I have bam files that I have split into unmapped, uniquely mapped and multimapped bam files from HISAT2 alignment. I am trying to merge the sorted unmapped and uniquely mapped bam files with the command

    samtools merge A1_merged.bam -b A1_unmapped.bam A1_unique.bam

and am getting an error

    [E::hts_open_format] Failed to open file BAMT
    samtools merge: fail to open "BAMT": No such file or directory

the square actually has a question mark in it but that didn't copy across. Anyone have any ideas on why this error is coming up and how to fix it?


      -b FILE    List of input BAM filenames, one per line [null]

`-b` would be necessary if the file names were in a separate text file.


It is simply 

    samtools merge A1_merged.bam A1_unmapped.bam A1_unique.bam

