I have been trying to run Minimap2 with fasta files of ~200Mb. I have 3 such files which I am trying to map onto a reference genome. The output sam file of first 2 files are about 500MB. But the third file gives a 2TB sam file and it has not completed running. Is there any reason of why this could be happening ? Any help would be appreciated.
The command I used is as follows:
minimap2 -a reference.mmi query.fasta -o output.sam -t 20