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 02-Jun-2021 18:25:28 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48448/2_msa/P48448_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48448/3_mltree/P48448.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48448/4_raxmlng_ancestral/P48448 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647528 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/P48448/2_msa/P48448_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 385 sites WARNING: Sequences sp_A3RF36_AL3A1_CANLF_9615 and tr_E2RB52_E2RB52_CANLF_9615 are exactly identical! WARNING: Sequences tr_K7DDP9_K7DDP9_PANTR_9598 and tr_A0A2R9AZE0_A0A2R9AZE0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0IZ66_A0A0E0IZ66_ORYNI_4536 and tr_B8BJI2_B8BJI2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0IZ66_A0A0E0IZ66_ORYNI_4536 and tr_A0A0E0R528_A0A0E0R528_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0IZ66_A0A0E0IZ66_ORYNI_4536 and tr_A0A0D3HJ19_A0A0D3HJ19_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0IZ66_A0A0E0IZ66_ORYNI_4536 and tr_A0A0E0BG62_A0A0E0BG62_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0IZ66_A0A0E0IZ66_ORYNI_4536 and tr_Q53NG8_Q53NG8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A1D5QTX0_A0A1D5QTX0_MACMU_9544 and tr_A0A2I3LLB9_A0A2I3LLB9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QTX0_A0A1D5QTX0_MACMU_9544 and tr_A0A2K5LLA3_A0A2K5LLA3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7BG63_F7BG63_MACMU_9544 and tr_A0A0D9R651_A0A0D9R651_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7C1D1_F7C1D1_MACMU_9544 and tr_G7PTU8_G7PTU8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7C1D1_F7C1D1_MACMU_9544 and tr_A0A2I3MS78_A0A2I3MS78_PAPAN_9555 are exactly identical! WARNING: Sequences tr_Q71LY7_Q71LY7_ORYSI_39946 and tr_I1PNG2_I1PNG2_ORYGL_4538 are exactly identical! WARNING: Sequences tr_Q71LY7_Q71LY7_ORYSI_39946 and tr_Q7XR89_Q7XR89_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0PC54_A0A0E0PC54_ORYRU_4529 and tr_A0A0D3FYG7_A0A0D3FYG7_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0PC54_A0A0E0PC54_ORYRU_4529 and tr_A0A0D9ZNP0_A0A0D9ZNP0_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_E3LUS8_E3LUS8_CAERE_31234 and tr_A0A261BXG3_A0A261BXG3_9PELO_1503980 are exactly identical! WARNING: Sequences tr_B3S5R6_B3S5R6_TRIAD_10228 and tr_A0A369RWV5_A0A369RWV5_9METZ_287889 are exactly identical! WARNING: Sequences tr_M4DC10_M4DC10_BRARP_51351 and tr_A0A078HGP8_A0A078HGP8_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4ETS3_M4ETS3_BRARP_51351 and tr_A0A0D3CFG2_A0A0D3CFG2_BRAOL_109376 are exactly identical! WARNING: Sequences tr_M7ZQL2_M7ZQL2_TRIUA_4572 and tr_A0A3B6HY41_A0A3B6HY41_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A015JW40_A0A015JW40_9GLOM_1432141 and tr_A0A2H5U2C8_A0A2H5U2C8_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015LAX1_A0A015LAX1_9GLOM_1432141 and tr_A0A2I1GB59_A0A2I1GB59_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015LAX1_A0A015LAX1_9GLOM_1432141 and tr_U9TKX5_U9TKX5_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A078HEY7_A0A078HEY7_BRANA_3708 and tr_A0A0D3DK98_A0A0D3DK98_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078HF71_A0A078HF71_BRANA_3708 and tr_A0A0D3BK14_A0A0D3BK14_BRAOL_109376 are exactly identical! WARNING: Sequences tr_V4T6Z5_V4T6Z5_9ROSI_85681 and tr_A0A2H5P793_A0A2H5P793_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2UTF8_A0A0D2UTF8_GOSRA_29730 and tr_A0A1U8N2I0_A0A1U8N2I0_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0V1D016_A0A0V1D016_TRIBR_45882 and tr_A0A0V0VZ81_A0A0V0VZ81_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D016_A0A0V1D016_TRIBR_45882 and tr_A0A0V0U854_A0A0V0U854_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3YME9_A0A1S3YME9_TOBAC_4097 and tr_A0A1U7XDH2_A0A1U7XDH2_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1D1W5E3_A0A1D1W5E3_RAMVA_947166 and tr_A0A1D1W5X1_A0A1D1W5X1_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A2G2ZA02_A0A2G2ZA02_CAPAN_4072 and tr_A0A2G3C783_A0A2G3C783_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2K5NL52_A0A2K5NL52_CERAT_9531 and tr_A0A2K6B8V5_A0A2K6B8V5_MACNE_9545 are exactly identical! WARNING: Duplicate sequences found: 34 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/P48448/4_raxmlng_ancestral/P48448.raxml.reduced.phy Alignment comprises 1 partitions and 385 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 385 Gaps: 3.40 % Invariant sites: 0.26 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48448/4_raxmlng_ancestral/P48448.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/P48448/3_mltree/P48448.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 97 / 7760 [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: -231698.847855 [00:00:00 -231698.847855] Initial branch length optimization [00:00:01 -230925.871189] Model parameter optimization (eps = 0.100000) [00:00:29] Tree #1, final logLikelihood: -229922.166868 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.198373,0.459077) (0.336914,0.605661) (0.254410,1.168810) (0.210303,1.937769) 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/P48448/4_raxmlng_ancestral/P48448.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48448/4_raxmlng_ancestral/P48448.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48448/4_raxmlng_ancestral/P48448.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P48448/4_raxmlng_ancestral/P48448.raxml.log Analysis started: 02-Jun-2021 18:25:28 / finished: 02-Jun-2021 18:26:01 Elapsed time: 33.259 seconds Consumed energy: 2.632 Wh