RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 04-Jun-2021 13:33:26 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P09622/2_msa/P09622_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P09622/3_mltree/P09622.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P09622/4_raxmlng_ancestral/P09622 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622802806 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P09622/2_msa/P09622_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 509 sites WARNING: Sequences tr_J3KFU3_J3KFU3_COCIM_246410 and tr_A0A0J6YFG4_A0A0J6YFG4_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2VSK7_B2VSK7_PYRTR_426418 and tr_A0A2W1GSK7_A0A2W1GSK7_9PLEO_45151 are exactly identical! WARNING: Sequences tr_Q2LZ16_Q2LZ16_DROPS_46245 and tr_B4GZR7_B4GZR7_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8NAT6_B8NAT6_ASPFN_332952 and tr_Q2U0D3_Q2U0D3_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NAT6_B8NAT6_ASPFN_332952 and tr_A0A1S9DCW3_A0A1S9DCW3_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UQ32_A0A179UQ32_BLAGS_559298 and tr_C5GRA5_C5GRA5_AJEDR_559297 are exactly identical! WARNING: Sequences tr_K7DCW7_K7DCW7_PANTR_9598 and sp_P09622_DLDH_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F9FWQ8_F9FWQ8_FUSOF_660025 and tr_A0A0D2XVZ1_A0A0D2XVZ1_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FWQ8_F9FWQ8_FUSOF_660025 and tr_S0E3X9_S0E3X9_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9FWQ8_F9FWQ8_FUSOF_660025 and tr_N4UE11_N4UE11_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FWQ8_F9FWQ8_FUSOF_660025 and tr_X0CUD2_X0CUD2_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FWQ8_F9FWQ8_FUSOF_660025 and tr_A0A2H3TJ66_A0A2H3TJ66_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FWQ8_F9FWQ8_FUSOF_660025 and tr_A0A2H3HMS2_A0A2H3HMS2_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FWQ8_F9FWQ8_FUSOF_660025 and tr_A0A365N2T1_A0A365N2T1_GIBIN_948311 are exactly identical! WARNING: Sequences tr_J5J2F3_J5J2F3_BEAB2_655819 and tr_A0A2N6NSP4_A0A2N6NSP4_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A0E0H9Y5_A0A0E0H9Y5_ORYNI_4536 and tr_A0A0E0PHV7_A0A0E0PHV7_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0HNB8_A0A0E0HNB8_ORYNI_4536 and tr_A0A0E0MVN3_A0A0E0MVN3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0HNB8_A0A0E0HNB8_ORYNI_4536 and tr_Q9ASP4_Q9ASP4_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2QNS6_A2QNS6_ASPNC_425011 and tr_G3XZ37_G3XZ37_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QNS6_A2QNS6_ASPNC_425011 and tr_A0A319ADR7_A0A319ADR7_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F7HRR6_F7HRR6_MACMU_9544 and tr_A0A2K6DLK1_A0A2K6DLK1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7XEW1_G7XEW1_ASPKW_1033177 and tr_A0A100IEI6_A0A100IEI6_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XEW1_G7XEW1_ASPKW_1033177 and tr_A0A146F124_A0A146F124_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XEW1_G7XEW1_ASPKW_1033177 and tr_A0A317W4W5_A0A317W4W5_9EURO_1448314 are exactly identical! WARNING: Sequences tr_F4NY10_F4NY10_BATDJ_684364 and tr_A0A177WLJ0_A0A177WLJ0_BATDE_403673 are exactly identical! WARNING: Sequences tr_I1NMR3_I1NMR3_ORYGL_4538 and tr_A0A0E0C165_A0A0E0C165_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_I1NMR3_I1NMR3_ORYGL_4538 and tr_A0A0D3EN96_A0A0D3EN96_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_G2YVZ6_G2YVZ6_BOTF4_999810 and tr_M7TM34_M7TM34_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_E3N753_E3N753_CAERE_31234 and tr_A0A261B5H6_A0A261B5H6_9PELO_1503980 are exactly identical! WARNING: Sequences tr_A8Y0F0_A8Y0F0_CAEBR_6238 and tr_A0A2G5TXX6_A0A2G5TXX6_9PELO_1611254 are exactly identical! WARNING: Sequences tr_F2SI59_F2SI59_TRIRC_559305 and tr_F2PL35_F2PL35_TRIEC_559882 are exactly identical! WARNING: Sequences tr_F2SI59_F2SI59_TRIRC_559305 and tr_A0A059J5G5_A0A059J5G5_9EURO_1215338 are exactly identical! WARNING: Sequences tr_F2SI59_F2SI59_TRIRC_559305 and tr_A0A178EZT5_A0A178EZT5_TRIRU_5551 are exactly identical! WARNING: Sequences tr_L0P7Y5_L0P7Y5_PNEJ8_1209962 and tr_A0A0W4ZFX2_A0A0W4ZFX2_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_M2TCN5_M2TCN5_COCSN_665912 and tr_W6YFT0_W6YFT0_COCCA_930089 are exactly identical! WARNING: Sequences tr_V2Y3Y4_V2Y3Y4_MONRO_1381753 and tr_A0A0W0G1U7_A0A0W0G1U7_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015JZB9_A0A015JZB9_9GLOM_1432141 and tr_A0A2H5TU05_A0A2H5TU05_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044TV88_A0A044TV88_ONCVO_6282 and tr_A0A182E8X7_A0A182E8X7_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A067FXK6_A0A067FXK6_CITSI_2711 and tr_A0A2H5N5V0_A0A2H5N5V0_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A084QBL2_A0A084QBL2_STAC4_1283841 and tr_A0A084R829_A0A084R829_STACH_1283842 are exactly identical! WARNING: Sequences tr_A0A096NF79_A0A096NF79_PAPAN_9555 and tr_A0A0D9RFY0_A0A0D9RFY0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NF79_A0A096NF79_PAPAN_9555 and tr_A0A2K5Y8F2_A0A2K5Y8F2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A078G360_A0A078G360_BRANA_3708 and tr_A0A0D3CP20_A0A0D3CP20_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A094F7B8_A0A094F7B8_9PEZI_1420912 and tr_A0A1B8GBX3_A0A1B8GBX3_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F8X452_A0A0F8X452_9EURO_308745 and tr_A0A2T5M9I4_A0A2T5M9I4_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0W8DYI0_A0A0W8DYI0_PHYNI_4790 and tr_W2L0G4_W2L0G4_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0V1CX15_A0A0V1CX15_TRIBR_45882 and tr_A0A0V0V4B5_A0A0V0V4B5_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CX15_A0A0V1CX15_TRIBR_45882 and tr_A0A0V1A9E5_A0A0V1A9E5_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CX15_A0A0V1CX15_TRIBR_45882 and tr_A0A0V0UET0_A0A0V0UET0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1LCP2_A0A0V1LCP2_9BILA_6335 and tr_A0A0V1P3M0_A0A0V1P3M0_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S4CPN2_A0A1S4CPN2_TOBAC_4097 and tr_A0A1U7XQY7_A0A1U7XQY7_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1V8UYN0_A0A1V8UYN0_9PEZI_1974281 and tr_A0A1V8SYG5_A0A1V8SYG5_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A1Y1X8X4_A0A1Y1X8X4_9FUNG_1314790 and tr_A0A1Y1Y6X8_A0A1Y1Y6X8_9FUNG_1314790 are exactly identical! WARNING: Duplicate sequences found: 53 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P09622/4_raxmlng_ancestral/P09622.raxml.reduced.phy Alignment comprises 1 partitions and 509 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 509 Gaps: 5.31 % Invariant sites: 1.18 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P09622/4_raxmlng_ancestral/P09622.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P09622/3_mltree/P09622.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 128 / 10240 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:00] Tree #1, initial LogLikelihood: -170486.514839 [00:00:00 -170486.514839] Initial branch length optimization [00:00:01 -169339.501011] Model parameter optimization (eps = 0.100000) [00:00:33] Tree #1, final logLikelihood: -168823.790906 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.277170,0.332525) (0.325142,0.581471) (0.202157,1.136268) (0.195531,2.501237) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Marginal ancestral probabilities saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P09622/4_raxmlng_ancestral/P09622.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P09622/4_raxmlng_ancestral/P09622.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P09622/4_raxmlng_ancestral/P09622.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P09622/4_raxmlng_ancestral/P09622.raxml.log Analysis started: 04-Jun-2021 13:33:26 / finished: 04-Jun-2021 13:34:04 Elapsed time: 37.746 seconds