Bugs when using minimap2 for mapping ultro long nanopore reads

[Archieyoung]

Hi Heng:
I am using minimap2 for mapping ultro long nanopore reads.
here is the minimap2 version:

minimap2 --version
2.12-r827

here is the commands to rum minimap2:

minimap2 -t 30 --MD -Y -L -a -x map-ont ref.hg38.fa input.fastq > out.sam

here is the read that causes the problem:
39b2c5d9-79c3-4feb-84ec-91ecc42aa75b.txt

I checked the output sam file and found that secondary alignment with "0S" CIGAR, then samtools raise the ERROR "CIGAR and query sequence are of different length''.

39b2c5d9-79c3-4feb-84ec-91ecc42aa75b    256     chr6_GL000251v2_alt     1416879 0       0S      *       0       0

Thanks,
Archie

[lh3]

Fixed via 7d80d6d.