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 03-Jun-2021 01:59:41 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P08397/2_msa/P08397_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P08397/3_mltree/P08397.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P08397/4_raxmlng_ancestral/P08397 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622674781 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/P08397/2_msa/P08397_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 361 sites WARNING: Sequences tr_B4QM08_B4QM08_DROSI_7240 and tr_Q9W0G4_Q9W0G4_DROME_7227 are exactly identical! WARNING: Sequences tr_B6Q4H6_B6Q4H6_TALMQ_441960 and tr_A0A093VLS5_A0A093VLS5_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2W5W6_B2W5W6_PYRTR_426418 and tr_A0A2W1DH67_A0A2W1DH67_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B8NYA7_B8NYA7_ASPFN_332952 and tr_Q2TYQ6_Q2TYQ6_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NYA7_B8NYA7_ASPFN_332952 and tr_A0A1S9DG13_A0A1S9DG13_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_H2Q4X6_H2Q4X6_PANTR_9598 and sp_P08397_HEM3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F9FKJ2_F9FKJ2_FUSOF_660025 and tr_W7MEJ9_W7MEJ9_GIBM7_334819 are exactly identical! WARNING: Sequences tr_F9FKJ2_F9FKJ2_FUSOF_660025 and tr_A0A0D2XYF8_A0A0D2XYF8_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FKJ2_F9FKJ2_FUSOF_660025 and tr_N4UK14_N4UK14_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FKJ2_F9FKJ2_FUSOF_660025 and tr_A0A2H3GKX6_A0A2H3GKX6_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FKJ2_F9FKJ2_FUSOF_660025 and tr_A0A2K0WBD4_A0A2K0WBD4_GIBNY_42673 are exactly identical! WARNING: Sequences tr_E9EJC7_E9EJC7_METRA_655844 and tr_A0A0D9NKT0_A0A0D9NKT0_METAN_1291518 are exactly identical! WARNING: Sequences tr_C6HL13_C6HL13_AJECH_544712 and tr_F0UE55_F0UE55_AJEC8_544711 are exactly identical! WARNING: Sequences tr_Q2U6C6_Q2U6C6_ASPOR_510516 and tr_A0A1S9D8W8_A0A1S9D8W8_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_Q2UDE4_Q2UDE4_ASPOR_510516 and tr_A0A1S9DPT9_A0A1S9DPT9_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A0E0G1X0_A0A0E0G1X0_ORYNI_4536 and tr_I1NXM7_I1NXM7_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0G1X0_A0A0E0G1X0_ORYNI_4536 and tr_A0A0E0NAE5_A0A0E0NAE5_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0G1X0_A0A0E0G1X0_ORYNI_4536 and tr_A0A0D3F181_A0A0D3F181_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0G1X0_A0A0E0G1X0_ORYNI_4536 and tr_A0A0D9YMV2_A0A0D9YMV2_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0G1X0_A0A0E0G1X0_ORYNI_4536 and sp_Q6H6D2_HEM3_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2Q9P7_A2Q9P7_ASPNC_425011 and tr_G3XT96_G3XT96_ASPNA_380704 are exactly identical! WARNING: Sequences tr_F6U3X9_F6U3X9_MACMU_9544 and tr_G7PP48_G7PP48_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6U3X9_F6U3X9_MACMU_9544 and tr_A0A0D9S3R9_A0A0D9S3R9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6U3X9_F6U3X9_MACMU_9544 and tr_A0A2K6AZR1_A0A2K6AZR1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7X5U3_G7X5U3_ASPKW_1033177 and tr_A0A146FMY2_A0A146FMY2_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7X8W3_G7X8W3_ASPKW_1033177 and tr_A0A146F6R9_A0A146F6R9_9EURO_1069201 are exactly identical! WARNING: Sequences tr_A0A0E0CG96_A0A0E0CG96_9ORYZ_40149 and tr_A0A0E0JW23_A0A0E0JW23_ORYPU_4537 are exactly identical! WARNING: Sequences tr_G2YHU6_G2YHU6_BOTF4_999810 and tr_M7TLT2_M7TLT2_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SV66_F2SV66_TRIRC_559305 and tr_A0A178F8H2_A0A178F8H2_TRIRU_5551 are exactly identical! WARNING: Sequences tr_F2PUS4_F2PUS4_TRIEC_559882 and tr_A0A059JEK1_A0A059JEK1_9EURO_1215338 are exactly identical! WARNING: Sequences tr_L0P9Y7_L0P9Y7_PNEJ8_1209962 and tr_A0A0W4ZNJ2_A0A0W4ZNJ2_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_W2PGX3_W2PGX3_PHYPN_761204 and tr_W2K0J1_W2K0J1_PHYPR_4792 are exactly identical! WARNING: Sequences tr_V4VEG2_V4VEG2_9ROSI_85681 and tr_A0A2H5P3G6_A0A2H5P3G6_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0F8U288_A0A0F8U288_9EURO_308745 and tr_A0A2T5MA88_A0A2T5MA88_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A100IN30_A0A100IN30_ASPNG_5061 and tr_A0A1L9NLI6_A0A1L9NLI6_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A1S3XSC6_A0A1S3XSC6_TOBAC_4097 and tr_A0A1U7XYW1_A0A1U7XYW1_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4DII9_A0A1S4DII9_TOBAC_4097 and tr_A0A1U7VYY0_A0A1U7VYY0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2I1E181_A0A2I1E181_9GLOM_588596 and tr_U9U875_U9U875_RHIID_747089 are exactly identical! WARNING: Duplicate sequences found: 38 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/P08397/4_raxmlng_ancestral/P08397.raxml.reduced.phy Alignment comprises 1 partitions and 361 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 361 Gaps: 12.81 % Invariant sites: 0.55 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P08397/4_raxmlng_ancestral/P08397.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/P08397/3_mltree/P08397.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 91 / 7280 [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: -178401.305003 [00:00:00 -178401.305003] Initial branch length optimization [00:00:00 -178042.160928] Model parameter optimization (eps = 0.100000) [00:00:22] Tree #1, final logLikelihood: -177453.273762 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.172847,0.230448) (0.265399,0.282977) (0.264264,0.935512) (0.297489,2.144089) 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/P08397/4_raxmlng_ancestral/P08397.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P08397/4_raxmlng_ancestral/P08397.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P08397/4_raxmlng_ancestral/P08397.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P08397/4_raxmlng_ancestral/P08397.raxml.log Analysis started: 03-Jun-2021 01:59:41 / finished: 03-Jun-2021 02:00:07 Elapsed time: 26.195 seconds Consumed energy: 1.913 Wh