constructing pangenome through psvcp

Question

[analyst]

I am building pangenome using psvcp tool. For that I have run following command:

python3 psvcp_v1.01-main/1Genome_construct_Pangenome.py gff_dir/ genome_list 

But it outputs following error:

Unknown option: t

USAGE: nucmer [options] <Reference> <Query>

Try '/usr/bin/nucmer -h' for more information. 1 nucmer ok awk: fatal: cannot open file `pan_dir_result/ref0_02428/ref0_02428.bed.Assemblytics_structural_variants.bed' for reading (No such file or directory) 2 Assemblytics ok index file pan_dir_result/ref0.fa.fai not found, generating... 3 final.bed ok 4 more_50.bed ok ins.more_50.bed is empty Unknown option: t

please guide to resolve this issue

Thankyou

[analyst]

Fixed the issue by updating nucmer version.

[IrisChang]

Hi, I am wondering if you fixed the error. I am also trying to construct a pangenome by psvcp. But I ran into the error that it output the empty bed2 file. Then 1Genome_construct_Pangenome.py stopped. Have you also had a similar issue?