The header line in the final VIRUSBreakend 2.12.0 summary.tsv file has one less header label than there are columns, with column 14 label as alternate_kmer_count#rname. It looks like the virusbreakend code needs a field separator inserted between the two header input sources, and probably, the leading "#" removed:
grep taxid_genus $file_summary_references_tsv | tr -d '\n' > $file_summary_coverage_tsv.tmp head -1 $prefix_adjusted.merged.bam.coverage | tr -d '\n' >> $file_summary_coverage_tsv.tmp