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 22:46:02 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08357/2_msa/Q08357_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08357/3_mltree/Q08357.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08357/4_raxmlng_ancestral/Q08357 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622663162 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/Q08357/2_msa/Q08357_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 652 sites WARNING: Sequences tr_Q4QH82_Q4QH82_LEIMA_5664 and tr_Q4QHL7_Q4QHL7_LEIMA_5664 are exactly identical! WARNING: Sequences tr_C3YE47_C3YE47_BRAFL_7739 and tr_C3YE61_C3YE61_BRAFL_7739 are exactly identical! WARNING: Sequences tr_F9G1R8_F9G1R8_FUSOF_660025 and tr_N4UWB8_N4UWB8_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9G1R8_F9G1R8_FUSOF_660025 and tr_X0CCK3_X0CCK3_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9G1R8_F9G1R8_FUSOF_660025 and tr_A0A2H3SX65_A0A2H3SX65_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A0A0E0G974_A0A0E0G974_ORYNI_4536 and tr_A2X6P4_A2X6P4_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0G974_A0A0E0G974_ORYNI_4536 and tr_I1P1R7_I1P1R7_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0G974_A0A0E0G974_ORYNI_4536 and tr_A0A0E0CMR5_A0A0E0CMR5_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0G974_A0A0E0G974_ORYNI_4536 and tr_A0A0E0NH73_A0A0E0NH73_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0G974_A0A0E0G974_ORYNI_4536 and tr_A0A0D3F730_A0A0D3F730_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0G974_A0A0E0G974_ORYNI_4536 and tr_A0A0D9YUD8_A0A0D9YUD8_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0G974_A0A0E0G974_ORYNI_4536 and tr_Q6ZH86_Q6ZH86_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A1D5RFC4_A0A1D5RFC4_MACMU_9544 and tr_G7PBR9_G7PBR9_MACFA_9541 are exactly identical! WARNING: Sequences tr_A4H5Y5_A4H5Y5_LEIBR_5660 and tr_A4H6C2_A4H6C2_LEIBR_5660 are exactly identical! WARNING: Sequences tr_F9XB41_F9XB41_ZYMTI_336722 and tr_A0A1X7RV31_A0A1X7RV31_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_F2PRR8_F2PRR8_TRIEC_559882 and tr_A0A059IXJ8_A0A059IXJ8_9EURO_1215338 are exactly identical! WARNING: Sequences tr_L2G1D8_L2G1D8_COLFN_1213859 and tr_T0LX38_T0LX38_COLGC_1237896 are exactly identical! WARNING: Sequences tr_M4E8V6_M4E8V6_BRARP_51351 and tr_A0A0D3DB14_A0A0D3DB14_BRAOL_109376 are exactly identical! WARNING: Sequences tr_N4URA0_N4URA0_FUSC1_1229664 and tr_X0DGJ4_X0DGJ4_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_N4URA0_N4URA0_FUSC1_1229664 and tr_A0A2H3SVC8_A0A2H3SVC8_FUSOX_5507 are exactly identical! WARNING: Sequences tr_N4URA0_N4URA0_FUSC1_1229664 and tr_A0A2H3I2Z9_A0A2H3I2Z9_FUSOX_327505 are exactly identical! WARNING: Sequences tr_A0A3B6NNV9_A0A3B6NNV9_WHEAT_4565 and tr_A0A3B6PLH1_A0A3B6PLH1_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A015I3L7_A0A015I3L7_9GLOM_1432141 and tr_U9U3V4_U9U3V4_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A094GUT3_A0A094GUT3_9PEZI_1420912 and tr_A0A1B8GSD5_A0A1B8GSD5_9PEZI_342668 are exactly identical! WARNING: Sequences tr_V4TIR2_V4TIR2_9ROSI_85681 and tr_A0A2H5N7S9_A0A2H5N7S9_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0V1CE22_A0A0V1CE22_TRIBR_45882 and tr_A0A0V0WQA4_A0A0V0WQA4_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CE22_A0A0V1CE22_TRIBR_45882 and tr_A0A0V0V6C8_A0A0V0V6C8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CE22_A0A0V1CE22_TRIBR_45882 and tr_A0A0V1KV47_A0A0V1KV47_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CE22_A0A0V1CE22_TRIBR_45882 and tr_A0A0V1NLA5_A0A0V1NLA5_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CE22_A0A0V1CE22_TRIBR_45882 and tr_A0A0V0UIM4_A0A0V0UIM4_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0UU60_A0A0V0UU60_9BILA_181606 and tr_A0A0V0TUK7_A0A0V0TUK7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1KZZ1_A0A0V1KZZ1_9BILA_6335 and tr_A0A0V1P4L4_A0A0V1P4L4_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A101MEI7_A0A101MEI7_9EURO_48697 and tr_A0A1V6NFF9_A0A1V6NFF9_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A1S3ZSM5_A0A1S3ZSM5_TOBAC_4097 and tr_A0A1U7V0U5_A0A1U7V0U5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2U1KLW5_A0A2U1KLW5_ARTAN_35608 and tr_A0A2U1N9S0_A0A2U1N9S0_ARTAN_35608 are exactly identical! WARNING: Duplicate sequences found: 35 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/Q08357/4_raxmlng_ancestral/Q08357.raxml.reduced.phy Alignment comprises 1 partitions and 652 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 652 Gaps: 26.87 % Invariant sites: 0.15 % NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08357/4_raxmlng_ancestral/Q08357.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/Q08357/3_mltree/Q08357.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 163 / 13040 [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: -268313.993139 [00:00:00 -268313.993139] Initial branch length optimization [00:00:02 -261236.890639] Model parameter optimization (eps = 0.100000) [00:00:51] Tree #1, final logLikelihood: -260373.005534 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.182006,0.252572) (0.215385,0.356222) (0.335673,0.968281) (0.266936,2.068957) 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/Q08357/4_raxmlng_ancestral/Q08357.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08357/4_raxmlng_ancestral/Q08357.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08357/4_raxmlng_ancestral/Q08357.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q08357/4_raxmlng_ancestral/Q08357.raxml.log Analysis started: 02-Jun-2021 22:46:02 / finished: 02-Jun-2021 22:46:59 Elapsed time: 57.263 seconds