Hi,
I’m running the latest version of nextalign, available here. Below you can find the command I’m running:
nextalign-MacOS-x86_64 --sequences sequences_test.fasta --reference reference.gb --genemap genemap.gff --genes E,M,N,ORF10,ORF14,ORF1a,ORF1b,ORF3a,ORF6,ORF7a,ORF7b,ORF8,ORF9b,S --output-dir output_files/ --output-basename test
I’m getting an Error: Invalid nucleotide: "L" that claims one of my sequences have an L somewhere, but in fact no letter L (neither upper of lowercase) is found in the file, not even in sequence headers. Any idea what may be happening?
I’m getting this error using a multifasta with these 10 genomes:
Wuhan/Hu-1/2019
HongKong/HKPU19_0402/2020
USA/WI-UW-159/2020
USA/WI-UW-237/2020
Wuhan/WH01/2019
Ghana/2828_S6/2020
France/GES-2843/2020
Singapore/95/2020
USA/CA-CZB-1088/2020
USA/IA-GMF-M00005/2020
Thank you