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 15:14:41 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95528/2_msa/O95528_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95528/3_mltree/O95528.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95528/4_raxmlng_ancestral/O95528 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622636081 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/O95528/2_msa/O95528_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 541 sites WARNING: Sequences tr_D8S624_D8S624_SELML_88036 and tr_D8SMJ7_D8SMJ7_SELML_88036 are exactly identical! WARNING: Sequences sp_Q0WWW9_XYLL3_ARATH_3702 and tr_D7MR67_D7MR67_ARALL_81972 are exactly identical! WARNING: Sequences tr_A0A0E0FFU0_A0A0E0FFU0_ORYNI_4536 and tr_B8AD38_B8AD38_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0FFU0_A0A0E0FFU0_ORYNI_4536 and tr_A0A0E0MR06_A0A0E0MR06_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0FFU0_A0A0E0FFU0_ORYNI_4536 and tr_A0A0D9Y2U9_A0A0D9Y2U9_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0H2H9_A0A0E0H2H9_ORYNI_4536 and tr_B8AVV5_B8AVV5_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0H2H9_A0A0E0H2H9_ORYNI_4536 and tr_A0A0E0PAX2_A0A0E0PAX2_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0H2H9_A0A0E0H2H9_ORYNI_4536 and tr_Q7XUE4_Q7XUE4_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0H7J2_A0A0E0H7J2_ORYNI_4536 and tr_A2XZ03_A2XZ03_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HWG6_A0A0E0HWG6_ORYNI_4536 and tr_Q7XIZ0_Q7XIZ0_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0I2V5_A0A0E0I2V5_ORYNI_4536 and tr_A2YN19_A2YN19_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0I2V5_A0A0E0I2V5_ORYNI_4536 and tr_I1QEN6_I1QEN6_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0I2V5_A0A0E0I2V5_ORYNI_4536 and tr_A0A0E0ALW5_A0A0E0ALW5_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0IFY4_A0A0E0IFY4_ORYNI_4536 and tr_B8BIF2_B8BIF2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0IFY4_A0A0E0IFY4_ORYNI_4536 and tr_Q7XBT2_Q7XBT2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0IHL9_A0A0E0IHL9_ORYNI_4536 and tr_A0A0E0QPD1_A0A0E0QPD1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0IHL9_A0A0E0IHL9_ORYNI_4536 and tr_A0A0P0XKW0_A0A0P0XKW0_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2ZG82_A2ZG82_ORYSI_39946 and tr_Q2R0P8_Q2R0P8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1NJZ6_I1NJZ6_ORYGL_4538 and tr_A0A0D3EJA3_A0A0D3EJA3_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1QFD1_I1QFD1_ORYGL_4538 and tr_A0A0D3FXD4_A0A0D3FXD4_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1QWB3_I1QWB3_ORYGL_4538 and tr_A0A0D3HH09_A0A0D3HH09_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1R1R3_I1R1R3_ORYGL_4538 and tr_A0A0D3HP94_A0A0D3HP94_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1R1R5_I1R1R5_ORYGL_4538 and tr_A0A0E0BLH7_A0A0E0BLH7_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0MY63_A0A0E0MY63_ORYRU_4529 and sp_Q94EC4_MST8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0QAD4_A0A0E0QAD4_ORYRU_4529 and tr_Q6ZFM7_Q6ZFM7_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_M4CEG5_M4CEG5_BRARP_51351 and tr_A0A078ISX5_A0A078ISX5_BRANA_3708 are exactly identical! WARNING: Sequences tr_M7YEB2_M7YEB2_TRIUA_4572 and tr_A0A3B6HZ70_A0A3B6HZ70_WHEAT_4565 are exactly identical! WARNING: Sequences tr_U5HH98_U5HH98_USTV1_683840 and tr_A0A2X0M7E2_A0A2X0M7E2_9BASI_796604 are exactly identical! WARNING: Sequences tr_A0A3B6FFH0_A0A3B6FFH0_WHEAT_4565 and tr_A0A3B6GKI6_A0A3B6GKI6_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A078FYN5_A0A078FYN5_BRANA_3708 and tr_A0A0D3BPJ1_A0A0D3BPJ1_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078GDA9_A0A078GDA9_BRANA_3708 and tr_A0A0D3C615_A0A0D3C615_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078HKD2_A0A078HKD2_BRANA_3708 and tr_A0A0D3AJF6_A0A0D3AJF6_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A1S3YEI6_A0A1S3YEI6_TOBAC_4097 and tr_A0A1U7WRK4_A0A1U7WRK4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3ZUZ8_A0A1S3ZUZ8_TOBAC_4097 and tr_A0A1U7XXM9_A0A1U7XXM9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4D4A5_A0A1S4D4A5_TOBAC_4097 and tr_A0A314L965_A0A314L965_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S3VXL0_A0A1S3VXL0_VIGRR_3916 and tr_A0A3Q0EPR6_A0A3Q0EPR6_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A2G2ZD64_A0A2G2ZD64_CAPAN_4072 and tr_A0A2G3CAH3_A0A2G3CAH3_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2H5NUR6_A0A2H5NUR6_CITUN_55188 and tr_A0A2H5NUS3_A0A2H5NUS3_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A2U1M885_A0A2U1M885_ARTAN_35608 and tr_A0A2U1N502_A0A2U1N502_ARTAN_35608 are exactly identical! WARNING: Duplicate sequences found: 39 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/O95528/4_raxmlng_ancestral/O95528.raxml.reduced.phy Alignment comprises 1 partitions and 541 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 541 Gaps: 19.38 % Invariant sites: 0.18 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95528/4_raxmlng_ancestral/O95528.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/O95528/3_mltree/O95528.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 136 / 10880 [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: -240067.400061 [00:00:00 -240067.400061] Initial branch length optimization [00:00:01 -238588.170028] Model parameter optimization (eps = 0.100000) [00:00:58] Tree #1, final logLikelihood: -237243.280464 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.245367,0.448646) (0.254077,0.464717) (0.276353,1.059112) (0.224203,2.137146) 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/O95528/4_raxmlng_ancestral/O95528.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95528/4_raxmlng_ancestral/O95528.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95528/4_raxmlng_ancestral/O95528.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95528/4_raxmlng_ancestral/O95528.raxml.log Analysis started: 02-Jun-2021 15:14:41 / finished: 02-Jun-2021 15:15:45 Elapsed time: 63.128 seconds