bwa_opts not applicable to nanopore data for the merge stage

[zhaoc1]

Hi,

I am running Circlator for nanopore sequencing data and my command is as following:

circlator all --merge_min_id 85 --merge_breaklen 1000 --threads {threads} --verbose \ --assembler canu --data_type nanopore-corrected --bwa_opts "-x ont2d" \ {input.contigs} {input.correctedReads} {params.outdir}

During the 04.merge stage: the bwa_opts is not passed to the bwa command, as the screen shot shown here (red line):

I don't see any other parameters that I can set up for other bwa_opts, and am wondering: can I missing anything, and how can I pass the bwa_opts to the bwa command during the merge stage?

Thank you!

Best, Chunyu