No Sequence Segments for secondary alignments in minimap2 while trying to run alignment on ONT data?

Question

[Adarsh]

Hello all, I was trying to align a set of ONT reads that I have against my reference and I noticed something strange in the generated SAM file. If a read has any secondary alignment, there are no sequence segments present in the output for it. Is this some default behavior for minimap2? I really need the secondary sequence segment for some further analysis. This is the command that I ran.

minimap2 -t 10 -ax map-ont reference.fasta combines_reads.fastq > alignment_out.sam 2> log.txt

I even tried the above command with --secondary=yes command but I still get an empty seq segment for secondary alignments. Could please help me with this?