Hi Yutang,

I haven't tried this before, but I think it should work if you just install Nucmer 4 yourself and then point to the executable with --aligner. And then you can pass whatever parameters you want (except for -p) via --nucmer-params.

Let me know if that works.

Hi Malonge,

Thank you very much for your reply. Yes, exactly, that's what I would like to try. I will try minimap2 first and then try Nucmer 4 later. If I make any progress, I will let you know here.

Best wishes,
Yutang

Hi Malonge,

Just to let you know, I installed mummer 4 in the ragtag conda environment and then added --nucmer-params '--maxmatch -t 30 -l 100 -c 500', it worked.

Thank you very much,
Yutang

Hi Malonge,

Just to let you know, when I removed --maxmatch from --nucmer-params, it didn't work anymore.

(ragtag) bash-4.2$ ./RAGTAG_h2.sh
usage: ragtag.py patch <target.fa> <query.fa>
ragtag_patch.py: error: argument --nucmer-params: expected one argument

Here's my command line:
ragtag.py patch target.fa query.fa -o ragtag_flye_h2_miop10 -u --aligner nucmer --nucmer-params '-t 30 -l 100 -c 500'

What could be wrong?

Best wishes,
Yutang

Do you get the same error using Nucmer 3? If so, please open up a separate issue.

Thank you very much for your reply. No problem for Nucmer 3.

idk iit seems like a problem with the argument parsing Maybe try --nucmer-params="-t 30 -l 100 -c 500". Or variations on that.

Some updates:

I used external Nucmer 4 (in a different conda environment) with multi-thread option to do alignment first and then copy the delta file to the folder where I am doing RagTag to run RagTag command. The delta file must have this name: ragtag.scaffold.asm.delta
Nucmer 4 command I used is following:
nucmer --maxmatch -t 50 -l 100 -c 500 --delta=ragtag.scaffold.asm.delta reference.fasta asm.fasta