I was using the eXpress to read my BAM files and got this error

Target 'some_target' exists in MultiFASTA but not alignment (SAM/BAM) file

Actually my FASTA reference was originally downloaded in Windows environment and then transferred to Unix environment therefore it contains some Windows specific characters which are responsible for this error. I run following command

tr -d '\r' output

Here INPUT is the name of my reference FASTA while OUTPUT is the name cleaned FASTA. This will convert the line endings in a text file from DOS (or Windows) to UNIX format. Hope this will help someone else too.