Incorrect number of contigs in the assembly

[ahmedelgoutbi]

Hi!
I need to assemble more than 30 yeast genomes that have been sequenced
with PacBio Sequel IIe (12.1 Mb each with roughly 40x coverage).
According to the reference genome (Saccharomyces cerevisiae S288C) the
chromosomes are 16 but I get a much higher number of contigs (70 - 100)
after assembling with WTDBG2 (see below for the full commands). Could
this be a problem related to repeated sequences that the algorithm
cannot solve? If so, should I adjust the parameters to refine the
assembly? Alternatively, is there any (or set of) parameter/s that I can
tweak to get a more congruent number of chromosomes?

These are the commands that I used to get the full assembly:

wtdbg2 -x rs -g 12.1m -i raw_data/raw.fasta.gz -t 16 -R -fo assemble_out wtpoa-cns -t 16 -i assemble.ctg.lay.gz -fo consensus.raw.fa minimap2 -t 16 -ax map-pb -r2k consensus.raw.fa raw_data/raw.fasta.gz | samtools sort -@4 > polished.bam samtools view -F0x900 polished.bam | wtpoa-cns -t 16 -d consensus.raw.fa -i - -fo polished.cns.fa busco -i polished.cns.fa -o yeast_genome -l saccharomycetes_odb10 -m genome -c 12