pddg+odgi+vg to perform pangenome analysis to cyanobacteria

Question

[snmdba]

I'm using a bioinformatics tool for the first time for an assignment, and I'm feeling completely lost. I want to perform a pangenome analysis using PGGB + ODGI + VG tools on five cyanobacteria genomes whose FASTA files I downloaded from NCBI. However, when I open my pangenome graph PDF, all I see is a small empty square. I've been struggling with various errors constantly (like my running step does not move even after an hour etc). Could you please help me? I'm open to any tutorials, articles, or any kind of guidance that could help me understand and complete this analysis.

[snmdba]

When I run the following command:

pggb -i alg.fa -o alg-pggb -n 5 -t 4 -p 98 -a 70 -l 10000 -s 500000

I get the error:

"ERROR: input alignment file 40, 50, 60, or 70 does not exist", 

even if I change the -a parameter to 50, 60, or 40.

Sometimes, I also get errors like:

"-a: command not found" or "-l: command not found".

I honestly have no idea what I'm doing wrong or what to do next.

[GenoMax]

Looking at the essential parameters described in the manual you should try to use only those first and see if you are able to get any progress: https://pggb.readthedocs.io/en/latest/rst/essential_parameters.html