constructing pangenome through psvcp
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Entering edit mode
27 days ago
analyst ▴ 50

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

psvcp pangenome • 254 views
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Entering edit mode

Fixed the issue by updating nucmer version.

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