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 14:02:06 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24752/2_msa/P24752_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24752/3_mltree/P24752.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24752/4_raxmlng_ancestral/P24752 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804526 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/P24752/2_msa/P24752_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 427 sites WARNING: Sequences tr_B6Q7E1_B6Q7E1_TALMQ_441960 and tr_A0A093Y570_A0A093Y570_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2VZ30_B2VZ30_PYRTR_426418 and tr_A0A2W1E4Z0_A0A2W1E4Z0_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G2XG43_G2XG43_VERDV_498257 and tr_A0A0G4MGW8_A0A0G4MGW8_9PEZI_100787 are exactly identical! WARNING: Sequences tr_B8NXL2_B8NXL2_ASPFN_332952 and tr_A0A1S9DGK4_A0A1S9DGK4_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_H2Q4P9_H2Q4P9_PANTR_9598 and sp_P24752_THIL_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q4P9_H2Q4P9_PANTR_9598 and tr_A0A2R9B6L3_A0A2R9B6L3_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FJY6_F9FJY6_FUSOF_660025 and tr_A0A0D2XPN3_A0A0D2XPN3_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FJY6_F9FJY6_FUSOF_660025 and tr_N4U1B1_N4U1B1_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FJY6_F9FJY6_FUSOF_660025 and tr_X0C154_X0C154_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FJY6_F9FJY6_FUSOF_660025 and tr_A0A2H3TLS2_A0A2H3TLS2_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FJY6_F9FJY6_FUSOF_660025 and tr_A0A2H3HKY2_A0A2H3HKY2_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FNR3_F9FNR3_FUSOF_660025 and tr_W7MC27_W7MC27_GIBM7_334819 are exactly identical! WARNING: Sequences tr_F9FNR3_F9FNR3_FUSOF_660025 and tr_A0A0D2XX83_A0A0D2XX83_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FNR3_F9FNR3_FUSOF_660025 and tr_S0DMY6_S0DMY6_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9FNR3_F9FNR3_FUSOF_660025 and tr_N4TL10_N4TL10_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FNR3_F9FNR3_FUSOF_660025 and tr_X0C3N6_X0C3N6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FNR3_F9FNR3_FUSOF_660025 and tr_A0A2H3T7S2_A0A2H3T7S2_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FNR3_F9FNR3_FUSOF_660025 and tr_A0A2H3HP50_A0A2H3HP50_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FNR3_F9FNR3_FUSOF_660025 and tr_A0A2K0W1U7_A0A2K0W1U7_GIBNY_42673 are exactly identical! WARNING: Sequences tr_F9FNR3_F9FNR3_FUSOF_660025 and tr_A0A365N8Y2_A0A365N8Y2_GIBIN_948311 are exactly identical! WARNING: Sequences tr_E9F1J9_E9F1J9_METRA_655844 and tr_A0A0D9P1Y0_A0A0D9P1Y0_METAN_1291518 are exactly identical! WARNING: Sequences tr_A0A0E0FF59_A0A0E0FF59_ORYNI_4536 and tr_B8ACV4_B8ACV4_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0IGV1_A0A0E0IGV1_ORYNI_4536 and tr_A2YYZ3_A2YYZ3_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0IGV1_A0A0E0IGV1_ORYNI_4536 and tr_A0A0D3H464_A0A0D3H464_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0IGV1_A0A0E0IGV1_ORYNI_4536 and tr_A0A0E0B067_A0A0E0B067_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0IGV1_A0A0E0IGV1_ORYNI_4536 and tr_Q6K3Z3_Q6K3Z3_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F6XC62_F6XC62_MACMU_9544 and tr_G7PNQ8_G7PNQ8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6XC62_F6XC62_MACMU_9544 and tr_A0A2K6CWR8_A0A2K6CWR8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7XYD6_G7XYD6_ASPKW_1033177 and tr_A0A146G2K0_A0A146G2K0_9EURO_1069201 are exactly identical! WARNING: Sequences tr_F4NXY0_F4NXY0_BATDJ_684364 and tr_A0A177WMG2_A0A177WMG2_BATDE_403673 are exactly identical! WARNING: Sequences tr_I1NJM5_I1NJM5_ORYGL_4538 and tr_A0A0D3EIT1_A0A0D3EIT1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0MQG9_A0A0E0MQG9_ORYRU_4529 and tr_Q9ASK5_Q9ASK5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F9XC90_F9XC90_ZYMTI_336722 and tr_A0A1X7RTQ5_A0A1X7RTQ5_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2XUB5_G2XUB5_BOTF4_999810 and tr_M7UEH3_M7UEH3_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_G2YZ82_G2YZ82_BOTF4_999810 and tr_M7TVA7_M7TVA7_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SCZ3_F2SCZ3_TRIRC_559305 and tr_A0A178ERN7_A0A178ERN7_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G3XQ18_G3XQ18_ASPNA_380704 and tr_A0A319AJ70_A0A319AJ70_9EURO_1450533 are exactly identical! WARNING: Sequences tr_S0DW03_S0DW03_GIBF5_1279085 and tr_A0A365NEH3_A0A365NEH3_GIBIN_948311 are exactly identical! WARNING: Sequences tr_U5H9N7_U5H9N7_USTV1_683840 and tr_A0A2X0LVN2_A0A2X0LVN2_9BASI_796604 are exactly identical! WARNING: Sequences tr_V2Z127_V2Z127_MONRO_1381753 and tr_A0A0W0FCZ4_A0A0W0FCZ4_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2RHM7_W2RHM7_PHYPN_761204 and tr_W2HLV1_W2HLV1_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0A1N7C7_A0A0A1N7C7_9FUNG_58291 and tr_A0A367JLP4_A0A367JLP4_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A164ZRC0_A0A164ZRC0_9HOMO_1314777 and tr_A0A166BW45_A0A166BW45_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A2V5HMP9_A0A2V5HMP9_9EURO_1450541 and tr_A0A2V5H2A4_A0A2V5H2A4_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 44 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/P24752/4_raxmlng_ancestral/P24752.raxml.reduced.phy Alignment comprises 1 partitions and 427 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 427 Gaps: 6.70 % Invariant sites: 2.58 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24752/4_raxmlng_ancestral/P24752.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/P24752/3_mltree/P24752.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 107 / 8560 [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: -170413.264275 [00:00:00 -170413.264275] Initial branch length optimization [00:00:01 -169975.142565] Model parameter optimization (eps = 0.100000) [00:00:26] Tree #1, final logLikelihood: -169504.329901 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.222917,0.315246) (0.331926,0.478577) (0.228238,1.155571) (0.216919,2.337872) 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/P24752/4_raxmlng_ancestral/P24752.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24752/4_raxmlng_ancestral/P24752.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24752/4_raxmlng_ancestral/P24752.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P24752/4_raxmlng_ancestral/P24752.raxml.log Analysis started: 04-Jun-2021 14:02:06 / finished: 04-Jun-2021 14:02:37 Elapsed time: 30.545 seconds