Minimap2 crashes during Flye run

[harmeet1990]

I am trying to polish a genome assembly using flye-minimap2 (with ONT reads) but it crashes with the following error message: flye-minimap2: align.c:284: mm_update_extra: Assertion `qoff == r->qe - r->qs && toff == r->re - r->rs' failed

Please find the entire stderr file in the attachment. Can you please help me out here? minimap.stderr.zip

[joehagmann]

I get the same error, but with the minimap2 binary and while aligning assembled chromosomes, each ~60 Mbp long, after 4 hrs. I use all-vs-all without self alignments (-X).

minimap2: align.c:284: mm_update_extra: Assertion 'qoff == r->qe - r->qs && toff == r->re - r->rs' failed.

The command I used: minimap2 -x asm20 -X -c -t50 -o mappings.paf chr1.fa.gz chr1.fa.gz

minimap2 version is 2.17-r1013-dirty

the fasta can be downloaded here: https://bit.ly/32aNTXs

Heng, could you have a look, please?

[lh3]

Please try the latest version first. Also, see #106 for the right way to do such alignment.

EDIT: Oh, I see you are using r1013, which should be close to the latest. I will have a look at some point.

[fenderglass]

@lh3 I've updated Flye to minimap 2.18, which hopefully should have solved this issue now.