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 19-Jun-2021 19:55:22 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/2_msa/P35520_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/3_mltree/P35520.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/4_raxmlng_ancestral/P35520 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624121722 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_040621/phylogeny-snakemake/results/P35520/2_msa/P35520_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 551 sites WARNING: Sequences tr_A0A0E1RXA8_A0A0E1RXA8_COCIM_246410 and tr_A0A0J6Y8R5_A0A0J6Y8R5_COCIT_404692 are exactly identical! WARNING: Sequences tr_J3KI41_J3KI41_COCIM_246410 and tr_A0A0J6XXC5_A0A0J6XXC5_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6Q8U6_B6Q8U6_TALMQ_441960 and tr_A0A093VLK5_A0A093VLK5_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B8NBZ9_B8NBZ9_ASPFN_332952 and tr_A0A1S9DDX3_A0A1S9DDX3_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179V230_A0A179V230_BLAGS_559298 and tr_A0A179TU37_A0A179TU37_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9FKU0_F9FKU0_FUSOF_660025 and tr_A0A0D2XET1_A0A0D2XET1_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FKU0_F9FKU0_FUSOF_660025 and tr_N4UEW5_N4UEW5_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FKU0_F9FKU0_FUSOF_660025 and tr_X0C2V0_X0C2V0_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FKU0_F9FKU0_FUSOF_660025 and tr_A0A2H3T2R4_A0A2H3T2R4_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FKU0_F9FKU0_FUSOF_660025 and tr_A0A2H3HL31_A0A2H3HL31_FUSOX_327505 are exactly identical! WARNING: Sequences tr_C6HT32_C6HT32_AJECH_544712 and tr_F0U9F4_F0U9F4_AJEC8_544711 are exactly identical! WARNING: Sequences sp_P0DN79_CBSL_HUMAN_9606 and sp_P35520_CBS_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A2QKG7_A2QKG7_ASPNC_425011 and tr_G3XV50_G3XV50_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QKG7_A2QKG7_ASPNC_425011 and tr_A0A319AG86_A0A319AG86_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XHD7_G7XHD7_ASPKW_1033177 and tr_A0A317UYW7_A0A317UYW7_9EURO_1448314 are exactly identical! WARNING: Sequences tr_B8B3S9_B8B3S9_ORYSI_39946 and tr_Q5Z8Y9_Q5Z8Y9_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F4P4C4_F4P4C4_BATDJ_684364 and tr_A0A177WHG6_A0A177WHG6_BATDE_403673 are exactly identical! WARNING: Sequences tr_E3MMP8_E3MMP8_CAERE_31234 and tr_A0A261CTT1_A0A261CTT1_9PELO_1503980 are exactly identical! WARNING: Sequences tr_A8WRM3_A8WRM3_CAEBR_6238 and tr_A0A2G5SMB0_A0A2G5SMB0_9PELO_1611254 are exactly identical! WARNING: Sequences tr_F2SCU1_F2SCU1_TRIRC_559305 and tr_A0A178ETH1_A0A178ETH1_TRIRU_5551 are exactly identical! WARNING: Sequences tr_U5HEA6_U5HEA6_USTV1_683840 and tr_A0A2X0NVI0_A0A2X0NVI0_9BASI_796604 are exactly identical! WARNING: Sequences tr_V2XBC2_V2XBC2_MONRO_1381753 and tr_A0A0W0FZ85_A0A0W0FZ85_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2PM91_W2PM91_PHYPN_761204 and tr_A0A0W8CA49_A0A0W8CA49_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PM91_W2PM91_PHYPN_761204 and tr_W2KGB8_W2KGB8_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QNX4_W2QNX4_PHYPN_761204 and tr_W2HD38_W2HD38_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2RD14_W2RD14_PHYPN_761204 and tr_A0A0W8CS04_A0A0W8CS04_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2RD14_W2RD14_PHYPN_761204 and tr_W2LEI1_W2LEI1_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015JN67_A0A015JN67_9GLOM_1432141 and tr_U9TWG8_U9TWG8_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A0A1NEP6_A0A0A1NEP6_9FUNG_58291 and tr_A0A367K1Z4_A0A367K1Z4_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0V1CES5_A0A0V1CES5_TRIBR_45882 and tr_A0A0V0UX03_A0A0V0UX03_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CES5_A0A0V1CES5_TRIBR_45882 and tr_A0A0V1P796_A0A0V1P796_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CES5_A0A0V1CES5_TRIBR_45882 and tr_A0A0V0TUD0_A0A0V0TUD0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A2S7P969_A0A2S7P969_9HELO_2070414 and tr_A0A2S7Q571_A0A2S7Q571_9HELO_2070412 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_040621/phylogeny-snakemake/results/P35520/4_raxmlng_ancestral/P35520.raxml.reduced.phy Alignment comprises 1 partitions and 551 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 551 Gaps: 20.26 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/4_raxmlng_ancestral/P35520.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_040621/phylogeny-snakemake/results/P35520/3_mltree/P35520.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 138 / 11040 [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: -228948.392352 [00:00:00 -228948.392352] Initial branch length optimization [00:00:01 -228061.778271] Model parameter optimization (eps = 0.100000) [00:00:31] Tree #1, final logLikelihood: -227213.004811 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.180705,0.311235) (0.241385,0.371451) (0.260962,0.813332) (0.316948,2.025088) 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_040621/phylogeny-snakemake/results/P35520/4_raxmlng_ancestral/P35520.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/4_raxmlng_ancestral/P35520.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/4_raxmlng_ancestral/P35520.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P35520/4_raxmlng_ancestral/P35520.raxml.log Analysis started: 19-Jun-2021 19:55:22 / finished: 19-Jun-2021 19:55:58 Elapsed time: 36.474 seconds