Rename <outname>.gfa.fa.gz to <outname>.sv.gfa.fa.gz, since this file corresponds to the sequences from <outname>.sv.gfa.gz (the minigraph SV graph) as extracted by gfatools gfa2fa.
cactus-pangenome writes this as its an important intermediate file for rerunning certain step-by-step commands, but it's not much use as a final output file.
Rename
<outname>.gfa.fa.gzto<outname>.sv.gfa.fa.gz, since this file corresponds to the sequences from<outname>.sv.gfa.gz(the minigraph SV graph) as extracted bygfatools gfa2fa.cactus-pangenomewrites this as its an important intermediate file for rerunning certain step-by-step commands, but it's not much use as a final output file.Also: add orang pangenome to the pangenomes list.
Resolves #1357