I am running GMAP on nanopore sequence aligning it to the human genome. The query file is approximately 2gb. The alignment is taking extremely long. It's been more than 12 hours and the output .sam file is so far only 130mb.
I am using following command:
path/to/gmapl -D /path/to/dir/ONT -d ONT /path/to/sample/fasta -t 4 -n 0 -f samse > /path/to/output/output.sam
Am I missing anything here?
Could someone please help me. Thanks