Changed stdout output in three scripts to stderr

These need to be changed:
- [x] abundance-dist
- [x] abundance-dist-single
- [x] annotate-partitions
- [x] count-median
- [x] count-overlap
- [x] do-partition
- [x] extract-paired-reads
- [x] extract-partitions
- [x] filter-abund
- [x] filter-abund-single
- [x] filter-stoptags
- [x] find-knots
- [x] load-graph
- [x] load-into-counting
- [x] make-initial-stoptags
- [x] merge-partitions
- [x] normalize-by-median
- [x] partition-graph
- [x] sample-reads-randomly

These don't need to be changed:
split-paired-reads
extract-long-sequences
fastq-to-fasta
interleave-reads