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 18:30:18 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25024/2_msa/P25024_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25024/3_mltree/P25024.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25024/4_raxmlng_ancestral/P25024 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647818 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/P25024/2_msa/P25024_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 350 sites WARNING: Sequences tr_M3XT32_M3XT32_MUSPF_9669 and sp_P56498_CXCR4_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XT32_M3XT32_MUSPF_9669 and tr_A0A2U3W623_A0A2U3W623_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XT32_M3XT32_MUSPF_9669 and tr_A0A2U3YFN5_A0A2U3YFN5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XT32_M3XT32_MUSPF_9669 and tr_A0A2Y9J9B6_A0A2Y9J9B6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3H6V3_A0A2I3H6V3_NOMLE_61853 and tr_G3QQ18_G3QQ18_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3H6V3_A0A2I3H6V3_NOMLE_61853 and tr_A0A2I3TX94_A0A2I3TX94_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3H6V3_A0A2I3H6V3_NOMLE_61853 and sp_P51686_CCR9_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RC17_G3RC17_GORGO_9595 and tr_H2QM91_H2QM91_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RC17_G3RC17_GORGO_9595 and sp_P51679_CCR4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RC17_G3RC17_GORGO_9595 and tr_A0A2R8ZA62_A0A2R8ZA62_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RDW5_G3RDW5_GORGO_9595 and tr_A0A2I3S7U4_A0A2I3S7U4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RDW5_G3RDW5_GORGO_9595 and tr_A0A2R9B3P4_A0A2R9B3P4_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RJP4_G3RJP4_GORGO_9595 and tr_H2NU74_H2NU74_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RJP4_G3RJP4_GORGO_9595 and tr_H2R9P0_H2R9P0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RJP4_G3RJP4_GORGO_9595 and sp_P32248_CCR7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RJP4_G3RJP4_GORGO_9595 and tr_A0A2R9CE39_A0A2R9CE39_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SIC0_G3SIC0_GORGO_9595 and tr_H2QYS8_H2QYS8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SIC0_G3SIC0_GORGO_9595 and sp_P49682_CXCR3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SIC0_G3SIC0_GORGO_9595 and tr_A0A2R9CB54_A0A2R9CB54_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SH35_A0A2I3SH35_PANTR_9598 and sp_P25025_CXCR2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3SH35_A0A2I3SH35_PANTR_9598 and tr_A0A2R8ZGE4_A0A2R8ZGE4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QNE3_H2QNE3_PANTR_9598 and tr_A0A2R8ZFQ0_A0A2R8ZFQ0_PANPA_9597 are exactly identical! WARNING: Sequences sp_P61072_CXCR4_PANTR_9598 and sp_P61073_CXCR4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A1D5Q373_A0A1D5Q373_MACMU_9544 and tr_G7NY39_G7NY39_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5Q373_A0A1D5Q373_MACMU_9544 and tr_A0A096NQ44_A0A096NQ44_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5Q373_A0A1D5Q373_MACMU_9544 and tr_A0A2K5NXR5_A0A2K5NXR5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5Q373_A0A1D5Q373_MACMU_9544 and tr_A0A2K6BC31_A0A2K6BC31_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5Q373_A0A1D5Q373_MACMU_9544 and tr_A0A2K6AAY8_A0A2K6AAY8_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6VQA9_F6VQA9_MACMU_9544 and tr_G7P491_G7P491_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WHR2_F6WHR2_MACMU_9544 and tr_A0A2I3LW21_A0A2I3LW21_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WHR2_F6WHR2_MACMU_9544 and tr_A0A0D9S306_A0A0D9S306_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6WHR2_F6WHR2_MACMU_9544 and tr_A0A2K5YEY1_A0A2K5YEY1_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GUA3_F7GUA3_MACMU_9544 and tr_G7NYB7_G7NYB7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GUA3_F7GUA3_MACMU_9544 and tr_A0A096NRU6_A0A096NRU6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GUA3_F7GUA3_MACMU_9544 and tr_A0A0D9SC57_A0A0D9SC57_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GUA3_F7GUA3_MACMU_9544 and tr_G9IT94_G9IT94_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GUA3_F7GUA3_MACMU_9544 and tr_A0A2K6AVR0_A0A2K6AVR0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HD60_F7HD60_MACMU_9544 and tr_A0A096NR01_A0A096NR01_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HLU2_F7HLU2_MACMU_9544 and tr_G8F5K4_G8F5K4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HLU2_F7HLU2_MACMU_9544 and tr_A0A096N7G2_A0A096N7G2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HLU2_F7HLU2_MACMU_9544 and tr_A0A0D9S3P4_A0A0D9S3P4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HLU2_F7HLU2_MACMU_9544 and tr_A0A2K5NDP1_A0A2K5NDP1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HLU2_F7HLU2_MACMU_9544 and tr_A0A2K6BXA4_A0A2K6BXA4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096N764_A0A096N764_PAPAN_9555 and tr_A0A2K5LAI7_A0A2K5LAI7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N764_A0A096N764_PAPAN_9555 and tr_A0A2K5YIP4_A0A2K5YIP4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9RFN8_A0A0D9RFN8_CHLSB_60711 and tr_A0A2K6ANL1_A0A2K6ANL1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D9RUS6_A0A0D9RUS6_CHLSB_60711 and tr_A0A2K5KP70_A0A2K5KP70_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9RUS6_A0A0D9RUS6_CHLSB_60711 and tr_A0A2K6C0G1_A0A2K6C0G1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D9RUS6_A0A0D9RUS6_CHLSB_60711 and tr_A0A2K5XJP9_A0A2K5XJP9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A087QIM8_A0A087QIM8_APTFO_9233 and tr_A0A099ZZT9_A0A099ZZT9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0MGE7_A0A2I0MGE7_COLLI_8932 and tr_A0A1V4K5V6_A0A1V4K5V6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A226NJ28_A0A226NJ28_CALSU_9009 and tr_A0A226P3P4_A0A226P3P4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RQJ1_A0A2D0RQJ1_ICTPU_7998 and tr_A0A2D0RS37_A0A2D0RS37_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KRT5_A0A2K5KRT5_CERAT_9531 and tr_A0A2K5ZZK3_A0A2K5ZZK3_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 54 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/P25024/4_raxmlng_ancestral/P25024.raxml.reduced.phy Alignment comprises 1 partitions and 350 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 350 Gaps: 8.54 % Invariant sites: 1.71 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25024/4_raxmlng_ancestral/P25024.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/P25024/3_mltree/P25024.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 88 / 7040 [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: -175853.507692 [00:00:00 -175853.507692] Initial branch length optimization [00:00:01 -171487.943211] Model parameter optimization (eps = 0.100000) [00:00:34] Tree #1, final logLikelihood: -171226.000538 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.172058,0.267516) (0.235138,0.464294) (0.416082,1.028222) (0.176722,2.359493) 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/P25024/4_raxmlng_ancestral/P25024.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25024/4_raxmlng_ancestral/P25024.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25024/4_raxmlng_ancestral/P25024.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P25024/4_raxmlng_ancestral/P25024.raxml.log Analysis started: 02-Jun-2021 18:30:18 / finished: 02-Jun-2021 18:30:56 Elapsed time: 37.926 seconds Consumed energy: 2.459 Wh