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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 03-Jun-2021 02:26:25 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX3/2_msa/Q9GZX3_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX3/3_mltree/Q9GZX3.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX3/4_raxmlng_ancestral/Q9GZX3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622676385 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/Q9GZX3/2_msa/Q9GZX3_nogap_msa.fasta [00:00:00] Loaded alignment with 598 taxa and 395 sites WARNING: Sequences tr_M3Z411_M3Z411_MUSPF_9669 and tr_A0A2Y9JN31_A0A2Y9JN31_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I2ZJP8_A0A2I2ZJP8_GORGO_9595 and tr_H2NC76_H2NC76_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2ZJP8_A0A2I2ZJP8_GORGO_9595 and tr_H2Q222_H2Q222_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZJP8_A0A2I2ZJP8_GORGO_9595 and sp_Q7LGC8_CHST3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZJP8_A0A2I2ZJP8_GORGO_9595 and tr_A0A2R9C0K7_A0A2R9C0K7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8KA42_A0A2J8KA42_PANTR_9598 and tr_A0A2R9AVP1_A0A2R9AVP1_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7B502_K7B502_PANTR_9598 and tr_A0A2R9CHK3_A0A2R9CHK3_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7CJK6_K7CJK6_PANTR_9598 and sp_Q9Y4C5_CHST2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7CJK6_K7CJK6_PANTR_9598 and tr_F7H292_F7H292_MACMU_9544 are exactly identical! WARNING: Sequences tr_K7CJK6_K7CJK6_PANTR_9598 and tr_A0A2R8NDX5_A0A2R8NDX5_CALJA_9483 are exactly identical! WARNING: Sequences tr_K7CJK6_K7CJK6_PANTR_9598 and tr_A0A2K6B5P3_A0A2K6B5P3_MACNE_9545 are exactly identical! WARNING: Sequences tr_K7CJK6_K7CJK6_PANTR_9598 and tr_A0A2K5XTM3_A0A2K5XTM3_MANLE_9568 are exactly identical! WARNING: Sequences tr_M4B058_M4B058_XIPMA_8083 and tr_A0A087YSM5_A0A087YSM5_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4B058_M4B058_XIPMA_8083 and tr_A0A087YSM6_A0A087YSM6_POEFO_48698 are exactly identical! WARNING: Sequences sp_O43916_CHST1_HUMAN_9606 and tr_F6TF94_F6TF94_MACMU_9544 are exactly identical! WARNING: Sequences sp_O43916_CHST1_HUMAN_9606 and tr_F6RNI1_F6RNI1_CALJA_9483 are exactly identical! WARNING: Sequences sp_O43916_CHST1_HUMAN_9606 and tr_A0A0D9SCY2_A0A0D9SCY2_CHLSB_60711 are exactly identical! WARNING: Sequences sp_O43916_CHST1_HUMAN_9606 and tr_A0A2K5KTU6_A0A2K5KTU6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7CNI9_F7CNI9_MACMU_9544 and tr_A0A2K5KIR6_A0A2K5KIR6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7CNI9_F7CNI9_MACMU_9544 and tr_A0A2K6B5A9_A0A2K6B5A9_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZEG7_H0ZEG7_TAEGU_59729 and tr_A0A091J7S5_A0A091J7S5_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A096N7J5_A0A096N7J5_PAPAN_9555 and tr_A0A2K5KH47_A0A2K5KH47_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N7J5_A0A096N7J5_PAPAN_9555 and tr_A0A2K5XCD7_A0A2K5XCD7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096P4S1_A0A096P4S1_PAPAN_9555 and tr_A0A0D9R802_A0A0D9R802_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096P4S1_A0A096P4S1_PAPAN_9555 and tr_A0A2K6DJZ3_A0A2K6DJZ3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096P4S1_A0A096P4S1_PAPAN_9555 and tr_A0A2K5ZVC6_A0A2K5ZVC6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091EY53_A0A091EY53_CORBR_85066 and tr_A0A091VE52_A0A091VE52_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A093S3Q0_A0A093S3Q0_9PASS_328815 and tr_A0A1V4KEW8_A0A1V4KEW8_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0M2F2_A0A2I0M2F2_COLLI_8932 and tr_A0A1V4K1I9_A0A1V4K1I9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A226MNR2_A0A226MNR2_CALSU_9009 and tr_A0A226PL37_A0A226PL37_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226N0Y2_A0A226N0Y2_CALSU_9009 and tr_A0A226PQG6_A0A226PQG6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4B9L1_A0A2U4B9L1_TURTR_9739 and tr_A0A2Y9NZJ5_A0A2Y9NZJ5_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BTI4_A0A2U4BTI4_TURTR_9739 and tr_A0A384A5N0_A0A384A5N0_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4CDE8_A0A2U4CDE8_TURTR_9739 and tr_A0A2Y9PQC5_A0A2Y9PQC5_DELLE_9749 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/Q9GZX3/4_raxmlng_ancestral/Q9GZX3.raxml.reduced.phy Alignment comprises 1 partitions and 395 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 395 Gaps: 11.96 % Invariant sites: 1.52 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX3/4_raxmlng_ancestral/Q9GZX3.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/Q9GZX3/3_mltree/Q9GZX3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 99 / 7920 [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: -90151.311707 [00:00:00 -90151.311707] Initial branch length optimization [00:00:01 -81604.298358] Model parameter optimization (eps = 0.100000) [00:00:22] Tree #1, final logLikelihood: -81497.689662 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.132963,0.210802) (0.231184,0.335531) (0.355676,0.898861) (0.280176,2.051206) 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/Q9GZX3/4_raxmlng_ancestral/Q9GZX3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX3/4_raxmlng_ancestral/Q9GZX3.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX3/4_raxmlng_ancestral/Q9GZX3.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9GZX3/4_raxmlng_ancestral/Q9GZX3.raxml.log Analysis started: 03-Jun-2021 02:26:25 / finished: 03-Jun-2021 02:26:50 Elapsed time: 24.907 seconds Consumed energy: 1.774 Wh