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 03-Jun-2021 02:00:36 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04424/2_msa/P04424_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04424/3_mltree/P04424.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04424/4_raxmlng_ancestral/P04424 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622674836 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/P04424/2_msa/P04424_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 464 sites WARNING: Sequences tr_J3KJ23_J3KJ23_COCIM_246410 and tr_A0A0J6Y3V6_A0A0J6Y3V6_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QVU4_B6QVU4_TALMQ_441960 and tr_A0A093VTD7_A0A093VTD7_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2W7L1_B2W7L1_PYRTR_426418 and tr_A0A2W1D4D9_A0A2W1D4D9_9PLEO_45151 are exactly identical! WARNING: Sequences tr_Q7S4I8_Q7S4I8_NEUCR_367110 and tr_G4UXL7_G4UXL7_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8NTR5_B8NTR5_ASPFN_332952 and tr_Q2U4A8_Q2U4A8_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NTR5_B8NTR5_ASPFN_332952 and tr_A0A0F0IJU4_A0A0F0IJU4_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8NTR5_B8NTR5_ASPFN_332952 and tr_A0A1S9DHK6_A0A1S9DHK6_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8NTR5_B8NTR5_ASPFN_332952 and tr_A0A2G7G1I1_A0A2G7G1I1_9EURO_656916 are exactly identical! WARNING: Sequences tr_H2RBX6_H2RBX6_PANTR_9598 and tr_A0A2R9BWX4_A0A2R9BWX4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0GLB2_A0A0E0GLB2_ORYNI_4536 and tr_A0A0D3FHJ1_A0A0D3FHJ1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A2Q942_A2Q942_ASPNC_425011 and tr_G3XSS3_G3XSS3_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2Q942_A2Q942_ASPNC_425011 and tr_A0A319AL13_A0A319AL13_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7X9G3_G7X9G3_ASPKW_1033177 and tr_A0A100I374_A0A100I374_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7X9G3_G7X9G3_ASPKW_1033177 and tr_A0A146FPK0_A0A146FPK0_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7X9G3_G7X9G3_ASPKW_1033177 and tr_A0A1L9NC31_A0A1L9NC31_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G7X9G3_G7X9G3_ASPKW_1033177 and tr_A0A317WF52_A0A317WF52_9EURO_1448314 are exactly identical! WARNING: Sequences tr_F4NS11_F4NS11_BATDJ_684364 and tr_A0A177W9V7_A0A177W9V7_BATDE_403673 are exactly identical! WARNING: Sequences tr_I1PAK6_I1PAK6_ORYGL_4538 and tr_A0A0E0NU02_A0A0E0NU02_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1PAK6_I1PAK6_ORYGL_4538 and tr_A0A0D9Z660_A0A0D9Z660_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F9XP57_F9XP57_ZYMTI_336722 and tr_A0A1X7S8F1_A0A1X7S8F1_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2YYL9_G2YYL9_BOTF4_999810 and tr_M7TZ45_M7TZ45_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_N4U3N7_N4U3N7_FUSC1_1229664 and tr_X0D1W4_X0D1W4_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_N4U3N7_N4U3N7_FUSC1_1229664 and tr_Q9C1T0_Q9C1T0_FUSOX_5507 are exactly identical! WARNING: Sequences tr_M2TK95_M2TK95_COCSN_665912 and tr_W6YBB2_W6YBB2_COCCA_930089 are exactly identical! WARNING: Sequences tr_V2X6U5_V2X6U5_MONRO_1381753 and tr_A0A0W0G9W0_A0A0W0G9W0_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2RDX2_W2RDX2_PHYPN_761204 and tr_A0A0W8C2W7_A0A0W8C2W7_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2RDX2_W2RDX2_PHYPN_761204 and tr_W2M4L4_W2M4L4_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A3B6HQN3_A0A3B6HQN3_WHEAT_4565 and tr_A0A3B6JL49_A0A3B6JL49_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A015IQV5_A0A015IQV5_9GLOM_1432141 and tr_A0A2I1EMD9_A0A2I1EMD9_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015IQV5_A0A015IQV5_9GLOM_1432141 and tr_U9STD7_U9STD7_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A067GNB8_A0A067GNB8_CITSI_2711 and tr_V4TBQ3_V4TBQ3_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A094F391_A0A094F391_9PEZI_1420912 and tr_A0A1B8GGF3_A0A1B8GGF3_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094F391_A0A094F391_9PEZI_1420912 and tr_A0A1B8EX51_A0A1B8EX51_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_A0A1S4BZ30_A0A1S4BZ30_TOBAC_4097 and tr_A0A1U7XWD9_A0A1U7XWD9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1R3RMZ4_A0A1R3RMZ4_ASPC5_602072 and tr_A0A317X8N6_A0A317X8N6_9EURO_1450535 are exactly identical! WARNING: Duplicate sequences found: 35 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/P04424/4_raxmlng_ancestral/P04424.raxml.reduced.phy Alignment comprises 1 partitions and 464 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 464 Gaps: 9.41 % Invariant sites: 0.22 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04424/4_raxmlng_ancestral/P04424.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/P04424/3_mltree/P04424.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 116 / 9280 [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: -188082.655853 [00:00:00 -188082.655853] Initial branch length optimization [00:00:00 -187602.618436] Model parameter optimization (eps = 0.100000) [00:00:25] Tree #1, final logLikelihood: -186804.632485 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.245605,0.396741) (0.348796,0.526213) (0.233485,1.011699) (0.172115,2.805117) 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/P04424/4_raxmlng_ancestral/P04424.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04424/4_raxmlng_ancestral/P04424.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04424/4_raxmlng_ancestral/P04424.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04424/4_raxmlng_ancestral/P04424.raxml.log Analysis started: 03-Jun-2021 02:00:36 / finished: 03-Jun-2021 02:01:05 Elapsed time: 28.978 seconds Consumed energy: 2.162 Wh