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 04-Jun-2021 13:38:01 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12081/2_msa/P12081_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12081/3_mltree/P12081.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12081/4_raxmlng_ancestral/P12081 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803081 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/P12081/2_msa/P12081_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 509 sites WARNING: Sequences tr_B2WAN2_B2WAN2_PYRTR_426418 and tr_A0A2W1ETI3_A0A2W1ETI3_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B8NSX8_B8NSX8_ASPFN_332952 and tr_A0A1S9D633_A0A1S9D633_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UFL3_A0A179UFL3_BLAGS_559298 and tr_C5GGB9_C5GGB9_AJEDR_559297 are exactly identical! WARNING: Sequences tr_G2HG51_G2HG51_PANTR_9598 and tr_A0A2R9BVQ3_A0A2R9BVQ3_PANPA_9597 are exactly identical! WARNING: Sequences tr_C6H2S2_C6H2S2_AJECH_544712 and tr_F0U5S6_F0U5S6_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A0I9N5H6_A0A0I9N5H6_BRUMA_6279 and tr_A0A0R3QK14_A0A0R3QK14_9BILA_42155 are exactly identical! WARNING: Sequences tr_A1CW52_A1CW52_NEOFI_331117 and tr_A0A0S7E1B5_A0A0S7E1B5_9EURO_293939 are exactly identical! WARNING: Sequences tr_G7MUZ2_G7MUZ2_MACMU_9544 and tr_G7P8H5_G7P8H5_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7MUZ3_G7MUZ3_MACMU_9544 and tr_G7P8H6_G7P8H6_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7X5S9_G7X5S9_ASPKW_1033177 and tr_A0A146FP36_A0A146FP36_9EURO_1069201 are exactly identical! WARNING: Sequences tr_F9XAF0_F9XAF0_ZYMTI_336722 and tr_A0A1X7RS79_A0A1X7RS79_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2YMN2_G2YMN2_BOTF4_999810 and tr_M7TLG1_M7TLG1_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_B3S1G9_B3S1G9_TRIAD_10228 and tr_A0A369SA01_A0A369SA01_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A0D2XDG5_A0A0D2XDG5_FUSO4_426428 and tr_N4TP89_N4TP89_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_A0A0D2XDG5_A0A0D2XDG5_FUSO4_426428 and tr_A0A2H3T412_A0A2H3T412_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A0A0D2XDG5_A0A0D2XDG5_FUSO4_426428 and tr_A0A2H3H538_A0A2H3H538_FUSOX_327505 are exactly identical! WARNING: Sequences tr_L2G4A9_L2G4A9_COLFN_1213859 and tr_T0JYX7_T0JYX7_COLGC_1237896 are exactly identical! WARNING: Sequences tr_M4DY38_M4DY38_BRARP_51351 and tr_A0A078HB62_A0A078HB62_BRANA_3708 are exactly identical! WARNING: Sequences tr_V2X3F1_V2X3F1_MONRO_1381753 and tr_A0A0W0EX60_A0A0W0EX60_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2PCX2_W2PCX2_PHYPN_761204 and tr_A0A0W8BXJ8_A0A0W8BXJ8_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PCX2_W2PCX2_PHYPN_761204 and tr_W2HGD8_W2HGD8_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015JJT8_A0A015JJT8_9GLOM_1432141 and tr_U9UCM5_U9UCM5_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044R448_A0A044R448_ONCVO_6282 and tr_A0A182E160_A0A182E160_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0F8XJE4_A0A0F8XJE4_9EURO_308745 and tr_A0A2T5MAH3_A0A2T5MAH3_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0L9T8Z7_A0A0L9T8Z7_PHAAN_3914 and tr_A0A1S3UU50_A0A1S3UU50_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A0L9T8Z7_A0A0L9T8Z7_PHAAN_3914 and tr_A0A3Q0FBD8_A0A3Q0FBD8_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A100I3Q4_A0A100I3Q4_ASPNG_5061 and tr_A0A1L9NBM7_A0A1L9NBM7_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A1C3YKS6_A0A1C3YKS6_GIBZE_229533 and tr_A0A2T4H0S8_A0A2T4H0S8_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A194VPH2_A0A194VPH2_9PEZI_105487 and tr_A0A194V8W1_A0A194V8W1_9PEZI_694573 are exactly identical! WARNING: Sequences tr_A0A319CF91_A0A319CF91_9EURO_1448315 and tr_A0A2V5IIG4_A0A2V5IIG4_9EURO_1450541 are exactly identical! WARNING: Duplicate sequences found: 30 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/P12081/4_raxmlng_ancestral/P12081.raxml.reduced.phy Alignment comprises 1 partitions and 509 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 509 Gaps: 8.26 % Invariant sites: 2.36 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12081/4_raxmlng_ancestral/P12081.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/P12081/3_mltree/P12081.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 128 / 10240 [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: -217432.033579 [00:00:00 -217432.033579] Initial branch length optimization [00:00:01 -215909.931141] Model parameter optimization (eps = 0.100000) [00:00:35] Tree #1, final logLikelihood: -215505.193813 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.190400,0.231135) (0.327538,0.391195) (0.232521,1.037129) (0.249540,2.351147) 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/P12081/4_raxmlng_ancestral/P12081.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12081/4_raxmlng_ancestral/P12081.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12081/4_raxmlng_ancestral/P12081.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12081/4_raxmlng_ancestral/P12081.raxml.log Analysis started: 04-Jun-2021 13:38:01 / finished: 04-Jun-2021 13:38:41 Elapsed time: 40.094 seconds