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 18:17:57 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56696/2_msa/P56696_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56696/3_mltree/P56696.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56696/4_raxmlng_ancestral/P56696 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647077 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/P56696/2_msa/P56696_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 695 sites WARNING: Sequences sp_Q61923_KCNA6_MOUSE_10090 and sp_P17659_KCNA6_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Z613_M3Z613_MUSPF_9669 and tr_A0A2Y9KVM7_A0A2Y9KVM7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A1Z856_A1Z856_DROME_7227 and tr_B4HME1_B4HME1_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1QKC9_G1QKC9_NOMLE_61853 and tr_G3R701_G3R701_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QKC9_G1QKC9_NOMLE_61853 and tr_A0A2I3S1D1_A0A2I3S1D1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QKC9_G1QKC9_NOMLE_61853 and tr_A0A2R9C3J4_A0A2R9C3J4_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3GUK9_G3GUK9_CRIGR_10029 and tr_A0A1U7R9N3_A0A1U7R9N3_MESAU_10036 are exactly identical! WARNING: Sequences tr_H2PZM5_H2PZM5_PANTR_9598 and tr_A0A2R8Z7H3_A0A2R8Z7H3_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7DI95_F7DI95_MACMU_9544 and tr_A0A2K5NHH6_A0A2K5NHH6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DI95_F7DI95_MACMU_9544 and tr_A0A2K6E1G7_A0A2K6E1G7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HL26_F7HL26_MACMU_9544 and tr_G7NW43_G7NW43_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HL26_F7HL26_MACMU_9544 and tr_A0A2I3MQT4_A0A2I3MQT4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HL26_F7HL26_MACMU_9544 and tr_A0A2K5KWS6_A0A2K5KWS6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HL26_F7HL26_MACMU_9544 and tr_A0A2K6B581_A0A2K6B581_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3VYC4_M3VYC4_FELCA_9685 and tr_A0A2U3X4T2_A0A2U3X4T2_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3VYC4_M3VYC4_FELCA_9685 and tr_A0A2U3Y7L2_A0A2U3Y7L2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_U3IS72_U3IS72_ANAPL_8839 and tr_A0A0A0A3C9_A0A0A0A3C9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A096NDD2_A0A096NDD2_PAPAN_9555 and tr_A0A2K5MPS2_A0A2K5MPS2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NDD2_A0A096NDD2_PAPAN_9555 and tr_A0A2K6DYU8_A0A2K6DYU8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3N4U3_A0A2I3N4U3_PAPAN_9555 and tr_A0A2K5L5Z3_A0A2K5L5Z3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3N4U3_A0A2I3N4U3_PAPAN_9555 and tr_A0A2K6DCZ5_A0A2K6DCZ5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091JFB6_A0A091JFB6_EGRGA_188379 and tr_A0A087QRU7_A0A087QRU7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JFB6_A0A091JFB6_EGRGA_188379 and tr_A0A0A0A824_A0A0A0A824_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091VLI6_A0A091VLI6_NIPNI_128390 and tr_A0A091G6X5_A0A091G6X5_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091WIM2_A0A091WIM2_OPIHO_30419 and tr_A0A099ZF49_A0A099ZF49_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A0V1D4B9_A0A0V1D4B9_TRIBR_45882 and tr_A0A0V0VKP7_A0A0V0VKP7_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D4B9_A0A0V1D4B9_TRIBR_45882 and tr_A0A0V1PHR2_A0A0V1PHR2_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1D4B9_A0A0V1D4B9_TRIBR_45882 and tr_A0A0V0TZ48_A0A0V0TZ48_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WBD0_A0A0V0WBD0_9BILA_92179 and tr_A0A0V1L3I5_A0A0V1L3I5_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0WBD0_A0A0V0WBD0_9BILA_92179 and tr_A0A0V0ZMT8_A0A0V0ZMT8_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0WBD0_A0A0V0WBD0_9BILA_92179 and tr_A0A0V1NPM6_A0A0V1NPM6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0WBD0_A0A0V0WBD0_9BILA_92179 and tr_A0A0V0TNR6_A0A0V0TNR6_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WHF8_A0A0V0WHF8_9BILA_92179 and tr_A0A0V1LGG3_A0A0V1LGG3_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A2D0PXA6_A0A2D0PXA6_ICTPU_7998 and tr_A0A2D0PXB4_A0A2D0PXB4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QMW3_A0A2D0QMW3_ICTPU_7998 and tr_A0A2D0QNH2_A0A2D0QNH2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QN80_A0A2D0QN80_ICTPU_7998 and tr_A0A2D0QNG8_A0A2D0QNG8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QQ42_A0A2D0QQ42_ICTPU_7998 and tr_A0A2D0QQV0_A0A2D0QQV0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RW07_A0A2D0RW07_ICTPU_7998 and tr_A0A2D0RWX1_A0A2D0RWX1_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 38 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/P56696/4_raxmlng_ancestral/P56696.raxml.reduced.phy Alignment comprises 1 partitions and 695 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 695 Gaps: 39.82 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56696/4_raxmlng_ancestral/P56696.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/P56696/3_mltree/P56696.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 174 / 13920 [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: -158180.711684 [00:00:00 -158180.711684] Initial branch length optimization [00:00:01 -157216.400974] Model parameter optimization (eps = 0.100000) [00:00:51] Tree #1, final logLikelihood: -156482.346174 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.152574,0.336375) (0.132769,0.365052) (0.339055,0.627735) (0.375601,1.830061) 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/P56696/4_raxmlng_ancestral/P56696.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56696/4_raxmlng_ancestral/P56696.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56696/4_raxmlng_ancestral/P56696.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P56696/4_raxmlng_ancestral/P56696.raxml.log Analysis started: 02-Jun-2021 18:17:57 / finished: 02-Jun-2021 18:18:55 Elapsed time: 57.689 seconds Consumed energy: 3.862 Wh