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sorted bam file generated from gff transcript fastas, how to get counts with HTseq?

I have a single cell miRNA analysis. I have generated a sorted bam file using STAR with the mirbase hairpin fastas and the hsa.gff3. I generated a genome index with star then performed alignment. Now however, I want to get the counts for my miRNAS, and HTseq complains:

*
    Warning: No features of type '{args.feature_type}' found. 
    The alignment file has no chromosomes in common with the GFF/GTF file. This will 
    result in zero feature counts. Please check if the references match, 
    e.g. if you are using 'chr1' or '1' as chromosome names.
*

So, since the hairpin fasta had no chromosome number in its identifier and my bam lacks this info, how do I approach this?

htseq bam
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updated by Ram Ram • written by RNAseqer RNAseqer

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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