Running htseq-count over BAM files
If your BAM file is using UCSC chromosome names (chr1, chr2, etc.) and your GTF file is using Ensembl chromosome names (1, 2, etc.) then htseq-count won't know how to match your alignments to any of the genes. The simplest solution is to not use htseq-count, but instead to use featureCounts, which will handle the chromosome name difference transparently (it's one of the few programs that does) and is much faster anyway. In the future, download your GTF and fasta files from the same source, don't mix and match them.