Hi , I have tried to align WGS reads to viral reference genomes using Stampy software that the command I used is:

stampy.py -t 16 -g viral_ref -h viral_ref --bamkeepgoodreads -M SampleName.bwa.bam -o sample.bwa.stampy.sam

Note: This is a hybrid mode which was performed by using an alignment file from BWA as an input.

However, I got this error:

stampy: Error: Found reference ID (gi|167006425|ref|NC_010314.1|) in BAM which is not in genome reference while re-mapping with --bamkeepgoodreads. Check that the correct genome reference was selected.

So I have no idea how this was happened since I used the same reference when I aligned reads by using BWA and I already checked whether that ID is in the reference file, which is:

gi|167006425|ref|NC_010314.1| Abaca bunchy top virus DNA-N, complete genome