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 22:50:54 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12694/2_msa/P12694_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12694/3_mltree/P12694.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12694/4_raxmlng_ancestral/P12694 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622663454 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/P12694/2_msa/P12694_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 445 sites WARNING: Sequences tr_J3KJ12_J3KJ12_COCIM_246410 and tr_A0A0J6Y0V9_A0A0J6Y0V9_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2VWK1_B2VWK1_PYRTR_426418 and tr_A0A2W1GA34_A0A2W1GA34_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B8NP77_B8NP77_ASPFN_332952 and tr_A0A1S9D6X9_A0A1S9D6X9_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8NP77_B8NP77_ASPFN_332952 and tr_A0A2G7FGB8_A0A2G7FGB8_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A179UGU7_A0A179UGU7_BLAGS_559298 and tr_C5GGX6_C5GGX6_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9FNW6_F9FNW6_FUSOF_660025 and tr_W7M2V7_W7M2V7_GIBM7_334819 are exactly identical! WARNING: Sequences tr_F9FNW6_F9FNW6_FUSOF_660025 and tr_S0DVS9_S0DVS9_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9FNW6_F9FNW6_FUSOF_660025 and tr_X0C0W4_X0C0W4_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FNW6_F9FNW6_FUSOF_660025 and tr_A0A2H3TUR9_A0A2H3TUR9_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FNW6_F9FNW6_FUSOF_660025 and tr_A0A365NDI9_A0A365NDI9_GIBIN_948311 are exactly identical! WARNING: Sequences tr_E9ENY1_E9ENY1_METRA_655844 and tr_A0A0D9PAB5_A0A0D9PAB5_METAN_1291518 are exactly identical! WARNING: Sequences tr_C6HD62_C6HD62_AJECH_544712 and tr_F0UTY3_F0UTY3_AJEC8_544711 are exactly identical! WARNING: Sequences tr_Q2UN01_Q2UN01_ASPOR_510516 and tr_A0A0F0I763_A0A0F0I763_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_A2QTN1_A2QTN1_ASPNC_425011 and tr_G3XMI6_G3XMI6_ASPNA_380704 are exactly identical! WARNING: Sequences tr_G7XXI8_G7XXI8_ASPKW_1033177 and tr_A0A100ILV2_A0A100ILV2_ASPNG_5061 are exactly identical! WARNING: Sequences tr_I1R4L9_I1R4L9_ORYGL_4538 and tr_A0A0E0BPV2_A0A0E0BPV2_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F9X9P8_F9X9P8_ZYMTI_336722 and tr_A0A1X7RRT2_A0A1X7RRT2_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F2SDR0_F2SDR0_TRIRC_559305 and tr_A0A178EUH9_A0A178EUH9_TRIRU_5551 are exactly identical! WARNING: Sequences tr_F1N5F2_F1N5F2_BOVIN_9913 and sp_P11178_ODBA_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M4DN25_M4DN25_BRARP_51351 and tr_A0A078IK13_A0A078IK13_BRANA_3708 are exactly identical! WARNING: Sequences tr_V2XSF8_V2XSF8_MONRO_1381753 and tr_A0A0W0G7M7_A0A0W0G7M7_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A2I3MBQ8_A0A2I3MBQ8_PAPAN_9555 and tr_A0A2K5KVA9_A0A2K5KVA9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MBQ8_A0A2I3MBQ8_PAPAN_9555 and tr_A0A2K6BX38_A0A2K6BX38_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D2SDF0_A0A0D2SDF0_GOSRA_29730 and tr_A0A1U8J9J2_A0A1U8J9J2_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0C9M909_A0A0C9M909_9FUNG_91626 and tr_A0A162ZSD9_A0A162ZSD9_MUCCL_747725 are exactly identical! WARNING: Sequences tr_A0A1S4A566_A0A1S4A566_TOBAC_4097 and tr_A0A1U7VFE1_A0A1U7VFE1_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4B8Q2_A0A1S4B8Q2_TOBAC_4097 and tr_A0A1U7USL2_A0A1U7USL2_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CF75_A0A1S4CF75_TOBAC_4097 and tr_A0A1U7Y9M4_A0A1U7Y9M4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1U8EUA7_A0A1U8EUA7_CAPAN_4072 and tr_A0A2G3B8B6_A0A2G3B8B6_CAPCH_80379 are exactly identical! WARNING: Duplicate sequences found: 29 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/P12694/4_raxmlng_ancestral/P12694.raxml.reduced.phy Alignment comprises 1 partitions and 445 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 445 Gaps: 10.73 % Invariant sites: 0.22 % NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12694/4_raxmlng_ancestral/P12694.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/P12694/3_mltree/P12694.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 112 / 8960 [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: -213387.092595 [00:00:00 -213387.092595] Initial branch length optimization [00:00:01 -212017.889942] Model parameter optimization (eps = 0.100000) [00:00:10] Tree #1, final logLikelihood: -212004.397901 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.188600,0.121858) (0.300159,0.424203) (0.191175,0.889777) (0.320066,2.123270) 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/P12694/4_raxmlng_ancestral/P12694.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12694/4_raxmlng_ancestral/P12694.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12694/4_raxmlng_ancestral/P12694.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P12694/4_raxmlng_ancestral/P12694.raxml.log Analysis started: 02-Jun-2021 22:50:54 / finished: 02-Jun-2021 22:51:09 Elapsed time: 14.718 seconds