Large number of reads cannot mapped successfully after prepare_mapped_reads.py

[duolinwang]

For example, after "get_refs_from_sam.py genome.fa basecalls_map.bam --min_coverage 0.5 --reverse > read_references_0.5.fasta" I got 3967 reads, but after "generate_per_read_params.py" and "prepare_mapped_reads.py", there are only 1062 reads mapped successfully (saved in the hdf5 file). Why so many reads cannot be mapped successfully? Which parameter can control it?