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 02:29:26 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P60484/2_msa/P60484_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P60484/3_mltree/P60484.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P60484/4_raxmlng_ancestral/P60484 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622676566 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/P60484/2_msa/P60484_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 403 sites WARNING: Sequences tr_F1NT98_F1NT98_CHICK_9031 and tr_A0A226P7B4_A0A226P7B4_COLVI_9014 are exactly identical! WARNING: Sequences sp_O08586_PTEN_MOUSE_10090 and tr_A0A1U7Q4N9_A0A1U7Q4N9_MESAU_10036 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_G3QF16_G3QF16_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_G1SVU9_G1SVU9_RABIT_9986 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and sp_P60483_PTEN_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_A0A2I3TNH3_A0A2I3TNH3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and sp_P60484_PTEN_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_F6VBA7_F6VBA7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_U3F9J7_U3F9J7_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_F2Z5H1_F2Z5H1_PIG_9823 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_D2GZ33_D2GZ33_AILME_9646 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_M3WPL8_M3WPL8_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_A0A096P5B4_A0A096P5B4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_A0A0D9R3M9_A0A0D9R3M9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_A0A1U7UMJ6_A0A1U7UMJ6_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_A0A2K5LKR0_A0A2K5LKR0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_A0A2K6B6A9_A0A2K6B6A9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_A0A2K5ZCM7_A0A2K5ZCM7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_A0A2U4BLH0_A0A2U4BLH0_TURTR_9739 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_A0A2Y9N7B6_A0A2Y9N7B6_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_A0A2Y9FLR7_A0A2Y9FLR7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_A0A384BYY7_A0A384BYY7_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1RNC7_G1RNC7_NOMLE_61853 and tr_A0A383ZVY4_A0A383ZVY4_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2I2YUW8_A0A2I2YUW8_GORGO_9595 and tr_H2QJD8_H2QJD8_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YUW8_A0A2I2YUW8_GORGO_9595 and sp_Q9HBL0_TENS1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A088AW82_A0A088AW82_APIME_7460 and tr_A0A2A3EHP8_A0A2A3EHP8_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NH16_A0A158NH16_ATTCE_12957 and tr_A0A151J1Z4_A0A151J1Z4_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NH16_A0A158NH16_ATTCE_12957 and tr_A0A195B6F6_A0A195B6F6_9HYME_520822 are exactly identical! WARNING: Sequences tr_G3SVY7_G3SVY7_LOXAF_9785 and tr_A0A2Y9D8M5_A0A2Y9D8M5_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0Z3J8_H0Z3J8_TAEGU_59729 and tr_A0A091ER46_A0A091ER46_CORBR_85066 are exactly identical! WARNING: Sequences tr_A0A0E0RGC4_A0A0E0RGC4_ORYRU_4529 and tr_Q2QT46_Q2QT46_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_W2R251_W2R251_PHYPN_761204 and tr_A0A0W8CGE1_A0A0W8CGE1_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2RGM6_W2RGM6_PHYPN_761204 and tr_W2HNT7_W2HNT7_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0D9RTC1_A0A0D9RTC1_CHLSB_60711 and tr_A0A2K5MYD3_A0A2K5MYD3_CERAT_9531 are exactly identical! WARNING: Sequences tr_V4UAC8_V4UAC8_9ROSI_85681 and tr_A0A2H5PRG1_A0A2H5PRG1_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0W8CLH4_A0A0W8CLH4_PHYNI_4790 and tr_W2K8Q2_W2K8Q2_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A093Q4K8_A0A093Q4K8_9PASS_328815 and tr_A0A091W8V2_A0A091W8V2_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A093Q4K8_A0A093Q4K8_9PASS_328815 and tr_A0A099ZZL0_A0A099ZZL0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091V410_A0A091V410_NIPNI_128390 and tr_A0A087QU08_A0A087QU08_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091V410_A0A091V410_NIPNI_128390 and tr_A0A099ZKX6_A0A099ZKX6_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091V410_A0A091V410_NIPNI_128390 and tr_A0A091IG12_A0A091IG12_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V1CY19_A0A0V1CY19_TRIBR_45882 and tr_A0A0V0WPE7_A0A0V0WPE7_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CY19_A0A0V1CY19_TRIBR_45882 and tr_A0A0V1KWE1_A0A0V1KWE1_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0ZW91_A0A0V0ZW91_9BILA_990121 and tr_A0A0V1NM97_A0A0V1NM97_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0ZW91_A0A0V0ZW91_9BILA_990121 and tr_A0A0V0TUI3_A0A0V0TUI3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3ZZS4_A0A1S3ZZS4_TOBAC_4097 and tr_A0A1U7UMI0_A0A1U7UMI0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4C3I1_A0A1S4C3I1_TOBAC_4097 and tr_A0A1U7V9P3_A0A1U7V9P3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1U8DWX6_A0A1U8DWX6_CAPAN_4072 and tr_A0A2G3BVF8_A0A2G3BVF8_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2K5MAS5_A0A2K5MAS5_CERAT_9531 and tr_A0A2K5Z1T0_A0A2K5Z1T0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3WLD5_A0A2U3WLD5_ODORO_9708 and tr_A0A2U3XMX7_A0A2U3XMX7_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 50 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/P60484/4_raxmlng_ancestral/P60484.raxml.reduced.phy Alignment comprises 1 partitions and 403 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 403 Gaps: 21.36 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P60484/4_raxmlng_ancestral/P60484.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/P60484/3_mltree/P60484.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 101 / 8080 [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: -195458.703242 [00:00:00 -195458.703242] Initial branch length optimization [00:00:00 -194626.049641] Model parameter optimization (eps = 0.100000) [00:00:25] Tree #1, final logLikelihood: -193957.852970 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.133704,0.318354) (0.180001,0.434165) (0.339513,0.887275) (0.346782,1.666878) 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/P60484/4_raxmlng_ancestral/P60484.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P60484/4_raxmlng_ancestral/P60484.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P60484/4_raxmlng_ancestral/P60484.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P60484/4_raxmlng_ancestral/P60484.raxml.log Analysis started: 03-Jun-2021 02:29:26 / finished: 03-Jun-2021 02:29:54 Elapsed time: 28.806 seconds Consumed energy: 1.696 Wh