I am getting a curious error when using bedtools to extract sequences from a reference fasta and a gff3 file.
/gpfs/gwngs/tools/bedtools2/bin/bedtools getfasta -s -fullHeader -fi ref.fa -bed ref.gff3
And I get a million lines saying, for example:
WARNING. chromosome (CP014594) was not found in the FASTA file. Skipping.
The thing is I grepped the fasta header for this chromosome and got:
There are no white spaces in the line. what's going on? i have tried inserting the prefix 'chr' into both files, and inserting a space between > and the chromosome name for the fasta file.