PAV Directory setup ln -s /net/eichler/vol28/projects/structural_variation/nobackups/pipelines/pav/2.3.4/runsnake ln -s /net/eichler/vol28/projects/structural_variation/nobackups/pipelines/pav/2.3.4/runlocal Contents of config.json { "reference": "/net/eichler/vol28/eee_shared/assemblies/hg38/no_alt/hg38.no_alt.fa", "assembly_table": "manifest.tab" } Contents of manifest.tab (a file of sample paths and names) NAME HAP1 HAP2 11918_s1 11918_s1.hifiasm.dip.hap1.p_ctg.gfa.fasta 11918_s1.hifiasm.dip.hap2.p_ctg.gfa.fasta 11918_p1 11918_p1.hifiasm.dip.hap1.p_ctg.gfa.fasta 11918_p1.hifiasm.dip.hap2.p_ctg.gfa.fasta Run module load miniconda/4.12.0 ./runsnake 30 -np # this is dry run ./runsnake 30 -p # actually submitting jobs