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 23-Jun-2021 00:28:09 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q14004/2_msa/Q14004_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q14004/3_mltree/Q14004.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q14004/4_raxmlng_ancestral/Q14004 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624397289 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/030621_run/phylogeny-snakemake/results/Q14004/2_msa/Q14004_nogap_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 1512 sites WARNING: Sequences sp_Q5ZKN1_CDK9_CHICK_9031 and tr_A0A226NP61_A0A226NP61_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q5ZKN1_CDK9_CHICK_9031 and tr_A0A226NXR4_A0A226NXR4_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q99J95_CDK9_MOUSE_10090 and tr_G3HV08_G3HV08_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q99J95_CDK9_MOUSE_10090 and sp_Q641Z4_CDK9_RAT_10116 are exactly identical! WARNING: Sequences sp_Q99J95_CDK9_MOUSE_10090 and tr_H0VGQ5_H0VGQ5_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3YQG9_M3YQG9_MUSPF_9669 and tr_A0A2U3YKG2_A0A2U3YKG2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G3R636_G3R636_GORGO_9595 and tr_H2QXX8_H2QXX8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R636_G3R636_GORGO_9595 and sp_P50750_CDK9_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R636_G3R636_GORGO_9595 and tr_A0A096P1Z7_A0A096P1Z7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3R636_G3R636_GORGO_9595 and tr_A0A2K5NJJ6_A0A2K5NJJ6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3R636_G3R636_GORGO_9595 and tr_A0A2K6D689_A0A2K6D689_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3R636_G3R636_GORGO_9595 and tr_A0A2K5XIA2_A0A2K5XIA2_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3R636_G3R636_GORGO_9595 and tr_A0A2R9B5G9_A0A2R9B5G9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QUG7_H2QUG7_PANTR_9598 and tr_A0A2R9C8V2_A0A2R9C8V2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0FZ19_A0A0E0FZ19_ORYNI_4536 and tr_A0A0E0CD63_A0A0E0CD63_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0FZ19_A0A0E0FZ19_ORYNI_4536 and tr_A0A0D3EYV3_A0A0D3EYV3_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0H2D9_A0A0E0H2D9_ORYNI_4536 and tr_A0A0D9ZMF4_A0A0D9ZMF4_9ORYZ_40148 are exactly identical! WARNING: Sequences sp_A2XUW1_CDKG2_ORYSI_39946 and sp_Q7XUF4_CDKG2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B8A9I9_B8A9I9_ORYSI_39946 and tr_I1NVD2_I1NVD2_ORYGL_4538 are exactly identical! WARNING: Sequences tr_B8A9I9_B8A9I9_ORYSI_39946 and tr_A0A0E0N7U0_A0A0E0N7U0_ORYRU_4529 are exactly identical! WARNING: Sequences tr_B8A9I9_B8A9I9_ORYSI_39946 and tr_A0A0E0JTU3_A0A0E0JTU3_ORYPU_4537 are exactly identical! WARNING: Sequences tr_I1PMG9_I1PMG9_ORYGL_4538 and tr_A0A0D3FXA7_A0A0D3FXA7_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1PV98_I1PV98_ORYGL_4538 and sp_Q6I5Y0_CDKC1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_C9E1C9_C9E1C9_PIG_9823 and tr_A0A1S3A3W0_A0A1S3A3W0_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M4FAI3_M4FAI3_BRARP_51351 and tr_A0A078GKF5_A0A078GKF5_BRANA_3708 are exactly identical! WARNING: Sequences tr_M7ZXC7_M7ZXC7_TRIUA_4572 and tr_A0A3B5Y140_A0A3B5Y140_WHEAT_4565 are exactly identical! WARNING: Sequences tr_V2YWG1_V2YWG1_MONRO_1381753 and tr_A0A0W0FJR6_A0A0W0FJR6_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A3B6ER56_A0A3B6ER56_WHEAT_4565 and tr_A0A3B6UAM5_A0A3B6UAM5_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A078IZZ0_A0A078IZZ0_BRANA_3708 and tr_A0A0D3AB36_A0A0D3AB36_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0A0KWT1_A0A0A0KWT1_CUCSA_3659 and tr_A0A1S3BNY3_A0A1S3BNY3_CUCME_3656 are exactly identical! WARNING: Sequences tr_V4SLA2_V4SLA2_9ROSI_85681 and tr_A0A2H5Q4P0_A0A2H5Q4P0_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2R6J1_A0A0D2R6J1_GOSRA_29730 and tr_A0A1U8LRG5_A0A1U8LRG5_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A075F2G7_A0A075F2G7_TOBAC_4097 and tr_A0A1U7Y1Y0_A0A1U7Y1Y0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3X3U8_A0A1S3X3U8_TOBAC_4097 and tr_A0A1J6IZX7_A0A1J6IZX7_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S4DB74_A0A1S4DB74_TOBAC_4097 and tr_A0A1U7V6D7_A0A1U7V6D7_NICSY_4096 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/030621_run/phylogeny-snakemake/results/Q14004/4_raxmlng_ancestral/Q14004.raxml.reduced.phy Alignment comprises 1 partitions and 1512 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1512 Gaps: 59.50 % Invariant sites: 0.73 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q14004/4_raxmlng_ancestral/Q14004.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/030621_run/phylogeny-snakemake/results/Q14004/3_mltree/Q14004.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 378 / 30240 [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: -406761.911310 [00:00:00 -406761.911310] Initial branch length optimization [00:00:03 -348781.733478] Model parameter optimization (eps = 0.100000) [00:01:24] Tree #1, final logLikelihood: -347820.500726 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.071299,0.102107) (0.067267,0.146538) (0.202287,0.526502) (0.659147,1.329534) 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/030621_run/phylogeny-snakemake/results/Q14004/4_raxmlng_ancestral/Q14004.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q14004/4_raxmlng_ancestral/Q14004.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q14004/4_raxmlng_ancestral/Q14004.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/Q14004/4_raxmlng_ancestral/Q14004.raxml.log Analysis started: 23-Jun-2021 00:28:09 / finished: 23-Jun-2021 00:29:48 Elapsed time: 98.147 seconds Consumed energy: 7.130 Wh