GFF file not recognized

[domenico-simone]

Hello,

I keep on getting a "GFF file is not in GFF3 file format!" error while running samtools mpileup + ivar variants. This is the command line:

samtools mpileup \
-aa -A -B \
--reference scaffolds.fasta \
test.bam | \
ivar variants \
-p ivar.out \
-r scaffolds.fasta \
-g test.gff

with these tool versions:

samtools v1.12
ivar v1.3.1

The gff file is output by Prokka (I have double-checked it's tab separated, and also have changed the source field from Prodigal to Genbank in case iVar is picky about source values). I have uploaded the files used in the command line here. What could be the issue?

Thank you for your support!

Domenico

[gkarthik]

Hello @domenico-simone , seems like the GFF file has a bunch of fasta sequences below. I removed those lines. Could you please check with this GFF file where I removed the lines? Thanks!

test.txt

[carlottaolivero]

Hi @gkarthik , I have the same problem with gff3 file for SARS-CoV-2 from NCBI.

The error message is the follow: "GFF file is not in GFF3 file format!" What is the problem here?
sequence.gff3.txt

If I try to skip at all this point (without adding "-g", it gives me "A GFF file containing the open reading frames (ORFs) has not been provided. Amino acid translation will not be done.".
I am not interested in the AA translation at the moment, is it possible to skip it?

Many thanks for your support,
Carlotta

[gkarthik]

Hello Carlotta, the message only indicates that you won't be able to do amino acid translation but you should be able to get the intra host variants without the translation.

I'll take a look at the GFF3 file you provided. Thanks!

[carlottaolivero]

Hi @gkarthik , I have managed to solve the problem (in the sense that the message "GFF file is not in GFF3 file format!" didn't appeared) downloading another gff3 file from a different website, not NCBI. Attached is the new file:
sequence.sorted.gff3.txt

Thanks a lot!!
.

[sebasfelt]

Hello,

I unfortunately have the same problem than above. Created a gff3 file through NCBI (https://www.ncbi.nlm.nih.gov/nuccore/KT992094.1?report=gbwithparts&log$=seqview) but I am getting the "GFF file is not in GFF3 file format!" error message. What could be the issue? Thanks for your time and help!!
RSVA2.txt

[sebasfelt]

Found a solution! Just used http://genometools.org/cgi-bin/gff3validator.cgi which helped me to find issue with file.