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?
THANKS
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 inID=
. And this is not always the case in your file.fin swimmer
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...
Is your gff3 file the output of
gff3_merge
without filtering? It appears that you have filtered to keep onlysource
(i.e., 2nd column) asmaker
. Perhaps you need to redogff3_merge
without filtering it's output to input into JBrowse, as some features of the gff3 file seem to be missing.Not sure that I understand... Yes, I did:
gff3_merge -d logfile
I did not do any filtering while merging.
Hi all, I highly want to know how to deal with the error "GFF3 parse error: some features reference other features that do not exist in the file (or in the same '###' scope)". I also depressed by the same bug. Any solution? Thanks.
Hi, As people below answered me - you have to find the problem with the file, either using a script kindly provided below, or manually. I ended up opening the file with R tools and correcting it semi-manually.