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 15:15:48 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00294/2_msa/O00294_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00294/3_mltree/O00294.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00294/4_raxmlng_ancestral/O00294 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622636148 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/O00294/2_msa/O00294_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 542 sites WARNING: Sequences tr_D8R328_D8R328_SELML_88036 and tr_D8SMF3_D8SMF3_SELML_88036 are exactly identical! WARNING: Sequences tr_D8R5X4_D8R5X4_SELML_88036 and tr_D8SG45_D8SG45_SELML_88036 are exactly identical! WARNING: Sequences tr_G3RQT8_G3RQT8_GORGO_9595 and tr_A0A2I3RTK4_A0A2I3RTK4_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2Q349_H2Q349_PANTR_9598 and tr_A0A2R9AQ07_A0A2R9AQ07_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0FW58_A0A0E0FW58_ORYNI_4536 and tr_A2WXB7_A2WXB7_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0FW58_A0A0E0FW58_ORYNI_4536 and tr_I1NTP2_I1NTP2_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0FW58_A0A0E0FW58_ORYNI_4536 and tr_A0A0E0CAR9_A0A0E0CAR9_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0FW58_A0A0E0FW58_ORYNI_4536 and tr_A0A0E0N5I2_A0A0E0N5I2_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0FW58_A0A0E0FW58_ORYNI_4536 and tr_A0A0D3EWP8_A0A0D3EWP8_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0FW58_A0A0E0FW58_ORYNI_4536 and tr_A0A0D9YHX0_A0A0D9YHX0_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0FW58_A0A0E0FW58_ORYNI_4536 and sp_Q8LJA9_TLP3_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2XGP5_A2XGP5_ORYSI_39946 and sp_Q10LG8_TLP6_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2ZID2_A2ZID2_ORYSI_39946 and tr_I1R4B9_I1R4B9_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2ZID2_A2ZID2_ORYSI_39946 and tr_A0A0E0RE64_A0A0E0RE64_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2ZID2_A2ZID2_ORYSI_39946 and tr_A0A0D3HRR6_A0A0D3HRR6_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A2ZID2_A2ZID2_ORYSI_39946 and sp_Q2QXB2_TLP14_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B8AZY9_B8AZY9_ORYSI_39946 and tr_I1PX84_I1PX84_ORYGL_4538 are exactly identical! WARNING: Sequences tr_B8AZY9_B8AZY9_ORYSI_39946 and sp_Q68Y48_TLP9_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B8B5W0_B8B5W0_ORYSI_39946 and sp_Q8H485_TLP11_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0NV24_A0A0E0NV24_ORYRU_4529 and tr_A0A0D9Z7D6_A0A0D9Z7D6_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_G7PQT0_G7PQT0_MACFA_9541 and tr_A0A2K6EAS3_A0A2K6EAS3_MACNE_9545 are exactly identical! WARNING: Sequences tr_M4D7M6_M4D7M6_BRARP_51351 and tr_A0A078K2K6_A0A078K2K6_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4FEU8_M4FEU8_BRARP_51351 and tr_A0A078I8U4_A0A078I8U4_BRANA_3708 are exactly identical! WARNING: Sequences tr_M7ZG02_M7ZG02_TRIUA_4572 and tr_A0A3B6KFD0_A0A3B6KFD0_WHEAT_4565 are exactly identical! WARNING: Sequences tr_M8A225_M8A225_TRIUA_4572 and tr_A0A3B6HUS0_A0A3B6HUS0_WHEAT_4565 are exactly identical! WARNING: Sequences tr_W2Q7I0_W2Q7I0_PHYPN_761204 and tr_W2L876_W2L876_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2R2P9_W2R2P9_PHYPN_761204 and tr_W2ICU6_W2ICU6_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2RF91_W2RF91_PHYPN_761204 and tr_A0A0W8DFZ9_A0A0W8DFZ9_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2RF91_W2RF91_PHYPN_761204 and tr_W2NJY3_W2NJY3_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A3B6EP02_A0A3B6EP02_WHEAT_4565 and tr_A0A3B6GYQ0_A0A3B6GYQ0_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A3B6EP02_A0A3B6EP02_WHEAT_4565 and tr_D8L9L6_D8L9L6_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A3B6INP1_A0A3B6INP1_WHEAT_4565 and tr_A0A3B6JGJ0_A0A3B6JGJ0_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067G8W6_A0A067G8W6_CITSI_2711 and tr_V4U0Y2_V4U0Y2_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067H6A1_A0A067H6A1_CITSI_2711 and tr_V4U0A5_V4U0A5_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A078GQJ5_A0A078GQJ5_BRANA_3708 and tr_A0A0D3C6S1_A0A0D3C6S1_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0A0L6H9_A0A0A0L6H9_CUCSA_3659 and tr_A0A1S3C2G0_A0A1S3C2G0_CUCME_3656 are exactly identical! WARNING: Sequences tr_V4SJ25_V4SJ25_9ROSI_85681 and tr_A0A2H5N7D7_A0A2H5N7D7_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2QMV3_A0A0D2QMV3_GOSRA_29730 and tr_A0A1U8K777_A0A1U8K777_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2RLI1_A0A0D2RLI1_GOSRA_29730 and tr_A0A1U8JSQ6_A0A1U8JSQ6_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0L9TX32_A0A0L9TX32_PHAAN_3914 and tr_A0A1S3V7Z2_A0A1S3V7Z2_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A0L9TZN1_A0A0L9TZN1_PHAAN_3914 and tr_A0A1S3V801_A0A1S3V801_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A0L9VG39_A0A0L9VG39_PHAAN_3914 and tr_A0A1S3VKM1_A0A1S3VKM1_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A0V0WJR8_A0A0V0WJR8_9BILA_92179 and tr_A0A0V1L8B4_A0A0V1L8B4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A151XIT9_A0A151XIT9_9HYME_64791 and tr_A0A195BXR6_A0A195BXR6_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A1S4C7Y4_A0A1S4C7Y4_TOBAC_4097 and tr_A0A1U7VIF0_A0A1U7VIF0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CXB6_A0A1S4CXB6_TOBAC_4097 and tr_A0A1U7XA72_A0A1U7XA72_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4D1L8_A0A1S4D1L8_TOBAC_4097 and tr_A0A1U7YCN9_A0A1U7YCN9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4D4R6_A0A1S4D4R6_TOBAC_4097 and tr_A0A1U7Y153_A0A1U7Y153_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3VJS8_A0A1S3VJS8_VIGRR_3916 and tr_A0A3Q0FH39_A0A3Q0FH39_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A2D0S0I0_A0A2D0S0I0_ICTPU_7998 and tr_A0A2D0S0I5_A0A2D0S0I5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2G2ZWD4_A0A2G2ZWD4_CAPAN_4072 and tr_A0A2G3CTT1_A0A2G3CTT1_CAPCH_80379 are exactly identical! WARNING: Duplicate sequences found: 51 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/O00294/4_raxmlng_ancestral/O00294.raxml.reduced.phy Alignment comprises 1 partitions and 542 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 542 Gaps: 37.03 % Invariant sites: 0.55 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00294/4_raxmlng_ancestral/O00294.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/O00294/3_mltree/O00294.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 136 / 10880 [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: -156160.002710 [00:00:00 -156160.002710] Initial branch length optimization [00:00:01 -155167.657391] Model parameter optimization (eps = 0.100000) [00:00:49] Tree #1, final logLikelihood: -154728.957300 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.152648,0.216291) (0.120966,0.334804) (0.245069,0.695451) (0.481317,1.570795) 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/O00294/4_raxmlng_ancestral/O00294.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00294/4_raxmlng_ancestral/O00294.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00294/4_raxmlng_ancestral/O00294.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O00294/4_raxmlng_ancestral/O00294.raxml.log Analysis started: 02-Jun-2021 15:15:48 / finished: 02-Jun-2021 15:16:42 Elapsed time: 54.702 seconds