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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 18:30:27 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P14598/2_msa/P14598_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P14598/3_mltree/P14598.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P14598/4_raxmlng_ancestral/P14598 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647827 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/020621_run/phylogeny-snakemake/results/P14598/2_msa/P14598_nogap_msa.fasta [00:00:00] Loaded alignment with 735 taxa and 390 sites WARNING: Sequences tr_G1RZ64_G1RZ64_NOMLE_61853 and tr_H2NBI2_H2NBI2_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RZ64_G1RZ64_NOMLE_61853 and tr_A0A2K5Y8Z2_A0A2K5Y8Z2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2ZS83_A0A2I2ZS83_GORGO_9595 and tr_A0A2I3SRN7_A0A2I3SRN7_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZS83_A0A2I2ZS83_GORGO_9595 and sp_Q5TCZ1_SPD2A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZS83_A0A2I2ZS83_GORGO_9595 and tr_F7EWU2_F7EWU2_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2ZS83_A0A2I2ZS83_GORGO_9595 and tr_A0A096P6H7_A0A096P6H7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PHD3_H2PHD3_PONAB_9601 and sp_A1X283_SPD2B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F9GBN3_F9GBN3_FUSOF_660025 and tr_A0A0D2XZS4_A0A0D2XZS4_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9GBN3_F9GBN3_FUSOF_660025 and tr_A0A2H3TI72_A0A2H3TI72_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9GBN3_F9GBN3_FUSOF_660025 and tr_A0A2H3GK38_A0A2H3GK38_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F6R7I6_F6R7I6_MACMU_9544 and tr_A0A2K5NWB1_A0A2K5NWB1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6R7I6_F6R7I6_MACMU_9544 and tr_A0A2K6CNX4_A0A2K6CNX4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MYE5_G7MYE5_MACMU_9544 and tr_A0A0D9RQE3_A0A0D9RQE3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7MYE5_G7MYE5_MACMU_9544 and tr_A0A2K5KJL5_A0A2K5KJL5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MYE5_G7MYE5_MACMU_9544 and tr_A0A2K6BGZ2_A0A2K6BGZ2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MYE5_G7MYE5_MACMU_9544 and tr_A0A2K5ZEW2_A0A2K5ZEW2_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0ZJA6_H0ZJA6_TAEGU_59729 and tr_A0A091FIS1_A0A091FIS1_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A0Q9WIK5_A0A0Q9WIK5_DROVI_7244 and tr_A0A0Q9XBW0_A0A0Q9XBW0_DROMO_7230 are exactly identical! WARNING: Sequences tr_W7MGS0_W7MGS0_GIBM7_334819 and tr_N4UP53_N4UP53_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_W7MGS0_W7MGS0_GIBM7_334819 and tr_X0CVA0_X0CVA0_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_W7MGS0_W7MGS0_GIBM7_334819 and tr_A0A2K0WIC3_A0A2K0WIC3_GIBNY_42673 are exactly identical! WARNING: Sequences tr_A0A096MQ72_A0A096MQ72_PAPAN_9555 and tr_A0A2K5Z934_A0A2K5Z934_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0F9ZXB5_A0A0F9ZXB5_TRIHA_5544 and tr_A0A2T3ZSY7_A0A2T3ZSY7_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A0A1N169_A0A0A1N169_9FUNG_58291 and tr_A0A367J357_A0A367J357_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A151PII8_A0A151PII8_ALLMI_8496 and tr_A0A3Q0GX81_A0A3Q0GX81_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091EB53_A0A091EB53_CORBR_85066 and tr_A0A093PHZ4_A0A093PHZ4_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091EB53_A0A091EB53_CORBR_85066 and tr_A0A091UMR8_A0A091UMR8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091EB53_A0A091EB53_CORBR_85066 and tr_A0A087QZD8_A0A087QZD8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091EB53_A0A091EB53_CORBR_85066 and tr_A0A091VCR1_A0A091VCR1_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091EB53_A0A091EB53_CORBR_85066 and tr_A0A099YYS6_A0A099YYS6_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091EB53_A0A091EB53_CORBR_85066 and tr_A0A0A0ABZ8_A0A0A0ABZ8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091VRD5_A0A091VRD5_NIPNI_128390 and tr_A0A0A0A7C7_A0A0A0A7C7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_I1RN36_I1RN36_GIBZE_229533 and tr_A0A1B8AKH9_A0A1B8AKH9_FUSPO_36050 are exactly identical! WARNING: Sequences tr_A0A1S3RMT0_A0A1S3RMT0_SALSA_8030 and tr_C0H923_C0H923_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A226MRR9_A0A226MRR9_CALSU_9009 and tr_A0A226PLV5_A0A226PLV5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0Q3R2_A0A2D0Q3R2_ICTPU_7998 and tr_A0A2D0Q4Y1_A0A2D0Q4Y1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0Q3R2_A0A2D0Q3R2_ICTPU_7998 and tr_A0A2D0Q6M3_A0A2D0Q6M3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZD5_A0A2D0SZD5_ICTPU_7998 and tr_A0A2D0SZW8_A0A2D0SZW8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2G4T0U5_A0A2G4T0U5_9FUNG_1340429 and tr_A0A367K5Y8_A0A367K5Y8_9FUNG_86630 are exactly identical! WARNING: Duplicate sequences found: 39 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P14598/4_raxmlng_ancestral/P14598.raxml.reduced.phy Alignment comprises 1 partitions and 390 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 390 Gaps: 31.04 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P14598/4_raxmlng_ancestral/P14598.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/020621_run/phylogeny-snakemake/results/P14598/3_mltree/P14598.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 98 / 7840 [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: -121406.714334 [00:00:00 -121406.714334] Initial branch length optimization [00:00:01 -119236.892018] Model parameter optimization (eps = 0.100000) [00:00:45] Tree #1, final logLikelihood: -118746.823325 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.068631,0.723966) (0.053985,0.659591) (0.404125,0.712506) (0.473259,1.324357) 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/020621_run/phylogeny-snakemake/results/P14598/4_raxmlng_ancestral/P14598.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P14598/4_raxmlng_ancestral/P14598.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P14598/4_raxmlng_ancestral/P14598.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P14598/4_raxmlng_ancestral/P14598.raxml.log Analysis started: 02-Jun-2021 18:30:27 / finished: 02-Jun-2021 18:31:16 Elapsed time: 48.175 seconds Consumed energy: 3.277 Wh