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 13:44:14 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5VT25/2_msa/Q5VT25_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5VT25/3_mltree/Q5VT25.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5VT25/4_raxmlng_ancestral/Q5VT25 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803454 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/Q5VT25/2_msa/Q5VT25_nogap_msa.fasta [00:00:00] Loaded alignment with 970 taxa and 1732 sites WARNING: Sequences tr_E1C8Z7_E1C8Z7_CHICK_9031 and tr_A0A091JI71_A0A091JI71_EGRGA_188379 are exactly identical! WARNING: Sequences tr_E1C8Z7_E1C8Z7_CHICK_9031 and tr_A0A091VNX0_A0A091VNX0_NIPNI_128390 are exactly identical! WARNING: Sequences tr_E1C8Z7_E1C8Z7_CHICK_9031 and tr_A0A091V6W0_A0A091V6W0_OPIHO_30419 are exactly identical! WARNING: Sequences tr_E1C8Z7_E1C8Z7_CHICK_9031 and tr_A0A099Z0Q2_A0A099Z0Q2_TINGU_94827 are exactly identical! WARNING: Sequences tr_E1C8Z7_E1C8Z7_CHICK_9031 and tr_A0A0A0AVM9_A0A0A0AVM9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_M3YGG8_M3YGG8_MUSPF_9669 and tr_E2R001_E2R001_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YGG8_M3YGG8_MUSPF_9669 and tr_A7MB32_A7MB32_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YGG8_M3YGG8_MUSPF_9669 and tr_A0A2Y9KWK1_A0A2Y9KWK1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_G1RIH6_G1RIH6_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and sp_Q5R8M1_STK38_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_H2QSW7_H2QSW7_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_I3MIC6_I3MIC6_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and sp_Q15208_STK38_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_F7D1P8_F7D1P8_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_U3E4E5_U3E4E5_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_G7P3B9_G7P3B9_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_A0A096NHS5_A0A096NHS5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_A0A0D9RD24_A0A0D9RD24_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_A0A2K5LUJ3_A0A2K5LUJ3_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_A0A2K6BFX2_A0A2K6BFX2_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_A0A2K5Y8D8_A0A2K5Y8D8_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_A0A2U3ZQ63_A0A2U3ZQ63_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_A0A2Y9JNH9_A0A2Y9JNH9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YS05_M3YS05_MUSPF_9669 and tr_A0A384CAX4_A0A384CAX4_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3ZBR7_M3ZBR7_NOMLE_61853 and tr_F7E684_F7E684_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3ZBR7_M3ZBR7_NOMLE_61853 and tr_U3BCV6_U3BCV6_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3ZBR7_M3ZBR7_NOMLE_61853 and tr_G7PK27_G7PK27_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3ZBR7_M3ZBR7_NOMLE_61853 and tr_A0A0D9R5M2_A0A0D9R5M2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3ZBR7_M3ZBR7_NOMLE_61853 and tr_A0A2K5NAH5_A0A2K5NAH5_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3ZBR7_M3ZBR7_NOMLE_61853 and tr_A0A2K5XRK9_A0A2K5XRK9_MANLE_9568 are exactly identical! WARNING: Sequences tr_H9G236_H9G236_MACMU_9544 and tr_A0A2K5Y2N1_A0A2K5Y2N1_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0YRN8_H0YRN8_TAEGU_59729 and tr_U3JKN9_U3JKN9_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0YRN8_H0YRN8_TAEGU_59729 and tr_A0A091F0Q9_A0A091F0Q9_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0YRN8_H0YRN8_TAEGU_59729 and tr_A0A093PK26_A0A093PK26_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0YRN8_H0YRN8_TAEGU_59729 and tr_A0A218UKX3_A0A218UKX3_9PASE_299123 are exactly identical! WARNING: Sequences tr_G7PIT5_G7PIT5_MACFA_9541 and tr_A0A2K6AXE1_A0A2K6AXE1_MACNE_9545 are exactly identical! WARNING: Sequences sp_A2VDV2_STK38_BOVIN_9913 and tr_F1MBL1_F1MBL1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_U3JMU5_U3JMU5_FICAL_59894 and tr_A0A093GAV0_A0A093GAV0_DRYPU_118200 are exactly identical! WARNING: Sequences tr_U3JMU5_U3JMU5_FICAL_59894 and tr_A0A218UH16_A0A218UH16_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A2I3LC55_A0A2I3LC55_PAPAN_9555 and tr_A0A2K6CYX4_A0A2K6CYX4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3LC55_A0A2I3LC55_PAPAN_9555 and tr_A0A2K6AB07_A0A2K6AB07_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I0M026_A0A2I0M026_COLLI_8932 and tr_A0A1V4KX44_A0A1V4KX44_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1DIC8_A0A0V1DIC8_TRIBR_45882 and tr_A0A0V1P6Z6_A0A0V1P6Z6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S3JV95_A0A1S3JV95_LINUN_7574 and tr_A0A1S3JVF2_A0A1S3JVF2_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3JV95_A0A1S3JV95_LINUN_7574 and tr_A0A1S3JW59_A0A1S3JW59_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1I7UMW1_A0A1I7UMW1_9PELO_1561998 and tr_A0A1I7UMW2_A0A1I7UMW2_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A2D0RMQ3_A0A2D0RMQ3_ICTPU_7998 and tr_A0A2D0RMQ7_A0A2D0RMQ7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RMQ3_A0A2D0RMQ3_ICTPU_7998 and tr_A0A2D0RNR4_A0A2D0RNR4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RMQ3_A0A2D0RMQ3_ICTPU_7998 and tr_A0A2D0RPB9_A0A2D0RPB9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5P066_A0A2K5P066_CERAT_9531 and tr_A0A2K5ZSQ5_A0A2K5ZSQ5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4C0C9_A0A2U4C0C9_TURTR_9739 and tr_A0A2Y9S7V7_A0A2Y9S7V7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4CIW0_A0A2U4CIW0_TURTR_9739 and tr_A0A2Y9ENU4_A0A2Y9ENU4_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 52 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/Q5VT25/4_raxmlng_ancestral/Q5VT25.raxml.reduced.phy Alignment comprises 1 partitions and 1732 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1732 Gaps: 35.73 % Invariant sites: 0.69 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5VT25/4_raxmlng_ancestral/Q5VT25.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/Q5VT25/3_mltree/Q5VT25.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 433 / 34640 [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: -509744.713189 [00:00:00 -509744.713189] Initial branch length optimization [00:00:04 -441181.016104] Model parameter optimization (eps = 0.100000) [00:02:03] Tree #1, final logLikelihood: -439923.856765 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.120729,0.275599) (0.127382,0.449205) (0.431447,0.873892) (0.320442,1.661671) 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/Q5VT25/4_raxmlng_ancestral/Q5VT25.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5VT25/4_raxmlng_ancestral/Q5VT25.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5VT25/4_raxmlng_ancestral/Q5VT25.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q5VT25/4_raxmlng_ancestral/Q5VT25.raxml.log Analysis started: 04-Jun-2021 13:44:14 / finished: 04-Jun-2021 13:46:32 Elapsed time: 138.426 seconds