papara called as:
papara -j 5 -r -t /home/acabello/acabello/genwork/acabello/raxml/pelagos_placement/raxml_ng/reference_tree.raxml.bestTree -s /home/acabello/acabello/genwork/acabello/raxml/pelagos_placement/allPelagos_Alignment_noCladeB4.phy -q /home/acabello/acabello/genwork/acabello/raxml/pelagos_placement/ASVs_V4_selectionTREE.fasta 
gap rate: 4141 44088
gap rate: 0.0939258
rate matrix: [2,2]((-0.0939258,0.0939258),(0.906074,-0.906074))
p: [2,2]((0.991062,0.00893822),(0.0862244,0.913776))
references container instantiated as: papara::references<pvec_pgap, sequence_model::tag_dna>
edges: 45
scoring scheme: -3 -1 2 -3
papara_core version 2.5
start scoring, using 5 threads
thread 1: 2.29472 gncup/s
thread 4: 2.27939 gncup/s
thread 3: 2.27647 gncup/s
thread 2: 2.2696 gncup/s
thread 0: 1.97081 gncup/s
scoring finished: 0.181836
0.536365
generating best scoring alignments
SUCCESS 0.536388