Error with GFF input file when using agat_sp_add_introns.pl and agat_convert_sp_gxf2gxf.pl

[mspopecki]

Hello!

I'm trying to add introns to my GFF file using the command agat_sp_add_introns.pl --gff MY.gff --out MY_introns.gff

Unfortunately, I got the below error. I also tried using the commands agat_convert_sp_gff2gtf.pl and agat_convert_sp_gxf2gxf.pl to remake the GFF file in case there were any issues, and also got the same error. How would you recommend proceeding? Thank you!!

    We found 1861 terms that are sequence_feature or is_a child of it.

--------------------------------- parsing file --------------------------------- => Number of line in file: 227414 => Number of comment lines: 350 => Fasta included: No => Number of features lines: 227064 => Number of feature lines with 1 fields (while 9 expected): 1 => Number of feature type (3rd column): 8

• Level1: 1 => gene
• level2: 1 => mRNA
• level3: 6 => three_prime_UTR five_prime_UTR exon CDS stop_codon start_codon

• unknown: 0 => => Version of the Bioperl GFF parser selected by AGAT: 3 Parsing: 99% [=====================================================*]0m00s Left ------------- EXCEPTION ------------- MSG: [}] does not look like GFF3 to me STACK AGAT::BioperlGFF::_from_gff3_string /PATH/lib/perl5/site_perl/AGAT/BioperlGFF.pm:634 STACK AGAT::BioperlGFF::from_gff_string /PATH/lib/perl5/site_perl/AGAT/BioperlGFF.pm:449 STACK AGAT::BioperlGFF::next_feature /PATH/lib/perl5/site_perl/AGAT/BioperlGFF.pm:406 STACK AGAT::OmniscientI::slurp_gff3_file_JD /PATH/lib/perl5/site_perl/AGAT/OmniscientI.pm:384 STACK toplevel /PATH/bin/agat_sp_add_introns.pl:68

[Juke34]

One line of your file contain only the value/character } Either a line contain 9 tabulated column or start by # and contains what ever you want. You are not in any of these cases. Open your file and check what is going on.