Minimap2 warning message

Question

[KVC_bioinfo]

Hello,

I am using Minimap2 for the Oxford nanopore reads. I made an index file for the human genome to be used as a reference. when I started the alignment I got following warning.

"For a multi-part index, no @SQ lines will be outputted"

I am not sure why I am getting this warning. Could someone help me here?

Thank you in advance.

[WouterDeCoster]

Please be as complete as possible when asking questions, and include the commands you used for building the index and running the alignment.

Also, don't forget to follow up on your previous questions and mark answers as accepted if it solves your question.

[KVC_bioinfo]

Thank you I have added the comment here with my command and I also took follow up on my past questions.

[KVC_bioinfo]

The command I used for building index:

minimap2 -d ref.mmi ref.fa

The command I used for alignment:

minimap2 -ax map-ont ref.fa ont-reads.fa > aln.sam

[Bioinfo]

Hello Please i want to know what that mean map-ont ??

[WouterDeCoster]

It's a preset combination of alignment parameters which the developer thought was the best for ONT data

Answer 1

[KVC_bioinfo]

I have got help from the authors of minimap2. I downloaded the reference from here which is very confusing. when Replaced the reference with this Minimap2 works fine.

[WouterDeCoster]

For future reference, see this thread https://github.com/lh3/minimap2/issues/58

[KVC_bioinfo]

Thank you for putting the reference here.