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-Jun-2021 18:13:47 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29371/2_msa/P29371_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29371/3_mltree/P29371.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29371/4_raxmlng_ancestral/P29371 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622646827 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/P29371/2_msa/P29371_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 465 sites WARNING: Sequences tr_B4QRK9_B4QRK9_DROSI_7240 and tr_B4HUF9_B4HUF9_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4R0W9_B4R0W9_DROSI_7240 and tr_B4HZI7_B4HZI7_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A2I3HFL3_A0A2I3HFL3_NOMLE_61853 and tr_A0A2J8W0K6_A0A2J8W0K6_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3HFL3_A0A2I3HFL3_NOMLE_61853 and tr_A0A2K6HM81_A0A2K6HM81_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HFL3_A0A2I3HFL3_NOMLE_61853 and sp_Q5IS62_NPY2R_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HFL3_A0A2I3HFL3_NOMLE_61853 and sp_P49146_NPY2R_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3HFL3_A0A2I3HFL3_NOMLE_61853 and tr_A0A2R8ZGI9_A0A2R8ZGI9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QP89_G3QP89_GORGO_9595 and tr_H2PEN1_H2PEN1_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QP89_G3QP89_GORGO_9595 and tr_H2QQD5_H2QQD5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QP89_G3QP89_GORGO_9595 and tr_A0A2R9CMK6_A0A2R9CMK6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2P5Q0_H2P5Q0_PONAB_9601 and sp_P25103_NK1R_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2P5Q0_H2P5Q0_PONAB_9601 and tr_A0A096N5A2_A0A096N5A2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2P5Q0_H2P5Q0_PONAB_9601 and tr_A0A0D9RTF5_A0A0D9RTF5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2P5Q0_H2P5Q0_PONAB_9601 and tr_A0A2K5Z4R7_A0A2K5Z4R7_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2P5Q0_H2P5Q0_PONAB_9601 and tr_A0A2R8ZV24_A0A2R8ZV24_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q293Q9_Q293Q9_DROPS_46245 and tr_B4GLR8_B4GLR8_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q29C90_Q29C90_DROPS_46245 and tr_B4GNG0_B4GNG0_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2QPZ4_H2QPZ4_PANTR_9598 and tr_A0A2R9AIG6_A0A2R9AIG6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NIG7_A0A158NIG7_ATTCE_12957 and tr_A0A195B6I0_A0A195B6I0_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A1D5R7E2_A0A1D5R7E2_MACMU_9544 and tr_G7PNH3_G7PNH3_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5R7E2_A0A1D5R7E2_MACMU_9544 and tr_A0A0D9S1B7_A0A0D9S1B7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_Q2WGM1_Q2WGM1_MACMU_9544 and tr_A0A2K6AW43_A0A2K6AW43_MACNE_9545 are exactly identical! WARNING: Sequences tr_Q9GK75_Q9GK75_MACMU_9544 and tr_G8F2E2_G8F2E2_MACFA_9541 are exactly identical! WARNING: Sequences tr_Q9GK75_Q9GK75_MACMU_9544 and tr_A0A096N011_A0A096N011_PAPAN_9555 are exactly identical! WARNING: Sequences tr_Q9GK75_Q9GK75_MACMU_9544 and tr_A0A0D9S1V8_A0A0D9S1V8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_Q9GK75_Q9GK75_MACMU_9544 and tr_A0A2K5XXT9_A0A2K5XXT9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3LFK4_A0A2I3LFK4_PAPAN_9555 and tr_A0A2K5KND0_A0A2K5KND0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LFK4_A0A2I3LFK4_PAPAN_9555 and tr_A0A2K6DXA9_A0A2K6DXA9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3LFK4_A0A2I3LFK4_PAPAN_9555 and tr_A0A2K5YL45_A0A2K5YL45_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151NUS9_A0A151NUS9_ALLMI_8496 and tr_A0A3Q0G8H7_A0A3Q0G8H7_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A2I0MEK0_A0A2I0MEK0_COLLI_8932 and tr_A0A1V4KI87_A0A1V4KI87_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1LM28_A0A0V1LM28_9BILA_6335 and tr_A0A0V0U2J8_A0A0V0U2J8_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3PIQ6_A0A1S3PIQ6_SALSA_8030 and tr_A0A060VP48_A0A060VP48_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A0M4ECI4_A0A0M4ECI4_DROBS_30019 and tr_A0A0M4EHF7_A0A0M4EHF7_DROBS_30019 are exactly identical! WARNING: Sequences tr_A0A1U7QMT5_A0A1U7QMT5_MESAU_10036 and sp_P51144_NK2R_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2D0PL24_A0A2D0PL24_ICTPU_7998 and tr_A0A2D0PMT5_A0A2D0PMT5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QMP6_A0A2D0QMP6_ICTPU_7998 and tr_A0A2D0QQ35_A0A2D0QQ35_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LBD6_A0A2K5LBD6_CERAT_9531 and tr_A0A2K5ZPY7_A0A2K5ZPY7_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 38 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/P29371/4_raxmlng_ancestral/P29371.raxml.reduced.phy Alignment comprises 1 partitions and 465 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 465 Gaps: 27.16 % Invariant sites: 0.22 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29371/4_raxmlng_ancestral/P29371.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/P29371/3_mltree/P29371.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 117 / 9360 [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: -193752.428529 [00:00:00 -193752.428529] Initial branch length optimization [00:00:01 -192838.998774] Model parameter optimization (eps = 0.100000) [00:00:32] Tree #1, final logLikelihood: -192127.056497 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.193346,0.290141) (0.199639,0.441591) (0.304631,0.841485) (0.302383,1.982255) 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/P29371/4_raxmlng_ancestral/P29371.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29371/4_raxmlng_ancestral/P29371.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29371/4_raxmlng_ancestral/P29371.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P29371/4_raxmlng_ancestral/P29371.raxml.log Analysis started: 02-Jun-2021 18:13:47 / finished: 02-Jun-2021 18:14:24 Elapsed time: 37.088 seconds Consumed energy: 2.676 Wh