I have a local Galaxy instance running and I am attempting to use a chloroplast genome as a custom genome for a class demonstration. I am using a FASTA nucleotide file and its corresponding GFF file, directly downloaded from NCBI and unmodified. The error message I get when trying to add the GFF data to my visualization in Trackster is:
Input error: Chromosome NC_007898.3 found in your input file but not in your genome file.
However, when I examine the files they seem to be completely standard, and the identifier NC_007898.3 is used throughout both. I have viewed the help regarding Genome ID mismatches (found in another thread on BioStars) and checked the obvious. Any other suggestions?
File heads look like this:
>gi|544163592|ref|NC_007898.3| Solanum lycopersicum chloroplast, complete genome
#!processor NCBI annotwriter
##sequence-region NC_007898.3 1 155461
NC_007898.3 RefSeq region 1 155461 . + . ID=id0;Dbxref=taxon:4081;Is_circular=true;Name=Pltd;authority=Lycopersicon esculentum (L.);common=tomato;cultivar=LA3023;gb-synonym=Lycopersicon esculentum;gbkey=Src;genome=chloroplast;mol_type=genomic DNA;old-name=Lycopersicon esculentum;specimen-voucher=Clemson University Genomics Institute
NC_007898.3 RefSeq gene 71636 71749 . - . ID=gene0