Hello i'm trying DiscoSnp++ and succesfully ran run_discoSnpRad.sh and discoRAD_finalization.sh. Since i'll use Structure i only need one SNP per locus, but it seems 1SNP_by_cluster.py doesn't ran with filter_paralogs.py called by discoRAD_finalization.sh (as explain in the header of 1SNP_by_cluster.py) wrapper, so i tried to run 1SNP_by_cluster.py manually but it filters out all the SNPs as follows
python3 1SNP_by_cluster.py discoRad_MslI_k_31_c_20_D_10_P_5_m_0_coherent_sorted_with_clusters.vcf nb SNP before : 158261 nb SNP after : 0
How can i make sure discoRAD_finalization.sh ran filter_paralogs.py and 1SNP_by_cluster.py ? how can i run 1SNP_by_cluster.py manually?