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 16:39:50 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/C9J2P7/2_msa/C9J2P7_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/C9J2P7/3_mltree/C9J2P7.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/C9J2P7/4_raxmlng_ancestral/C9J2P7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626097190 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/C9J2P7/2_msa/C9J2P7_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 530 sites WARNING: Sequences tr_G3RHX2_G3RHX2_GORGO_9595 and tr_K7ALA5_K7ALA5_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3RP02_A0A2I3RP02_PANTR_9598 and sp_Q9H9J4_UBP42_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3RP02_A0A2I3RP02_PANTR_9598 and tr_A0A2R9A8W9_A0A2R9A8W9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0G470_A0A0E0G470_ORYNI_4536 and tr_A0A0E0NCB1_A0A0E0NCB1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0G470_A0A0E0G470_ORYNI_4536 and tr_A0A0D3F2Z6_A0A0D3F2Z6_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0G470_A0A0E0G470_ORYNI_4536 and tr_A0A0D9YPT2_A0A0D9YPT2_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0HLU9_A0A0E0HLU9_ORYNI_4536 and tr_B8B3I9_B8B3I9_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HLU9_A0A0E0HLU9_ORYNI_4536 and tr_I1Q034_I1Q034_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0HLU9_A0A0E0HLU9_ORYNI_4536 and tr_A0A0E0PUD1_A0A0E0PUD1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0IDE5_A0A0E0IDE5_ORYNI_4536 and tr_I1QJH5_I1QJH5_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0IDE5_A0A0E0IDE5_ORYNI_4536 and tr_A0A0E0QKA9_A0A0E0QKA9_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0IDE5_A0A0E0IDE5_ORYNI_4536 and tr_A0A0D3H1D6_A0A0D3H1D6_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0IDE5_A0A0E0IDE5_ORYNI_4536 and tr_Q6ZJC2_Q6ZJC2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A1D5QFX6_A0A1D5QFX6_MACMU_9544 and tr_F6QBN6_F6QBN6_MACMU_9544 are exactly identical! WARNING: Sequences tr_H9EXL0_H9EXL0_MACMU_9544 and tr_A0A2K6CGC7_A0A2K6CGC7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A2YFR5_A2YFR5_ORYSI_39946 and tr_A0A0E0ACP6_A0A0E0ACP6_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_I1NYX5_I1NYX5_ORYGL_4538 and tr_Q0E2F9_Q0E2F9_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1QKR8_I1QKR8_ORYGL_4538 and tr_A0A0D3G9M5_A0A0D3G9M5_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_M4EEX9_M4EEX9_BRARP_51351 and tr_A0A0D3CK94_A0A0D3CK94_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A096NT88_A0A096NT88_PAPAN_9555 and tr_A0A2K6AH76_A0A2K6AH76_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9RYQ6_A0A0D9RYQ6_CHLSB_60711 and tr_A0A2K5MZY7_A0A2K5MZY7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D2RBZ9_A0A0D2RBZ9_GOSRA_29730 and tr_A0A1U8JTB7_A0A1U8JTB7_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0V1DGS7_A0A0V1DGS7_TRIBR_45882 and tr_A0A0V0UXV3_A0A0V0UXV3_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DGS7_A0A0V1DGS7_TRIBR_45882 and tr_A0A0V0U1S9_A0A0V0U1S9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3Z1S6_A0A1S3Z1S6_TOBAC_4097 and tr_A0A1U7WC27_A0A1U7WC27_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3ZT29_A0A1S3ZT29_TOBAC_4097 and tr_A0A1U7W257_A0A1U7W257_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4BFN6_A0A1S4BFN6_TOBAC_4097 and tr_A0A1U7WUW4_A0A1U7WUW4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CLX9_A0A1S4CLX9_TOBAC_4097 and tr_A0A1U7V562_A0A1U7V562_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A226MLW9_A0A226MLW9_CALSU_9009 and tr_A0A226PTH7_A0A226PTH7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2N5S3Q2_A0A2N5S3Q2_9BASI_200324 and tr_A0A2N5VWQ6_A0A2N5VWQ6_9BASI_200324 are exactly identical! WARNING: Duplicate sequences found: 30 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/C9J2P7/4_raxmlng_ancestral/C9J2P7.raxml.reduced.phy Alignment comprises 1 partitions and 530 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 530 Gaps: 22.31 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/C9J2P7/4_raxmlng_ancestral/C9J2P7.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/C9J2P7/3_mltree/C9J2P7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 133 / 10640 [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: -260889.243330 [00:00:00 -260889.243330] Initial branch length optimization [00:00:01 -248764.634515] Model parameter optimization (eps = 0.100000) 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 17:53:00 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/C9J2P7/2_msa/C9J2P7_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/C9J2P7/3_mltree/C9J2P7.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/C9J2P7/4_raxmlng_ancestral/C9J2P7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101580 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 WARNING: The model you specified on the command line (LG4X) will be ignored since the binary MSA file already contains a model definition. If you want to change the model, please re-run RAxML-NG with the original PHYLIP/FASTA alignment and --redo option. [00:00:00] Loading binary alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/C9J2P7/4_raxmlng_ancestral/C9J2P7.raxml.rba [00:00:00] Alignment comprises 1001 taxa, 1 partitions and 530 patterns Partition 0: noname Model: LG4X+R4 Alignment sites: 530 Gaps: 22.31 % Invariant sites: 0.00 % Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] NOTE: Resuming execution from checkpoint (logLH: -248764.63, ML trees: 0, bootstraps: 0) [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 133 / 10640 [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: -248764.634515 [00:00:00 -248764.634515] Model parameter optimization (eps = 0.100000) [00:00:31] Tree #1, final logLikelihood: -248295.000022 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.137136,0.196962) (0.149102,0.254169) (0.244299,0.692260) (0.469462,1.631598) 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/C9J2P7/4_raxmlng_ancestral/C9J2P7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/C9J2P7/4_raxmlng_ancestral/C9J2P7.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/C9J2P7/4_raxmlng_ancestral/C9J2P7.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/C9J2P7/4_raxmlng_ancestral/C9J2P7.raxml.log Analysis started: 12-Jul-2021 17:53:00 / finished: 12-Jul-2021 17:53:36 Elapsed time: 36.257 seconds (this run) / 37.704 seconds (total with restarts) Consumed energy: 2.834 Wh