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 13:53:28 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15125/2_msa/Q15125_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15125/3_mltree/Q15125.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15125/4_raxmlng_ancestral/Q15125 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804008 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/Q15125/2_msa/Q15125_nogap_msa.fasta [00:00:00] Loaded alignment with 852 taxa and 230 sites WARNING: Sequences tr_J3KAW8_J3KAW8_COCIM_246410 and tr_E9CY70_E9CY70_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3KAW8_J3KAW8_COCIM_246410 and tr_A0A0J6YFG7_A0A0J6YFG7_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2WKZ3_B2WKZ3_PYRTR_426418 and tr_A0A2W1GZW5_A0A2W1GZW5_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3RQ64_G3RQ64_GORGO_9595 and tr_H2RA53_H2RA53_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RQ64_G3RQ64_GORGO_9595 and tr_A0A2R9CDM9_A0A2R9CDM9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G2WUJ3_G2WUJ3_VERDV_498257 and tr_A0A0G4MSF4_A0A0G4MSF4_9PEZI_100787 are exactly identical! WARNING: Sequences tr_A0A179UKN9_A0A179UKN9_BLAGS_559298 and tr_C5G8P8_C5G8P8_AJEDR_559297 are exactly identical! WARNING: Sequences tr_E9F8M6_E9F8M6_METRA_655844 and tr_A0A0D9NPB7_A0A0D9NPB7_METAN_1291518 are exactly identical! WARNING: Sequences tr_C6HB72_C6HB72_AJECH_544712 and tr_F0UDM7_F0UDM7_AJEC8_544711 are exactly identical! WARNING: Sequences tr_Q2UFT4_Q2UFT4_ASPOR_510516 and tr_A0A1S9E1G7_A0A1S9E1G7_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_Q2UQJ9_Q2UQJ9_ASPOR_510516 and tr_A0A1S9DU56_A0A1S9DU56_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A0E0FEY2_A0A0E0FEY2_ORYNI_4536 and tr_A0A0E0MQA0_A0A0E0MQA0_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0FEY2_A0A0E0FEY2_ORYNI_4536 and tr_A0A0D3EIL7_A0A0D3EIL7_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0FEY2_A0A0E0FEY2_ORYNI_4536 and tr_A0A0D9Y226_A0A0D9Y226_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A2QAY8_A2QAY8_ASPNC_425011 and tr_G3XRP9_G3XRP9_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QAY8_A2QAY8_ASPNC_425011 and tr_A0A319B185_A0A319B185_9EURO_1450533 are exactly identical! WARNING: Sequences tr_B8ACS4_B8ACS4_ORYSI_39946 and sp_Q9FTZ2_EBP_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G2Y463_G2Y463_BOTF4_999810 and tr_M7U630_M7U630_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_N4TU97_N4TU97_FUSC1_1229664 and tr_X0DFP6_X0DFP6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_N4UWM1_N4UWM1_FUSC1_1229664 and tr_X0CUJ8_X0CUJ8_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_N4UWM1_N4UWM1_FUSC1_1229664 and tr_A0A2H3GJS1_A0A2H3GJS1_FUSOX_327505 are exactly identical! WARNING: Sequences tr_A0A015K6H5_A0A015K6H5_9GLOM_1432141 and tr_A0A2I1FUD5_A0A2I1FUD5_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015K6H5_A0A015K6H5_9GLOM_1432141 and tr_U9UDC6_U9UDC6_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A0D3GHA0_A0A0D3GHA0_9ORYZ_65489 and tr_A0A0E0AAA8_A0A0E0AAA8_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A067E3D8_A0A067E3D8_CITSI_2711 and tr_V4UCQ2_V4UCQ2_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A094DYV9_A0A094DYV9_9PEZI_1420912 and tr_A0A2P2SW85_A0A2P2SW85_9PEZI_342668 are exactly identical! WARNING: Sequences tr_V4SJ37_V4SJ37_9ROSI_85681 and tr_A0A2H5Q055_A0A2H5Q055_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A1S4BQJ6_A0A1S4BQJ6_TOBAC_4097 and tr_A0A1U7XH78_A0A1U7XH78_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1U8H250_A0A1U8H250_CAPAN_4072 and tr_A0A2G3CBV5_A0A2G3CBV5_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2U4C135_A0A2U4C135_TURTR_9739 and tr_A0A2Y9MER2_A0A2Y9MER2_DELLE_9749 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/Q15125/4_raxmlng_ancestral/Q15125.raxml.reduced.phy Alignment comprises 1 partitions and 230 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 230 Gaps: 12.84 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15125/4_raxmlng_ancestral/Q15125.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/Q15125/3_mltree/Q15125.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 58 / 4640 [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: -120644.187137 [00:00:00 -120644.187137] Initial branch length optimization [00:00:00 -120367.922903] Model parameter optimization (eps = 0.100000) [00:00:19] Tree #1, final logLikelihood: -119923.345336 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.148319,0.368276) (0.333856,0.498579) (0.347341,1.226341) (0.170484,2.070377) 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/Q15125/4_raxmlng_ancestral/Q15125.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15125/4_raxmlng_ancestral/Q15125.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15125/4_raxmlng_ancestral/Q15125.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q15125/4_raxmlng_ancestral/Q15125.raxml.log Analysis started: 04-Jun-2021 13:53:28 / finished: 04-Jun-2021 13:53:49 Elapsed time: 20.934 seconds