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 02-Jun-2021 15:01:00 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00367/2_msa/P00367_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00367/3_mltree/P00367.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00367/4_raxmlng_ancestral/P00367 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622635260 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/P00367/2_msa/P00367_nogap_msa.fasta [00:00:00] Loaded alignment with 836 taxa and 558 sites WARNING: Sequences tr_B4R1F7_B4R1F7_DROSI_7240 and tr_B4HFD8_B4HFD8_DROSE_7238 are exactly identical! WARNING: Sequences tr_Q298M7_Q298M7_DROPS_46245 and tr_B4G4C1_B4G4C1_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2I3T898_A0A2I3T898_PANTR_9598 and tr_A0A2R8ZT50_A0A2R8ZT50_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q38946_DHE2_ARATH_3702 and tr_D7M0I9_D7M0I9_ARALL_81972 are exactly identical! WARNING: Sequences tr_A0A0E0GAG9_A0A0E0GAG9_ORYNI_4536 and tr_I1P2N0_I1P2N0_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GAG9_A0A0E0GAG9_ORYNI_4536 and tr_A0A0D3F898_A0A0D3F898_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0GAG9_A0A0E0GAG9_ORYNI_4536 and sp_Q6H3Y7_DHE3_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0GUV4_A0A0E0GUV4_ORYNI_4536 and sp_A2XMV1_DHE1_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GUV4_A0A0E0GUV4_ORYNI_4536 and tr_A0A0E0D848_A0A0E0D848_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0GUV4_A0A0E0GUV4_ORYNI_4536 and tr_A0A0E0P2G3_A0A0E0P2G3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GUV4_A0A0E0GUV4_ORYNI_4536 and tr_A0A0D3FQ37_A0A0D3FQ37_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0GUV4_A0A0E0GUV4_ORYNI_4536 and tr_A0A0D9ZEB9_A0A0D9ZEB9_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0GUV4_A0A0E0GUV4_ORYNI_4536 and sp_Q852M0_DHE1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0H3S7_A0A0E0H3S7_ORYNI_4536 and sp_A2XW22_DHE2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0H3S7_A0A0E0H3S7_ORYNI_4536 and tr_I1PNI2_I1PNI2_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0H3S7_A0A0E0H3S7_ORYNI_4536 and tr_A0A0E0PC82_A0A0E0PC82_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0H3S7_A0A0E0H3S7_ORYNI_4536 and tr_A0A0D3FYJ4_A0A0D3FYJ4_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0H3S7_A0A0E0H3S7_ORYNI_4536 and tr_A0A0D9ZNS4_A0A0D9ZNS4_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0H3S7_A0A0E0H3S7_ORYNI_4536 and sp_Q33E23_DHE2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0K0JSW1_A0A0K0JSW1_BRUMA_6279 and tr_A0A0N4TSG0_A0A0N4TSG0_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A0K0JY49_A0A0K0JY49_BRUMA_6279 and tr_A0A0R3QRG7_A0A0R3QRG7_9BILA_42155 are exactly identical! WARNING: Sequences tr_F4NVN3_F4NVN3_BATDJ_684364 and tr_A0A177W9A7_A0A177W9A7_BATDE_403673 are exactly identical! WARNING: Sequences tr_A8X0P1_A8X0P1_CAEBR_6238 and tr_A0A2G5U5G5_A0A2G5U5G5_9PELO_1611254 are exactly identical! WARNING: Sequences tr_M4F5S2_M4F5S2_BRARP_51351 and tr_A0A078G808_A0A078G808_BRANA_3708 are exactly identical! WARNING: Sequences tr_A0A015NH11_A0A015NH11_9GLOM_1432141 and tr_A0A2H5SXI4_A0A2H5SXI4_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A078GXY3_A0A078GXY3_BRANA_3708 and tr_A0A0D3AFR8_A0A0D3AFR8_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0D2S5E9_A0A0D2S5E9_GOSRA_29730 and tr_A0A1U8IV10_A0A1U8IV10_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0A1MX20_A0A0A1MX20_9FUNG_58291 and tr_A0A367JY57_A0A367JY57_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A091IJG7_A0A091IJG7_EGRGA_188379 and tr_A0A091V5H8_A0A091V5H8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IJG7_A0A091IJG7_EGRGA_188379 and tr_A0A087QH96_A0A087QH96_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IJG7_A0A091IJG7_EGRGA_188379 and tr_A0A0A0B0J5_A0A0A0B0J5_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1S3YRG3_A0A1S3YRG3_TOBAC_4097 and tr_A0A1U7YEB9_A0A1U7YEB9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4B8W9_A0A1S4B8W9_TOBAC_4097 and tr_A0A1U7VHC4_A0A1U7VHC4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4DCK2_A0A1S4DCK2_TOBAC_4097 and tr_A0A1U7VP65_A0A1U7VP65_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1U8E9N3_A0A1U8E9N3_CAPAN_4072 and tr_A0A2G3BI10_A0A2G3BI10_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2K5NNM1_A0A2K5NNM1_CERAT_9531 and tr_A0A2K5YUC7_A0A2K5YUC7_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 36 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/P00367/4_raxmlng_ancestral/P00367.raxml.reduced.phy Alignment comprises 1 partitions and 558 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 558 Gaps: 26.68 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00367/4_raxmlng_ancestral/P00367.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/P00367/3_mltree/P00367.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 140 / 11200 [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: -156657.932168 [00:00:00 -156657.932168] Initial branch length optimization [00:00:01 -154715.332300] Model parameter optimization (eps = 0.100000) [00:00:32] Tree #1, final logLikelihood: -153980.490011 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.186129,0.389911) (0.208944,0.469310) (0.337764,0.781515) (0.267162,2.116315) 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/P00367/4_raxmlng_ancestral/P00367.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00367/4_raxmlng_ancestral/P00367.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00367/4_raxmlng_ancestral/P00367.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P00367/4_raxmlng_ancestral/P00367.raxml.log Analysis started: 02-Jun-2021 15:01:00 / finished: 02-Jun-2021 15:01:37 Elapsed time: 37.097 seconds