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-Aug-2021 10:13:58 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKN8/2_msa/A6NKN8_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKN8/3_mltree/A6NKN8.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKN8/4_raxmlng_ancestral/A6NKN8 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1627888438 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/300621_run/phylogeny-snakemake/results/A6NKN8/2_msa/A6NKN8_nogap_msa.fasta [00:00:00] Loaded alignment with 156 taxa and 68 sites WARNING: Sequences sp_P63054_PCP4_MOUSE_10090 and sp_P63055_PCP4_RAT_10116 are exactly identical! WARNING: Sequences sp_P63054_PCP4_MOUSE_10090 and tr_A0A1U7QSJ8_A0A1U7QSJ8_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_G1RRW7_G1RRW7_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_G3R093_G3R093_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_H2P365_H2P365_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_J9PBP8_J9PBP8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_H2QL15_H2QL15_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_F6SRG1_F6SRG1_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and sp_P48539_PCP4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_H9EPH8_H9EPH8_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A286ZI58_A0A286ZI58_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A096NJ12_A0A096NJ12_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A1S3WS82_A0A1S3WS82_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A1U7U993_A0A1U7U993_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2K5NWH4_A0A2K5NWH4_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2K6DYS2_A0A2K6DYS2_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2K5YGP8_A0A2K5YGP8_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2U3V1E5_A0A2U3V1E5_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2U3WQC6_A0A2U3WQC6_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2U3YMS5_A0A2U3YMS5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2Y9LG75_A0A2Y9LG75_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A2Y9SBI3_A0A2Y9SBI3_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3YB87_M3YB87_MUSPF_9669 and tr_A0A384CZD1_A0A384CZD1_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1RVZ4_G1RVZ4_NOMLE_61853 and tr_H2N508_H2N508_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RVZ4_G1RVZ4_NOMLE_61853 and tr_H9FYP4_H9FYP4_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RVZ4_G1RVZ4_NOMLE_61853 and tr_A0A2K5Z886_A0A2K5Z886_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1PPL2_G1PPL2_MYOLU_59463 and tr_G1LIJ2_G1LIJ2_AILME_9646 are exactly identical! WARNING: Sequences tr_G1PPL2_G1PPL2_MYOLU_59463 and tr_G7P0Z1_G7P0Z1_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2Q0G7_H2Q0G7_PANTR_9598 and sp_A6NKN8_PC4L1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q0G7_H2Q0G7_PANTR_9598 and tr_A0A2R9AUB3_A0A2R9AUB3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A287CTQ0_A0A287CTQ0_ICTTR_43179 and tr_A0A286XUW8_A0A286XUW8_CAVPO_10141 are exactly identical! WARNING: Sequences tr_A0A287CTQ0_A0A287CTQ0_ICTTR_43179 and tr_A0A2I2V204_A0A2I2V204_FELCA_9685 are exactly identical! WARNING: Sequences tr_H0WYL0_H0WYL0_OTOGA_30611 and sp_Q148C4_PCP4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_R0KEN3_R0KEN3_ANAPL_8839 are exactly identical! WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A091ETK0_A0A091ETK0_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A091K1X0_A0A091K1X0_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A093PRY3_A0A093PRY3_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A091VW12_A0A091VW12_NIPNI_128390 are exactly identical! WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A087R974_A0A087R974_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A093HLY8_A0A093HLY8_STRCA_441894 are exactly identical! WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A091VYN2_A0A091VYN2_OPIHO_30419 are exactly identical! WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A099ZEX3_A0A099ZEX3_TINGU_94827 are exactly identical! WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A0A0AXU0_A0A0A0AXU0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A093IXJ4_A0A093IXJ4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_U3KI80_U3KI80_FICAL_59894 and tr_A0A091I7Z8_A0A091I7Z8_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091V0R8_A0A091V0R8_NIPNI_128390 and tr_A0A0A0A8L1_A0A0A0A8L1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1S3G455_A0A1S3G455_DIPOR_10020 and tr_A0A2Y9S0Q3_A0A2Y9S0Q3_TRIMA_127582 are exactly identical! WARNING: Sequences tr_B9EM62_B9EM62_SALSA_8030 and tr_A0A060W927_A0A060W927_ONCMY_8022 are exactly identical! WARNING: Duplicate sequences found: 48 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKN8/4_raxmlng_ancestral/A6NKN8.raxml.reduced.phy Alignment comprises 1 partitions and 68 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 68 Gaps: 13.45 % Invariant sites: 13.24 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKN8/4_raxmlng_ancestral/A6NKN8.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/300621_run/phylogeny-snakemake/results/A6NKN8/3_mltree/A6NKN8.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 17 / 1360 [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: -3675.417967 [00:00:00 -3675.417967] Initial branch length optimization [00:00:00 -3244.514785] Model parameter optimization (eps = 0.100000) [00:00:03] Tree #1, final logLikelihood: -3213.512373 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.154670,0.033226) (0.175810,1.066397) (0.281969,0.302214) (0.387550,1.863404) 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/300621_run/phylogeny-snakemake/results/A6NKN8/4_raxmlng_ancestral/A6NKN8.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKN8/4_raxmlng_ancestral/A6NKN8.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKN8/4_raxmlng_ancestral/A6NKN8.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NKN8/4_raxmlng_ancestral/A6NKN8.raxml.log Analysis started: 02-Aug-2021 10:13:58 / finished: 02-Aug-2021 10:14:02 Elapsed time: 3.497 seconds Consumed energy: 0.327 Wh