I believe the code in msg.pl around these lines should also check that stampy index files like *.stidx exist when using stampy.
BWA INDEXING
foreach $sp ( keys %genomes ) {
unless( -e "$genomes_fa{$sp}.bwt" and -e "$genomes_fa{$sp}.ann" ) {
To have hit this error MSG must have stopped after creating the bwt and ann files but before creating the stampy files which should be a rare issue. (Or this could happen if you previously run with BWA mapping and then switch to stampy and do a rerun).
I believe the code in msg.pl around these lines should also check that stampy index files like *.stidx exist when using stampy.
BWA INDEXING
foreach $sp ( keys %genomes ) {
unless( -e "$genomes_fa{$sp}.bwt" and -e "$genomes_fa{$sp}.ann" ) {
To have hit this error MSG must have stopped after creating the bwt and ann files but before creating the stampy files which should be a rare issue. (Or this could happen if you previously run with BWA mapping and then switch to stampy and do a rerun).