Phasing problem using "samtools phase"
This is what I see in my samtools phase (v1.10)

Usage:   samtools phase [options] &lt;in.bam&gt;


samtools phase only takes a bam file as an input. But you are specifying a .fasta file as an input. If you want to specify the reference genome, you should be using the argument "--reference" as described here

      --reference FILE
           Reference sequence FASTA FILE [null]