Unable to run ntroot on my own VCF file

[dfermin]

Hello

I just created a fresh conda environment with the latest version of ntroot.
I'm trying to use it to predict the genetic ancestry of the human samples I have in my vcf file mydata.MAF005.vcf.gz

Here is the command I am running:

REF=./ntroot.data/GRCh38.fa.gz
L_VCF=./ntroot.data/1000GP_integrated_snv_v2a_27022019.GRCh38.phased_gt1.vcf.gz
THREADS=24
SRC_VCF=../mydata.MAF005.vcf.gz

ntroot -k 55 --reference $REF --genome $SRC_VCF -t $THREADS -l $L_VCF -v

The snakemake code failed to run.
I've confirmed that the chromosome names match between my $SRC_VCF file and both $REF and $L_VCF
My $SRC_VCF is sorted and indexed.
I've attached the log file here in case it helps.

Any suggestions for how to run it would be greatly appreciated.

Thanks!

2026-04-09T164607.222937.snakemake.log

[lcoombe]

Hi @dfermin,

If you already have a VCF file, and want to predict ancestry from that (as opposed to inputting reads or a genome), you should use the --custom_vcf option. Here is an example command:

ntroot -r GRCh38.fa.gz --custom_vcf third_party.vcf -l 1000GP_integrated_snv_v2a_27022019.GRCh38.phased_gt1.vcf.gz

The command you have there would be for when you want to predict ancestry from an assembled genome, hence why you're getting an error.

I hope that helps - thank you for your interest in ntRoot!
Lauren