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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 02-Jul-2021 07:47:51 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P28482/2_msa/P28482_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P28482/3_mltree/P28482 --seed 2 --threads 5 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P28482/2_msa/P28482_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 331 sites WARNING: Sequences tr_Q8UWG6_Q8UWG6_CHICK_9031 and tr_A0A218V2J1_A0A218V2J1_9PASE_299123 are exactly identical! WARNING: Sequences tr_Q8UWG6_Q8UWG6_CHICK_9031 and tr_A0A226PZA8_A0A226PZA8_COLVI_9014 are exactly identical! WARNING: Sequences sp_P63085_MK01_MOUSE_10090 and sp_P63086_MK01_RAT_10116 are exactly identical! WARNING: Sequences sp_P63085_MK01_MOUSE_10090 and tr_A0A1U7QEZ9_A0A1U7QEZ9_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q63844_MK03_MOUSE_10090 and sp_P21708_MK03_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XVL2_M3XVL2_MUSPF_9669 and tr_G1P5Y1_G1P5Y1_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3XVL2_M3XVL2_MUSPF_9669 and tr_F6PMR8_F6PMR8_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3XVL2_M3XVL2_MUSPF_9669 and tr_D2HUM0_D2HUM0_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XVL2_M3XVL2_MUSPF_9669 and tr_A0A2R8ZMR6_A0A2R8ZMR6_PANPA_9597 are exactly identical! WARNING: Sequences tr_F5HEA9_F5HEA9_PHANO_321614 and tr_E3RZ08_E3RZ08_PYRTT_861557 are exactly identical! WARNING: Sequences tr_F5HEA9_F5HEA9_PHANO_321614 and tr_B2WNL7_B2WNL7_PYRTR_426418 are exactly identical! WARNING: Sequences tr_F5HEA9_F5HEA9_PHANO_321614 and tr_E5AFE2_E5AFE2_LEPMJ_985895 are exactly identical! WARNING: Sequences tr_F5HEA9_F5HEA9_PHANO_321614 and tr_A0A163J5G2_A0A163J5G2_DIDRA_5454 are exactly identical! WARNING: Sequences tr_F5HEA9_F5HEA9_PHANO_321614 and tr_A0A178AXY3_A0A178AXY3_9PLEO_765868 are exactly identical! WARNING: Sequences tr_F5HEA9_F5HEA9_PHANO_321614 and tr_A0A177DAJ6_A0A177DAJ6_ALTAL_5599 are exactly identical! WARNING: Sequences tr_F5HEA9_F5HEA9_PHANO_321614 and tr_A0A1Y2LZ12_A0A1Y2LZ12_EPING_105696 are exactly identical! WARNING: Sequences tr_F5HEA9_F5HEA9_PHANO_321614 and tr_A0A2W1G9X5_A0A2W1G9X5_9PLEO_45151 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and tr_A0A2I2YZW1_A0A2I2YZW1_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and tr_E2R2N2_E2R2N2_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and tr_H2QLB4_H2QLB4_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and sp_P28482_MK01_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and tr_F7FMZ6_F7FMZ6_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and tr_A0A286ZPF5_A0A286ZPF5_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and tr_A0A2I3LQV7_A0A2I3LQV7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and tr_A0A0D9RMI9_A0A0D9RMI9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and tr_A0A2K5LSN3_A0A2K5LSN3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and tr_A0A2U4AL99_A0A2U4AL99_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and tr_A0A2U3VYF5_A0A2U3VYF5_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and tr_A0A2Y9IWM6_A0A2Y9IWM6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and tr_A0A2Y9LEH4_A0A2Y9LEH4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2I3G715_A0A2I3G715_NOMLE_61853 and tr_A0A2Y9SG06_A0A2Y9SG06_PHYCD_9755 are exactly identical! WARNING: Sequences tr_J3KJS5_J3KJS5_COCIM_246410 and tr_E9CVF8_E9CVF8_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3KJS5_J3KJS5_COCIM_246410 and tr_A0A0J7AWG4_A0A0J7AWG4_COCIT_404692 are exactly identical! WARNING: Sequences tr_D8QQG3_D8QQG3_SELML_88036 and tr_D8R8H3_D8R8H3_SELML_88036 are exactly identical! WARNING: Sequences tr_H2NQJ9_H2NQJ9_PONAB_9601 and tr_H2RA86_H2RA86_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NQJ9_H2NQJ9_PONAB_9601 and sp_P27361_MK03_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NQJ9_H2NQJ9_PONAB_9601 and tr_A0A096NHR1_A0A096NHR1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2NQJ9_H2NQJ9_PONAB_9601 and tr_A0A0D9R1K1_A0A0D9R1K1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2NQJ9_H2NQJ9_PONAB_9601 and tr_A0A2K6BWG8_A0A2K6BWG8_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2NQJ9_H2NQJ9_PONAB_9601 and tr_A0A2K5Z0A7_A0A2K5Z0A7_MANLE_9568 are exactly identical! WARNING: Sequences tr_C1GB79_C1GB79_PARBD_502780 and tr_C1H2P0_C1H2P0_PARBA_502779 are exactly identical! WARNING: Sequences tr_C0NH76_C0NH76_AJECG_447093 and tr_F0U7W4_F0U7W4_AJEC8_544711 are exactly identical! WARNING: Sequences tr_C0NH76_C0NH76_AJECG_447093 and tr_A6R6J2_A6R6J2_AJECN_339724 are exactly identical! WARNING: Sequences tr_G1MQT8_G1MQT8_MELGA_9103 and tr_H0ZE69_H0ZE69_TAEGU_59729 are exactly identical! WARNING: Sequences tr_G1MQT8_G1MQT8_MELGA_9103 and tr_U3IEQ1_U3IEQ1_ANAPL_8839 are exactly identical! WARNING: Sequences tr_G1MQT8_G1MQT8_MELGA_9103 and tr_A0A091ESG6_A0A091ESG6_CORBR_85066 are exactly identical! WARNING: Sequences tr_G1MQT8_G1MQT8_MELGA_9103 and tr_A0A093PWS9_A0A093PWS9_9PASS_328815 are exactly identical! WARNING: Sequences tr_G1MQT8_G1MQT8_MELGA_9103 and tr_A0A091IHL4_A0A091IHL4_CALAN_9244 are exactly identical! WARNING: Sequences tr_B8P2A6_B8P2A6_POSPM_561896 and tr_A0A1X6MWN9_A0A1X6MWN9_9APHY_670580 are exactly identical! WARNING: Sequences tr_B8P7P9_B8P7P9_POSPM_561896 and tr_A0A1X6MXF3_A0A1X6MXF3_9APHY_670580 are exactly identical! WARNING: Sequences tr_B8PJ10_B8PJ10_POSPM_561896 and tr_A0A1X6NGQ2_A0A1X6NGQ2_9APHY_670580 are exactly identical! WARNING: Sequences tr_V5IKE7_V5IKE7_NEUCR_367110 and tr_G4UVH4_G4UVH4_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8N223_B8N223_ASPFN_332952 and tr_Q2ULI1_Q2ULI1_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N223_B8N223_ASPFN_332952 and tr_A0A0L1IND9_A0A0L1IND9_ASPNO_1509407 are exactly identical! WARNING: Sequences tr_B8N223_B8N223_ASPFN_332952 and tr_A0A1S9DN62_A0A1S9DN62_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179U8X0_A0A179U8X0_BLAGS_559298 and tr_A0A179U8D3_A0A179U8D3_AJEDR_559297 are exactly identical! WARNING: Sequences tr_W5P0L9_W5P0L9_SHEEP_9940 and tr_E1B8P9_E1B8P9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5Q1R8_W5Q1R8_SHEEP_9940 and tr_F1MI27_F1MI27_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F9FEW2_F9FEW2_FUSOF_660025 and tr_C7YP45_C7YP45_NECH7_660122 are exactly identical! WARNING: Sequences tr_F9FEW2_F9FEW2_FUSOF_660025 and tr_W7M8C1_W7M8C1_GIBM7_334819 are exactly identical! WARNING: Sequences tr_F9FEW2_F9FEW2_FUSOF_660025 and tr_A0A0C4DHU3_A0A0C4DHU3_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FEW2_F9FEW2_FUSOF_660025 and tr_S0E3W7_S0E3W7_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9FEW2_F9FEW2_FUSOF_660025 and tr_N4UA45_N4UA45_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FEW2_F9FEW2_FUSOF_660025 and tr_X0D3M7_X0D3M7_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FEW2_F9FEW2_FUSOF_660025 and tr_A0A1V1TAH6_A0A1V1TAH6_9FUNG_1813822 are exactly identical! WARNING: Sequences tr_F9FEW2_F9FEW2_FUSOF_660025 and tr_A0A2H3T2R5_A0A2H3T2R5_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FEW2_F9FEW2_FUSOF_660025 and tr_A0A2H3HWV2_A0A2H3HWV2_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FEW2_F9FEW2_FUSOF_660025 and tr_A0A2K0WQ18_A0A2K0WQ18_GIBNY_42673 are exactly identical! WARNING: Sequences tr_F9FEW2_F9FEW2_FUSOF_660025 and tr_A0A365N2K8_A0A365N2K8_GIBIN_948311 are exactly identical! WARNING: Sequences tr_E9EWV4_E9EWV4_METRA_655844 and tr_E9DS25_E9DS25_METAQ_655827 are exactly identical! WARNING: Sequences tr_E9EWV4_E9EWV4_METRA_655844 and tr_A0A0B2X709_A0A0B2X709_METAS_1081103 are exactly identical! WARNING: Sequences tr_E9EWV4_E9EWV4_METRA_655844 and tr_A0A0B4HPY9_A0A0B4HPY9_METMF_1276143 are exactly identical! WARNING: Sequences tr_E9EWV4_E9EWV4_METRA_655844 and tr_A0A0D9PCZ2_A0A0D9PCZ2_METAN_1291518 are exactly identical! WARNING: Sequences tr_J4KQI8_J4KQI8_BEAB2_655819 and tr_A0A0A2V4U1_A0A0A2V4U1_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J4KQI8_J4KQI8_BEAB2_655819 and tr_A0A167CV07_A0A167CV07_9HYPO_1081107 are exactly identical! WARNING: Sequences tr_J4KQI8_J4KQI8_BEAB2_655819 and tr_A0A2N6NSN0_A0A2N6NSN0_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A088AJ01_A0A088AJ01_APIME_7460 and tr_A0A2A3EL41_A0A2A3EL41_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158P1W9_A0A158P1W9_ATTCE_12957 and tr_F4W648_F4W648_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158P1W9_A0A158P1W9_ATTCE_12957 and tr_A0A195AWA8_A0A195AWA8_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158P1W9_A0A158P1W9_ATTCE_12957 and tr_A0A195ERA1_A0A195ERA1_9HYME_34720 are exactly identical! WARNING: Sequences tr_G9NYK9_G9NYK9_HYPAI_452589 and tr_Q2WGK5_Q2WGK5_TRIHA_5544 are exactly identical! WARNING: Sequences tr_G9NYK9_G9NYK9_HYPAI_452589 and tr_A0A2T3ZWY3_A0A2T3ZWY3_TRIHA_983964 are exactly identical! WARNING: Sequences tr_J3NVC8_J3NVC8_GAGT3_644352 and tr_G4N0Z0_G4N0Z0_MAGO7_242507 are exactly identical! WARNING: Sequences tr_J3NVC8_J3NVC8_GAGT3_644352 and tr_A0A0C4DUI1_A0A0C4DUI1_MAGP6_644358 are exactly identical! WARNING: Sequences tr_A0A0I9N6G9_A0A0I9N6G9_BRUMA_6279 and tr_A0A2K6WJU9_A0A2K6WJU9_ONCVO_6282 are exactly identical! WARNING: Sequences tr_A0A0I9N6G9_A0A0I9N6G9_BRUMA_6279 and tr_A0A0R3QUT5_A0A0R3QUT5_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A0I9N6G9_A0A0I9N6G9_BRUMA_6279 and tr_A0A182EBC9_A0A182EBC9_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A1DP05_A1DP05_NEOFI_331117 and tr_A0A0K8LJF5_A0A0K8LJF5_9EURO_91492 are exactly identical! WARNING: Sequences tr_A1DP05_A1DP05_NEOFI_331117 and tr_A0A2I1CBQ2_A0A2I1CBQ2_9EURO_1392255 are exactly identical! WARNING: Sequences tr_A2QSG8_A2QSG8_ASPNC_425011 and tr_G7XLY7_G7XLY7_ASPKW_1033177 are exactly identical! WARNING: Sequences tr_A2QSG8_A2QSG8_ASPNC_425011 and tr_G3YFU1_G3YFU1_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QSG8_A2QSG8_ASPNC_425011 and tr_A0A100IQ13_A0A100IQ13_ASPNG_5061 are exactly identical! WARNING: Sequences tr_A2QSG8_A2QSG8_ASPNC_425011 and tr_A0A1L9UND4_A0A1L9UND4_9EURO_767769 are exactly identical! WARNING: Sequences tr_A2QSG8_A2QSG8_ASPNC_425011 and tr_A0A318ZYD5_A0A318ZYD5_9EURO_1450533 are exactly identical! WARNING: Sequences tr_D5GC39_D5GC39_TUBMM_656061 and tr_A0A317T1L8_A0A317T1L8_9PEZI_42249 are exactly identical! WARNING: Sequences tr_G9MQI4_G9MQI4_HYPVG_413071 and tr_A0A2T3ZJ00_A0A2T3ZJ00_9HYPO_1042311 are exactly identical! WARNING: Sequences tr_G9MQI4_G9MQI4_HYPVG_413071 and tr_A0A2T4AZH2_A0A2T4AZH2_9HYPO_58853 are exactly identical! WARNING: Sequences tr_H1VA10_H1VA10_COLHI_759273 and tr_E3QLR0_E3QLR0_COLGM_645133 are exactly identical! WARNING: Sequences tr_H1VA10_H1VA10_COLHI_759273 and tr_L2GIQ8_L2GIQ8_COLFN_1213859 are exactly identical! WARNING: Sequences tr_H1VA10_H1VA10_COLHI_759273 and tr_N4UTY5_N4UTY5_COLOR_1213857 are exactly identical! WARNING: Sequences tr_H1VA10_H1VA10_COLHI_759273 and tr_T0JLU8_T0JLU8_COLGC_1237896 are exactly identical! WARNING: Sequences tr_H1VA10_H1VA10_COLHI_759273 and tr_A0A010S4M5_A0A010S4M5_9PEZI_1445577 are exactly identical! WARNING: Sequences tr_H1VA10_H1VA10_COLHI_759273 and tr_A0A066XR12_A0A066XR12_COLSU_1173701 are exactly identical! WARNING: Sequences tr_H1VA10_H1VA10_COLHI_759273 and tr_A0A135T9V1_A0A135T9V1_9PEZI_1209931 are exactly identical! WARNING: Sequences tr_H1VA10_H1VA10_COLHI_759273 and tr_A0A166WL81_A0A166WL81_9PEZI_708197 are exactly identical! WARNING: Sequences tr_H1VA10_H1VA10_COLHI_759273 and tr_A0A161YHF5_A0A161YHF5_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_H1VA10_H1VA10_COLHI_759273 and tr_A0A1G4BSE1_A0A1G4BSE1_9PEZI_1209926 are exactly identical! WARNING: Sequences tr_H1VA10_H1VA10_COLHI_759273 and tr_A0A1Q8S0W0_A0A1Q8S0W0_9PEZI_708187 are exactly identical! WARNING: Sequences tr_F9XD87_F9XD87_ZYMTI_336722 and tr_A0A0F4H0Y8_A0A0F4H0Y8_9PEZI_1047168 are exactly identical! WARNING: Sequences tr_F9XD87_F9XD87_ZYMTI_336722 and tr_A0A1X7RW24_A0A1X7RW24_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2XRF8_G2XRF8_BOTF4_999810 and tr_M7UCJ8_M7UCJ8_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_A0A287BLM6_A0A287BLM6_PIG_9823 and tr_A0A2Y9PDR5_A0A2Y9PDR5_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A287BLM6_A0A287BLM6_PIG_9823 and tr_A0A2Y9SSQ5_A0A2Y9SSQ5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_E3N6Z0_E3N6Z0_CAERE_31234 and tr_A0A261C567_A0A261C567_9PELO_1503980 are exactly identical! WARNING: Sequences tr_E6ZV08_E6ZV08_SPORE_999809 and tr_A0A0F7RZY7_A0A0F7RZY7_9BASI_49012 are exactly identical! WARNING: Sequences tr_G0RHV5_G0RHV5_HYPJQ_431241 and tr_A0A2T4C6I4_A0A2T4C6I4_TRILO_983965 are exactly identical! WARNING: Sequences tr_B3S523_B3S523_TRIAD_10228 and tr_A0A369SI29_A0A369SI29_9METZ_287889 are exactly identical! WARNING: Sequences sp_P46196_MK01_BOVIN_9913 and tr_M3XFY0_M3XFY0_FELCA_9685 are exactly identical! WARNING: Sequences tr_K9FDB7_K9FDB7_PEND2_1170229 and tr_A0A0A2JY81_A0A0A2JY81_PENEN_27334 are exactly identical! WARNING: Sequences tr_K9FDB7_K9FDB7_PEND2_1170229 and tr_W6R7K2_W6R7K2_PENRF_1365484 are exactly identical! WARNING: Sequences tr_K9FDB7_K9FDB7_PEND2_1170229 and tr_A0A0G4P4S3_A0A0G4P4S3_PENCA_1429867 are exactly identical! WARNING: Sequences tr_K9FDB7_K9FDB7_PEND2_1170229 and tr_A0A101MRG7_A0A101MRG7_9EURO_48697 are exactly identical! WARNING: Sequences tr_K9FDB7_K9FDB7_PEND2_1170229 and tr_A0A1V6N8N0_A0A1V6N8N0_9EURO_60169 are exactly identical! WARNING: Sequences tr_K9FDB7_K9FDB7_PEND2_1170229 and tr_A0A1V6RV80_A0A1V6RV80_9EURO_29845 are exactly identical! WARNING: Sequences tr_K9FDB7_K9FDB7_PEND2_1170229 and tr_A0A1V6RJM9_A0A1V6RJM9_9EURO_60172 are exactly identical! WARNING: Sequences tr_L0P9Z0_L0P9Z0_PNEJ8_1209962 and tr_A0A0W4ZL45_A0A0W4ZL45_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_S3CBN3_S3CBN3_OPHP1_1262450 and tr_U7Q7Q6_U7Q7Q6_SPOS1_1391915 are exactly identical! WARNING: Sequences tr_M3AVQ5_M3AVQ5_PSEFD_383855 and tr_A0A2I0RZ29_A0A2I0RZ29_9PEZI_348901 are exactly identical! WARNING: Sequences tr_M2TCC8_M2TCC8_COCSN_665912 and tr_R0IIH3_R0IIH3_SETT2_671987 are exactly identical! WARNING: Sequences tr_M2TCC8_M2TCC8_COCSN_665912 and tr_M2UET7_M2UET7_COCH5_701091 are exactly identical! WARNING: Sequences tr_M2TCC8_M2TCC8_COCSN_665912 and tr_W6YPH4_W6YPH4_COCCA_930089 are exactly identical! WARNING: Sequences tr_M2TCC8_M2TCC8_COCSN_665912 and tr_W6ZMT6_W6ZMT6_COCMI_930090 are exactly identical! WARNING: Sequences tr_M2TCC8_M2TCC8_COCSN_665912 and tr_A0A364N2H5_A0A364N2H5_9PLEO_183478 are exactly identical! WARNING: Sequences tr_V2X6M5_V2X6M5_MONRO_1381753 and tr_A0A0W0FIK4_A0A0W0FIK4_9AGAR_221103 are exactly identical! WARNING: Sequences tr_V2X8U7_V2X8U7_MONRO_1381753 and tr_A0A0W0FWS7_A0A0W0FWS7_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2QZC7_W2QZC7_PHYPN_761204 and tr_W2G2Z4_W2G2Z4_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W9WZU4_W9WZU4_9EURO_1182543 and tr_A0A0D2E760_A0A0D2E760_9EURO_348802 are exactly identical! WARNING: Sequences tr_A0A015L1L2_A0A015L1L2_9GLOM_1432141 and tr_A0A1C9IHM9_A0A1C9IHM9_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015L1L2_A0A015L1L2_9GLOM_1432141 and tr_U9ULE8_U9ULE8_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015L1L2_A0A015L1L2_9GLOM_1432141 and tr_A0A2Z6R5A4_A0A2Z6R5A4_9GLOM_94130 are exactly identical! WARNING: Sequences tr_A0A059J2J1_A0A059J2J1_9EURO_1215338 and tr_A0A178ES75_A0A178ES75_TRIRU_5551 are exactly identical! WARNING: Sequences tr_A0A074WNZ4_A0A074WNZ4_9PEZI_1043004 and tr_A0A074W3S0_A0A074W3S0_9PEZI_1043003 are exactly identical! WARNING: Sequences tr_A0A084QBL1_A0A084QBL1_STAC4_1283841 and tr_A0A084R836_A0A084R836_STACH_1283842 are exactly identical! WARNING: Sequences tr_A0A094F240_A0A094F240_9PEZI_1420912 and tr_A0A1B8E2U5_A0A1B8E2U5_9PEZI_1524831 are exactly identical! WARNING: Sequences tr_A0A094F240_A0A094F240_9PEZI_1420912 and tr_A0A1B8G931_A0A1B8G931_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094F240_A0A094F240_9PEZI_1420912 and tr_A0A1B8EQ21_A0A1B8EQ21_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_A0A0F8X8Z1_A0A0F8X8Z1_9EURO_308745 and tr_A0A2T5LPC4_A0A2T5LPC4_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0G2FQA4_A0A0G2FQA4_9PEZI_1214573 and tr_A0A2P5HLF5_A0A2P5HLF5_9PEZI_158607 are exactly identical! WARNING: Sequences tr_A0A0K0F5T3_A0A0K0F5T3_STRVS_75913 and tr_A0A0N5BEK0_A0A0N5BEK0_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0M9EUQ7_A0A0M9EUQ7_FUSLA_179993 and tr_I1RQN9_I1RQN9_GIBZE_229533 are exactly identical! WARNING: Sequences tr_A0A0M9EUQ7_A0A0M9EUQ7_FUSLA_179993 and tr_A0A1B8ANW8_A0A1B8ANW8_FUSPO_36050 are exactly identical! WARNING: Sequences tr_A0A0M9EUQ7_A0A0M9EUQ7_FUSLA_179993 and tr_A0A2T4GN21_A0A2T4GN21_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A0D1ZJJ0_A0A0D1ZJJ0_9EURO_569365 and tr_A0A178ZFD9_A0A178ZFD9_9EURO_1367422 are exactly identical! WARNING: Sequences tr_A0A0V0RKD6_A0A0V0RKD6_9BILA_6336 and tr_A0A0V0WMA4_A0A0V0WMA4_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RKD6_A0A0V0RKD6_9BILA_6336 and tr_A0A0V0VHW0_A0A0V0VHW0_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0RKD6_A0A0V0RKD6_9BILA_6336 and tr_A0A0V1LQ42_A0A0V1LQ42_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0RKD6_A0A0V0RKD6_9BILA_6336 and tr_A0A0V0ZP97_A0A0V0ZP97_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0RKD6_A0A0V0RKD6_9BILA_6336 and tr_A0A0V1MR09_A0A0V1MR09_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V0RKD6_A0A0V0RKD6_9BILA_6336 and tr_A0A0V1P3A5_A0A0V1P3A5_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0RKD6_A0A0V0RKD6_9BILA_6336 and tr_A0A0V1I965_A0A0V1I965_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A194X3P6_A0A194X3P6_9HELO_149040 and tr_A0A1L7WXV4_A0A1L7WXV4_9HELO_576137 are exactly identical! WARNING: Sequences tr_A0A194X3P6_A0A194X3P6_9HELO_149040 and tr_A0A2V1CQ62_A0A2V1CQ62_9HELO_1485229 are exactly identical! WARNING: Sequences tr_A0A146FA49_A0A146FA49_9EURO_1069201 and tr_A0A1L9NQ58_A0A1L9NQ58_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A164ZXP2_A0A164ZXP2_9HOMO_1314777 and tr_A0A166FD10_A0A166FD10_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A164ZY95_A0A164ZY95_9HOMO_1314777 and tr_A0A166FDL3_A0A166FDL3_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A194W6H1_A0A194W6H1_9PEZI_105487 and tr_A0A194V2X2_A0A194V2X2_9PEZI_694573 are exactly identical! WARNING: Sequences tr_A0A194W6H1_A0A194W6H1_9PEZI_105487 and tr_A0A1J7J0E4_A0A1J7J0E4_9PEZI_1408157 are exactly identical! WARNING: Sequences tr_A0A168PIZ5_A0A168PIZ5_ABSGL_4829 and tr_A0A1X2I3I4_A0A1X2I3I4_9FUNG_90262 are exactly identical! WARNING: Sequences tr_A0A1S3R5W8_A0A1S3R5W8_SALSA_8030 and tr_A0A060XIU8_A0A060XIU8_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1B7MMQ7_A0A1B7MMQ7_9HOMO_1314800 and tr_A0A1J8Q2Z0_A0A1J8Q2Z0_9HOMO_180088 are exactly identical! WARNING: Sequences tr_A0A1B7MVJ6_A0A1B7MVJ6_9HOMO_1314800 and tr_A0A1J8QQU2_A0A1J8QQU2_9HOMO_180088 are exactly identical! WARNING: Sequences tr_A0A1R3S1A5_A0A1R3S1A5_ASPC5_602072 and tr_A0A319EMI6_A0A319EMI6_9EURO_1448318 are exactly identical! WARNING: Sequences tr_A0A1R3S1A5_A0A1R3S1A5_ASPC5_602072 and tr_A0A395H8A7_A0A395H8A7_9EURO_1448316 are exactly identical! WARNING: Sequences tr_A0A1V8U515_A0A1V8U515_9PEZI_1974281 and tr_A0A1V8V298_A0A1V8V298_9PEZI_1974281 are exactly identical! WARNING: Sequences tr_A0A1V8U515_A0A1V8U515_9PEZI_1974281 and tr_A0A1V8SRS7_A0A1V8SRS7_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A1Y1ZCH9_A0A1Y1ZCH9_9PLEO_1231657 and tr_A0A2V1D9X4_A0A2V1D9X4_9PLEO_97972 are exactly identical! WARNING: Sequences tr_A0A1Y2DP20_A0A1Y2DP20_9PEZI_1141098 and tr_A0A1Y2W0T2_A0A1Y2W0T2_9PEZI_1001833 are exactly identical! WARNING: Sequences tr_A0A229XE04_A0A229XE04_9EURO_1245748 and tr_A0A397HSP5_A0A397HSP5_9EURO_41047 are exactly identical! WARNING: Sequences tr_A0A2H3DFL2_A0A2H3DFL2_ARMGA_47427 and tr_A0A2H3BIC9_A0A2H3BIC9_9AGAR_1076256 are exactly identical! WARNING: Sequences tr_A0A2H3DFL2_A0A2H3DFL2_ARMGA_47427 and tr_A0A284QR22_A0A284QR22_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2H3E2X1_A0A2H3E2X1_ARMGA_47427 and tr_A0A2H3B7K7_A0A2H3B7K7_9AGAR_1076256 are exactly identical! WARNING: Sequences tr_A0A2H3E2X1_A0A2H3E2X1_ARMGA_47427 and tr_A0A284RRI8_A0A284RRI8_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2S7PJF4_A0A2S7PJF4_9HELO_2070414 and tr_A0A2S7R0M3_A0A2S7R0M3_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A2G4T1P2_A0A2G4T1P2_9FUNG_1340429 and tr_A0A367JL46_A0A367JL46_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A2P8A8H5_A0A2P8A8H5_9PEZI_40998 and tr_A0A2K1QRB1_A0A2K1QRB1_9PEZI_2082308 are exactly identical! WARNING: Sequences tr_A0A2U4A994_A0A2U4A994_TURTR_9739 and tr_A0A384AGR0_A0A384AGR0_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3VPZ0_A0A2U3VPZ0_ODORO_9708 and tr_A0A2U3Z2Q3_A0A2U3Z2Q3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A317WVW7_A0A317WVW7_9EURO_1448321 and tr_A0A319EKP4_A0A319EKP4_9EURO_1448320 are exactly identical! WARNING: Sequences tr_A0A317WVW7_A0A317WVW7_9EURO_1448321 and tr_A0A2V5I0K3_A0A2V5I0K3_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A2Y9RRM5_A0A2Y9RRM5_TRIMA_127582 and tr_A0A384B9K1_A0A384B9K1_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A369H6Z1_A0A369H6Z1_9HYPO_2039874 and tr_A0A367LAT8_A0A367LAT8_9HYPO_1330021 are exactly identical! WARNING: Duplicate sequences found: 191 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/P28482/3_mltree/P28482.raxml.reduced.phy Alignment comprises 1 partitions and 330 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 331 / 330 Gaps: 1.25 % Invariant sites: 6.04 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P28482/3_mltree/P28482.raxml.rba Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 330 / 26400 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -323959.891688] Initial branch length optimization [00:00:08 -257825.425574] Model parameter optimization (eps = 10.000000) [00:01:03 -256866.372606] AUTODETECT spr round 1 (radius: 5) [00:04:54 -167876.598044] AUTODETECT spr round 2 (radius: 10) [00:08:56 -128516.437951] AUTODETECT spr round 3 (radius: 15) [00:13:40 -107531.073694] AUTODETECT spr round 4 (radius: 20) [00:18:21 -93306.089426] AUTODETECT spr round 5 (radius: 25) [00:23:33 -90573.514413] SPR radius for FAST iterations: 25 (autodetect) [00:23:33 -90573.514413] Model parameter optimization (eps = 3.000000) [00:24:01 -90552.253802] FAST spr round 1 (radius: 25) [00:28:36 -74128.211741] FAST spr round 2 (radius: 25) [00:31:48 -67232.065577] FAST spr round 3 (radius: 25) [00:34:38 -65267.473899] FAST spr round 4 (radius: 25) [00:36:59 -65019.875161] FAST spr round 5 (radius: 25) [00:39:18 -65015.364540] FAST spr round 6 (radius: 25) [00:41:20 -65015.364078] Model parameter optimization (eps = 1.000000) [00:41:35 -65013.873343] SLOW spr round 1 (radius: 5) [00:44:36 -65002.567548] SLOW spr round 2 (radius: 5) [00:47:33 -64999.815723] SLOW spr round 3 (radius: 5) [00:50:17 -64999.815510] SLOW spr round 4 (radius: 10) [00:53:14 -64999.815171] SLOW spr round 5 (radius: 15) [00:59:09 -64999.815034] SLOW spr round 6 (radius: 20) [01:07:41 -64993.164700] SLOW spr round 7 (radius: 5) [01:11:45 -64992.769776] SLOW spr round 8 (radius: 5) [01:15:12 -64992.769316] SLOW spr round 9 (radius: 10) [01:18:33 -64982.971057] SLOW spr round 10 (radius: 5) [01:22:16 -64982.658117] SLOW spr round 11 (radius: 5) [01:25:26 -64982.657668] SLOW spr round 12 (radius: 10) [01:28:33 -64980.498756] SLOW spr round 13 (radius: 5) [01:32:13 -64980.498426] SLOW spr round 14 (radius: 10) [01:35:44 -64980.498215] SLOW spr round 15 (radius: 15) [01:37:09] [worker #1] ML tree search #2, logLikelihood: -64962.649357 [01:40:58 -64980.498013] SLOW spr round 16 (radius: 20) [01:49:42 -64980.497819] SLOW spr round 17 (radius: 25) [01:59:06] [worker #2] ML tree search #3, logLikelihood: -64972.122980 [01:59:39 -64980.497630] Model parameter optimization (eps = 0.100000) [01:59:48] [worker #0] ML tree search #1, logLikelihood: -64980.355164 [01:59:48 -319203.584403] Initial branch length optimization [01:59:56 -255301.586316] Model parameter optimization (eps = 10.000000) [02:00:54 -254324.341283] AUTODETECT spr round 1 (radius: 5) [02:01:18] [worker #4] ML tree search #5, logLikelihood: -64969.142065 [02:04:47 -168249.884216] AUTODETECT spr round 2 (radius: 10) [02:08:48 -129430.502026] AUTODETECT spr round 3 (radius: 15) [02:13:36 -101957.952170] AUTODETECT spr round 4 (radius: 20) [02:18:55 -85250.695764] AUTODETECT spr round 5 (radius: 25) [02:25:18 -82991.167838] SPR radius for FAST iterations: 25 (autodetect) [02:25:18 -82991.167838] Model parameter optimization (eps = 3.000000) [02:25:43 -82975.132156] FAST spr round 1 (radius: 25) [02:30:05 -65916.823424] FAST spr round 2 (radius: 25) [02:33:10 -65069.272557] FAST spr round 3 (radius: 25) [02:35:48 -65011.094347] FAST spr round 4 (radius: 25) [02:38:10 -65007.130779] FAST spr round 5 (radius: 25) [02:40:16 -65007.130299] Model parameter optimization (eps = 1.000000) [02:40:31 -65005.999697] SLOW spr round 1 (radius: 5) [02:43:31 -64992.644185] SLOW spr round 2 (radius: 5) [02:46:18 -64992.390614] SLOW spr round 3 (radius: 5) [02:49:01 -64992.390489] SLOW spr round 4 (radius: 10) [02:51:53 -64992.390457] SLOW spr round 5 (radius: 15) [02:57:48 -64991.446811] SLOW spr round 6 (radius: 5) [03:01:37 -64991.446612] SLOW spr round 7 (radius: 10) [03:05:19 -64991.446581] SLOW spr round 8 (radius: 15) [03:10:24 -64991.446552] SLOW spr round 9 (radius: 20) [03:19:00 -64991.446523] SLOW spr round 10 (radius: 25) [03:20:19] [worker #3] ML tree search #4, logLikelihood: -64969.949099 [03:29:14 -64989.482863] SLOW spr round 11 (radius: 5) [03:30:07] [worker #4] ML tree search #10, logLikelihood: -64970.177869 [03:33:21 -64989.452124] SLOW spr round 12 (radius: 10) [03:37:22 -64988.708417] SLOW spr round 13 (radius: 5) [03:40:57 -64988.707715] SLOW spr round 14 (radius: 10) [03:44:17 -64988.707580] SLOW spr round 15 (radius: 15) [03:49:32 -64988.707546] SLOW spr round 16 (radius: 20) [03:58:07 -64988.707531] SLOW spr round 17 (radius: 25) [03:59:45] [worker #2] ML tree search #8, logLikelihood: -64949.992042 [04:00:02] [worker #1] ML tree search #7, logLikelihood: -64976.838572 [04:08:14 -64985.816065] SLOW spr round 18 (radius: 5) [04:12:18 -64985.815632] SLOW spr round 19 (radius: 10) [04:16:18 -64985.815622] SLOW spr round 20 (radius: 15) [04:21:22 -64985.815618] SLOW spr round 21 (radius: 20) [04:30:04 -64985.815614] SLOW spr round 22 (radius: 25) [04:40:14 -64985.815611] Model parameter optimization (eps = 0.100000) [04:40:22] [worker #0] ML tree search #6, logLikelihood: -64985.781177 [04:40:22 -320771.496667] Initial branch length optimization [04:40:30 -255396.161726] Model parameter optimization (eps = 10.000000) [04:41:20 -254415.305296] AUTODETECT spr round 1 (radius: 5) [04:45:25 -169582.554611] AUTODETECT spr round 2 (radius: 10) [04:49:32 -130235.975745] AUTODETECT spr round 3 (radius: 15) [04:54:20 -105427.188711] AUTODETECT spr round 4 (radius: 20) [04:58:52 -94697.038477] AUTODETECT spr round 5 (radius: 25) [05:04:05 -90621.326929] SPR radius for FAST iterations: 25 (autodetect) [05:04:05 -90621.326929] Model parameter optimization (eps = 3.000000) [05:04:35 -90612.472586] FAST spr round 1 (radius: 25) [05:08:26 -74069.522477] FAST spr round 2 (radius: 25) [05:11:13 -71484.997916] FAST spr round 3 (radius: 25) [05:13:33 -71169.183072] FAST spr round 4 (radius: 25) [05:15:47] [worker #4] ML tree search #15, logLikelihood: -64970.787705 [05:15:48 -71105.054500] FAST spr round 5 (radius: 25) [05:17:45 -71103.025846] FAST spr round 6 (radius: 25) [05:19:39 -71102.423581] FAST spr round 7 (radius: 25) [05:21:32 -71102.423565] Model parameter optimization (eps = 1.000000) [05:21:43 -71101.506203] SLOW spr round 1 (radius: 5) [05:24:33 -71093.320329] SLOW spr round 2 (radius: 5) [05:27:22 -71092.572453] SLOW spr round 3 (radius: 5) [05:30:08 -71092.016506] SLOW spr round 4 (radius: 5) [05:31:47] [worker #3] ML tree search #9, logLikelihood: -64963.697036 [05:32:49 -71092.016287] SLOW spr round 5 (radius: 10) [05:35:39 -71087.612154] SLOW spr round 6 (radius: 5) [05:39:14 -71087.299759] SLOW spr round 7 (radius: 5) [05:42:18 -71087.299300] SLOW spr round 8 (radius: 10) [05:42:47] [worker #1] ML tree search #12, logLikelihood: -64958.198383 [05:45:14 -71087.299211] SLOW spr round 9 (radius: 15) [05:50:06 -71086.430708] SLOW spr round 10 (radius: 5) [05:53:46 -71086.430577] SLOW spr round 11 (radius: 10) [05:56:20] [worker #2] ML tree search #13, logLikelihood: -64954.552530 [05:57:14 -71086.430572] SLOW spr round 12 (radius: 15) [06:01:50 -71086.430567] SLOW spr round 13 (radius: 20) [06:08:45 -71086.430562] SLOW spr round 14 (radius: 25) [06:16:11 -71086.249428] SLOW spr round 15 (radius: 5) [06:20:01 -71086.249328] SLOW spr round 16 (radius: 10) [06:23:43 -71086.249322] SLOW spr round 17 (radius: 15) [06:28:19 -71084.363790] SLOW spr round 18 (radius: 5) [06:32:03 -71080.411492] SLOW spr round 19 (radius: 5) [06:35:12 -71080.411485] SLOW spr round 20 (radius: 10) [06:38:13 -71080.411479] SLOW spr round 21 (radius: 15) [06:42:55 -71080.411472] SLOW spr round 22 (radius: 20) [06:49:23 -71077.621528] SLOW spr round 23 (radius: 5) [06:53:10 -71077.476118] SLOW spr round 24 (radius: 5) [06:56:22 -71077.476111] SLOW spr round 25 (radius: 10) [06:59:25 -71077.476103] SLOW spr round 26 (radius: 15) [07:04:05 -71077.476096] SLOW spr round 27 (radius: 20) [07:08:06] [worker #3] ML tree search #14, logLikelihood: -64984.691753 [07:10:31 -71077.476088] SLOW spr round 28 (radius: 25) [07:18:43 -71077.476080] Model parameter optimization (eps = 0.100000) [07:18:51] [worker #0] ML tree search #11, logLikelihood: -71077.454364 [07:18:51 -321766.747245] Initial branch length optimization [07:18:58 -254787.060425] Model parameter optimization (eps = 10.000000) [07:20:28 -253805.965064] AUTODETECT spr round 1 (radius: 5) [07:24:37 -169552.001219] AUTODETECT spr round 2 (radius: 10) [07:29:18 -122241.316015] AUTODETECT spr round 3 (radius: 15) [07:29:27] [worker #1] ML tree search #17, logLikelihood: -64971.387572 [07:34:06 -100259.407775] AUTODETECT spr round 4 (radius: 20) [07:39:49 -85713.381995] AUTODETECT spr round 5 (radius: 25) [07:45:16] [worker #4] ML tree search #20, logLikelihood: -64977.597998 [07:46:23 -82219.932027] SPR radius for FAST iterations: 25 (autodetect) [07:46:23 -82219.932027] Model parameter optimization (eps = 3.000000) [07:46:50 -82170.661395] FAST spr round 1 (radius: 25) [07:51:33 -66690.444432] FAST spr round 2 (radius: 25) [07:54:57 -65172.939811] FAST spr round 3 (radius: 25) [07:57:48 -65034.750880] FAST spr round 4 (radius: 25) [08:00:15 -65028.448141] FAST spr round 5 (radius: 25) [08:02:30 -65028.446952] Model parameter optimization (eps = 1.000000) [08:02:47 -65023.612546] SLOW spr round 1 (radius: 5) [08:04:42] [worker #2] ML tree search #18, logLikelihood: -64987.427450 [08:05:57 -65008.381780] SLOW spr round 2 (radius: 5) [08:09:08 -65008.312467] SLOW spr round 3 (radius: 10) [08:12:29 -64997.230998] SLOW spr round 4 (radius: 5) [08:16:37 -64997.062548] SLOW spr round 5 (radius: 5) [08:20:16 -64997.062307] SLOW spr round 6 (radius: 10) [08:23:42 -64997.062297] SLOW spr round 7 (radius: 15) [08:29:29 -64991.288675] SLOW spr round 8 (radius: 5) [08:33:45 -64988.885338] SLOW spr round 9 (radius: 5) [08:37:17 -64988.885316] SLOW spr round 10 (radius: 10) [08:40:44 -64988.577895] SLOW spr round 11 (radius: 5) [08:41:06] [worker #3] ML tree search #19, logLikelihood: -64959.874508 [08:44:35 -64988.577887] SLOW spr round 12 (radius: 10) [08:48:20 -64988.577887] SLOW spr round 13 (radius: 15) [08:53:46 -64988.577887] SLOW spr round 14 (radius: 20) [09:02:36 -64987.786550] SLOW spr round 15 (radius: 5) [09:07:02 -64983.353744] SLOW spr round 16 (radius: 5) [09:10:44 -64983.352506] SLOW spr round 17 (radius: 10) [09:14:17 -64983.352320] SLOW spr round 18 (radius: 15) [09:19:54 -64982.625695] SLOW spr round 19 (radius: 5) [09:24:04 -64982.348669] SLOW spr round 20 (radius: 5) [09:27:35 -64982.348571] SLOW spr round 21 (radius: 10) [09:31:00 -64982.348554] SLOW spr round 22 (radius: 15) [09:36:37 -64982.348539] SLOW spr round 23 (radius: 20) [09:45:10 -64982.348525] SLOW spr round 24 (radius: 25) [09:55:31 -64982.348511] Model parameter optimization (eps = 0.100000) [09:55:42] [worker #0] ML tree search #16, logLikelihood: -64982.228561 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.362802,0.286956) (0.325961,0.536191) (0.200227,1.532447) (0.111010,3.731897) 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 Final LogLikelihood: -64949.992042 AIC score: 133909.984083 / AICc score: 8177969.984083 / BIC score: 141533.231426 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=331). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P28482/3_mltree/P28482.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P28482/3_mltree/P28482.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P28482/3_mltree/P28482.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P28482/3_mltree/P28482.raxml.log Analysis started: 02-Jul-2021 07:47:51 / finished: 02-Jul-2021 17:43:34 Elapsed time: 35742.553 seconds Consumed energy: 3154.218 Wh (= 16 km in an electric car, or 79 km with an e-scooter!)