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 02:47:52 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60931/2_msa/O60931_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60931/3_mltree/O60931.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60931/4_raxmlng_ancestral/O60931 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677672 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/O60931/2_msa/O60931_nogap_msa.fasta [00:00:00] Loaded alignment with 983 taxa and 367 sites WARNING: Sequences tr_B6HWC2_B6HWC2_PENRW_500485 and tr_W6QA09_W6QA09_PENRF_1365484 are exactly identical! WARNING: Sequences tr_B6HWC2_B6HWC2_PENRW_500485 and tr_A0A0G4PZF0_A0A0G4PZF0_PENCA_1429867 are exactly identical! WARNING: Sequences tr_A0A0E1RZ10_A0A0E1RZ10_COCIM_246410 and tr_A0A0J6YDI1_A0A0J6YDI1_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QMP2_B6QMP2_TALMQ_441960 and tr_A0A093UYA0_A0A093UYA0_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WAH2_B2WAH2_PYRTR_426418 and tr_A0A2W1EC70_A0A2W1EC70_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B5DVI6_B5DVI6_DROPS_46245 and tr_B4GZF9_B4GZF9_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A179ULA6_A0A179ULA6_BLAGS_559298 and tr_C5GBB2_C5GBB2_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2QBW8_H2QBW8_PANTR_9598 and tr_A0A2R9BNZ7_A0A2R9BNZ7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A2Q8N4_A2Q8N4_ASPNC_425011 and tr_G3XSA5_G3XSA5_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2Q8N4_A2Q8N4_ASPNC_425011 and tr_A0A318ZTI8_A0A318ZTI8_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7X9J8_G7X9J8_ASPKW_1033177 and tr_A0A124BUQ5_A0A124BUQ5_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7X9J8_G7X9J8_ASPKW_1033177 and tr_A0A1L9NCI0_A0A1L9NCI0_ASPTU_767770 are exactly identical! WARNING: Sequences tr_F4NY54_F4NY54_BATDJ_684364 and tr_A0A177WM02_A0A177WM02_BATDE_403673 are exactly identical! WARNING: Sequences tr_I1R5J4_I1R5J4_ORYGL_4538 and tr_A0A0E0RFY8_A0A0E0RFY8_ORYRU_4529 are exactly identical! WARNING: Sequences tr_I1R5J4_I1R5J4_ORYGL_4538 and tr_A0A0D3HTA4_A0A0D3HTA4_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1R5J4_I1R5J4_ORYGL_4538 and tr_Q2QTY6_Q2QTY6_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G2YV60_G2YV60_BOTF4_999810 and tr_M7TVK4_M7TVK4_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SUK2_F2SUK2_TRIRC_559305 and tr_A0A178F7Z3_A0A178F7Z3_TRIRU_5551 are exactly identical! WARNING: Sequences tr_A0A0D2XCP8_A0A0D2XCP8_FUSO4_426428 and tr_A0A2H3H458_A0A2H3H458_FUSOX_327505 are exactly identical! WARNING: Sequences tr_M4E9U8_M4E9U8_BRARP_51351 and tr_A0A078HVT9_A0A078HVT9_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4ENG1_M4ENG1_BRARP_51351 and tr_A0A078EF13_A0A078EF13_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4ENG1_M4ENG1_BRARP_51351 and tr_A0A0D3C0W2_A0A0D3C0W2_BRAOL_109376 are exactly identical! WARNING: Sequences tr_U5GZM2_U5GZM2_USTV1_683840 and tr_A0A2X0MQ73_A0A2X0MQ73_9BASI_796604 are exactly identical! WARNING: Sequences tr_W2PYY1_W2PYY1_PHYPN_761204 and tr_A0A0W8BVJ1_A0A0W8BVJ1_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PYY1_W2PYY1_PHYPN_761204 and tr_W2N2U0_W2N2U0_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A067EAG1_A0A067EAG1_CITSI_2711 and tr_V4U3E3_V4U3E3_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A078HF03_A0A078HF03_BRANA_3708 and tr_A0A0D3C095_A0A0D3C095_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A094EGW3_A0A094EGW3_9PEZI_1420912 and tr_A0A1B8G898_A0A1B8G898_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094EGW3_A0A094EGW3_9PEZI_1420912 and tr_A0A1B8CIK2_A0A1B8CIK2_9PEZI_1622147 are exactly identical! WARNING: Sequences tr_A0A0F8W2V1_A0A0F8W2V1_9EURO_308745 and tr_A0A2T5M4D4_A0A2T5M4D4_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0V1CM59_A0A0V1CM59_TRIBR_45882 and tr_A0A0V0VCD8_A0A0V0VCD8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CM59_A0A0V1CM59_TRIBR_45882 and tr_A0A0V1L549_A0A0V1L549_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CM59_A0A0V1CM59_TRIBR_45882 and tr_A0A0V1PCH6_A0A0V1PCH6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CM59_A0A0V1CM59_TRIBR_45882 and tr_A0A0V0TVM3_A0A0V0TVM3_9BILA_144512 are exactly identical! WARNING: Sequences tr_I1RSK7_I1RSK7_GIBZE_229533 and tr_A0A2T4H3X7_A0A2T4H3X7_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A1S3YAM0_A0A1S3YAM0_TOBAC_4097 and tr_A0A1U7VWN9_A0A1U7VWN9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3YCV8_A0A1S3YCV8_TOBAC_4097 and tr_A0A1U7YNK0_A0A1U7YNK0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1R3RSA9_A0A1R3RSA9_ASPC5_602072 and tr_A0A317XFX1_A0A317XFX1_9EURO_1450535 are exactly identical! WARNING: Sequences tr_A0A2P5FBS8_A0A2P5FBS8_TREOI_63057 and tr_A0A2P5B5H4_A0A2P5B5H4_PARAD_3476 are exactly identical! WARNING: Duplicate sequences found: 39 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/O60931/4_raxmlng_ancestral/O60931.raxml.reduced.phy Alignment comprises 1 partitions and 367 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 367 Gaps: 32.39 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60931/4_raxmlng_ancestral/O60931.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/O60931/3_mltree/O60931.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 92 / 7360 [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: -180034.180211 [00:00:00 -180034.180211] Initial branch length optimization [00:00:01 -178254.988226] Model parameter optimization (eps = 0.100000) [00:00:37] Tree #1, final logLikelihood: -177657.782984 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.167728,0.327412) (0.277350,0.536815) (0.348356,1.110835) (0.206566,1.981121) 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/O60931/4_raxmlng_ancestral/O60931.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60931/4_raxmlng_ancestral/O60931.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60931/4_raxmlng_ancestral/O60931.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/O60931/4_raxmlng_ancestral/O60931.raxml.log Analysis started: 03-Jun-2021 02:47:52 / finished: 03-Jun-2021 02:48:33 Elapsed time: 41.159 seconds Consumed energy: 3.445 Wh