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 02-Jun-2021 18:22:29 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96CW9/2_msa/Q96CW9_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96CW9/3_mltree/Q96CW9.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96CW9/4_raxmlng_ancestral/Q96CW9 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647349 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/Q96CW9/2_msa/Q96CW9_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 530 sites WARNING: Sequences tr_A0A1D5P1P1_A0A1D5P1P1_CHICK_9031 and sp_Q90923_NET3_CHICK_9031 are exactly identical! WARNING: Sequences tr_A0A1I7Q444_A0A1I7Q444_CHICK_9031 and sp_Q90922_NET1_CHICK_9031 are exactly identical! WARNING: Sequences tr_A0A1I7Q444_A0A1I7Q444_CHICK_9031 and tr_A0A226MGT8_A0A226MGT8_CALSU_9009 are exactly identical! WARNING: Sequences tr_G3RF36_G3RF36_GORGO_9595 and tr_H2Q0R2_H2Q0R2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RF36_G3RF36_GORGO_9595 and sp_Q13753_LAMC2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RF36_G3RF36_GORGO_9595 and tr_A0A2R9B9I9_A0A2R9B9I9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RG19_G3RG19_GORGO_9595 and tr_H2QMK9_H2QMK9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RJD2_G3RJD2_GORGO_9595 and sp_Q9Y2I2_NTNG1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RJD2_G3RJD2_GORGO_9595 and tr_G7MIC2_G7MIC2_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RJD2_G3RJD2_GORGO_9595 and tr_A0A2K5KW05_A0A2K5KW05_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RJD2_G3RJD2_GORGO_9595 and tr_A0A2K6BCQ1_A0A2K6BCQ1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RJD2_G3RJD2_GORGO_9595 and tr_A0A2K5Z4U3_A0A2K5Z4U3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3RJD2_G3RJD2_GORGO_9595 and tr_A0A2R9CK20_A0A2R9CK20_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PTR5_H2PTR5_PONAB_9601 and tr_A0A2R9B8T1_A0A2R9B8T1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QC90_H2QC90_PANTR_9598 and tr_I3LX86_I3LX86_ICTTR_43179 are exactly identical! WARNING: Sequences tr_H2QC90_H2QC90_PANTR_9598 and sp_O95631_NET1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QC90_H2QC90_PANTR_9598 and tr_U3DL39_U3DL39_CALJA_9483 are exactly identical! WARNING: Sequences tr_F7BDD8_F7BDD8_MACMU_9544 and tr_A0A2K6CFY0_A0A2K6CFY0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BDD8_F7BDD8_MACMU_9544 and tr_A0A2K5ZQ84_A0A2K5ZQ84_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7EV15_F7EV15_MACMU_9544 and tr_A0A2K6C3G7_A0A2K6C3G7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A287A555_A0A287A555_PIG_9823 and sp_Q2HXW4_NET1_PIG_9823 are exactly identical! WARNING: Sequences tr_B3RK07_B3RK07_TRIAD_10228 and tr_A0A369S4Q1_A0A369S4Q1_9METZ_287889 are exactly identical! WARNING: Sequences tr_G7NV41_G7NV41_MACFA_9541 and tr_A0A0D9S6L6_A0A0D9S6L6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MUU2_A0A096MUU2_PAPAN_9555 and tr_A0A2K5P838_A0A2K5P838_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MUU2_A0A096MUU2_PAPAN_9555 and tr_A0A2K6E936_A0A2K6E936_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096MYW4_A0A096MYW4_PAPAN_9555 and tr_A0A2K5KKZ0_A0A2K5KKZ0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NL57_A0A096NL57_PAPAN_9555 and tr_A0A2K5NS94_A0A2K5NS94_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NL57_A0A096NL57_PAPAN_9555 and tr_A0A2K6D9X2_A0A2K6D9X2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A194QVU4_A0A194QVU4_PAPMA_76193 and tr_A0A194Q4T3_A0A194Q4T3_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A099YTG0_A0A099YTG0_TINGU_94827 and tr_A0A0A0A3I8_A0A0A0A3I8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1CEK2_A0A0V1CEK2_TRIBR_45882 and tr_A0A0V0UWQ8_A0A0V0UWQ8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1KWB4_A0A0V1KWB4_9BILA_6335 and tr_A0A0V1PG22_A0A0V1PG22_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1MAZ0_A0A0V1MAZ0_9BILA_268474 and tr_A0A0V1HC59_A0A0V1HC59_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3JDP2_A0A1S3JDP2_LINUN_7574 and tr_A0A1S3JF50_A0A1S3JF50_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3JDW4_A0A1S3JDW4_LINUN_7574 and tr_A0A1S3JED4_A0A1S3JED4_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A226MVL1_A0A226MVL1_CALSU_9009 and tr_A0A226NTU1_A0A226NTU1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NPP8_A0A226NPP8_CALSU_9009 and tr_A0A226P128_A0A226P128_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PHN8_A0A2D0PHN8_ICTPU_7998 and tr_A0A2D0PIZ3_A0A2D0PIZ3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PJ17_A0A2D0PJ17_ICTPU_7998 and tr_A0A2D0PKH8_A0A2D0PKH8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PJ17_A0A2D0PJ17_ICTPU_7998 and tr_A0A2D0PLH4_A0A2D0PLH4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2Y9Q6I1_A0A2Y9Q6I1_DELLE_9749 and tr_A0A2Y9T6H0_A0A2Y9T6H0_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 41 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/Q96CW9/4_raxmlng_ancestral/Q96CW9.raxml.reduced.phy Alignment comprises 1 partitions and 530 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 530 Gaps: 36.70 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96CW9/4_raxmlng_ancestral/Q96CW9.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/Q96CW9/3_mltree/Q96CW9.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: -166161.293760 [00:00:00 -166161.293760] Initial branch length optimization [00:00:01 -164428.171950] Model parameter optimization (eps = 0.100000) [00:01:23] Tree #1, final logLikelihood: -163643.363205 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.150408,0.332938) (0.081218,1.697252) (0.417995,0.696473) (0.350378,1.486830) 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/Q96CW9/4_raxmlng_ancestral/Q96CW9.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96CW9/4_raxmlng_ancestral/Q96CW9.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96CW9/4_raxmlng_ancestral/Q96CW9.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96CW9/4_raxmlng_ancestral/Q96CW9.raxml.log Analysis started: 02-Jun-2021 18:22:29 / finished: 02-Jun-2021 18:23:57 Elapsed time: 88.469 seconds Consumed energy: 8.177 Wh