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 02-Jun-2021 18:09:58 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P23769/2_msa/P23769_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P23769/3_mltree/P23769.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P23769/4_raxmlng_ancestral/P23769 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622646598 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/P23769/2_msa/P23769_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 480 sites WARNING: Sequences sp_P23824_GATA2_CHICK_9031 and tr_G1N5I0_G1N5I0_MELGA_9103 are exactly identical! WARNING: Sequences sp_P23824_GATA2_CHICK_9031 and tr_A0A226PTL6_A0A226PTL6_COLVI_9014 are exactly identical! WARNING: Sequences tr_M3XRU8_M3XRU8_MUSPF_9669 and tr_A0A2Y9KJH7_A0A2Y9KJH7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z0W6_M3Z0W6_MUSPF_9669 and tr_A0A2Y9L6Y8_A0A2Y9L6Y8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1RVX7_G1RVX7_NOMLE_61853 and tr_H2RAN3_H2RAN3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RVX7_G1RVX7_NOMLE_61853 and sp_P23769_GATA2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RVX7_G1RVX7_NOMLE_61853 and tr_A0A2R8ZVR6_A0A2R8ZVR6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3GR59_G3GR59_CRIGR_10029 and tr_A0A1U8C3B3_A0A1U8C3B3_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3RS51_G3RS51_GORGO_9595 and tr_A0A2I3TBK1_A0A2I3TBK1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RS51_G3RS51_GORGO_9595 and tr_A0A2R9B5B4_A0A2R9B5B4_PANPA_9597 are exactly identical! WARNING: Sequences tr_B8PHC3_B8PHC3_POSPM_561896 and tr_A0A1X6N659_A0A1X6N659_9APHY_670580 are exactly identical! WARNING: Sequences tr_I5APP3_I5APP3_DROPS_46245 and tr_B4GML7_B4GML7_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q299A5_Q299A5_DROPS_46245 and tr_B4G4Y3_B4G4Y3_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2I3SFW5_A0A2I3SFW5_PANTR_9598 and sp_P43694_GATA4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8MPF8_A0A2J8MPF8_PANTR_9598 and tr_A0A096MVE0_A0A096MVE0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2J8MPF8_A0A2J8MPF8_PANTR_9598 and tr_A0A0D9RYJ6_A0A0D9RYJ6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2J8MPF8_A0A2J8MPF8_PANTR_9598 and tr_A0A2K5KM52_A0A2K5KM52_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2J8MPF8_A0A2J8MPF8_PANTR_9598 and tr_A0A2K6BWV0_A0A2K6BWV0_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2QKQ9_H2QKQ9_PANTR_9598 and sp_Q9BWX5_GATA5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R285_H2R285_PANTR_9598 and tr_A0A2R8ZRJ9_A0A2R8ZRJ9_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7GBH5_F7GBH5_MACMU_9544 and tr_G7Q2N4_G7Q2N4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GBH5_F7GBH5_MACMU_9544 and tr_A0A2K6E1V7_A0A2K6E1V7_MACNE_9545 are exactly identical! WARNING: Sequences tr_B3S690_B3S690_TRIAD_10228 and tr_A0A369SKD1_A0A369SKD1_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A096N2A9_A0A096N2A9_PAPAN_9555 and tr_A0A2K5LP02_A0A2K5LP02_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N377_A0A096N377_PAPAN_9555 and tr_A0A0D9RL84_A0A0D9RL84_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096N377_A0A096N377_PAPAN_9555 and tr_A0A2K5L663_A0A2K5L663_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N377_A0A096N377_PAPAN_9555 and tr_A0A2K5YEX9_A0A2K5YEX9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096P3E2_A0A096P3E2_PAPAN_9555 and tr_A0A2K5ZIC9_A0A2K5ZIC9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A1MZP7_A0A0A1MZP7_9FUNG_58291 and tr_A0A2G4SMG9_A0A2G4SMG9_9FUNG_1340429 are exactly identical! WARNING: Sequences tr_A0A0A1MZP7_A0A0A1MZP7_9FUNG_58291 and tr_A0A367K9V8_A0A367K9V8_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A091EXZ5_A0A091EXZ5_CORBR_85066 and tr_A0A0A0AF25_A0A0A0AF25_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091EXZ5_A0A091EXZ5_CORBR_85066 and tr_A0A093GKB3_A0A093GKB3_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091EXZ5_A0A091EXZ5_CORBR_85066 and tr_A0A091HVM5_A0A091HVM5_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V1CI24_A0A0V1CI24_TRIBR_45882 and tr_A0A0V0USE9_A0A0V0USE9_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CI24_A0A0V1CI24_TRIBR_45882 and tr_A0A0V1LT67_A0A0V1LT67_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CI24_A0A0V1CI24_TRIBR_45882 and tr_A0A0V1A6Q8_A0A0V1A6Q8_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CI24_A0A0V1CI24_TRIBR_45882 and tr_A0A0V1NLI0_A0A0V1NLI0_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CI24_A0A0V1CI24_TRIBR_45882 and tr_A0A0V0U6P0_A0A0V0U6P0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3JFM4_A0A1S3JFM4_LINUN_7574 and tr_A0A1S3JFS3_A0A1S3JFS3_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3LDJ1_A0A1S3LDJ1_SALSA_8030 and tr_B5X0Q3_B5X0Q3_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A226NA23_A0A226NA23_CALSU_9009 and tr_A0A226PCR6_A0A226PCR6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PI50_A0A2D0PI50_ICTPU_7998 and tr_W5UMM1_W5UMM1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R3U8_A0A2D0R3U8_ICTPU_7998 and tr_W5UQD2_W5UQD2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SIE7_A0A2D0SIE7_ICTPU_7998 and tr_W5UD88_W5UD88_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0TAH6_A0A2D0TAH6_ICTPU_7998 and tr_A0A2D0TAI3_A0A2D0TAI3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KWR3_A0A2K5KWR3_CERAT_9531 and tr_A0A2K6BE94_A0A2K6BE94_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5KWR3_A0A2K5KWR3_CERAT_9531 and tr_A0A2K6A373_A0A2K6A373_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4B6F9_A0A2U4B6F9_TURTR_9739 and tr_A0A2Y9P1J9_A0A2Y9P1J9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B6F9_A0A2U4B6F9_TURTR_9739 and tr_A0A2Y9EJS0_A0A2Y9EJS0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3VSV7_A0A2U3VSV7_ODORO_9708 and tr_A0A2U3YCA3_A0A2U3YCA3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9MEW3_A0A2Y9MEW3_DELLE_9749 and tr_A0A2Y9S257_A0A2Y9S257_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/020621_run/phylogeny-snakemake/results/P23769/4_raxmlng_ancestral/P23769.raxml.reduced.phy Alignment comprises 1 partitions and 480 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 480 Gaps: 40.82 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P23769/4_raxmlng_ancestral/P23769.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/P23769/3_mltree/P23769.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 120 / 9600 [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: -278180.298297 [00:00:00 -278180.298297] Initial branch length optimization [00:00:01 -175888.821195] Model parameter optimization (eps = 0.100000) [00:02:00] Tree #1, final logLikelihood: -174414.792660 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.280515,1.656091) (0.109707,0.046931) (0.193246,0.336661) (0.416532,1.116923) 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/P23769/4_raxmlng_ancestral/P23769.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P23769/4_raxmlng_ancestral/P23769.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P23769/4_raxmlng_ancestral/P23769.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P23769/4_raxmlng_ancestral/P23769.raxml.log Analysis started: 02-Jun-2021 18:09:58 / finished: 02-Jun-2021 18:12:03 Elapsed time: 125.100 seconds Consumed energy: 7.352 Wh