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 12-Jul-2021 17:48:16 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/2_msa/Q13627_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/3_mltree/Q13627.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/4_raxmlng_ancestral/Q13627 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101296 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/Q13627/2_msa/Q13627_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 763 sites WARNING: Sequences tr_B2WIP7_B2WIP7_PYRTR_426418 and tr_A0A2W1EVT9_A0A2W1EVT9_9PLEO_45151 are exactly identical! WARNING: Sequences tr_C0NXA2_C0NXA2_AJECG_447093 and tr_F0UHG7_F0UHG7_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A179V1H8_A0A179V1H8_BLAGS_559298 and tr_C5GS77_C5GS77_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2QL08_H2QL08_PANTR_9598 and sp_Q13627_DYR1A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7D9F3_K7D9F3_PANTR_9598 and sp_Q9Y463_DYR1B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F9G0R5_F9G0R5_FUSOF_660025 and tr_N4USN2_N4USN2_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9G0R5_F9G0R5_FUSOF_660025 and tr_X0DKF1_X0DKF1_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9G0R5_F9G0R5_FUSOF_660025 and tr_A0A2H3TRJ8_A0A2H3TRJ8_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A2R2K4_A2R2K4_ASPNC_425011 and tr_G3XNJ8_G3XNJ8_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2R2K4_A2R2K4_ASPNC_425011 and tr_A0A319AQP3_A0A319AQP3_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F7FBT7_F7FBT7_MACMU_9544 and tr_A0A2K5ZRQ1_A0A2K5ZRQ1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7XJE7_G7XJE7_ASPKW_1033177 and tr_A0A100IKQ2_A0A100IKQ2_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XJE7_G7XJE7_ASPKW_1033177 and tr_A0A146FHA3_A0A146FHA3_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XJE7_G7XJE7_ASPKW_1033177 and tr_A0A1L9NKT5_A0A1L9NKT5_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G7XJE7_G7XJE7_ASPKW_1033177 and tr_A0A1L9UZ78_A0A1L9UZ78_9EURO_767769 are exactly identical! WARNING: Sequences tr_G7XWD5_G7XWD5_ASPKW_1033177 and tr_A0A100IN07_A0A100IN07_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XWD5_G7XWD5_ASPKW_1033177 and tr_A0A146FWP0_A0A146FWP0_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XWD5_G7XWD5_ASPKW_1033177 and tr_A0A1L9NID3_A0A1L9NID3_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G7XWD5_G7XWD5_ASPKW_1033177 and tr_A0A317VBL4_A0A317VBL4_9EURO_1448314 are exactly identical! WARNING: Sequences tr_G2YI01_G2YI01_BOTF4_999810 and tr_M7TP45_M7TP45_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_A0A0D2XZP9_A0A0D2XZP9_FUSO4_426428 and tr_A0A2H3H385_A0A2H3H385_FUSOX_327505 are exactly identical! WARNING: Sequences tr_U5H4F3_U5H4F3_USTV1_683840 and tr_A0A2X0P6T1_A0A2X0P6T1_9BASI_796604 are exactly identical! WARNING: Sequences tr_V2XCA4_V2XCA4_MONRO_1381753 and tr_A0A0W0G820_A0A0W0G820_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015LPX9_A0A015LPX9_9GLOM_1432141 and tr_A0A2H5TV43_A0A2H5TV43_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A068SBI9_A0A068SBI9_9FUNG_1263082 and tr_A0A068SGN4_A0A068SGN4_9FUNG_1263082 are exactly identical! WARNING: Sequences tr_A0A096NJ33_A0A096NJ33_PAPAN_9555 and tr_A0A2K5P1R8_A0A2K5P1R8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NJ33_A0A096NJ33_PAPAN_9555 and tr_A0A2K6B4V6_A0A2K6B4V6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A094E4V5_A0A094E4V5_9PEZI_1420912 and tr_A0A2P2SVN3_A0A2P2SVN3_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F0I044_A0A0F0I044_ASPPU_1403190 and tr_A0A2G7FIM5_A0A2G7FIM5_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0F8TZH8_A0A0F8TZH8_9EURO_308745 and tr_A0A2T5LVG1_A0A2T5LVG1_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A087R962_A0A087R962_APTFO_9233 and tr_A0A091VZ88_A0A091VZ88_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A1S3K7Y7_A0A1S3K7Y7_LINUN_7574 and tr_A0A1S3K8H6_A0A1S3K8H6_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3K7Y7_A0A1S3K7Y7_LINUN_7574 and tr_A0A1S3K8H9_A0A1S3K8H9_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3K7Y7_A0A1S3K7Y7_LINUN_7574 and tr_A0A1S3K908_A0A1S3K908_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3NBF7_A0A1S3NBF7_SALSA_8030 and tr_A0A1S3RXL0_A0A1S3RXL0_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1R3RA30_A0A1R3RA30_ASPC5_602072 and tr_A0A317V3Q8_A0A317V3Q8_9EURO_1450535 are exactly identical! WARNING: Sequences tr_A0A2K5MZG1_A0A2K5MZG1_CERAT_9531 and tr_A0A2K6E229_A0A2K6E229_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5MZG1_A0A2K5MZG1_CERAT_9531 and tr_A0A2K5YAA4_A0A2K5YAA4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2N5T2P5_A0A2N5T2P5_9BASI_200324 and tr_A0A2N5W1Q9_A0A2N5W1Q9_9BASI_200324 are exactly identical! WARNING: Sequences tr_A0A2U4AB97_A0A2U4AB97_TURTR_9739 and tr_A0A2Y9LNG7_A0A2Y9LNG7_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 40 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/Q13627/4_raxmlng_ancestral/Q13627.raxml.reduced.phy Alignment comprises 1 partitions and 763 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 763 Gaps: 33.28 % Invariant sites: 1.70 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/4_raxmlng_ancestral/Q13627.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/Q13627/3_mltree/Q13627.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 191 / 15280 [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: -243788.508498 [00:00:00 -243788.508498] Initial branch length optimization [00:00:02 -227584.925357] Model parameter optimization (eps = 0.100000) [00:00:57] Tree #1, final logLikelihood: -227101.081688 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.111990,0.121845) (0.133007,0.197656) (0.224430,0.547751) (0.530573,1.577790) 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/Q13627/4_raxmlng_ancestral/Q13627.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/4_raxmlng_ancestral/Q13627.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/4_raxmlng_ancestral/Q13627.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q13627/4_raxmlng_ancestral/Q13627.raxml.log Analysis started: 12-Jul-2021 17:48:16 / finished: 12-Jul-2021 17:49:20 Elapsed time: 64.484 seconds Consumed energy: 3.745 Wh