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Could not parse the header line

Error using samtools mpileup

samtools mpileup SAMPLE_sorted.bam
"Could not parse the header line:... "

The problem can be due to a comma in the gene/contig ID

Samtools mpileup is adding information to the original contig ID separated by comma. 
and gets confused if the gene ID already includes a comma:  1005929-1007642,1007542-1008571

Remove all comma from your gene or contig ID names before running samtools.