Understanding minimap2 output (PAF format)

Question

[Rogerio Ribeiro]

Hi all! I used minimap2 in order to align a (subset) of transcripts from an older project to the set of transcripts I generated to my project. The command I used was the following:

minimap2 my_transcriptome.fasta --secondary=no oldproject_transcripts.fasta > minimap_output.txt

As is my understanding, minimap flags the highest-scoring alignment as the primary. However, after analyzing my output, I´m pretty sure my rationale is wrong, as I got several primary alignments reported to the same query. Can someone explain why this happens? Thanks in advance

partial output:

Caros006251.1_4 5238    1052    3241    -   CATHA.6748.1    2205    14  2201    1446    2198    60  tp:A:P  cm:i:212    s1:i:1444   s2:i:471    dv:f:0.0445 rl:i:18
Caros006251.1_4 5238    8   812 +   CATHA.11089.1   3445    1248    2052    683 804 6   tp:A:P  cm:i:119    s1:i:683    s2:i:666    dv:f:0.0193 rl:i:18