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 17-Jul-2021 07:59:50 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6P4F2/2_msa/Q6P4F2_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6P4F2/3_mltree/Q6P4F2.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6P4F2/4_raxmlng_ancestral/Q6P4F2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626497990 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_300621/phylogeny-snakemake/results/Q6P4F2/2_msa/Q6P4F2_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 186 sites WARNING: Sequences tr_B4QMS4_B4QMS4_DROSI_7240 and tr_B4HKN6_B4HKN6_DROSE_7238 are exactly identical! WARNING: Sequences tr_Q8SZA8_Q8SZA8_DROME_7227 and tr_B4HU46_B4HU46_DROSE_7238 are exactly identical! WARNING: Sequences tr_J3K8H3_J3K8H3_COCIM_246410 and tr_E9DBF3_E9DBF3_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3K8H3_J3K8H3_COCIM_246410 and tr_A0A0J6YAC5_A0A0J6YAC5_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2WHN3_B2WHN3_PYRTR_426418 and tr_A0A2W1HGK1_A0A2W1HGK1_9PLEO_45151 are exactly identical! WARNING: Sequences tr_C0NTR7_C0NTR7_AJECG_447093 and tr_C6HEH4_C6HEH4_AJECH_544712 are exactly identical! WARNING: Sequences tr_C0NTR7_C0NTR7_AJECG_447093 and tr_F0UQ84_F0UQ84_AJEC8_544711 are exactly identical! WARNING: Sequences tr_Q7S0K4_Q7S0K4_NEUCR_367110 and tr_G4UFE2_G4UFE2_NEUT9_510952 are exactly identical! WARNING: Sequences tr_Q2LZ88_Q2LZ88_DROPS_46245 and tr_B4HAG0_B4HAG0_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8NQI7_B8NQI7_ASPFN_332952 and tr_Q2UA03_Q2UA03_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NQI7_B8NQI7_ASPFN_332952 and tr_A0A1S9DRM2_A0A1S9DRM2_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_H2QFB4_H2QFB4_PANTR_9598 and tr_A0A2R8ZDJ1_A0A2R8ZDJ1_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FC45_F9FC45_FUSOF_660025 and tr_A0A0D2XV15_A0A0D2XV15_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FC45_F9FC45_FUSOF_660025 and tr_S0DX78_S0DX78_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9FC45_F9FC45_FUSOF_660025 and tr_N4UIH5_N4UIH5_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FC45_F9FC45_FUSOF_660025 and tr_X0DS94_X0DS94_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FC45_F9FC45_FUSOF_660025 and tr_A0A2H3TBT8_A0A2H3TBT8_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FC45_F9FC45_FUSOF_660025 and tr_A0A2H3HSI8_A0A2H3HSI8_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FC45_F9FC45_FUSOF_660025 and tr_A0A2K0VVD3_A0A2K0VVD3_GIBNY_42673 are exactly identical! WARNING: Sequences tr_E9F812_E9F812_METRA_655844 and tr_A0A0B4HM85_A0A0B4HM85_METMF_1276143 are exactly identical! WARNING: Sequences tr_A0A088A406_A0A088A406_APIME_7460 and tr_A0A2A3EMB0_A0A2A3EMB0_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A0E0IK97_A0A0E0IK97_ORYNI_4536 and tr_A0A0E0B3E7_A0A0E0B3E7_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0IK97_A0A0E0IK97_ORYNI_4536 and tr_Q69LJ8_Q69LJ8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2QUP2_A2QUP2_ASPNC_425011 and tr_G3XLR1_G3XLR1_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QUP2_A2QUP2_ASPNC_425011 and tr_A0A319BVI3_A0A319BVI3_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XN12_G7XN12_ASPKW_1033177 and tr_A0A146FPP9_A0A146FPP9_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XN12_G7XN12_ASPKW_1033177 and tr_A0A1L9NG47_A0A1L9NG47_ASPTU_767770 are exactly identical! WARNING: Sequences tr_B8B6V2_B8B6V2_ORYSI_39946 and tr_Q7XIU2_Q7XIU2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0QRW2_A0A0E0QRW2_ORYRU_4529 and tr_A0A0D3H7A1_A0A0D3H7A1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_G2YDM5_G2YDM5_BOTF4_999810 and tr_M7U8J4_M7U8J4_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SYS5_F2SYS5_TRIRC_559305 and tr_A0A178F4M3_A0A178F4M3_TRIRU_5551 are exactly identical! WARNING: Sequences tr_L2G1U9_L2G1U9_COLFN_1213859 and tr_T0L1L7_T0L1L7_COLGC_1237896 are exactly identical! WARNING: Sequences tr_M2SYB8_M2SYB8_COCSN_665912 and tr_W6YSN7_W6YSN7_COCMI_930090 are exactly identical! WARNING: Sequences tr_W2PD42_W2PD42_PHYPN_761204 and tr_A0A0W8AZG2_A0A0W8AZG2_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A044TE75_A0A044TE75_ONCVO_6282 and tr_A0A182E2M6_A0A182E2M6_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A2I3MIV0_A0A2I3MIV0_PAPAN_9555 and tr_A0A2K6AAX5_A0A2K6AAX5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A094E420_A0A094E420_9PEZI_1420912 and tr_A0A1B8GJB4_A0A1B8GJB4_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F8WDK3_A0A0F8WDK3_9EURO_308745 and tr_A0A2T5LXK7_A0A2T5LXK7_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0N0DH59_A0A0N0DH59_FUSLA_179993 and tr_I1RPY0_I1RPY0_GIBZE_229533 are exactly identical! WARNING: Sequences tr_A0A0N0DH59_A0A0N0DH59_FUSLA_179993 and tr_A0A2T4GN23_A0A2T4GN23_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A0A1NMV8_A0A0A1NMV8_9FUNG_58291 and tr_A0A2G4SWU8_A0A2G4SWU8_9FUNG_1340429 are exactly identical! WARNING: Sequences tr_A0A0A1NMV8_A0A0A1NMV8_9FUNG_58291 and tr_A0A367K2U3_A0A367K2U3_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0G4LQ57_A0A0G4LQ57_9PEZI_100787 and tr_A0A0G4N790_A0A0G4N790_9PEZI_100787 are exactly identical! WARNING: Sequences tr_A0A0V1CJ32_A0A0V1CJ32_TRIBR_45882 and tr_A0A0V0VPL3_A0A0V0VPL3_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CJ32_A0A0V1CJ32_TRIBR_45882 and tr_A0A0V1NLB1_A0A0V1NLB1_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CJ32_A0A0V1CJ32_TRIBR_45882 and tr_A0A0V0TSR9_A0A0V0TSR9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A2K5P4H0_A0A2K5P4H0_CERAT_9531 and tr_A0A2K6BWR5_A0A2K6BWR5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2S7NY69_A0A2S7NY69_9HELO_2070414 and tr_A0A2S7R4N0_A0A2S7R4N0_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A319DFJ0_A0A319DFJ0_9EURO_1448315 and tr_A0A2V5I9E0_A0A2V5I9E0_9EURO_1450541 are exactly identical! WARNING: Duplicate sequences found: 49 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6P4F2/4_raxmlng_ancestral/Q6P4F2.raxml.reduced.phy Alignment comprises 1 partitions and 186 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 186 Gaps: 21.55 % Invariant sites: 0.54 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6P4F2/4_raxmlng_ancestral/Q6P4F2.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_300621/phylogeny-snakemake/results/Q6P4F2/3_mltree/Q6P4F2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 47 / 3760 [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: -91707.935848 [00:00:00 -91707.935848] Initial branch length optimization [00:00:01 -88289.151669] Model parameter optimization (eps = 0.100000) [00:00:25] Tree #1, final logLikelihood: -87985.478967 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.231548,0.155291) (0.167565,0.242974) (0.275842,0.732473) (0.325045,2.219022) 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_300621/phylogeny-snakemake/results/Q6P4F2/4_raxmlng_ancestral/Q6P4F2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6P4F2/4_raxmlng_ancestral/Q6P4F2.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6P4F2/4_raxmlng_ancestral/Q6P4F2.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q6P4F2/4_raxmlng_ancestral/Q6P4F2.raxml.log Analysis started: 17-Jul-2021 07:59:50 / finished: 17-Jul-2021 08:00:17 Elapsed time: 27.057 seconds