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 17:20:32 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/2_msa/Q00577_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/3_mltree/Q00577.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/4_raxmlng_ancestral/Q00577 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099632 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/Q00577/2_msa/Q00577_nogap_msa.fasta [00:00:00] Loaded alignment with 406 taxa and 322 sites WARNING: Sequences tr_A0A2I3H6G0_A0A2I3H6G0_NOMLE_61853 and sp_Q9UJV8_PURG_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3H6G0_A0A2I3H6G0_NOMLE_61853 and tr_I0FR81_I0FR81_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_H2QW00_H2QW00_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_F7IME5_F7IME5_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_A0A2K5NIA8_A0A2K5NIA8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_A0A2K6CUE0_A0A2K6CUE0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_A0A2K5XJR1_A0A2K5XJR1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2ZCM4_A0A2I2ZCM4_GORGO_9595 and tr_A0A2R9B1C9_A0A2R9B1C9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PGR4_H2PGR4_PONAB_9601 and tr_H0WMM7_H0WMM7_OTOGA_30611 are exactly identical! WARNING: Sequences tr_H2PGR4_H2PGR4_PONAB_9601 and sp_Q00577_PURA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PGR4_H2PGR4_PONAB_9601 and tr_F6T2C6_F6T2C6_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PGR4_H2PGR4_PONAB_9601 and tr_A0A2R8MMW8_A0A2R8MMW8_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2PGR4_H2PGR4_PONAB_9601 and tr_A0A0D9S9H0_A0A0D9S9H0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2PGR4_H2PGR4_PONAB_9601 and tr_A0A1S2ZD82_A0A1S2ZD82_ERIEU_9365 are exactly identical! WARNING: Sequences tr_H2PGR4_H2PGR4_PONAB_9601 and tr_A0A2U4AGJ4_A0A2U4AGJ4_TURTR_9739 are exactly identical! WARNING: Sequences tr_H2PGR4_H2PGR4_PONAB_9601 and tr_A0A2U3VRJ7_A0A2U3VRJ7_ODORO_9708 are exactly identical! WARNING: Sequences tr_H2PGR4_H2PGR4_PONAB_9601 and tr_A0A2Y9IT58_A0A2Y9IT58_ENHLU_391180 are exactly identical! WARNING: Sequences tr_H2PGR4_H2PGR4_PONAB_9601 and tr_A0A2Y9PHA3_A0A2Y9PHA3_DELLE_9749 are exactly identical! WARNING: Sequences tr_H2PGR4_H2PGR4_PONAB_9601 and tr_A0A2Y9SEJ6_A0A2Y9SEJ6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_H2PM71_H2PM71_PONAB_9601 and tr_H2RGZ5_H2RGZ5_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PM71_H2PM71_PONAB_9601 and tr_I2CY42_I2CY42_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PM71_H2PM71_PONAB_9601 and tr_F6PGI5_F6PGI5_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2PM71_H2PM71_PONAB_9601 and tr_A0A0D9SE08_A0A0D9SE08_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2PM71_H2PM71_PONAB_9601 and tr_A0A2K5L1U7_A0A2K5L1U7_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2PM71_H2PM71_PONAB_9601 and tr_A0A2K6ATK1_A0A2K6ATK1_MACNE_9545 are exactly identical! WARNING: Sequences tr_M4B0T7_M4B0T7_XIPMA_8083 and tr_A0A087YLM3_A0A087YLM3_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NMT9_A0A158NMT9_ATTCE_12957 and tr_A0A195EWT1_A0A195EWT1_9HYME_34720 are exactly identical! WARNING: Sequences tr_B3RKP5_B3RKP5_TRIAD_10228 and tr_A0A369SCN4_A0A369SCN4_9METZ_287889 are exactly identical! WARNING: Sequences tr_M3WKB0_M3WKB0_FELCA_9685 and tr_A0A2U3ZNT6_A0A2U3ZNT6_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A091E2A4_A0A091E2A4_FUKDA_885580 and tr_A0A1U7T937_A0A1U7T937_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A091EVR8_A0A091EVR8_CORBR_85066 and tr_A0A093PXU5_A0A093PXU5_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091EVR8_A0A091EVR8_CORBR_85066 and tr_A0A091VGJ9_A0A091VGJ9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091EVR8_A0A091EVR8_CORBR_85066 and tr_A0A087R119_A0A087R119_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091EVR8_A0A091EVR8_CORBR_85066 and tr_A0A0A0AIG8_A0A0A0AIG8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1CYY4_A0A0V1CYY4_TRIBR_45882 and tr_A0A0V0V8K1_A0A0V0V8K1_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CYY4_A0A0V1CYY4_TRIBR_45882 and tr_A0A0V1PBX8_A0A0V1PBX8_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CYY4_A0A0V1CYY4_TRIBR_45882 and tr_A0A0V0U9G0_A0A0V0U9G0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WBC2_A0A0V0WBC2_9BILA_92179 and tr_A0A0V1KY99_A0A0V1KY99_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A151WVA1_A0A151WVA1_9HYME_64791 and tr_A0A151JBS4_A0A151JBS4_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A151WVA1_A0A151WVA1_9HYME_64791 and tr_A0A195BC11_A0A195BC11_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A1S3HVH5_A0A1S3HVH5_LINUN_7574 and tr_A0A1S3HVI1_A0A1S3HVI1_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3HVH5_A0A1S3HVH5_LINUN_7574 and tr_A0A1S3HVJ2_A0A1S3HVJ2_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3HVH5_A0A1S3HVH5_LINUN_7574 and tr_A0A1S3HY90_A0A1S3HY90_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3L1P4_A0A1S3L1P4_SALSA_8030 and tr_A0A060Y9L0_A0A060Y9L0_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3RQC6_A0A1S3RQC6_SALSA_8030 and tr_A0A060XIQ4_A0A060XIQ4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3SVX6_A0A1S3SVX6_SALSA_8030 and tr_A0A060Z1L3_A0A060Z1L3_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226MU76_A0A226MU76_CALSU_9009 and tr_A0A226P4I0_A0A226P4I0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4BN77_A0A2U4BN77_TURTR_9739 and tr_A0A2Y9PUE8_A0A2Y9PUE8_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BN77_A0A2U4BN77_TURTR_9739 and tr_A0A2Y9S4R1_A0A2Y9S4R1_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3XK48_A0A2U3XK48_LEPWE_9713 and tr_A0A2Y9J2F3_A0A2Y9J2F3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2Y9N135_A0A2Y9N135_DELLE_9749 and tr_A0A2Y9T8H8_A0A2Y9T8H8_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 51 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/Q00577/4_raxmlng_ancestral/Q00577.raxml.reduced.phy Alignment comprises 1 partitions and 322 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 322 Gaps: 26.39 % Invariant sites: 0.31 % NOTE: Binary MSA file already exists: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/4_raxmlng_ancestral/Q00577.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/Q00577/3_mltree/Q00577.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 81 / 6480 [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: -37015.486137 [00:00:00 -37015.486137] Initial branch length optimization [00:00:00 -32638.807572] Model parameter optimization (eps = 0.100000) [00:00:26] Tree #1, final logLikelihood: -32260.907686 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.227829,0.421442) (0.146260,0.750060) (0.300045,0.460919) (0.325866,2.013047) 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/Q00577/4_raxmlng_ancestral/Q00577.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/4_raxmlng_ancestral/Q00577.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/4_raxmlng_ancestral/Q00577.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00577/4_raxmlng_ancestral/Q00577.raxml.log Analysis started: 12-Jul-2021 17:20:32 / finished: 12-Jul-2021 17:20:59 Elapsed time: 27.332 seconds Consumed energy: 2.002 Wh