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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 15:03:07 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04844/2_msa/Q04844_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04844/3_mltree/Q04844.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04844/4_raxmlng_ancestral/Q04844 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622635387 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04844/2_msa/Q04844_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 493 sites WARNING: Sequences tr_B4QT69_B4QT69_DROSI_7240 and sp_P17644_ACH2_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QT69_B4QT69_DROSI_7240 and tr_B4HH26_B4HH26_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4QT71_B4QT71_DROSI_7240 and sp_P25162_ACH4_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QT71_B4QT71_DROSI_7240 and tr_B4HH28_B4HH28_DROSE_7238 are exactly identical! WARNING: Sequences tr_F1NHP4_F1NHP4_CHICK_9031 and sp_P09480_ACHA2_CHICK_9031 are exactly identical! WARNING: Sequences sp_P09478_ACH1_DROME_7227 and tr_B4HH23_B4HH23_DROSE_7238 are exactly identical! WARNING: Sequences sp_P09478_ACH1_DROME_7227 and tr_B3N1Q7_B3N1Q7_DROAN_7217 are exactly identical! WARNING: Sequences sp_P09478_ACH1_DROME_7227 and tr_A0A1W4URW6_A0A1W4URW6_DROFC_30025 are exactly identical! WARNING: Sequences tr_G3QW49_G3QW49_GORGO_9595 and tr_H2Q056_H2Q056_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QW49_G3QW49_GORGO_9595 and sp_P17787_ACHB2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QW49_G3QW49_GORGO_9595 and tr_A0A2R9AJA2_A0A2R9AJA2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8SKI9_A0A2J8SKI9_PONAB_9601 and tr_A0A2J8KCH2_A0A2J8KCH2_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2J8SKI9_A0A2J8SKI9_PONAB_9601 and sp_P32297_ACHA3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_B5DWV2_B5DWV2_DROPS_46245 and tr_B4GE91_B4GE91_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2K6HRQ5_A0A2K6HRQ5_PANTR_9598 and sp_Q15825_ACHA6_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q9W8_H2Q9W8_PANTR_9598 and tr_A0A2R9A6Q4_A0A2R9A6Q4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R3V0_H2R3V0_PANTR_9598 and tr_A0A2R9CRT0_A0A2R9CRT0_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q5IS52_ACHA2_PANTR_9598 and tr_A0A2R9C9T0_A0A2R9C9T0_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q5IS75_ACHB3_PANTR_9598 and sp_Q05901_ACHB3_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5IS75_ACHB3_PANTR_9598 and tr_A0A2R9BDF1_A0A2R9BDF1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G7PBS1_G7PBS1_MACFA_9541 and tr_A0A2K6ADP0_A0A2K6ADP0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096MXP4_A0A096MXP4_PAPAN_9555 and tr_A0A2K5NCC7_A0A2K5NCC7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MXP4_A0A096MXP4_PAPAN_9555 and tr_A0A2K5Y862_A0A2K5Y862_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151NE18_A0A151NE18_ALLMI_8496 and tr_A0A1U7STT8_A0A1U7STT8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091F5H0_A0A091F5H0_CORBR_85066 and tr_A0A0A0AJI6_A0A0A0AJI6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091VVF9_A0A091VVF9_NIPNI_128390 and tr_A0A099ZFC7_A0A099ZFC7_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091VVF9_A0A091VVF9_NIPNI_128390 and tr_A0A091G8N7_A0A091G8N7_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091VVF9_A0A091VVF9_NIPNI_128390 and tr_A0A0A0B1M4_A0A0A0B1M4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091VVF9_A0A091VVF9_NIPNI_128390 and tr_A0A093IHR7_A0A093IHR7_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A2K5KQC0_A0A2K5KQC0_CERAT_9531 and tr_A0A2K5YK65_A0A2K5YK65_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5KT26_A0A2K5KT26_CERAT_9531 and tr_A0A2K5XV71_A0A2K5XV71_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 31 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04844/4_raxmlng_ancestral/Q04844.raxml.reduced.phy Alignment comprises 1 partitions and 493 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 493 Gaps: 12.19 % Invariant sites: 1.62 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04844/4_raxmlng_ancestral/Q04844.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04844/3_mltree/Q04844.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 124 / 9920 [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: -156747.504706 [00:00:00 -156747.504706] Initial branch length optimization [00:00:01 -143325.637052] Model parameter optimization (eps = 0.100000) [00:02:57] Tree #1, final logLikelihood: -142849.225700 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.276690,0.254754) (0.221175,0.323862) (0.295106,1.070664) (0.207029,2.617614) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04844/4_raxmlng_ancestral/Q04844.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04844/4_raxmlng_ancestral/Q04844.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04844/4_raxmlng_ancestral/Q04844.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q04844/4_raxmlng_ancestral/Q04844.raxml.log Analysis started: 02-Jun-2021 15:03:07 / finished: 02-Jun-2021 15:06:09 Elapsed time: 181.881 seconds