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 12-Jul-2021 17:31:00 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/2_msa/Q96CM4_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/3_mltree/Q96CM4.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/4_raxmlng_ancestral/Q96CM4 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100260 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/Q96CM4/2_msa/Q96CM4_nogap_msa.fasta [00:00:00] Loaded alignment with 462 taxa and 212 sites WARNING: Sequences tr_A0A1L1RYW6_A0A1L1RYW6_CHICK_9031 and tr_U3HZ60_U3HZ60_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A2I3STE4_A0A2I3STE4_PANTR_9598 and tr_A0A2R9C0H1_A0A2R9C0H1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R1V8_H2R1V8_PANTR_9598 and sp_Q96CM4_NXNL1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A0E0FUC5_A0A0E0FUC5_ORYNI_4536 and tr_B8AAX8_B8AAX8_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0FUC5_A0A0E0FUC5_ORYNI_4536 and tr_I1NSC6_I1NSC6_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0FUC5_A0A0E0FUC5_ORYNI_4536 and tr_A0A0E0N3J1_A0A0E0N3J1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0FUC5_A0A0E0FUC5_ORYNI_4536 and tr_A0A0D3EUZ5_A0A0D3EUZ5_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0FUC5_A0A0E0FUC5_ORYNI_4536 and sp_Q0JIL1_NRX2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0H5R5_A0A0E0H5R5_ORYNI_4536 and tr_B8ATV8_B8ATV8_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0H5R5_A0A0E0H5R5_ORYNI_4536 and tr_I1PPJ9_I1PPJ9_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0H5R5_A0A0E0H5R5_ORYNI_4536 and tr_A0A0E0PDV1_A0A0E0PDV1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0H5R5_A0A0E0H5R5_ORYNI_4536 and tr_A0A0D3FZZ1_A0A0D3FZZ1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0H5R5_A0A0E0H5R5_ORYNI_4536 and sp_Q7XPE8_NRX3_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0K0K0J2_A0A0K0K0J2_BRUMA_6279 and tr_A0A0N4TBR2_A0A0N4TBR2_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A0K0K0J2_A0A0K0K0J2_BRUMA_6279 and tr_A0A0R3R431_A0A0R3R431_9BILA_42155 are exactly identical! WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V0SM09_A0A0V0SM09_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V1DG63_A0A0V1DG63_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V0WQT2_A0A0V0WQT2_9BILA_92179 are exactly identical! WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V0VF13_A0A0V0VF13_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V1LQ31_A0A0V1LQ31_9BILA_6335 are exactly identical! WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V1A2V4_A0A0V1A2V4_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V1PP89_A0A0V1PP89_9BILA_92180 are exactly identical! WARNING: Sequences tr_E5SC51_E5SC51_TRISP_6334 and tr_A0A0V0UCD0_A0A0V0UCD0_9BILA_144512 are exactly identical! WARNING: Sequences tr_I1PC51_I1PC51_ORYGL_4538 and tr_A0A0D3FJM5_A0A0D3FJM5_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A8WTV6_A8WTV6_CAEBR_6238 and tr_A0A2G5V3V4_A0A2G5V3V4_9PELO_1611254 are exactly identical! WARNING: Sequences tr_A0A044VHD1_A0A044VHD1_ONCVO_6282 and tr_A0A182EJ26_A0A182EJ26_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A044VHD7_A0A044VHD7_ONCVO_6282 and tr_A0A182EI61_A0A182EI61_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0D9R4R0_A0A0D9R4R0_CHLSB_60711 and tr_A0A2K5N2K4_A0A2K5N2K4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9R4R0_A0A0D9R4R0_CHLSB_60711 and tr_A0A2K6AVK7_A0A2K6AVK7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D2NXV3_A0A0D2NXV3_GOSRA_29730 and tr_A0A1U8NN36_A0A1U8NN36_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0V1D3L6_A0A0V1D3L6_TRIBR_45882 and tr_A0A0V0WJ51_A0A0V0WJ51_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1D3L6_A0A0V1D3L6_TRIBR_45882 and tr_A0A0V0VDC8_A0A0V0VDC8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D3L6_A0A0V1D3L6_TRIBR_45882 and tr_A0A0V1L3U2_A0A0V1L3U2_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1D3L6_A0A0V1D3L6_TRIBR_45882 and tr_A0A0V0TXP9_A0A0V0TXP9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0VCE7_A0A0V0VCE7_9BILA_181606 and tr_A0A0V0ZZB5_A0A0V0ZZB5_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0VCE7_A0A0V0VCE7_9BILA_181606 and tr_A0A0V0TXU1_A0A0V0TXU1_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0YIH6_A0A0V0YIH6_TRIPS_6337 and tr_A0A0V1NA69_A0A0V1NA69_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V0YIH6_A0A0V0YIH6_TRIPS_6337 and tr_A0A0V1I9F4_A0A0V1I9F4_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S4BT60_A0A1S4BT60_TOBAC_4097 and tr_A0A1U7Y411_A0A1U7Y411_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CQA3_A0A1S4CQA3_TOBAC_4097 and tr_A0A1U7V7K4_A0A1U7V7K4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1I7VQM2_A0A1I7VQM2_LOALO_7209 and tr_A0A1I7VWJ0_A0A1I7VWJ0_LOALO_7209 are exactly identical! WARNING: Sequences tr_A0A2D0Q3D2_A0A2D0Q3D2_ICTPU_7998 and tr_A0A2D0Q4K5_A0A2D0Q4K5_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 42 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/Q96CM4/4_raxmlng_ancestral/Q96CM4.raxml.reduced.phy Alignment comprises 1 partitions and 212 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 212 Gaps: 28.54 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/4_raxmlng_ancestral/Q96CM4.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/Q96CM4/3_mltree/Q96CM4.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 53 / 4240 [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: -50188.386763 [00:00:00 -50188.386763] Initial branch length optimization [00:00:00 -49460.268386] Model parameter optimization (eps = 0.100000) [00:00:09] Tree #1, final logLikelihood: -49294.079259 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.099712,0.242586) (0.105684,0.348379) (0.316288,0.726383) (0.478316,1.482801) 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/Q96CM4/4_raxmlng_ancestral/Q96CM4.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/4_raxmlng_ancestral/Q96CM4.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/4_raxmlng_ancestral/Q96CM4.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q96CM4/4_raxmlng_ancestral/Q96CM4.raxml.log Analysis started: 12-Jul-2021 17:31:00 / finished: 12-Jul-2021 17:31:11 Elapsed time: 10.697 seconds