get two sets of haplotype genomes by purge_dups

[gdmdxl]

Hi, thank you for your purge_dups. It is very helpful for our work!

I have a question about the result file. My input files include three: the canu output file asm.fa, the ONT third-generation sequencing data, and the illumina second-generation sequencing data.
Because my species has a high heterozygosity, the result asm.fa generated by canu has more bubbles. So I want to get two sets of haplotype genomes by purge_dups. I run the program as follows:

Step 4. Merge hap.fa and $hap_asm and redo the above steps to get a decent haplotig set.

We got two purged.fa files and two hap.fa files. Can these two purged.fa files be used as my ideal result?
Also, the two files are similar in size, but the number of sequences is different. One is 1100 sequences and the other is 880 sequences. Is this normal?

Looking forward to your reply！