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 02:44:28 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBX5/2_msa/Q9UBX5_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBX5/3_mltree/Q9UBX5.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBX5/4_raxmlng_ancestral/Q9UBX5 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677468 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/Q9UBX5/2_msa/Q9UBX5_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 448 sites WARNING: Sequences tr_F1NX60_F1NX60_CHICK_9031 and sp_O73775_FBLN1_CHICK_9031 are exactly identical! WARNING: Sequences tr_M3Y8S3_M3Y8S3_MUSPF_9669 and tr_A0A2Y9JIY1_A0A2Y9JIY1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YJA0_M3YJA0_MUSPF_9669 and tr_A0A2Y9JNF3_A0A2Y9JNF3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3HAN1_A0A2I3HAN1_NOMLE_61853 and tr_G3QH75_G3QH75_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HAN1_A0A2I3HAN1_NOMLE_61853 and tr_A0A2R9AKA2_A0A2R9AKA2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QLA9_G3QLA9_GORGO_9595 and tr_H2NN62_H2NN62_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QLA9_G3QLA9_GORGO_9595 and tr_A0A2I3RTE4_A0A2I3RTE4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QLA9_G3QLA9_GORGO_9595 and sp_P35555_FBN1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QLA9_G3QLA9_GORGO_9595 and tr_F1SN67_F1SN67_PIG_9823 are exactly identical! WARNING: Sequences tr_G3QLA9_G3QLA9_GORGO_9595 and sp_P98133_FBN1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G3QLA9_G3QLA9_GORGO_9595 and tr_A0A2R9CMD1_A0A2R9CMD1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QLA9_G3QLA9_GORGO_9595 and tr_A0A2Y9PJL6_A0A2Y9PJL6_DELLE_9749 are exactly identical! WARNING: Sequences tr_G3QLA9_G3QLA9_GORGO_9595 and tr_A0A2Y9RXM1_A0A2Y9RXM1_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2J8XCL5_A0A2J8XCL5_PONAB_9601 and tr_G7NA36_G7NA36_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2J8XCL5_A0A2J8XCL5_PONAB_9601 and tr_A0A096NP06_A0A096NP06_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2J8XCL5_A0A2J8XCL5_PONAB_9601 and tr_A0A0D9RPF4_A0A0D9RPF4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2J8XCL5_A0A2J8XCL5_PONAB_9601 and tr_A0A2K5KXY1_A0A2K5KXY1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2J8XCL5_A0A2J8XCL5_PONAB_9601 and tr_A0A2K6DZ29_A0A2K6DZ29_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2J8XCL5_A0A2J8XCL5_PONAB_9601 and tr_A0A2K5YW69_A0A2K5YW69_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2NM18_H2NM18_PONAB_9601 and tr_A0A2I3S9Z3_A0A2I3S9Z3_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NM18_H2NM18_PONAB_9601 and sp_Q9UBX5_FBLN5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_B5DR05_B5DR05_DROPS_46245 and tr_B4H2A4_B4H2A4_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2R429_H2R429_PANTR_9598 and tr_A0A2R9BKP0_A0A2R9BKP0_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2REY4_H2REY4_PANTR_9598 and sp_Q12805_FBLN3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_G7PBA1_G7PBA1_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_A0A096NM08_A0A096NM08_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_A0A2K5L3Z1_A0A2K5L3Z1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_A0A2K6BW09_A0A2K6BW09_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6UHI1_F6UHI1_MACMU_9544 and tr_A0A2K6CJU3_A0A2K6CJU3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6UHI1_F6UHI1_MACMU_9544 and tr_A0A2K5ZZV8_A0A2K5ZZV8_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7EB76_F7EB76_MACMU_9544 and tr_G7PM02_G7PM02_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7EB76_F7EB76_MACMU_9544 and tr_A0A2K6CH16_A0A2K6CH16_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096MQ74_A0A096MQ74_PAPAN_9555 and tr_A0A0D9RGS8_A0A0D9RGS8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MQ74_A0A096MQ74_PAPAN_9555 and tr_A0A2K5LUR3_A0A2K5LUR3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MQ74_A0A096MQ74_PAPAN_9555 and tr_A0A2K6AJP7_A0A2K6AJP7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096ND84_A0A096ND84_PAPAN_9555 and tr_A0A2K5N0D6_A0A2K5N0D6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096ND84_A0A096ND84_PAPAN_9555 and tr_A0A2K6DUB3_A0A2K6DUB3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096ND84_A0A096ND84_PAPAN_9555 and tr_A0A2K5Y1P0_A0A2K5Y1P0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3MQ48_A0A2I3MQ48_PAPAN_9555 and tr_A0A2K5LFG6_A0A2K5LFG6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MQ48_A0A2I3MQ48_PAPAN_9555 and tr_A0A2K6CT24_A0A2K6CT24_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A087R5P4_A0A087R5P4_APTFO_9233 and tr_A0A091FSW9_A0A091FSW9_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A0A0A2Z6_A0A0A0A2Z6_CHAVO_50402 and tr_A0A2I0MK74_A0A2I0MK74_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A226MPL4_A0A226MPL4_CALSU_9009 and tr_A0A226P3S0_A0A226P3S0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0SH52_A0A2D0SH52_ICTPU_7998 and tr_W5UBK9_W5UBK9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LG61_A0A2K5LG61_CERAT_9531 and tr_A0A2K6C2A2_A0A2K6C2A2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2A3EPY8_A0A2A3EPY8_APICC_94128 and tr_A0A2A3ERD3_A0A2A3ERD3_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A2U4BY46_A0A2U4BY46_TURTR_9739 and tr_A0A2Y9Q5P9_A0A2Y9Q5P9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C001_A0A2U4C001_TURTR_9739 and tr_A0A2Y9NKJ3_A0A2Y9NKJ3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C001_A0A2U4C001_TURTR_9739 and tr_A0A384AVN5_A0A384AVN5_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 49 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/Q9UBX5/4_raxmlng_ancestral/Q9UBX5.raxml.reduced.phy Alignment comprises 1 partitions and 448 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 448 Gaps: 25.54 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBX5/4_raxmlng_ancestral/Q9UBX5.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/Q9UBX5/3_mltree/Q9UBX5.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 112 / 8960 [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: -196594.090217 [00:00:00 -196594.090217] Initial branch length optimization [00:00:01 -194190.410378] Model parameter optimization (eps = 0.100000) [00:01:12] Tree #1, final logLikelihood: -193505.964806 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.192962,0.204779) (0.098116,0.756141) (0.416207,0.956785) (0.292715,1.667407) 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/Q9UBX5/4_raxmlng_ancestral/Q9UBX5.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBX5/4_raxmlng_ancestral/Q9UBX5.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBX5/4_raxmlng_ancestral/Q9UBX5.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9UBX5/4_raxmlng_ancestral/Q9UBX5.raxml.log Analysis started: 03-Jun-2021 02:44:28 / finished: 03-Jun-2021 02:45:45 Elapsed time: 77.083 seconds Consumed energy: 7.294 Wh