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 23-Jun-2021 00:31:02 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P18074/2_msa/P18074_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P18074/3_mltree/P18074.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P18074/4_raxmlng_ancestral/P18074 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624397462 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/030621_run/phylogeny-snakemake/results/P18074/2_msa/P18074_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 760 sites WARNING: Sequences tr_J3KB80_J3KB80_COCIM_246410 and tr_E9CXR0_E9CXR0_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3KB80_J3KB80_COCIM_246410 and tr_A0A0J6YG17_A0A0J6YG17_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QC92_B6QC92_TALMQ_441960 and tr_A0A093VBI5_A0A093VBI5_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B5E1L9_B5E1L9_DROPS_46245 and tr_B4H4V2_B4H4V2_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8N4P3_B8N4P3_ASPFN_332952 and tr_A0A0F0IHD7_A0A0F0IHD7_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8N4P3_B8N4P3_ASPFN_332952 and tr_A0A1S9DQ74_A0A1S9DQ74_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8N4P3_B8N4P3_ASPFN_332952 and tr_A0A2G7FX24_A0A2G7FX24_9EURO_656916 are exactly identical! WARNING: Sequences tr_E9EZ49_E9EZ49_METRA_655844 and tr_A0A0B4HNR9_A0A0B4HNR9_METMF_1276143 are exactly identical! WARNING: Sequences tr_E9EZ49_E9EZ49_METRA_655844 and tr_A0A0D9PB70_A0A0D9PB70_METAN_1291518 are exactly identical! WARNING: Sequences tr_A2QRS5_A2QRS5_ASPNC_425011 and tr_G3YEQ3_G3YEQ3_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QRS5_A2QRS5_ASPNC_425011 and tr_A0A319A787_A0A319A787_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F7BIL7_F7BIL7_MACMU_9544 and tr_A0A2K6DVB0_A0A2K6DVB0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7XKF8_G7XKF8_ASPKW_1033177 and tr_A0A100IJ96_A0A100IJ96_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XKF8_G7XKF8_ASPKW_1033177 and tr_A0A146FSS3_A0A146FSS3_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XKF8_G7XKF8_ASPKW_1033177 and tr_A0A1L9NPT0_A0A1L9NPT0_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G7XKF8_G7XKF8_ASPKW_1033177 and tr_A0A317W753_A0A317W753_9EURO_1448314 are exactly identical! WARNING: Sequences tr_F9XEJ8_F9XEJ8_ZYMTI_336722 and tr_A0A0F4GN34_A0A0F4GN34_9PEZI_1047168 are exactly identical! WARNING: Sequences tr_F9XEJ8_F9XEJ8_ZYMTI_336722 and tr_A0A1X7RXA8_A0A1X7RXA8_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_A0A0D2YCB6_A0A0D2YCB6_FUSO4_426428 and tr_A0A2K0WWD5_A0A2K0WWD5_GIBNY_42673 are exactly identical! WARNING: Sequences tr_S0EGI5_S0EGI5_GIBF5_1279085 and tr_A0A365NIM3_A0A365NIM3_GIBIN_948311 are exactly identical! WARNING: Sequences tr_N4UZI0_N4UZI0_FUSC1_1229664 and tr_A0A2H3U1T4_A0A2H3U1T4_FUSOX_5507 are exactly identical! WARNING: Sequences tr_M2T400_M2T400_COCSN_665912 and tr_M2UYQ7_M2UYQ7_COCH5_701091 are exactly identical! WARNING: Sequences tr_M2T400_M2T400_COCSN_665912 and tr_W6YY68_W6YY68_COCCA_930089 are exactly identical! WARNING: Sequences tr_M2T400_M2T400_COCSN_665912 and tr_W6ZDX5_W6ZDX5_COCMI_930090 are exactly identical! WARNING: Sequences tr_W2PP97_W2PP97_PHYPN_761204 and tr_W2IBZ9_W2IBZ9_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015IV18_A0A015IV18_9GLOM_1432141 and tr_A0A2I1G4L0_A0A2I1G4L0_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015IV18_A0A015IV18_9GLOM_1432141 and tr_U9TRU9_U9TRU9_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A067FRJ1_A0A067FRJ1_CITSI_2711 and tr_V4TZX9_V4TZX9_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A084QEI4_A0A084QEI4_STAC4_1283841 and tr_A0A084RBU4_A0A084RBU4_STACH_1283842 are exactly identical! WARNING: Sequences tr_X0CV41_X0CV41_FUSOX_1089458 and tr_A0A2H3GQC0_A0A2H3GQC0_FUSOX_327505 are exactly identical! WARNING: Sequences tr_A0A0V0UQY2_A0A0V0UQY2_9BILA_181606 and tr_A0A0V1LPA3_A0A0V1LPA3_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0UQY2_A0A0V0UQY2_9BILA_181606 and tr_A0A0V0ZFR8_A0A0V0ZFR8_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0UQY2_A0A0V0UQY2_9BILA_181606 and tr_A0A0V1NSZ8_A0A0V1NSZ8_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0UQY2_A0A0V0UQY2_9BILA_181606 and tr_A0A0V0TKA4_A0A0V0TKA4_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1C3YN55_A0A1C3YN55_GIBZE_229533 and tr_A0A2T4GV83_A0A2T4GV83_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A161W1N1_A0A161W1N1_9PEZI_708197 and tr_A0A161W8G5_A0A161W8G5_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_A0A1S3YNQ8_A0A1S3YNQ8_TOBAC_4097 and tr_A0A1U7W1Z5_A0A1U7W1Z5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2G2Y0I5_A0A2G2Y0I5_CAPAN_4072 and tr_A0A2G3C3N8_A0A2G3C3N8_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2N5SCB1_A0A2N5SCB1_9BASI_200324 and tr_A0A2N5UN64_A0A2N5UN64_9BASI_200324 are exactly identical! WARNING: Sequences tr_A0A2V5I179_A0A2V5I179_9EURO_1450541 and tr_A0A2V5GYZ4_A0A2V5GYZ4_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 40 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P18074/4_raxmlng_ancestral/P18074.raxml.reduced.phy Alignment comprises 1 partitions and 760 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 760 Gaps: 7.41 % Invariant sites: 0.13 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P18074/4_raxmlng_ancestral/P18074.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/030621_run/phylogeny-snakemake/results/P18074/3_mltree/P18074.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 190 / 15200 [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: -253628.113263 [00:00:00 -253628.113263] Initial branch length optimization [00:00:02 -252861.954196] Model parameter optimization (eps = 0.100000) [00:01:03] Tree #1, final logLikelihood: -251597.773874 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.273016,0.390302) (0.287963,0.512213) (0.296013,1.077430) (0.143008,2.985914) 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/030621_run/phylogeny-snakemake/results/P18074/4_raxmlng_ancestral/P18074.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P18074/4_raxmlng_ancestral/P18074.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P18074/4_raxmlng_ancestral/P18074.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/P18074/4_raxmlng_ancestral/P18074.raxml.log Analysis started: 23-Jun-2021 00:31:02 / finished: 23-Jun-2021 00:32:13 Elapsed time: 70.964 seconds Consumed energy: 6.100 Wh