.all.id.map
map_gff_ids Corav.Jeff.all.id.map Corav.Jeff.all.gff
 
I’ve attached the map file itself, as well as a subset of the gff file.
 
Any help with this is much appreciated!
 
Best,
 
Kelly Vining, Ph.D.
Assistant Professor, Department of Horticulture
4071 Agriculture and Life Sciences Bldg
Oregon State University
Corvallis, Oregon 97331
 
<Corav.Jeff.all.id.map><Corav.Jeff.First1000Lines.gff>_______________________________________________
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