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 02-Jun-2021 14:10:30 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P16219/2_msa/P16219_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P16219/3_mltree/P16219.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P16219/4_raxmlng_ancestral/P16219 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622632230 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/P16219/2_msa/P16219_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 412 sites WARNING: Sequences tr_J3KAZ8_J3KAZ8_COCIM_246410 and tr_E9CY24_E9CY24_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3KAZ8_J3KAZ8_COCIM_246410 and tr_A0A0J6YK26_A0A0J6YK26_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QAV8_B6QAV8_TALMQ_441960 and tr_A0A093VF69_A0A093VF69_TALMA_1077442 are exactly identical! WARNING: Sequences tr_G3QI49_G3QI49_GORGO_9595 and tr_H2Q719_H2Q719_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QI49_G3QI49_GORGO_9595 and tr_A0A0D9S4L4_A0A0D9S4L4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QI49_G3QI49_GORGO_9595 and tr_A0A2R8ZI63_A0A2R8ZI63_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q294T1_Q294T1_DROPS_46245 and tr_B4GMN1_B4GMN1_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q2M0E5_Q2M0E5_DROPS_46245 and tr_B4GRR0_B4GRR0_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8MZJ2_B8MZJ2_ASPFN_332952 and tr_Q2UQH2_Q2UQH2_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8MZJ2_B8MZJ2_ASPFN_332952 and tr_A0A0F0I4V8_A0A0F0I4V8_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8MZJ2_B8MZJ2_ASPFN_332952 and tr_A0A2G7FVA5_A0A2G7FVA5_9EURO_656916 are exactly identical! WARNING: Sequences tr_B8NUG5_B8NUG5_ASPFN_332952 and tr_A0A1S9DHY9_A0A1S9DHY9_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_F9FME3_F9FME3_FUSOF_660025 and tr_W7MLG8_W7MLG8_GIBM7_334819 are exactly identical! WARNING: Sequences tr_F9FME3_F9FME3_FUSOF_660025 and tr_A0A0D2XWP3_A0A0D2XWP3_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FME3_F9FME3_FUSOF_660025 and tr_N4UG87_N4UG87_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FME3_F9FME3_FUSOF_660025 and tr_X0CEF0_X0CEF0_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FME3_F9FME3_FUSOF_660025 and tr_A0A2H3T8U8_A0A2H3T8U8_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FME3_F9FME3_FUSOF_660025 and tr_A0A2H3I217_A0A2H3I217_FUSOX_327505 are exactly identical! WARNING: Sequences tr_E9F435_E9F435_METRA_655844 and tr_A0A0B4HE50_A0A0B4HE50_METMF_1276143 are exactly identical! WARNING: Sequences tr_C6HNX7_C6HNX7_AJECH_544712 and tr_F0UGF1_F0UGF1_AJEC8_544711 are exactly identical! WARNING: Sequences sp_P45954_ACDSB_HUMAN_9606 and tr_A0A2R9BHF8_A0A2R9BHF8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A2QAV9_A2QAV9_ASPNC_425011 and tr_G3XRH8_G3XRH8_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QAV9_A2QAV9_ASPNC_425011 and tr_A0A319B1G2_A0A319B1G2_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XID5_G7XID5_ASPKW_1033177 and tr_A0A124BVH4_A0A124BVH4_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XID5_G7XID5_ASPKW_1033177 and tr_A0A146FB81_A0A146FB81_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XID5_G7XID5_ASPKW_1033177 and tr_A0A1L9N6P9_A0A1L9N6P9_ASPTU_767770 are exactly identical! WARNING: Sequences tr_E3NRT0_E3NRT0_CAERE_31234 and tr_A0A261BU63_A0A261BU63_9PELO_1503980 are exactly identical! WARNING: Sequences tr_V2X593_V2X593_MONRO_1381753 and tr_A0A0W0EVM6_A0A0W0EVM6_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2Q743_W2Q743_PHYPN_761204 and tr_W2J1T5_W2J1T5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015I1G5_A0A015I1G5_9GLOM_1432141 and tr_A0A2I1EFH5_A0A2I1EFH5_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015I1G5_A0A015I1G5_9GLOM_1432141 and tr_U9SXE2_U9SXE2_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015JR09_A0A015JR09_9GLOM_1432141 and tr_A0A2H5TP58_A0A2H5TP58_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A0F0ILJ7_A0A0F0ILJ7_ASPPU_1403190 and tr_A0A2G7G4U0_A0A2G7G4U0_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0F8WWW2_A0A0F8WWW2_9EURO_308745 and tr_A0A2T5M375_A0A2T5M375_9EURO_1392256 are exactly identical! WARNING: Sequences tr_I1RZ38_I1RZ38_GIBZE_229533 and tr_A0A2T4GDJ3_A0A2T4GDJ3_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A164VD59_A0A164VD59_9HOMO_1314777 and tr_A0A165Z246_A0A165Z246_9HOMO_1314776 are exactly identical! WARNING: Duplicate sequences found: 36 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/P16219/4_raxmlng_ancestral/P16219.raxml.reduced.phy Alignment comprises 1 partitions and 412 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 412 Gaps: 5.50 % Invariant sites: 1.21 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P16219/4_raxmlng_ancestral/P16219.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/P16219/3_mltree/P16219.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 103 / 8240 [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: -172409.491071 [00:00:00 -172409.491071] Initial branch length optimization [00:00:01 -171352.955622] Model parameter optimization (eps = 0.100000) [00:00:24] Tree #1, final logLikelihood: -170706.060448 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.242955,0.358140) (0.326335,0.482986) (0.229029,1.042258) (0.201681,2.561792) 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/P16219/4_raxmlng_ancestral/P16219.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P16219/4_raxmlng_ancestral/P16219.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P16219/4_raxmlng_ancestral/P16219.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P16219/4_raxmlng_ancestral/P16219.raxml.log Analysis started: 02-Jun-2021 14:10:30 / finished: 02-Jun-2021 14:10:58 Elapsed time: 28.212 seconds