Question: Maker Gff3 file issues
gravatar for alslonik
11 weeks ago by
alslonik70 wrote:

Hi community,

This is really a technical question, I hope it is OK to post it here...

I am trying to import the gff3 file from Maker to my Jbrowse to view the annotations. I am using the maker2jbrowse script and getting constant errors. There are no indications that Maker did produce a problematic file, the logs are w/o errors. Still I am getting this output:

GFF3 parse error: some features reference other features that do not exist in the file (or in the same '###' scope).

Head of my gff3 file:

##gff-version 3
Chr6    .   contig  1   41368575    .   .   .   ID=Chr6;Name=Chr6
Chr6    maker   gene    9418414 9419484 .   -   .   ID=maker-Chr6-exonerate_protein2genome-gene-94.9;Name=maker-Chr6-exonerate_protein2genome-gene-94.9
Chr6    maker   mRNA    9418414 9419484 594 -   .   ID=maker-Chr6-exonerate_protein2genome-gene-94.9-mRNA-1;Parent=maker-Chr6-exonerate_protein2genome-gene-94.9;Name=maker-Chr6-exonerate_protein2genome-gene-94.9-mRNA-1;_AED=0.31;_eAED=0.43;_QI=0|0|0|1|0|0|2|0|197
Chr6    maker   exon    9418414 9418727 .   -   .   ID=maker-Chr6-exonerate_protein2genome-gene-94.9-mRNA-1:exon:382;Parent=maker-Chr6-exonerate_protein2genome-gene-94.9-mRNA-1
Chr6    maker   exon    9419205 9419484 .   -   .   ID=maker-Chr6-exonerate_protein2genome-gene-94.9-mRNA-1:exon:381;Parent=maker-Chr6-exonerate_protein2genome-gene-94.9-mRNA-1
Chr6    maker   CDS 9419205 9419484 .   -   0   ID=maker-Chr6-exonerate_protein2genome-gene-94.9-mRNA-1:cds;Parent=maker-Chr6-exonerate_protein2genome-gene-94.9-mRNA-1
Chr6    maker   CDS 9418414 9418727 .   -   2   ID=maker-Chr6-exonerate_protein2genome-gene-94.9-mRNA-1:cds;Parent=maker-Chr6-exonerate_protein2genome-gene-94.9-mRNA-1
Chr6    maker   gene    9469345 9471102 .   -   .   ID=maker-Chr6-exonerate_protein2genome-gene-94.15;Name=maker-Chr6-exonerate_protein2genome-gene-94.15
Chr6    maker   mRNA    9469345 9471102 588 -   .   ID=maker-Chr6-exonerate_protein2genome-gene-94.15-mRNA-1;Parent=maker-Chr6-exonerate_protein2genome-gene-94.15;Name=maker-Chr6-exonerate_protein

The file is 2.1 Gb large. How do I check for the validity of the file and more importantly how do I fix the file in case it is not valid?


ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by alslonik70

Hello alslonik ,

I don't know Maker or worked with Jbrowse. But the error message is quite clear to me. In a ggf3 file the value given in Parent= link to an entry in the file where you have the same value in ID=. And this is not always the case in your file.

fin swimmer

ADD REPLYlink written 11 weeks ago by finswimmer9.8k

Thanks, finswimmer, I understand what you mean. The question is how do I deal with this? Are there any ways to fix this in a gff3 file? Also, maybe it is a matter of sorting the file correctly? I have never worked with gff3 before, hence the questions...

ADD REPLYlink written 11 weeks ago by alslonik70

Is your gff3 file the output of gff3_merge without filtering? It appears that you have filtered to keep only source (i.e., 2nd column) as maker. Perhaps you need to redo gff3_merge without filtering it's output to input into JBrowse, as some features of the gff3 file seem to be missing.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by jean.elbers510

Not sure that I understand... Yes, I did:

gff3_merge -d logfile

I did not do any filtering while merging.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by alslonik70
gravatar for Juke-34
11 weeks ago by
Juke-341.8k wrote:

I got often this kind of problem using MAKER on our cluster (LSF + openMPI). I never succeeded to find where the problem is coming from. I end up with some parent features missing or duplicated features. I have developed a library to standardise any kind of GTF/GFF that fix all kind of problem and produce a full gff3 output.

Clone this repository and install it: Then just do: -gff input.gff -o output.gff You can even add this option -v 1 to have a look at what problem is corrected.

ADD COMMENTlink written 11 weeks ago by Juke-341.8k

WOW. Thanks, Juke-34 I am going to try it. Al least I am not the only one!!! And I ran Maker with open MPI too... Thank you very much!

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by alslonik70

Hi, an update. Your script throws me a list of awful errors and no output:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: OBO File Format Error - 
Cannot find tag format-version and/ default-namespace . These are required header.

STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/
STACK: Bio::OntologyIO::obo::_header /usr/share/perl5/Bio/OntologyIO/
STACK: Bio::OntologyIO::obo::parse /usr/share/perl5/Bio/OntologyIO/
STACK: BILS::Handler::GXFhandler::try {...}  /home/alex/bin/GAAS/annotation/BILS/Handler/
STACK: Try::Tiny::try /usr/share/perl5/Try/
STACK: BILS::Handler::GXFhandler::_handle_ontology /home/alex/bin/GAAS/annotation/BILS/Handler/
STACK: BILS::Handler::GXFhandler::slurp_gff3_file_JD /home/alex/bin/GAAS/annotation/BILS/Handler/

Let's continue without feature-ontology information.
No data retrieved among the feature-ontology.
=>GFF version parser used: 3

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: [  -   .   ID=Chr7:hsp:23258:;Parent=Chr7:hit:14758:;Target=gb|OWM91437.1| 350 575;Gap=M85 I4 M44 I4 M62 I4 M5 D7 M18] does not look like GFF3 to me
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/
STACK: Bio::Tools::GFF::_from_gff3_string /usr/share/perl5/Bio/Tools/
STACK: Bio::Tools::GFF::from_gff_string /usr/share/perl5/Bio/Tools/
STACK: Bio::Tools::GFF::next_feature /usr/share/perl5/Bio/Tools/
STACK: BILS::Handler::GXFhandler::slurp_gff3_file_JD /home/alex/bin/GAAS/annotation/BILS/Handler/

Does this mean that the file is corrupted? What do you think it means about my Maker run? Thanks again...

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by alslonik70

Sounds like a line in your file is not 9 columns. That cannot be fixed by the tool. You have to find this line manualy ( the one cited in the error) and fix it. I have already seen that... it’s rare but few times one line is split and written over 2 lines ...

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Juke-341.8k
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