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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 02-Jun-2021 18:14:58 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15882/2_msa/P15882_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15882/3_mltree/P15882.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15882/4_raxmlng_ancestral/P15882 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622646898 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15882/2_msa/P15882_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 459 sites WARNING: Sequences tr_A0A2I3HQR3_A0A2I3HQR3_NOMLE_61853 and tr_A0A096N3U5_A0A096N3U5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HQR3_A0A2I3HQR3_NOMLE_61853 and tr_A0A2K5MMT3_A0A2K5MMT3_CERAT_9531 are exactly identical! WARNING: Sequences tr_B6QT21_B6QT21_TALMQ_441960 and tr_A0A093XW31_A0A093XW31_TALMA_1077442 are exactly identical! WARNING: Sequences tr_G3RAD4_G3RAD4_GORGO_9595 and tr_H2PMI5_H2PMI5_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RAD4_G3RAD4_GORGO_9595 and tr_H2R2E9_H2R2E9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RAD4_G3RAD4_GORGO_9595 and sp_P52757_CHIO_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RAD4_G3RAD4_GORGO_9595 and tr_F7DU99_F7DU99_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3RAD4_G3RAD4_GORGO_9595 and tr_A0A2R9AIP2_A0A2R9AIP2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RFQ2_G3RFQ2_GORGO_9595 and sp_B2RTY4_MYO9A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RFQ2_G3RFQ2_GORGO_9595 and tr_A0A2R9BBY5_A0A2R9BBY5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SBI9_G3SBI9_GORGO_9595 and tr_H2QJ06_H2QJ06_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SBI9_G3SBI9_GORGO_9595 and sp_P15882_CHIN_HUMAN_9606 are exactly identical! WARNING: Sequences tr_B8P0Y7_B8P0Y7_POSPM_561896 and tr_B8PK46_B8PK46_POSPM_561896 are exactly identical! WARNING: Sequences tr_B8NUZ1_B8NUZ1_ASPFN_332952 and tr_Q2U511_Q2U511_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NUZ1_B8NUZ1_ASPFN_332952 and tr_A0A1S9DIS5_A0A1S9DIS5_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_F7B042_F7B042_MACMU_9544 and tr_A0A0D9QUL6_A0A0D9QUL6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7B042_F7B042_MACMU_9544 and tr_A0A2K5LLX3_A0A2K5LLX3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7XFP6_G7XFP6_ASPKW_1033177 and tr_A0A317UYD0_A0A317UYD0_9EURO_1448314 are exactly identical! WARNING: Sequences tr_G7XNV7_G7XNV7_ASPKW_1033177 and tr_G3YHD0_G3YHD0_ASPNA_380704 are exactly identical! WARNING: Sequences tr_G7XNV7_G7XNV7_ASPKW_1033177 and tr_A0A100IIE9_A0A100IIE9_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XNV7_G7XNV7_ASPKW_1033177 and tr_A0A1L9NPF1_A0A1L9NPF1_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G7XNV7_G7XNV7_ASPKW_1033177 and tr_A0A319AFC5_A0A319AFC5_9EURO_1450533 are exactly identical! WARNING: Sequences tr_A0A287APY3_A0A287APY3_PIG_9823 and tr_A0A2U3ZPH2_A0A2U3ZPH2_ODORO_9708 are exactly identical! WARNING: Sequences tr_A8XLU9_A8XLU9_CAEBR_6238 and tr_A0A2G5UMW2_A0A2G5UMW2_9PELO_1611254 are exactly identical! WARNING: Sequences tr_F2SH16_F2SH16_TRIRC_559305 and tr_A0A178F0Q0_A0A178F0Q0_TRIRU_5551 are exactly identical! WARNING: Sequences tr_A0A044UTH6_A0A044UTH6_ONCVO_6282 and tr_A0A182E3L0_A0A182E3L0_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0F8XAF2_A0A0F8XAF2_9EURO_308745 and tr_A0A2T5M2J2_A0A2T5M2J2_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A091JAG8_A0A091JAG8_EGRGA_188379 and tr_A0A087R0N8_A0A087R0N8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JH32_A0A091JH32_EGRGA_188379 and tr_A0A091UU05_A0A091UU05_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091V4G4_A0A091V4G4_NIPNI_128390 and tr_A0A091WGW6_A0A091WGW6_OPIHO_30419 are exactly identical! WARNING: Sequences tr_W6Y492_W6Y492_COCCA_930089 and tr_W6YUG0_W6YUG0_COCMI_930090 are exactly identical! WARNING: Sequences tr_A0A0V1CUP5_A0A0V1CUP5_TRIBR_45882 and tr_A0A0V1PQ30_A0A0V1PQ30_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CUP5_A0A0V1CUP5_TRIBR_45882 and tr_A0A0V0TQN8_A0A0V0TQN8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A100IP11_A0A100IP11_ASPNG_5061 and tr_A0A1L9N2P4_A0A1L9N2P4_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A0E0SKR3_A0A0E0SKR3_GIBZE_229533 and tr_A0A2T4GLX9_A0A2T4GLX9_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A226MVN1_A0A226MVN1_CALSU_9009 and tr_A0A226P4L8_A0A226P4L8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NE75_A0A226NE75_CALSU_9009 and tr_A0A226PDI3_A0A226PDI3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3BW51_A0A2H3BW51_9AGAR_1076256 and tr_A0A284QLT2_A0A284QLT2_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2D0S770_A0A2D0S770_ICTPU_7998 and tr_A0A2D0S781_A0A2D0S781_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SCM0_A0A2D0SCM0_ICTPU_7998 and tr_A0A2D0SDD2_A0A2D0SDD2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SCM0_A0A2D0SCM0_ICTPU_7998 and tr_A0A2D0SDZ1_A0A2D0SDZ1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2N5S8F8_A0A2N5S8F8_9BASI_200324 and tr_A0A2N5UIC1_A0A2N5UIC1_9BASI_200324 are exactly identical! WARNING: Sequences tr_A0A2U4AAZ6_A0A2U4AAZ6_TURTR_9739 and tr_A0A2Y9MTT5_A0A2Y9MTT5_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4AAZ6_A0A2U4AAZ6_TURTR_9739 and tr_A0A2Y9SNZ7_A0A2Y9SNZ7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4AJC0_A0A2U4AJC0_TURTR_9739 and tr_A0A2Y9N7Z8_A0A2Y9N7Z8_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 45 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15882/4_raxmlng_ancestral/P15882.raxml.reduced.phy Alignment comprises 1 partitions and 459 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 459 Gaps: 19.09 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15882/4_raxmlng_ancestral/P15882.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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15882/3_mltree/P15882.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 115 / 9200 [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: -198674.979291 [00:00:00 -198674.979291] Initial branch length optimization [00:00:01 -197649.146215] Model parameter optimization (eps = 0.100000) [00:00:33] Tree #1, final logLikelihood: -196766.847028 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.169407,0.483444) (0.131939,0.482964) (0.392846,0.913647) (0.305808,1.620157) 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15882/4_raxmlng_ancestral/P15882.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15882/4_raxmlng_ancestral/P15882.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15882/4_raxmlng_ancestral/P15882.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15882/4_raxmlng_ancestral/P15882.raxml.log Analysis started: 02-Jun-2021 18:14:58 / finished: 02-Jun-2021 18:15:36 Elapsed time: 37.985 seconds Consumed energy: 3.144 Wh