the speed is very slow

[songrunxian]

My dear professor:

this process is 10min
bowtie2 -p 20 --reorder --mm --score-min=C,-15,0 -q -x /ref/boetiew2_index_rice -U anchors.fq.gz -S bowtieresult.sam

this process need 2hours:
bowtie2 -p 20 --reorder --mm --score-min=C,-15,0 -q -x /ref/boetiew2_index_rice -U anchors.fq.gz | find_circ.py --genome=genome.fa --prefix=find_circ --name=result --stats=stats.txt > splice_sites.bed

How can we let the speed faster