Error when attempting stringtie assembly: no reference transcripts found. Using WBcel235 from NCBI

Hello, I’m trying to run stringtie as precursor to analysis with dexseq2. For my annotation file, I’m using WBcel235 downloaded from NCBI.

When I run stringtie, I get the following error:

" An error occurred with this dataset: format gtf database ce11 WARNING: no reference transcripts were found for the genomic sequences where reads were mapped! Please make sure the -G annotation file uses the same naming convention for the genome sequences."

I get the gist of this - Galaxy somehow doesn’t like the format of my annotation file. But I am not sure entirely what is wrong with it, or how to fix this. I’ve copied the first few lines of my annotation file below.

Any help would be greatly appreciated.

#gtf-version 2.2
#!genome-build WBcel235
#!genome-build-accession NCBI_Assembly:GCF_000002985.6
#!annotation-source WormBase WS283
NC_003279.8 RefSeq gene 3747 3909 . - . gene_id “CELE_Y74C9A.6”; transcript_id “”; db_xref “GeneID:353377”; gbkey “Gene”; gene “Y74C9A.6”; gene_biotype “snoRNA”; locus_tag “CELE_Y74C9A.6”;
NC_003279.8 RefSeq transcript 3747 3909 . - . gene_id “CELE_Y74C9A.6”; transcript_id “NR_001477.2”; db_x