running psvcp_v1.01 pipeline on example data aiming to construct linear pangenome

Question

[analyst]

I am trying to run psvcp_v1.01 on example data using following command:

$ python3 ../Construct_pan_and_Call_sv.py genome_gff_dir_example genome_list -fqd fq_dir_example -o step1

But it gives following error:

> 1 nucmer ok awk: cannot open
> pan_dir_result/ref0_Lemont_0-2M/ref0_Lemont_0-2M.bed.Assemblytics_structural_variants.bed **(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  
1 nucmer ok awk: cannot open
> pan_dir_result/ref1_CN1_0-2M/ref1_CN1_0-2M.bed.Assemblytics_structural_variants.bed
> **(No such file or directory)**  
2 Assemblytics ok index file
> pan_dir_result/ref1.fa.fai not found, generating...  
3 final.bed ok  
4 more_50.bed ok ins.more_50.bed is empty next round  
1 nucmer ok awk:
> cannot open
> pan_dir_result/ref2_R498_0-2M/ref2_R498_0-2M.bed.Assemblytics_structural_variants.bed
> **(No such file or directory)**  
2 Assemblytics ok index file
> pan_dir_result/ref2.fa.fai not found, generating...  
3 final.bed ok  
4 more_50.bed ok ins.more_50.bed is empty next round  
1 nucmer ok awk:
> cannot open
> pan_dir_result/ref3_FH838_0-2M/ref3_FH838_0-2M.bed.Assemblytics_structural_variants.bed
> **(No such file or directory)**  
2 Assemblytics ok index file
> pan_dir_result/ref3.fa.fai not found, generating...  
3 final.bed ok  
4 more_50.bed ok ins.more_50.bed is empty next round

Every required tool is installed.

Please guide. Thanks

[GenoMax]

Seems toe be looking for

pan_dir_result/

from where you are running your command. Do you have the said directory/folders/files available?

[analyst]

Thanks GenoMax! The issue was resolved by installing python3-is-python