Converting to tskit format: file not found

[LuisGFdez]

Hi, I'm using SINGER to infer the ARG from some simulations. Below is the command line I'm using to infer the tree:

 singer_software/singer_master -Ne 1000 -m 1e-7 recomb_map recom_ratemap.csv -vcf example_sim -output infer_vcf -start 0 -end 20010

And this is the command I'm using to convert the output to tskit format:

 singer_software/convert_to_tskit -input infer_vcf -output trees_tskit -start 0 -end 20010

However, I keep encountering this error regardless of the step size parameter I specify:

FileNotFoundError: infer_vcf_nodes_100.txt not found.

Why is it looking for the file infer_vcf_nodes_100.txt when I only have 99 files?

Additionally, is there a specific format required for the recombination rate map? It seems the software isn't using the file I provided.

Any insight is appreciated.
recom_ratemap.csv

example_sim.zip

[zhangming-m]

i think you can try
singer_software/convert_to_tskit -input infer_vcf -output trees_tskit -start 0 -end 99

[YunDeng98]

@LuisGFdez I think @zhangming-m is correct. The map format is like multiple rows with (x, y, rate_between_x_and_y)