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 18:27:22 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96JS3/2_msa/Q96JS3_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96JS3/3_mltree/Q96JS3.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96JS3/4_raxmlng_ancestral/Q96JS3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647642 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/Q96JS3/2_msa/Q96JS3_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 809 sites WARNING: Sequences tr_A0A2I2Y5T7_A0A2I2Y5T7_GORGO_9595 and sp_Q5RAE6_ZNF24_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2Y5T7_A0A2I2Y5T7_GORGO_9595 and tr_H2QEF6_H2QEF6_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Y5T7_A0A2I2Y5T7_GORGO_9595 and tr_A0A2R8ZDP9_A0A2R8ZDP9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QQX3_G3QQX3_GORGO_9595 and sp_P17029_ZKSC1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NPY3_H2NPY3_PONAB_9601 and tr_A0A2R9ATI4_A0A2R9ATI4_PANPA_9597 are exactly identical! WARNING: Sequences tr_E2RHC3_E2RHC3_CANLF_9615 and tr_A0A2I2U772_A0A2I2U772_FELCA_9685 are exactly identical! WARNING: Sequences tr_E2RHC3_E2RHC3_CANLF_9615 and tr_A0A2U3W860_A0A2U3W860_ODORO_9708 are exactly identical! WARNING: Sequences tr_H2QSK4_H2QSK4_PANTR_9598 and sp_Q6R2W3_SCND3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QV13_H2QV13_PANTR_9598 and tr_A0A2R9BHM6_A0A2R9BHM6_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7AAB1_K7AAB1_PANTR_9598 and sp_Q8NF99_ZN397_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7AAB1_K7AAB1_PANTR_9598 and tr_A0A2R9C8P1_A0A2R9C8P1_PANPA_9597 are exactly identical! WARNING: Sequences sp_P0DP91_ERPG3_HUMAN_9606 and sp_Q8N328_PGBD3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A1D5Q7E3_A0A1D5Q7E3_MACMU_9544 and tr_A0A2K6BFA3_A0A2K6BFA3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5Q7E3_A0A1D5Q7E3_MACMU_9544 and tr_A0A2K5YES9_A0A2K5YES9_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6Q028_F6Q028_MACMU_9544 and tr_G7P3T3_G7P3T3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6Q028_F6Q028_MACMU_9544 and tr_A0A2K6C2K0_A0A2K6C2K0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6SLB4_F6SLB4_MACMU_9544 and tr_G7PTA6_G7PTA6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6SZV8_F6SZV8_MACMU_9544 and tr_G7Q0C6_G7Q0C6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6UAQ9_F6UAQ9_MACMU_9544 and tr_G7P0C1_G7P0C1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7AE32_F7AE32_MACMU_9544 and tr_A0A2K6AP59_A0A2K6AP59_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7AE32_F7AE32_MACMU_9544 and tr_A0A2K5ZR07_A0A2K5ZR07_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7EAK6_F7EAK6_MACMU_9544 and tr_A0A096NLL3_A0A096NLL3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7EAK6_F7EAK6_MACMU_9544 and tr_A0A2K6AQX7_A0A2K6AQX7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7EH74_F7EH74_MACMU_9544 and tr_G7P3S3_G7P3S3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7EH74_F7EH74_MACMU_9544 and tr_A0A096NLJ7_A0A096NLJ7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7EH74_F7EH74_MACMU_9544 and tr_A0A2K5M129_A0A2K5M129_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7EH74_F7EH74_MACMU_9544 and tr_A0A2K6DJK3_A0A2K6DJK3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7EHB8_F7EHB8_MACMU_9544 and tr_G7P3S2_G7P3S2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7EHB8_F7EHB8_MACMU_9544 and tr_A0A096NLJ5_A0A096NLJ5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7EHB8_F7EHB8_MACMU_9544 and tr_A0A2K5ZYA8_A0A2K5ZYA8_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HLR2_F7HLR2_MACMU_9544 and tr_G7PWN1_G7PWN1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HLR2_F7HLR2_MACMU_9544 and tr_A0A096N8R3_A0A096N8R3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HLR2_F7HLR2_MACMU_9544 and tr_A0A2K5M7K8_A0A2K5M7K8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HLR2_F7HLR2_MACMU_9544 and tr_A0A2K6BEP4_A0A2K6BEP4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HLR2_F7HLR2_MACMU_9544 and tr_A0A2K5Z933_A0A2K5Z933_MANLE_9568 are exactly identical! WARNING: Sequences tr_G8F2T8_G8F2T8_MACFA_9541 and tr_A0A096NDF2_A0A096NDF2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G8F2T8_G8F2T8_MACFA_9541 and tr_A0A2K5L4M7_A0A2K5L4M7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G8F2T8_G8F2T8_MACFA_9541 and tr_A0A2K5ZXT3_A0A2K5ZXT3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096MV28_A0A096MV28_PAPAN_9555 and tr_A0A0D9RZ13_A0A0D9RZ13_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MV28_A0A096MV28_PAPAN_9555 and tr_A0A2K5YUJ0_A0A2K5YUJ0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096N6I7_A0A096N6I7_PAPAN_9555 and tr_A0A2K5M1J2_A0A2K5M1J2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N6I7_A0A096N6I7_PAPAN_9555 and tr_A0A2K6A111_A0A2K6A111_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NLL7_A0A096NLL7_PAPAN_9555 and tr_A0A2K5KSJ7_A0A2K5KSJ7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NLL7_A0A096NLL7_PAPAN_9555 and tr_A0A2K5ZI32_A0A2K5ZI32_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5N265_A0A2K5N265_CERAT_9531 and tr_A0A2K6EBM2_A0A2K6EBM2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2U3V908_A0A2U3V908_TURTR_9739 and tr_A0A2Y9P6G0_A0A2Y9P6G0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V908_A0A2U3V908_TURTR_9739 and tr_A0A383YWF6_A0A383YWF6_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4CA67_A0A2U4CA67_TURTR_9739 and tr_A0A2U4CA79_A0A2U4CA79_TURTR_9739 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/020621_run/phylogeny-snakemake/results/Q96JS3/4_raxmlng_ancestral/Q96JS3.raxml.reduced.phy Alignment comprises 1 partitions and 809 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 809 Gaps: 51.37 % Invariant sites: 0.62 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96JS3/4_raxmlng_ancestral/Q96JS3.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/Q96JS3/3_mltree/Q96JS3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 203 / 16240 [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: -179960.134813 [00:00:00 -179960.134813] Initial branch length optimization [00:00:02 -178171.398172] Model parameter optimization (eps = 0.100000) [00:01:15] Tree #1, final logLikelihood: -177435.512063 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.078496,0.410323) (0.094084,1.188848) (0.382841,0.632753) (0.444579,1.380398) 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/Q96JS3/4_raxmlng_ancestral/Q96JS3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96JS3/4_raxmlng_ancestral/Q96JS3.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96JS3/4_raxmlng_ancestral/Q96JS3.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96JS3/4_raxmlng_ancestral/Q96JS3.raxml.log Analysis started: 02-Jun-2021 18:27:22 / finished: 02-Jun-2021 18:28:45 Elapsed time: 82.913 seconds Consumed energy: 4.791 Wh