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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 04-Jun-2021 13:51:21 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O60674/2_msa/O60674_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O60674/3_mltree/O60674.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O60674/4_raxmlng_ancestral/O60674 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803881 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O60674/2_msa/O60674_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 1132 sites WARNING: Sequences tr_B4QCQ4_B4QCQ4_DROSI_7240 and sp_Q9V9J3_SRC42_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QCQ4_B4QCQ4_DROSI_7240 and tr_B4II23_B4II23_DROSE_7238 are exactly identical! WARNING: Sequences tr_M3XNR7_M3XNR7_MUSPF_9669 and tr_A0A2Y9ITG3_A0A2Y9ITG3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XY32_M3XY32_MUSPF_9669 and tr_G1LBE7_G1LBE7_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XY32_M3XY32_MUSPF_9669 and tr_A0A2Y9KGR5_A0A2Y9KGR5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3R096_G3R096_GORGO_9595 and tr_A0A2I3TMU8_A0A2I3TMU8_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2N5B2_H2N5B2_PONAB_9601 and tr_A0A2I3T3D1_A0A2I3T3D1_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2N5B2_H2N5B2_PONAB_9601 and sp_P04629_NTRK1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2N5B2_H2N5B2_PONAB_9601 and tr_A0A2R9B3Y6_A0A2R9B3Y6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2N755_H2N755_PONAB_9601 and tr_H2PZ66_H2PZ66_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2N755_H2N755_PONAB_9601 and sp_P23458_JAK1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QTL3_H2QTL3_PANTR_9598 and sp_P42685_FRK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QTL3_H2QTL3_PANTR_9598 and tr_A0A2R9BRU0_A0A2R9BRU0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A087ZQN7_A0A087ZQN7_APIME_7460 and tr_A0A0L7QY19_A0A0L7QY19_9HYME_597456 are exactly identical! WARNING: Sequences tr_A0A087ZQN7_A0A087ZQN7_APIME_7460 and tr_A0A2A3E5Z4_A0A2A3E5Z4_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NHS2_A0A158NHS2_ATTCE_12957 and tr_A0A195AWS6_A0A195AWS6_9HYME_520822 are exactly identical! WARNING: Sequences sp_P00519_ABL1_HUMAN_9606 and tr_A0A0D9RQJ3_A0A0D9RQJ3_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q07912_ACK1_HUMAN_9606 and tr_F6SXS7_F6SXS7_MACMU_9544 are exactly identical! WARNING: Sequences tr_F6YLX1_F6YLX1_MACMU_9544 and tr_A0A2I3LGP0_A0A2I3LGP0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6YLX1_F6YLX1_MACMU_9544 and tr_A0A2K5ZKJ8_A0A2K5ZKJ8_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3SZ92_G3SZ92_LOXAF_9785 and tr_A0A2Y9DJL9_A0A2Y9DJL9_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G3SZ92_G3SZ92_LOXAF_9785 and tr_A0A2Y9NX24_A0A2Y9NX24_DELLE_9749 are exactly identical! WARNING: Sequences tr_H0ZH03_H0ZH03_TAEGU_59729 and tr_U3JYF1_U3JYF1_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZH03_H0ZH03_TAEGU_59729 and tr_A0A218V922_A0A218V922_9PASE_299123 are exactly identical! WARNING: Sequences tr_F4WY89_F4WY89_ACREC_103372 and tr_A0A195CB93_A0A195CB93_9HYME_456900 are exactly identical! WARNING: Sequences tr_G7NZ43_G7NZ43_MACFA_9541 and tr_A0A0D9R851_A0A0D9R851_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A091IT27_A0A091IT27_EGRGA_188379 and tr_A0A091VYQ6_A0A091VYQ6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IT27_A0A091IT27_EGRGA_188379 and tr_A0A087QR73_A0A087QR73_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IT27_A0A091IT27_EGRGA_188379 and tr_A0A093HY04_A0A093HY04_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091IT27_A0A091IT27_EGRGA_188379 and tr_A0A091XV06_A0A091XV06_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091IT27_A0A091IT27_EGRGA_188379 and tr_A0A091GHA4_A0A091GHA4_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091IT27_A0A091IT27_EGRGA_188379 and tr_A0A0A0AGC2_A0A0A0AGC2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091IT27_A0A091IT27_EGRGA_188379 and tr_A0A091J0E6_A0A091J0E6_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091JMK4_A0A091JMK4_EGRGA_188379 and tr_A0A093HFK6_A0A093HFK6_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091JMK4_A0A091JMK4_EGRGA_188379 and tr_A0A091WJZ2_A0A091WJZ2_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JMK4_A0A091JMK4_EGRGA_188379 and tr_A0A0A0ARF2_A0A0A0ARF2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091V5B4_A0A091V5B4_NIPNI_128390 and tr_A0A087QT21_A0A087QT21_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091V5B4_A0A091V5B4_NIPNI_128390 and tr_A0A093I0Q1_A0A093I0Q1_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091V5B4_A0A091V5B4_NIPNI_128390 and tr_A0A099Z788_A0A099Z788_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A2D0SR82_A0A2D0SR82_ICTPU_7998 and tr_A0A2D0SSC0_A0A2D0SSC0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T1D5_A0A2D0T1D5_ICTPU_7998 and tr_W5UG95_W5UG95_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T7Y0_A0A2D0T7Y0_ICTPU_7998 and tr_A0A2D0T8L0_A0A2D0T8L0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5NXD9_A0A2K5NXD9_CERAT_9531 and tr_A0A2K6E1K6_A0A2K6E1K6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5P604_A0A2K5P604_CERAT_9531 and tr_A0A2K6DLP3_A0A2K6DLP3_MACNE_9545 are exactly identical! WARNING: Duplicate sequences found: 44 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O60674/4_raxmlng_ancestral/O60674.raxml.reduced.phy Alignment comprises 1 partitions and 1132 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1132 Gaps: 43.77 % Invariant sites: 0.09 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O60674/4_raxmlng_ancestral/O60674.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O60674/3_mltree/O60674.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 283 / 22640 [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: -340511.139015 [00:00:00 -340511.139015] Initial branch length optimization [00:00:02 -316039.779427] Model parameter optimization (eps = 0.100000) [00:01:27] Tree #1, final logLikelihood: -315189.890508 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.150612,0.375647) (0.119597,0.491982) (0.379014,0.774393) (0.350777,1.685053) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O60674/4_raxmlng_ancestral/O60674.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O60674/4_raxmlng_ancestral/O60674.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O60674/4_raxmlng_ancestral/O60674.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O60674/4_raxmlng_ancestral/O60674.raxml.log Analysis started: 04-Jun-2021 13:51:21 / finished: 04-Jun-2021 13:52:58 Elapsed time: 97.555 seconds