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 02-Jun-2021 18:22:13 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06418/2_msa/Q06418_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06418/3_mltree/Q06418.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06418/4_raxmlng_ancestral/Q06418 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647333 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/Q06418/2_msa/Q06418_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 890 sites WARNING: Sequences tr_A0A1D5P6T3_A0A1D5P6T3_CHICK_9031 and tr_G1N117_G1N117_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q60751_IGF1R_MOUSE_10090 and sp_P24062_IGF1R_RAT_10116 are exactly identical! WARNING: Sequences tr_G3R4W2_G3R4W2_GORGO_9595 and tr_A0A2I3RAJ1_A0A2I3RAJ1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R4W2_G3R4W2_GORGO_9595 and tr_A0A2I3S7G9_A0A2I3S7G9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R4W2_G3R4W2_GORGO_9595 and tr_H9YUX8_H9YUX8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3R4W2_G3R4W2_GORGO_9595 and tr_G7PRB8_G7PRB8_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3R4W2_G3R4W2_GORGO_9595 and tr_A0A2K6B7I9_A0A2K6B7I9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3R4W2_G3R4W2_GORGO_9595 and tr_A0A2K5XNT4_A0A2K5XNT4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3R4W2_G3R4W2_GORGO_9595 and tr_A0A2R9BA11_A0A2R9BA11_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RAQ4_G3RAQ4_GORGO_9595 and tr_H2QA49_H2QA49_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RAQ4_G3RAQ4_GORGO_9595 and sp_P08069_IGF1R_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RAQ4_G3RAQ4_GORGO_9595 and tr_A0A2R8ZYJ5_A0A2R8ZYJ5_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q2IBF2_MET_GORGO_9595 and sp_P08581_MET_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A0A0MXS4_A0A0A0MXS4_PONAB_9601 and sp_Q2IBD8_MET_PONAB_9601 are exactly identical! WARNING: Sequences tr_J9P743_J9P743_CANLF_9615 and sp_Q75ZY9_MET_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3T1S4_A0A2I3T1S4_PANTR_9598 and tr_A0A2R9BKS2_A0A2R9BKS2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H0WNV1_H0WNV1_OTOGA_30611 and sp_Q2QLH6_MET_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G3T807_G3T807_LOXAF_9785 and sp_Q108U6_MET_LOXAF_9785 are exactly identical! WARNING: Sequences tr_H0Z2V6_H0Z2V6_TAEGU_59729 and tr_A0A218V5K2_A0A218V5K2_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZEE4_H0ZEE4_TAEGU_59729 and tr_A0A218V095_A0A218V095_9PASE_299123 are exactly identical! WARNING: Sequences tr_G7P9I7_G7P9I7_MACFA_9541 and tr_A0A2I3MLM3_A0A2I3MLM3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7P9I7_G7P9I7_MACFA_9541 and tr_A0A2K5L870_A0A2K5L870_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7P9I7_G7P9I7_MACFA_9541 and tr_A0A2K6D2L3_A0A2K6D2L3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PYV6_G7PYV6_MACFA_9541 and tr_A0A0A0MW58_A0A0A0MW58_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A0A0MVB9_A0A0A0MVB9_PAPAN_9555 and tr_A0A2K6AMU0_A0A2K6AMU0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3M4K4_A0A2I3M4K4_PAPAN_9555 and tr_A0A2K5NV40_A0A2K5NV40_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151MFN4_A0A151MFN4_ALLMI_8496 and tr_A0A1U7S4W8_A0A1U7S4W8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NYQ1_A0A151NYQ1_ALLMI_8496 and tr_A0A3Q0H314_A0A3Q0H314_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091J0U9_A0A091J0U9_EGRGA_188379 and tr_A0A087RB90_A0A087RB90_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091J0U9_A0A091J0U9_EGRGA_188379 and tr_A0A091V3R3_A0A091V3R3_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JHP5_A0A091JHP5_EGRGA_188379 and tr_A0A091URD2_A0A091URD2_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JHP5_A0A091JHP5_EGRGA_188379 and tr_A0A087RGY7_A0A087RGY7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JHP5_A0A091JHP5_EGRGA_188379 and tr_A0A091GMR3_A0A091GMR3_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091VGU9_A0A091VGU9_NIPNI_128390 and tr_A0A087R5C7_A0A087R5C7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091VGU9_A0A091VGU9_NIPNI_128390 and tr_A0A093K1W3_A0A093K1W3_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091VGU9_A0A091VGU9_NIPNI_128390 and tr_A0A091VPT0_A0A091VPT0_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A195EXC2_A0A195EXC2_9HYME_34720 and tr_A0A195C704_A0A195C704_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A226NMH2_A0A226NMH2_CALSU_9009 and tr_A0A226NXN8_A0A226NXN8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QNU4_A0A2D0QNU4_ICTPU_7998 and tr_A0A2D0QPB5_A0A2D0QPB5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RPL8_A0A2D0RPL8_ICTPU_7998 and tr_W5U9F6_W5U9F6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5MLR5_A0A2K5MLR5_CERAT_9531 and tr_A0A2K6D6I9_A0A2K6D6I9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2Y9QAK7_A0A2Y9QAK7_DELLE_9749 and tr_A0A2Y9TH39_A0A2Y9TH39_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9QAK7_A0A2Y9QAK7_DELLE_9749 and tr_A0A384AV05_A0A384AV05_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 43 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/Q06418/4_raxmlng_ancestral/Q06418.raxml.reduced.phy Alignment comprises 1 partitions and 890 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 890 Gaps: 29.63 % Invariant sites: 0.45 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06418/4_raxmlng_ancestral/Q06418.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/Q06418/3_mltree/Q06418.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 223 / 17840 [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: -337079.038481 [00:00:00 -337079.038481] Initial branch length optimization [00:00:02 -303800.143990] Model parameter optimization (eps = 0.100000) [00:01:01] Tree #1, final logLikelihood: -303205.185937 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.092136,0.165594) (0.110893,0.264355) (0.422213,0.825977) (0.374759,1.618881) 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/Q06418/4_raxmlng_ancestral/Q06418.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06418/4_raxmlng_ancestral/Q06418.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06418/4_raxmlng_ancestral/Q06418.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06418/4_raxmlng_ancestral/Q06418.raxml.log Analysis started: 02-Jun-2021 18:22:13 / finished: 02-Jun-2021 18:23:23 Elapsed time: 69.983 seconds Consumed energy: 4.028 Wh