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 14:17:33 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34913/2_msa/P34913_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34913/3_mltree/P34913.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34913/4_raxmlng_ancestral/P34913 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805453 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/P34913/2_msa/P34913_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 555 sites WARNING: Sequences tr_G1RHG6_G1RHG6_NOMLE_61853 and tr_G3QD12_G3QD12_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RHG6_G1RHG6_NOMLE_61853 and sp_Q8IUS5_EPHX4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_J3K2C7_J3K2C7_COCIM_246410 and tr_A0A0J6YMZ4_A0A0J6YMZ4_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2WHB7_B2WHB7_PYRTR_426418 and tr_A0A2W1H6Z5_A0A2W1H6Z5_9PLEO_45151 are exactly identical! WARNING: Sequences tr_H2PZE0_H2PZE0_PANTR_9598 and tr_A0A2R9BZY5_A0A2R9BZY5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0FJJ5_A0A0E0FJJ5_ORYNI_4536 and tr_A2WN01_A2WN01_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GVX6_A0A0E0GVX6_ORYNI_4536 and tr_Q850X2_Q850X2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F7GW92_F7GW92_MACMU_9544 and tr_A0A096N6Q8_A0A096N6Q8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GW92_F7GW92_MACMU_9544 and tr_A0A0D9S6S2_A0A0D9S6S2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GW92_F7GW92_MACMU_9544 and tr_A0A2K5LE46_A0A2K5LE46_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GW92_F7GW92_MACMU_9544 and tr_A0A2K6CD51_A0A2K6CD51_MACNE_9545 are exactly identical! WARNING: Sequences tr_A2Y2M8_A2Y2M8_ORYSI_39946 and tr_Q0DJJ0_Q0DJJ0_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2ZN48_A2ZN48_ORYSI_39946 and tr_A0A0E0RKG9_A0A0E0RKG9_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2ZN48_A2ZN48_ORYSI_39946 and tr_A0A0D3HX56_A0A0D3HX56_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A2ZN48_A2ZN48_ORYSI_39946 and tr_A0A0E0BVP0_A0A0E0BVP0_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_I1NLZ9_I1NLZ9_ORYGL_4538 and tr_A0A0E0C4Z7_A0A0E0C4Z7_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_I1PH02_I1PH02_ORYGL_4538 and tr_A0A0D9ZFA2_A0A0D9ZFA2_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0MU35_A0A0E0MU35_ORYRU_4529 and tr_Q9S7P1_Q9S7P1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0MU43_A0A0E0MU43_ORYRU_4529 and tr_Q5NBT2_Q5NBT2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G2YSP7_G2YSP7_BOTF4_999810 and tr_M7THL9_M7THL9_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_W2Q1B7_W2Q1B7_PHYPN_761204 and tr_A0A0W8CHT2_A0A0W8CHT2_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2Q1B7_W2Q1B7_PHYPN_761204 and tr_W2N5E8_W2N5E8_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2R448_W2R448_PHYPN_761204 and tr_A0A0W8DD54_A0A0W8DD54_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2R448_W2R448_PHYPN_761204 and tr_W2GHL5_W2GHL5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A067H5C3_A0A067H5C3_CITSI_2711 and tr_V4U658_V4U658_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067HGN0_A0A067HGN0_CITSI_2711 and tr_V4TVV1_V4TVV1_9ROSI_85681 are exactly identical! WARNING: Sequences tr_X0D3K0_X0D3K0_FUSOX_1089458 and tr_A0A2H3TF42_A0A2H3TF42_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A0A0D2S289_A0A0D2S289_GOSRA_29730 and tr_A0A1U8IPF4_A0A1U8IPF4_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2SGS4_A0A0D2SGS4_GOSRA_29730 and tr_A0A1U8K347_A0A1U8K347_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A1S3WY84_A0A1S3WY84_TOBAC_4097 and tr_A0A1U7XFV6_A0A1U7XFV6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3YAP7_A0A1S3YAP7_TOBAC_4097 and tr_A0A1U7VGP3_A0A1U7VGP3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4B580_A0A1S4B580_TOBAC_4097 and tr_A0A1U7V6V6_A0A1U7V6V6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4BAP0_A0A1S4BAP0_TOBAC_4097 and tr_A0A1U7XZN9_A0A1U7XZN9_NICSY_4096 are exactly identical! WARNING: Duplicate sequences found: 33 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/P34913/4_raxmlng_ancestral/P34913.raxml.reduced.phy Alignment comprises 1 partitions and 555 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 555 Gaps: 44.27 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34913/4_raxmlng_ancestral/P34913.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/P34913/3_mltree/P34913.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 139 / 11120 [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: -205398.738740 [00:00:00 -205398.738740] Initial branch length optimization [00:00:01 -204108.035416] Model parameter optimization (eps = 0.100000) [00:00:54] Tree #1, final logLikelihood: -203512.020492 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.113676,0.545206) (0.195086,0.454312) (0.363357,0.873682) (0.327882,1.622339) 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/P34913/4_raxmlng_ancestral/P34913.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34913/4_raxmlng_ancestral/P34913.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34913/4_raxmlng_ancestral/P34913.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P34913/4_raxmlng_ancestral/P34913.raxml.log Analysis started: 04-Jun-2021 14:17:33 / finished: 04-Jun-2021 14:18:32 Elapsed time: 59.437 seconds