syri is not detecting huge indels

[ivaneskos]

I am running syri on mitochondrial genomes. I have some strange results for part of the genomes. For example, for this pair of mitogenomes, the nucmere pairwise alignment shows the presence of at least 2 huge indels (figure in .ps format). By the way, syri output vcf doesn't contain any indels, only a small number of SNPs. Can you please help me to find the issue?
My script (minimap2 + syri):

minimap2 -t 12 -ax asm5 --eqx $reference $assemblies/${i}.fasta > $syri_pangenome_sam_files/${i}.IPO323.sam
syri -c $syri_pangenome_sam_files/${i}.IPO323.sam --nc 12 -F S -r $reference -q $assemblies/${i}.fasta --dir $syri_output --prefix ${i}.IPO323

Input files: 2 fastas + .ps file on the google-drive https://drive.google.com/drive/folders/1Ukn-Romyv3guribQYWgV4XnxsQ1wnAQn?usp=sharing

[mnshgl0110]

Sorry for a delayed response. Is this issue resolved? If not, then could you please share syri.log and syri.out files?