Error given while trying to index a BAM file with Samtools Index - NO COOR?
By now this will be of little interest to the original poster, but for future reference:
$ samtools sort -n -T ~/[etc] -o sample${r}bowtiemapping_sorted.bam [etc]
$ samtools index sample${r}bowtiemapping_sorted.bam
[E::hts_idx_push] NO_COOR reads not in a single block at the end 1652 -1.

This error message indicates (admittedly somewhat obscurely) that the reads are not sorted by coordinate — in particular, there are mapped reads appearing after the unplaced unmapped reads (those with RNAME *) that should be at the very end of the file.
This is because samtools sort -n has been used to sort the reads by name instead. Remove -n to sort by position, which is what is needed to prepare a BAM file for indexing with samtools index.