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 12-Jul-2021 17:22:09 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/2_msa/Q7L5A8_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/3_mltree/Q7L5A8.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/4_raxmlng_ancestral/Q7L5A8 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099729 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/300621_run/phylogeny-snakemake/results/Q7L5A8/2_msa/Q7L5A8_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 372 sites WARNING: Sequences tr_J3KAL8_J3KAL8_COCIM_246410 and tr_A0A0J6YK01_A0A0J6YK01_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QBT3_B6QBT3_TALMQ_441960 and tr_A0A093UUJ7_A0A093UUJ7_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WJL3_B2WJL3_PYRTR_426418 and tr_A0A2W1HNE1_A0A2W1HNE1_9PLEO_45151 are exactly identical! WARNING: Sequences tr_A0A179UVJ0_A0A179UVJ0_BLAGS_559298 and tr_C5GME5_C5GME5_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2QBI4_H2QBI4_PANTR_9598 and tr_A0A2R8ZJK9_A0A2R8ZJK9_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FF95_F9FF95_FUSOF_660025 and tr_A0A0D2XVA2_A0A0D2XVA2_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FF95_F9FF95_FUSOF_660025 and tr_N4UAV0_N4UAV0_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FF95_F9FF95_FUSOF_660025 and tr_X0CT35_X0CT35_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FF95_F9FF95_FUSOF_660025 and tr_A0A2H3T082_A0A2H3T082_FUSOX_5507 are exactly identical! WARNING: Sequences tr_C6HNJ0_C6HNJ0_AJECH_544712 and tr_F0UFR1_F0UFR1_AJEC8_544711 are exactly identical! WARNING: Sequences tr_J5JKS8_J5JKS8_BEAB2_655819 and tr_A0A2N6NWB1_A0A2N6NWB1_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A0E0ITA6_A0A0E0ITA6_ORYNI_4536 and tr_A2XMJ0_A2XMJ0_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0ITA6_A0A0E0ITA6_ORYNI_4536 and tr_I1PG27_I1PG27_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0ITA6_A0A0E0ITA6_ORYNI_4536 and tr_A0A0D3FPS3_A0A0D3FPS3_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0ITA6_A0A0E0ITA6_ORYNI_4536 and tr_A0A0D9ZDX2_A0A0D9ZDX2_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A2QB78_A2QB78_ASPNC_425011 and tr_A0A319B0Y8_A0A319B0Y8_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F7HMN1_F7HMN1_MACMU_9544 and tr_A0A2K5MM77_A0A2K5MM77_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7XIR1_G7XIR1_ASPKW_1033177 and tr_A0A124BVE4_A0A124BVE4_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XIR1_G7XIR1_ASPKW_1033177 and tr_A0A1L9N6E3_A0A1L9N6E3_ASPTU_767770 are exactly identical! WARNING: Sequences tr_B8BN49_B8BN49_ORYSI_39946 and tr_I1R831_I1R831_ORYGL_4538 are exactly identical! WARNING: Sequences tr_B8BN49_B8BN49_ORYSI_39946 and tr_Q0ILR7_Q0ILR7_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0P224_A0A0E0P224_ORYRU_4529 and tr_Q9AY73_Q9AY73_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_L2G8D6_L2G8D6_COLFN_1213859 and tr_T0LLV8_T0LLV8_COLGC_1237896 are exactly identical! WARNING: Sequences tr_M4DZ62_M4DZ62_BRARP_51351 and tr_A0A078G1H8_A0A078G1H8_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4DZ62_M4DZ62_BRARP_51351 and tr_A0A078GF95_A0A078GF95_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4DZ62_M4DZ62_BRARP_51351 and tr_A0A0D3C3S2_A0A0D3C3S2_BRAOL_109376 are exactly identical! WARNING: Sequences tr_S0E0M0_S0E0M0_GIBF5_1279085 and tr_A0A365MJ03_A0A365MJ03_GIBIN_948311 are exactly identical! WARNING: Sequences tr_U5HJ78_U5HJ78_USTV1_683840 and tr_A0A2X0MLE8_A0A2X0MLE8_9BASI_796604 are exactly identical! WARNING: Sequences tr_A0A015N7V5_A0A015N7V5_9GLOM_1432141 and tr_A0A2H5TAW8_A0A2H5TAW8_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A2K6VRR4_A0A2K6VRR4_ONCVO_6282 and tr_A0A182ED95_A0A182ED95_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0D3HX02_A0A0D3HX02_9ORYZ_65489 and tr_A0A0E0BVI8_A0A0E0BVI8_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A078I5V5_A0A078I5V5_BRANA_3708 and tr_A0A0D3C122_A0A0D3C122_BRAOL_109376 are exactly identical! WARNING: Sequences tr_V4UD48_V4UD48_9ROSI_85681 and tr_A0A2H5N1W2_A0A2H5N1W2_CITUN_55188 are exactly identical! WARNING: Sequences tr_V4UIH0_V4UIH0_9ROSI_85681 and tr_A0A2H5N120_A0A2H5N120_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0A1PEE7_A0A0A1PEE7_9FUNG_58291 and tr_A0A367KCC7_A0A367KCC7_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0V1CQU7_A0A0V1CQU7_TRIBR_45882 and tr_A0A0V0TS13_A0A0V0TS13_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0P1BLJ4_A0A0P1BLJ4_9BASI_401625 and tr_A0A316W4Y8_A0A316W4Y8_9BASI_1522189 are exactly identical! WARNING: Sequences tr_A0A165BJD0_A0A165BJD0_EXIGL_1314781 and tr_A0A165DCP1_A0A165DCP1_EXIGL_1314781 are exactly identical! WARNING: Sequences tr_A0A1S3XTK4_A0A1S3XTK4_TOBAC_4097 and tr_A0A1U7W494_A0A1U7W494_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3YYM5_A0A1S3YYM5_TOBAC_4097 and sp_P49098_CYB5_TOBAC_4097 are exactly identical! WARNING: Sequences tr_A0A1S3YYM5_A0A1S3YYM5_TOBAC_4097 and tr_A0A1J6J6L0_A0A1J6J6L0_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S3YYM5_A0A1S3YYM5_TOBAC_4097 and tr_A0A1U7XR80_A0A1U7XR80_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CRV3_A0A1S4CRV3_TOBAC_4097 and tr_A0A1U7W897_A0A1U7W897_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2H3C1H3_A0A2H3C1H3_9AGAR_1076256 and tr_A0A284QYF1_A0A284QYF1_9AGAR_47428 are exactly identical! WARNING: Duplicate sequences found: 44 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/4_raxmlng_ancestral/Q7L5A8.raxml.reduced.phy Alignment comprises 1 partitions and 372 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 372 Gaps: 24.11 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/4_raxmlng_ancestral/Q7L5A8.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/300621_run/phylogeny-snakemake/results/Q7L5A8/3_mltree/Q7L5A8.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 93 / 7440 [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: -177190.513721 [00:00:00 -177190.513721] Initial branch length optimization [00:00:01 -173689.905718] Model parameter optimization (eps = 0.100000) [00:00:34] Tree #1, final logLikelihood: -172942.150376 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.155852,0.420825) (0.288811,0.496148) (0.325777,1.029587) (0.229560,1.985123) 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/300621_run/phylogeny-snakemake/results/Q7L5A8/4_raxmlng_ancestral/Q7L5A8.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/4_raxmlng_ancestral/Q7L5A8.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/4_raxmlng_ancestral/Q7L5A8.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/4_raxmlng_ancestral/Q7L5A8.raxml.log Analysis started: 12-Jul-2021 17:22:09 / finished: 12-Jul-2021 17:22:46 Elapsed time: 37.425 seconds Consumed energy: 3.242 Wh