constructing pangenome through psvcp
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
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IrisChang •
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Bushra Bibi
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written
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Bushra Bibi
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Fixed the issue by updating nucmer version.
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?