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 14:17:42 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07550/2_msa/P07550_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07550/3_mltree/P07550.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07550/4_raxmlng_ancestral/P07550 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805462 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/P07550/2_msa/P07550_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 413 sites WARNING: Sequences tr_B4R032_B4R032_DROSI_7240 and sp_Q9VCZ3_OCTB1_DROME_7227 are exactly identical! WARNING: Sequences tr_B4R032_B4R032_DROSI_7240 and tr_B4HEA3_B4HEA3_DROSE_7238 are exactly identical! WARNING: Sequences tr_M3Z6H4_M3Z6H4_MUSPF_9669 and tr_A0A2Y9ITW1_A0A2Y9ITW1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z6H4_M3Z6H4_MUSPF_9669 and tr_A0A384C6Q9_A0A384C6Q9_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I2YZU4_A0A2I2YZU4_GORGO_9595 and tr_H2QS18_H2QS18_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YZU4_A0A2I2YZU4_GORGO_9595 and sp_P21728_DRD1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YZU4_A0A2I2YZU4_GORGO_9595 and tr_A0A2R8ZF27_A0A2R8ZF27_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QRR6_G3QRR6_GORGO_9595 and sp_P07550_ADRB2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RNJ9_G3RNJ9_GORGO_9595 and tr_A0A2J8NJA4_A0A2J8NJA4_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PH04_H2PH04_PONAB_9601 and tr_A0A2R9C269_A0A2R9C269_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PHF2_H2PHF2_PONAB_9601 and sp_O77680_DRD1_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PHF2_H2PHF2_PONAB_9601 and tr_G7P6Y1_G7P6Y1_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2PHF2_H2PHF2_PONAB_9601 and tr_A0A096MZY6_A0A096MZY6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PHF2_H2PHF2_PONAB_9601 and tr_A0A0D9RAW0_A0A0D9RAW0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2PHF2_H2PHF2_PONAB_9601 and tr_A0A2K5KKQ1_A0A2K5KKQ1_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2PHF2_H2PHF2_PONAB_9601 and tr_A0A2K6ATP0_A0A2K6ATP0_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PHF2_H2PHF2_PONAB_9601 and tr_A0A2K5XYI3_A0A2K5XYI3_MANLE_9568 are exactly identical! WARNING: Sequences tr_Q29BK0_Q29BK0_DROPS_46245 and tr_B4GP31_B4GP31_DROPE_7234 are exactly identical! WARNING: Sequences tr_F1PI21_F1PI21_CANLF_9615 and tr_A0A2U3WYJ9_A0A2U3WYJ9_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1PI21_F1PI21_CANLF_9615 and tr_A0A2U3XM84_A0A2U3XM84_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2I3T596_A0A2I3T596_PANTR_9598 and tr_A0A2R9CKI2_A0A2R9CKI2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QJW8_H2QJW8_PANTR_9598 and sp_P25100_ADA1D_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M4AYK8_M4AYK8_XIPMA_8083 and tr_A0A087YRH2_A0A087YRH2_POEFO_48698 are exactly identical! WARNING: Sequences tr_K1PY13_K1PY13_CRAGI_29159 and tr_K1QX81_K1QX81_CRAGI_29159 are exactly identical! WARNING: Sequences tr_A0A1D5QIZ4_A0A1D5QIZ4_MACMU_9544 and sp_P47899_ADRB1_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A1D5QIZ4_A0A1D5QIZ4_MACMU_9544 and tr_A0A2K5KWY9_A0A2K5KWY9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7H268_F7H268_MACMU_9544 and tr_A0A2K6AX76_A0A2K6AX76_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H268_F7H268_MACMU_9544 and tr_A0A2K5XF26_A0A2K5XF26_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q28509_ADRB2_MACMU_9544 and tr_G7P8M7_G7P8M7_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q28509_ADRB2_MACMU_9544 and tr_A0A2K6AMT4_A0A2K6AMT4_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q28524_ADRB3_MACMU_9544 and tr_A0A2K5NSK0_A0A2K5NSK0_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q28524_ADRB3_MACMU_9544 and tr_A0A2K6CSA4_A0A2K6CSA4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F4WR97_F4WR97_ACREC_103372 and tr_A0A151ITH2_A0A151ITH2_9HYME_471704 are exactly identical! WARNING: Sequences tr_I3L8T6_I3L8T6_PIG_9823 and sp_P50130_DRD1_PIG_9823 are exactly identical! WARNING: Sequences tr_G7P8M6_G7P8M6_MACFA_9541 and tr_A0A2K5MCV0_A0A2K5MCV0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7P8M6_G7P8M6_MACFA_9541 and tr_A0A2K6CJI8_A0A2K6CJI8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7P8M6_G7P8M6_MACFA_9541 and tr_A0A2K5YPK8_A0A2K5YPK8_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7PCY2_G7PCY2_MACFA_9541 and tr_A0A2I3M6I3_A0A2I3M6I3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PCY2_G7PCY2_MACFA_9541 and tr_A0A2K6BZS0_A0A2K6BZS0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PCY2_G7PCY2_MACFA_9541 and tr_A0A2K6AD94_A0A2K6AD94_MANLE_9568 are exactly identical! WARNING: Sequences tr_F1MYI6_F1MYI6_BOVIN_9913 and sp_P18130_ADA1A_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A096N3C3_A0A096N3C3_PAPAN_9555 and tr_A0A2K5NYB0_A0A2K5NYB0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NVC9_A0A096NVC9_PAPAN_9555 and tr_A0A2K6DY91_A0A2K6DY91_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A151M6R6_A0A151M6R6_ALLMI_8496 and tr_A0A1U7SDX7_A0A1U7SDX7_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091WUI3_A0A091WUI3_NIPNI_128390 and tr_A0A087REN6_A0A087REN6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091WJB7_A0A091WJB7_OPIHO_30419 and tr_A0A0A0AHT7_A0A0A0AHT7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0MML6_A0A2I0MML6_COLLI_8932 and tr_A0A1V4JKG9_A0A1V4JKG9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1U7Q2D3_A0A1U7Q2D3_MESAU_10036 and sp_P18841_ADA1B_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A1U7Q3C3_A0A1U7Q3C3_MESAU_10036 and sp_P04274_ADRB2_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A226N274_A0A226N274_CALSU_9009 and tr_A0A226PNI9_A0A226PNI9_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5L4H5_A0A2K5L4H5_CERAT_9531 and tr_A0A2K5XIQ5_A0A2K5XIQ5_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 51 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/P07550/4_raxmlng_ancestral/P07550.raxml.reduced.phy Alignment comprises 1 partitions and 413 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 413 Gaps: 19.17 % Invariant sites: 1.21 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07550/4_raxmlng_ancestral/P07550.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/P07550/3_mltree/P07550.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 104 / 8320 [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: -139676.957929 [00:00:00 -139676.957929] Initial branch length optimization [00:00:01 -129067.591194] Model parameter optimization (eps = 0.100000) [00:00:34] Tree #1, final logLikelihood: -128778.722203 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.198074,0.147311) (0.209577,0.246471) (0.276529,0.785506) (0.315820,2.222633) 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/P07550/4_raxmlng_ancestral/P07550.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07550/4_raxmlng_ancestral/P07550.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07550/4_raxmlng_ancestral/P07550.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P07550/4_raxmlng_ancestral/P07550.raxml.log Analysis started: 04-Jun-2021 14:17:42 / finished: 04-Jun-2021 14:18:20 Elapsed time: 38.360 seconds