nothing found on a metagenome search?

[Sung-hub]

I used PacBio long read data (assembly or raw data) with two different size selection (Cut at 15kb with blue pippin) or non-sized selection.
All cases show there is nothing found.

log file showed:
Loading database...
Converting sample reads to k-mers...
Plasmids done: 19776 of 19782
Clustering results...
Nothing found...
Done!

I used command line below:
$ nohup perl plasmidseeker.pl -d ./db_w20 -i ~/LIB209522_PureWorm/m84124_240809_211430_s3.fastq -b e_coli_sakai_ref.fna -o ~/LIB209522_PureWorm/PS_results.txt --ponly 2> asm.log &
I used e_coli_sakai_ref.fna as closest reference, since it is metagenome. Do I change to different reference or just remove refence?

I am not sure there is no plasmid in this metagenome. Please let me know how you think.