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shingocat / lrscaf

TGS scaffolding
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lrscaf throws an error with ont mapped reads from minimap2 #36

Open andrewkern opened 2 years ago

andrewkern commented 2 years ago

Hi there-- thanks for the software!

I'm running into an error when I map ONT reads using minimap2 using the appropriate options. i.e. if i prepare my alignment as 

minimap2 -t 24 -ax map-ont -o out.mm ref.fa reads.fastq.gz

lrscaf throws an error like

2021-12-02 20:06:17  [ ERROR ]  agis.ps.file.MMReader   On lines: 1 For input string: "ptg000088l"
2021-12-02 20:06:18  [ ERROR ]  PathBuilder ： The Edges could not be empty!

however if I prepare my alignment without the -ax map-ont flag i.e.,

minimap2 -t 24  -o out.mm ref.fa reads.fastq.gz

then in that case lrscaf runs without problem. i believe others have seen this in closed issues e.g., #17

thanks for your help

tim-oconnor commented 2 years ago

Hey @andrewkern, did you ever find a solution to this? Or did you just use the default minimap2 settings (as others did)? Thanks for any tips. Tim

andrewkern commented 2 years ago

no I never did. I just used default settings eventually.

tim-oconnor commented 2 years ago

Gotcha, thanks for responding!