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 05-Jul-2021 03:09:33 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P68400/2_msa/P68400_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P68400/3_mltree/P68400 --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/P68400/2_msa/P68400_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 319 sites WARNING: Sequences tr_B4NT68_B4NT68_DROSI_7240 and sp_P08181_CSK2A_DROME_7227 are exactly identical! WARNING: Sequences tr_B4NT68_B4NT68_DROSI_7240 and tr_B4JYW2_B4JYW2_DROGR_7222 are exactly identical! WARNING: Sequences tr_B4NT68_B4NT68_DROSI_7240 and tr_B4IKT0_B4IKT0_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4NT68_B4NT68_DROSI_7240 and tr_B5DSA2_B5DSA2_DROPS_46245 are exactly identical! WARNING: Sequences tr_B4NT68_B4NT68_DROSI_7240 and tr_A0A0P8XWP5_A0A0P8XWP5_DROAN_7217 are exactly identical! WARNING: Sequences tr_B4NT68_B4NT68_DROSI_7240 and tr_B4GE77_B4GE77_DROPE_7234 are exactly identical! WARNING: Sequences tr_B4NT68_B4NT68_DROSI_7240 and tr_B4MCA6_B4MCA6_DROVI_7244 are exactly identical! WARNING: Sequences tr_B4NT68_B4NT68_DROSI_7240 and tr_A0A0Q9WZD3_A0A0Q9WZD3_DROMO_7230 are exactly identical! WARNING: Sequences tr_B4NT68_B4NT68_DROSI_7240 and tr_A0A0M3QX82_A0A0M3QX82_DROBS_30019 are exactly identical! WARNING: Sequences tr_B4NT68_B4NT68_DROSI_7240 and tr_A0A1W4VSK9_A0A1W4VSK9_DROFC_30025 are exactly identical! WARNING: Sequences tr_E2AW17_E2AW17_CAMFO_104421 and tr_A0A026VYW4_A0A026VYW4_OOCBI_2015173 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_G1N6J4_G1N6J4_MELGA_9103 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_F6VCI6_F6VCI6_MONDO_13616 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_K7GIG0_K7GIG0_PELSI_13735 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_G3VX45_G3VX45_SARHA_9305 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_H0Z8S4_H0Z8S4_TAEGU_59729 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_U3JT45_U3JT45_FICAL_59894 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A151NX96_A0A151NX96_ALLMI_8496 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A0Q3RZE4_A0A0Q3RZE4_AMAAE_12930 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A091EU85_A0A091EU85_CORBR_85066 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A091JEJ8_A0A091JEJ8_EGRGA_188379 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A093PMS6_A0A093PMS6_9PASS_328815 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A091V228_A0A091V228_NIPNI_128390 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A087R8Q2_A0A087R8Q2_APTFO_9233 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A093HZT4_A0A093HZT4_STRCA_441894 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A091WFP4_A0A091WFP4_OPIHO_30419 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A099Z576_A0A099Z576_TINGU_94827 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A091G8J4_A0A091G8J4_9AVES_55661 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A0A0B1J4_A0A0A0B1J4_CHAVO_50402 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A2I0LIS4_A0A2I0LIS4_COLLI_8932 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A093GN01_A0A093GN01_DRYPU_118200 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A091I711_A0A091I711_CALAN_9244 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A1U7RWQ0_A0A1U7RWQ0_ALLSI_38654 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A1V4KKK6_A0A1V4KKK6_PATFA_372326 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A218US37_A0A218US37_9PASE_299123 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A226NJH3_A0A226NJH3_CALSU_9009 are exactly identical! WARNING: Sequences sp_P21868_CSK21_CHICK_9031 and tr_A0A226PER4_A0A226PER4_COLVI_9014 are exactly identical! WARNING: Sequences sp_P21869_CSK22_CHICK_9031 and tr_A0A091VHU9_A0A091VHU9_NIPNI_128390 are exactly identical! WARNING: Sequences sp_P21869_CSK22_CHICK_9031 and tr_A0A226MTR7_A0A226MTR7_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A0D1EA57_A0A0D1EA57_USTMA_237631 and tr_V5GJT6_V5GJT6_KALBG_1365824 are exactly identical! WARNING: Sequences sp_O54833_CSK22_MOUSE_10090 and sp_P20427_CSK22_BOVIN_9913 are exactly identical! WARNING: Sequences sp_O54833_CSK22_MOUSE_10090 and tr_M3WZB7_M3WZB7_FELCA_9685 are exactly identical! WARNING: Sequences sp_O54833_CSK22_MOUSE_10090 and tr_A0A2U3VLT7_A0A2U3VLT7_ODORO_9708 are exactly identical! WARNING: Sequences sp_O54833_CSK22_MOUSE_10090 and tr_A0A2Y9DBK3_A0A2Y9DBK3_TRIMA_127582 are exactly identical! WARNING: Sequences sp_O54833_CSK22_MOUSE_10090 and tr_A0A2Y9KZ01_A0A2Y9KZ01_ENHLU_391180 are exactly identical! WARNING: Sequences sp_O54833_CSK22_MOUSE_10090 and tr_A0A2Y9LQ77_A0A2Y9LQ77_DELLE_9749 are exactly identical! WARNING: Sequences sp_O54833_CSK22_MOUSE_10090 and tr_A0A2Y9STA9_A0A2Y9STA9_PHYCD_9755 are exactly identical! WARNING: Sequences sp_O54833_CSK22_MOUSE_10090 and tr_A0A383YY34_A0A383YY34_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_M3Z2K4_M3Z2K4_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_G1RE63_G1RE63_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_G1PF23_G1PF23_MYOLU_59463 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_G3RVT9_G3RVT9_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A2J8VIA6_A0A2J8VIA6_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_G1TQ31_G1TQ31_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_E2RHZ1_E2RHZ1_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_K7D8P4_K7D8P4_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_W5QCL6_W5QCL6_SHEEP_9940 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and sp_P19139_CSK21_RAT_10116 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_I3MC13_I3MC13_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_H0WLB6_H0WLB6_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_H0V659_H0V659_CAVPO_10141 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and sp_P68400_CSK21_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A1D5RD87_A0A1D5RD87_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_G3SRS0_G3SRS0_LOXAF_9785 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_F7I6P7_F7I6P7_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_F2Z5I5_F2Z5I5_PIG_9823 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_G1M663_G1M663_AILME_9646 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and sp_P68399_CSK21_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_L5JYB0_L5JYB0_PTEAL_9402 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_M3W025_M3W025_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A096NV36_A0A096NV36_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A091DTP5_A0A091DTP5_FUKDA_885580 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A0D9RDK2_A0A0D9RDK2_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A1S2ZQS3_A0A1S2ZQS3_ERIEU_9365 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A1S3EQY8_A0A1S3EQY8_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A1U7THT6_A0A1U7THT6_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A2K5NY87_A0A2K5NY87_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A2K6B4C2_A0A2K6B4C2_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A2K5ZH87_A0A2K5ZH87_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A2R9AMW1_A0A2R9AMW1_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A2U4CLU6_A0A2U4CLU6_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A2U3VEH9_A0A2U3VEH9_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A2U3XDH1_A0A2U3XDH1_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A2Y9QHP6_A0A2Y9QHP6_TRIMA_127582 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A2Y9IUN2_A0A2Y9IUN2_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A2Y9PZA0_A0A2Y9PZA0_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A2Y9FJJ8_A0A2Y9FJJ8_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A384D347_A0A384D347_URSMA_29073 are exactly identical! WARNING: Sequences sp_Q60737_CSK21_MOUSE_10090 and tr_A0A384B285_A0A384B285_BALAS_310752 are exactly identical! WARNING: Sequences tr_B6HFA6_B6HFA6_PENRW_500485 and tr_W6QSN6_W6QSN6_PENRF_1365484 are exactly identical! WARNING: Sequences tr_B6HFA6_B6HFA6_PENRW_500485 and tr_A0A0M8P8T7_A0A0M8P8T7_9EURO_229535 are exactly identical! WARNING: Sequences tr_B6HFA6_B6HFA6_PENRW_500485 and tr_A0A0G4PRX7_A0A0G4PRX7_PENCA_1429867 are exactly identical! WARNING: Sequences tr_B6HFA6_B6HFA6_PENRW_500485 and tr_A0A101MPA7_A0A101MPA7_9EURO_48697 are exactly identical! WARNING: Sequences tr_B6HFA6_B6HFA6_PENRW_500485 and tr_A0A1V6NY21_A0A1V6NY21_9EURO_60169 are exactly identical! WARNING: Sequences tr_B6HFA6_B6HFA6_PENRW_500485 and tr_A0A1V6QQJ3_A0A1V6QQJ3_9EURO_60172 are exactly identical! WARNING: Sequences tr_B6HFA6_B6HFA6_PENRW_500485 and tr_A0A1V6YV80_A0A1V6YV80_PENNA_60175 are exactly identical! WARNING: Sequences tr_H2LQZ6_H2LQZ6_ORYLA_8090 and tr_A0A3B5Q5S7_A0A3B5Q5S7_XIPMA_8083 are exactly identical! WARNING: Sequences tr_H2LQZ6_H2LQZ6_ORYLA_8090 and tr_I3J3S0_I3J3S0_ORENI_8128 are exactly identical! WARNING: Sequences tr_H2LQZ6_H2LQZ6_ORYLA_8090 and tr_A0A087XG04_A0A087XG04_POEFO_48698 are exactly identical! WARNING: Sequences tr_H2LQZ6_H2LQZ6_ORYLA_8090 and tr_A0A2I4B8W4_A0A2I4B8W4_9TELE_52670 are exactly identical! WARNING: Sequences tr_H2LQZ6_H2LQZ6_ORYLA_8090 and tr_A0A2U9AYK8_A0A2U9AYK8_SCOMX_52904 are exactly identical! WARNING: Sequences tr_B0CP69_B0CP69_LACBS_486041 and tr_A0A0C9X0H6_A0A0C9X0H6_9AGAR_1095629 are exactly identical! WARNING: Sequences tr_A0A0E1S066_A0A0E1S066_COCIM_246410 and tr_E9CTB8_E9CTB8_COCPS_443226 are exactly identical! WARNING: Sequences tr_A0A0E1S066_A0A0E1S066_COCIM_246410 and tr_A0A0J6YR22_A0A0J6YR22_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QM16_B6QM16_TALMQ_441960 and tr_A0A093XL27_A0A093XL27_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2WCA7_B2WCA7_PYRTR_426418 and tr_A0A2W1DZZ7_A0A2W1DZZ7_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G2WTA6_G2WTA6_VERDV_498257 and tr_C9SH98_C9SH98_VERA1_526221 are exactly identical! WARNING: Sequences tr_G2WTA6_G2WTA6_VERDV_498257 and tr_A0A0G4MQX8_A0A0G4MQX8_9PEZI_100787 are exactly identical! WARNING: Sequences tr_C1G5N0_C1G5N0_PARBD_502780 and tr_C1H2B4_C1H2B4_PARBA_502779 are exactly identical! WARNING: Sequences sp_Q8TG13_CSK2A_NEUCR_367110 and tr_G4U7M4_G4U7M4_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8MXX7_B8MXX7_ASPFN_332952 and tr_Q2URW4_Q2URW4_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8MXX7_B8MXX7_ASPFN_332952 and tr_A0A0F0I5Y6_A0A0F0I5Y6_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_A0A179UM63_A0A179UM63_BLAGS_559298 and tr_C5GUI6_C5GUI6_AJEDR_559297 are exactly identical! WARNING: Sequences tr_Q5KF69_Q5KF69_CRYNJ_214684 and tr_E6R816_E6R816_CRYGW_367775 are exactly identical! WARNING: Sequences tr_K7CVS9_K7CVS9_PANTR_9598 and sp_P19784_CSK22_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7CVS9_K7CVS9_PANTR_9598 and tr_H9ENR6_H9ENR6_MACMU_9544 are exactly identical! WARNING: Sequences tr_K7CVS9_K7CVS9_PANTR_9598 and tr_A0A096NJ04_A0A096NJ04_PAPAN_9555 are exactly identical! WARNING: Sequences tr_K7CVS9_K7CVS9_PANTR_9598 and tr_A0A0D9QXL1_A0A0D9QXL1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_K7CVS9_K7CVS9_PANTR_9598 and tr_A0A2K5L3Z6_A0A2K5L3Z6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6ZR68_F6ZR68_HORSE_9796 and tr_W5NT21_W5NT21_SHEEP_9940 are exactly identical! WARNING: Sequences tr_F6ZR68_F6ZR68_HORSE_9796 and tr_G5AUG4_G5AUG4_HETGA_10181 are exactly identical! WARNING: Sequences tr_F6ZR68_F6ZR68_HORSE_9796 and tr_F1MJ55_F1MJ55_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F9FXH8_F9FXH8_FUSOF_660025 and tr_W7LA97_W7LA97_GIBM7_334819 are exactly identical! WARNING: Sequences tr_F9FXH8_F9FXH8_FUSOF_660025 and tr_A0A0D2XAT1_A0A0D2XAT1_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FXH8_F9FXH8_FUSOF_660025 and tr_S0DKC5_S0DKC5_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9FXH8_F9FXH8_FUSOF_660025 and tr_N4TQL2_N4TQL2_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FXH8_F9FXH8_FUSOF_660025 and tr_X0DPH4_X0DPH4_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FXH8_F9FXH8_FUSOF_660025 and tr_A0A2H3SVA0_A0A2H3SVA0_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FXH8_F9FXH8_FUSOF_660025 and tr_A0A2H3HV64_A0A2H3HV64_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FXH8_F9FXH8_FUSOF_660025 and tr_A0A2K0V9Y3_A0A2K0V9Y3_GIBNY_42673 are exactly identical! WARNING: Sequences tr_A0A3B5QML5_A0A3B5QML5_XIPMA_8083 and tr_A0A087XZ89_A0A087XZ89_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A087ZW71_A0A087ZW71_APIME_7460 and tr_A0A0N0BJQ2_A0A0N0BJQ2_9HYME_166423 are exactly identical! WARNING: Sequences tr_A0A087ZW71_A0A087ZW71_APIME_7460 and tr_A0A2A3EL85_A0A2A3EL85_APICC_94128 are exactly identical! WARNING: Sequences tr_I3J500_I3J500_ORENI_8128 and tr_G3PBW0_G3PBW0_GASAC_69293 are exactly identical! WARNING: Sequences tr_A0A3B5KLY4_A0A3B5KLY4_TAKRU_31033 and tr_H3DM83_H3DM83_TETNG_99883 are exactly identical! WARNING: Sequences tr_G9P9Z2_G9P9Z2_HYPAI_452589 and tr_A0A2T3Z778_A0A2T3Z778_9HYPO_1042311 are exactly identical! WARNING: Sequences tr_J3MI55_J3MI55_ORYBR_4533 and tr_A0A0E0ITQ2_A0A0E0ITQ2_ORYNI_4536 are exactly identical! WARNING: Sequences tr_J3MI55_J3MI55_ORYBR_4533 and tr_A2YHJ1_A2YHJ1_ORYSI_39946 are exactly identical! WARNING: Sequences tr_J3MI55_J3MI55_ORYBR_4533 and tr_I1Q7J7_I1Q7J7_ORYGL_4538 are exactly identical! WARNING: Sequences tr_J3MI55_J3MI55_ORYBR_4533 and tr_A0A0E0Q3C5_A0A0E0Q3C5_ORYRU_4529 are exactly identical! WARNING: Sequences tr_J3MI55_J3MI55_ORYBR_4533 and tr_A0A0D3GLK5_A0A0D3GLK5_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_J3MI55_J3MI55_ORYBR_4533 and tr_A0A0E0AF67_A0A0E0AF67_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_J3MI55_J3MI55_ORYBR_4533 and tr_A0A0D9WUU6_A0A0D9WUU6_9ORYZ_77586 are exactly identical! WARNING: Sequences tr_J3MI55_J3MI55_ORYBR_4533 and tr_Q8H386_Q8H386_ORYSJ_39947 are exactly identical! WARNING: Sequences sp_O64816_CSK2P_ARATH_3702 and tr_D7LEN3_D7LEN3_ARALL_81972 are exactly identical! WARNING: Sequences tr_A0A0E0GIR1_A0A0E0GIR1_ORYNI_4536 and tr_A0A0E0NRA3_A0A0E0NRA3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GU55_A0A0E0GU55_ORYNI_4536 and tr_B8AK92_B8AK92_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GU55_A0A0E0GU55_ORYNI_4536 and tr_I1PFR4_I1PFR4_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GU55_A0A0E0GU55_ORYNI_4536 and tr_A0A0E0D784_A0A0E0D784_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0GU55_A0A0E0GU55_ORYNI_4536 and tr_A0A0D3FPE5_A0A0D3FPE5_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0GU55_A0A0E0GU55_ORYNI_4536 and tr_A0A0E0KJC3_A0A0E0KJC3_ORYPU_4537 are exactly identical! WARNING: Sequences tr_A1DB93_A1DB93_NEOFI_331117 and tr_A0A0S7E546_A0A0S7E546_9EURO_293939 are exactly identical! WARNING: Sequences tr_A1DB93_A1DB93_NEOFI_331117 and tr_A0A2I1C030_A0A2I1C030_9EURO_1392255 are exactly identical! WARNING: Sequences tr_A2R8Q7_A2R8Q7_ASPNC_425011 and tr_G3Y6R3_G3Y6R3_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2R8Q7_A2R8Q7_ASPNC_425011 and tr_A0A100ILL6_A0A100ILL6_ASPNG_5061 are exactly identical! WARNING: Sequences tr_A2R8Q7_A2R8Q7_ASPNC_425011 and tr_A0A1L9N4F4_A0A1L9N4F4_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A2R8Q7_A2R8Q7_ASPNC_425011 and tr_A0A319AM27_A0A319AM27_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G9MIM3_G9MIM3_HYPVG_413071 and tr_A0A0F9XSJ5_A0A0F9XSJ5_TRIHA_5544 are exactly identical! WARNING: Sequences tr_G9MIM3_G9MIM3_HYPVG_413071 and tr_A0A2T4AD36_A0A2T4AD36_TRIHA_983964 are exactly identical! WARNING: Sequences tr_F4PC49_F4PC49_BATDJ_684364 and tr_A0A177WY49_A0A177WY49_BATDE_403673 are exactly identical! WARNING: Sequences tr_B4FFS6_B4FFS6_MAIZE_4577 and sp_P28523_CSK2A_MAIZE_4577 are exactly identical! WARNING: Sequences tr_H0Z2U6_H0Z2U6_TAEGU_59729 and tr_U3JWL2_U3JWL2_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0Z2U6_H0Z2U6_TAEGU_59729 and tr_A0A091F373_A0A091F373_CORBR_85066 are exactly identical! WARNING: Sequences tr_F4WU82_F4WU82_ACREC_103372 and tr_A0A151X092_A0A151X092_9HYME_64791 are exactly identical! WARNING: Sequences tr_F4WU82_F4WU82_ACREC_103372 and tr_A0A151J3G8_A0A151J3G8_9HYME_471704 are exactly identical! WARNING: Sequences tr_F4WU82_F4WU82_ACREC_103372 and tr_A0A151I5B1_A0A151I5B1_9HYME_520822 are exactly identical! WARNING: Sequences tr_F4WU82_F4WU82_ACREC_103372 and tr_A0A151JW70_A0A151JW70_9HYME_34720 are exactly identical! WARNING: Sequences tr_F4WU82_F4WU82_ACREC_103372 and tr_A0A195C1G2_A0A195C1G2_9HYME_456900 are exactly identical! WARNING: Sequences tr_F9XBZ2_F9XBZ2_ZYMTI_336722 and tr_A0A0F4GS26_A0A0F4GS26_9PEZI_1047168 are exactly identical! WARNING: Sequences tr_F9XBZ2_F9XBZ2_ZYMTI_336722 and tr_A0A1X7RU70_A0A1X7RU70_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_A8XFP5_A8XFP5_CAEBR_6238 and tr_A0A2G5VLH3_A0A2G5VLH3_9PELO_1611254 are exactly identical! WARNING: Sequences tr_F2SIT4_F2SIT4_TRIRC_559305 and tr_A0A178F2W9_A0A178F2W9_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G0RNL8_G0RNL8_HYPJQ_431241 and tr_A0A2T4C8S5_A0A2T4C8S5_TRILO_983965 are exactly identical! WARNING: Sequences tr_F2PGZ4_F2PGZ4_TRIEC_559882 and tr_A0A059J6X2_A0A059J6X2_9EURO_1215338 are exactly identical! WARNING: Sequences tr_M0WZZ0_M0WZZ0_HORVV_112509 and tr_M7YN39_M7YN39_TRIUA_4572 are exactly identical! WARNING: Sequences tr_M0WZZ0_M0WZZ0_HORVV_112509 and tr_A0A3B6KN37_A0A3B6KN37_WHEAT_4565 are exactly identical! WARNING: Sequences tr_M0WZZ0_M0WZZ0_HORVV_112509 and tr_A0A3B6MYA7_A0A3B6MYA7_WHEAT_4565 are exactly identical! WARNING: Sequences tr_M4ETQ0_M4ETQ0_BRARP_51351 and tr_A0A078HQ81_A0A078HQ81_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4F4P4_M4F4P4_BRARP_51351 and tr_A0A078H1G0_A0A078H1G0_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4F4P4_M4F4P4_BRARP_51351 and tr_A0A078IYN0_A0A078IYN0_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4F4P4_M4F4P4_BRARP_51351 and tr_A0A0D3DRT0_A0A0D3DRT0_BRAOL_109376 are exactly identical! WARNING: Sequences tr_M4FFR8_M4FFR8_BRARP_51351 and tr_A0A078IEW0_A0A078IEW0_BRANA_3708 are exactly identical! WARNING: Sequences tr_U3J9H3_U3J9H3_ANAPL_8839 and tr_A0A091JGJ4_A0A091JGJ4_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3J9H3_U3J9H3_ANAPL_8839 and tr_A0A093PWQ5_A0A093PWQ5_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3J9H3_U3J9H3_ANAPL_8839 and tr_A0A093HAH8_A0A093HAH8_STRCA_441894 are exactly identical! WARNING: Sequences tr_U3J9H3_U3J9H3_ANAPL_8839 and tr_A0A091WPK0_A0A091WPK0_OPIHO_30419 are exactly identical! WARNING: Sequences tr_U3J9H3_U3J9H3_ANAPL_8839 and tr_A0A091G2R1_A0A091G2R1_9AVES_55661 are exactly identical! WARNING: Sequences tr_U3J9H3_U3J9H3_ANAPL_8839 and tr_A0A099ZZ39_A0A099ZZ39_CHAVO_50402 are exactly identical! WARNING: Sequences tr_U3J9H3_U3J9H3_ANAPL_8839 and tr_A0A2I0M7Q9_A0A2I0M7Q9_COLLI_8932 are exactly identical! WARNING: Sequences tr_M2T1V2_M2T1V2_COCSN_665912 and tr_M2V2F6_M2V2F6_COCH5_701091 are exactly identical! WARNING: Sequences tr_M2T1V2_M2T1V2_COCSN_665912 and tr_W6XPV4_W6XPV4_COCCA_930089 are exactly identical! WARNING: Sequences tr_M2T1V2_M2T1V2_COCSN_665912 and tr_W6YY67_W6YY67_COCMI_930090 are exactly identical! WARNING: Sequences tr_A0A3B1JP92_A0A3B1JP92_ASTMX_7994 and tr_A0A2D0RAK8_A0A2D0RAK8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_W2PU74_W2PU74_PHYPN_761204 and tr_A0A0W8C7U3_A0A0W8C7U3_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PU74_W2PU74_PHYPN_761204 and tr_A0A0W8CLW4_A0A0W8CLW4_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PU74_W2PU74_PHYPN_761204 and tr_W2MVU3_W2MVU3_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W9XAH0_W9XAH0_9EURO_1182543 and tr_A0A0D1Z7B5_A0A0D1Z7B5_9EURO_569365 are exactly identical! WARNING: Sequences tr_W9XAH0_W9XAH0_9EURO_1182543 and tr_A0A178ZWC0_A0A178ZWC0_9EURO_1367422 are exactly identical! WARNING: Sequences tr_A0A017SGX6_A0A017SGX6_9EURO_1388766 and tr_A0A1L9VY24_A0A1L9VY24_ASPGL_1160497 are exactly identical! WARNING: Sequences tr_A0A067GH58_A0A067GH58_CITSI_2711 and tr_V4SFE7_V4SFE7_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A084QP54_A0A084QP54_STAC4_1283841 and tr_A0A084RJ22_A0A084RJ22_STACH_1283842 are exactly identical! WARNING: Sequences tr_A0A078J4K3_A0A078J4K3_BRANA_3708 and tr_A0A0D3A9L5_A0A0D3A9L5_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0A0LNA2_A0A0A0LNA2_CUCSA_3659 and tr_A0A1S3BAN9_A0A1S3BAN9_CUCME_3656 are exactly identical! WARNING: Sequences tr_V4UIZ4_V4UIZ4_9ROSI_85681 and tr_A0A2H5PCX3_A0A2H5PCX3_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2SPH7_A0A0D2SPH7_GOSRA_29730 and tr_A0A1U8K8K4_A0A1U8K8K4_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0F8V516_A0A0F8V516_9EURO_308745 and tr_A0A2T5M5R4_A0A2T5M5R4_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0M9EUA7_A0A0M9EUA7_FUSLA_179993 and tr_I1RAY2_I1RAY2_GIBZE_229533 are exactly identical! WARNING: Sequences tr_A0A0M9EUA7_A0A0M9EUA7_FUSLA_179993 and tr_A0A1B8B1Z9_A0A1B8B1Z9_FUSPO_36050 are exactly identical! WARNING: Sequences tr_A0A0M9EUA7_A0A0M9EUA7_FUSLA_179993 and tr_A0A2T4H8A7_A0A2T4H8A7_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A0M9EUA7_A0A0M9EUA7_FUSLA_179993 and tr_A0A2L2T1B0_A0A2L2T1B0_9HYPO_56646 are exactly identical! WARNING: Sequences tr_A0A0L9TPJ8_A0A0L9TPJ8_PHAAN_3914 and tr_A0A1S3UTP3_A0A1S3UTP3_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A0L9UQK4_A0A0L9UQK4_PHAAN_3914 and tr_A0A1S3VS89_A0A1S3VS89_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A194RGM1_A0A194RGM1_PAPMA_76193 and tr_A0A194PUN6_A0A194PUN6_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A0D2FFN7_A0A0D2FFN7_9EURO_5601 and tr_A0A1C1CL40_A0A1C1CL40_9EURO_86049 are exactly identical! WARNING: Sequences tr_A0A0V0SDZ5_A0A0V0SDZ5_9BILA_6336 and tr_A0A0V1D5K2_A0A0V1D5K2_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0SDZ5_A0A0V0SDZ5_9BILA_6336 and tr_A0A0V0WMT7_A0A0V0WMT7_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0SDZ5_A0A0V0SDZ5_9BILA_6336 and tr_A0A0V0VWI8_A0A0V0VWI8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0SDZ5_A0A0V0SDZ5_9BILA_6336 and tr_A0A0V1LLG4_A0A0V1LLG4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0SDZ5_A0A0V0SDZ5_9BILA_6336 and tr_A0A0V0ZT31_A0A0V0ZT31_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0SDZ5_A0A0V0SDZ5_9BILA_6336 and tr_A0A0V0YEY1_A0A0V0YEY1_TRIPS_6337 are exactly identical! WARNING: Sequences tr_A0A0V0SDZ5_A0A0V0SDZ5_9BILA_6336 and tr_A0A0V1MK36_A0A0V1MK36_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V0SDZ5_A0A0V0SDZ5_9BILA_6336 and tr_A0A0V1P8P5_A0A0V1P8P5_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0SDZ5_A0A0V0SDZ5_9BILA_6336 and tr_A0A0V1I5T1_A0A0V1I5T1_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A0V0SDZ5_A0A0V0SDZ5_9BILA_6336 and tr_A0A0V0U6Q7_A0A0V0U6Q7_9BILA_144512 are exactly identical! WARNING: Sequences tr_Q70Z24_Q70Z24_TOBAC_4097 and tr_A0A314LCJ5_A0A314LCJ5_NICAT_49451 are exactly identical! WARNING: Sequences tr_Q70Z25_Q70Z25_TOBAC_4097 and tr_A0A1U7W1B7_A0A1U7W1B7_NICSY_4096 are exactly identical! WARNING: Sequences tr_Q8LP30_Q8LP30_TOBAC_4097 and tr_A0A1U7YFP7_A0A1U7YFP7_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3J7U8_A0A1S3J7U8_LINUN_7574 and tr_A0A1S3J7V5_A0A1S3J7V5_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3KML5_A0A1S3KML5_SALSA_8030 and tr_A0A060X2A6_A0A060X2A6_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3M4L7_A0A1S3M4L7_SALSA_8030 and tr_A0A060XPP9_A0A060XPP9_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3P7C5_A0A1S3P7C5_SALSA_8030 and tr_A0A060X538_A0A060X538_ONCMY_8022 are exactly identical! WARNING: Sequences tr_B9EMZ5_B9EMZ5_SALSA_8030 and tr_A0A060Y9U0_A0A060Y9U0_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1B8EFM1_A0A1B8EFM1_9PEZI_1524831 and tr_A0A1B8GA86_A0A1B8GA86_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A1B8EFM1_A0A1B8EFM1_9PEZI_1524831 and tr_A0A1B8C918_A0A1B8C918_9PEZI_1622147 are exactly identical! WARNING: Sequences tr_A0A1B8EFM1_A0A1B8EFM1_9PEZI_1524831 and tr_A0A1B8F0S9_A0A1B8F0S9_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_A0A1B7NJJ9_A0A1B7NJJ9_9HOMO_1314800 and tr_A0A1J8QDT0_A0A1J8QDT0_9HOMO_180088 are exactly identical! WARNING: Sequences tr_A0A1I7UG64_A0A1I7UG64_9PELO_1561998 and tr_A0A1I7UG65_A0A1I7UG65_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1F5LMB5_A0A1F5LMB5_9EURO_1835702 and tr_A0A1V6QHH4_A0A1V6QHH4_9EURO_416450 are exactly identical! WARNING: Sequences tr_A0A1L9WPS7_A0A1L9WPS7_ASPAC_690307 and tr_A0A319DR94_A0A319DR94_9EURO_1448315 are exactly identical! WARNING: Sequences tr_A0A1L9WPS7_A0A1L9WPS7_ASPAC_690307 and tr_A0A2V5JFT6_A0A2V5JFT6_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A1L9WPS7_A0A1L9WPS7_ASPAC_690307 and tr_A0A2V5H437_A0A2V5H437_9EURO_1450538 are exactly identical! WARNING: Sequences tr_A0A1L8EM01_A0A1L8EM01_XENLA_8355 and tr_A0A1L8ETF4_A0A1L8ETF4_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A1R3RPF8_A0A1R3RPF8_ASPC5_602072 and tr_A0A319E9P2_A0A319E9P2_9EURO_1448318 are exactly identical! WARNING: Sequences tr_A0A1V8UYU3_A0A1V8UYU3_9PEZI_1974281 and tr_A0A1V8SF57_A0A1V8SF57_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A1V8UYU3_A0A1V8UYU3_9PEZI_1974281 and tr_A0A1V8SN48_A0A1V8SN48_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A2D0PXH0_A0A2D0PXH0_ICTPU_7998 and tr_A0A2D0PXI1_A0A2D0PXI1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A1U8GN25_A0A1U8GN25_CAPAN_4072 and tr_A0A2G3CLH0_A0A2G3CLH0_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2G5HLU0_A0A2G5HLU0_CERBT_122368 and tr_A0A2I0S448_A0A2I0S448_9PEZI_348901 are exactly identical! WARNING: Sequences tr_A0A2G5HLU0_A0A2G5HLU0_CERBT_122368 and tr_A0A2S6CFN3_A0A2S6CFN3_9PEZI_357750 are exactly identical! WARNING: Sequences tr_A0A2K5XTX7_A0A2K5XTX7_MANLE_9568 and tr_A0A2R9BZ77_A0A2R9BZ77_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A318ZUK8_A0A318ZUK8_9EURO_1450539 and tr_A0A395I1R7_A0A395I1R7_9EURO_1450537 are exactly identical! WARNING: Duplicate sequences found: 251 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/P68400/3_mltree/P68400.raxml.reduced.phy Alignment comprises 1 partitions and 318 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 319 / 318 Gaps: 0.62 % Invariant sites: 5.96 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P68400/3_mltree/P68400.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 / 318 / 25440 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -220377.880111] Initial branch length optimization [00:00:09 -190238.444026] Model parameter optimization (eps = 10.000000) [00:01:02 -189682.184673] AUTODETECT spr round 1 (radius: 5) [00:04:09 -106711.316299] AUTODETECT spr round 2 (radius: 10) [00:06:55 -80279.315248] AUTODETECT spr round 3 (radius: 15) [00:10:09 -67527.202928] AUTODETECT spr round 4 (radius: 20) [00:13:57 -63733.437735] AUTODETECT spr round 5 (radius: 25) [00:17:55 -63390.448856] SPR radius for FAST iterations: 25 (autodetect) [00:17:55 -63390.448856] Model parameter optimization (eps = 3.000000) [00:18:13 -63381.794936] FAST spr round 1 (radius: 25) [00:21:23 -53049.527207] FAST spr round 2 (radius: 25) [00:24:02 -48595.745192] FAST spr round 3 (radius: 25) [00:26:20 -45471.266213] FAST spr round 4 (radius: 25) [00:28:35 -45067.669520] FAST spr round 5 (radius: 25) [00:30:29 -45043.790082] FAST spr round 6 (radius: 25) [00:32:11 -45042.747072] FAST spr round 7 (radius: 25) [00:33:53 -45041.043332] FAST spr round 8 (radius: 25) [00:35:31 -45041.023302] Model parameter optimization (eps = 1.000000) [00:35:47 -45013.949911] SLOW spr round 1 (radius: 5) [00:38:06 -44998.015496] SLOW spr round 2 (radius: 5) [00:40:26 -44993.392855] SLOW spr round 3 (radius: 5) [00:42:45 -44988.552673] SLOW spr round 4 (radius: 5) [00:45:05 -44988.551200] SLOW spr round 5 (radius: 10) [00:47:33 -44985.786224] SLOW spr round 6 (radius: 5) [00:50:49 -44983.394305] SLOW spr round 7 (radius: 5) [00:53:34 -44983.106360] SLOW spr round 8 (radius: 5) [00:55:59 -44983.106307] SLOW spr round 9 (radius: 10) [00:58:24 -44983.106250] SLOW spr round 10 (radius: 15) [01:02:20 -44983.106185] SLOW spr round 11 (radius: 20) [01:05:41] [worker #4] ML tree search #5, logLikelihood: -44999.628904 [01:08:06 -44983.106120] SLOW spr round 12 (radius: 25) [01:14:51 -44983.106099] Model parameter optimization (eps = 0.100000) [01:15:01] [worker #0] ML tree search #1, logLikelihood: -44982.895888 [01:15:01 -220879.674154] Initial branch length optimization [01:15:09 -190945.044956] Model parameter optimization (eps = 10.000000) [01:15:49 -190393.395617] AUTODETECT spr round 1 (radius: 5) [01:15:53] [worker #1] ML tree search #2, logLikelihood: -44991.573218 [01:16:52] [worker #3] ML tree search #4, logLikelihood: -44996.331668 [01:18:50 -105639.555409] AUTODETECT spr round 2 (radius: 10) [01:21:40 -72138.025571] AUTODETECT spr round 3 (radius: 15) [01:24:50 -65886.466219] AUTODETECT spr round 4 (radius: 20) [01:29:09 -56988.813494] AUTODETECT spr round 5 (radius: 25) [01:29:56] [worker #2] ML tree search #3, logLikelihood: -44989.713710 [01:34:08 -54242.163178] SPR radius for FAST iterations: 25 (autodetect) [01:34:08 -54242.163178] Model parameter optimization (eps = 3.000000) [01:34:28 -54225.218781] FAST spr round 1 (radius: 25) [01:37:39 -45428.051652] FAST spr round 2 (radius: 25) [01:39:59 -45092.215231] FAST spr round 3 (radius: 25) [01:42:03 -45054.964903] FAST spr round 4 (radius: 25) [01:43:52 -45035.210777] FAST spr round 5 (radius: 25) [01:45:34 -45035.168356] Model parameter optimization (eps = 1.000000) [01:45:50 -45029.455789] SLOW spr round 1 (radius: 5) [01:48:12 -45016.761924] SLOW spr round 2 (radius: 5) [01:50:34 -45010.199859] SLOW spr round 3 (radius: 5) [01:52:56 -45009.973922] SLOW spr round 4 (radius: 5) [01:55:12 -45009.973762] SLOW spr round 5 (radius: 10) [01:57:41 -45009.942211] SLOW spr round 6 (radius: 15) [02:01:50 -45008.329757] SLOW spr round 7 (radius: 5) [02:05:11 -45008.235890] SLOW spr round 8 (radius: 10) [02:08:02 -45008.235837] SLOW spr round 9 (radius: 15) [02:11:36] [worker #1] ML tree search #7, logLikelihood: -45002.165013 [02:11:38 -45008.235804] SLOW spr round 10 (radius: 20) [02:16:48 -45008.235776] SLOW spr round 11 (radius: 25) [02:23:11 -45008.235752] Model parameter optimization (eps = 0.100000) [02:23:21] [worker #0] ML tree search #6, logLikelihood: -45008.061291 [02:23:21 -222193.427185] Initial branch length optimization [02:23:21] [worker #4] ML tree search #10, logLikelihood: -44997.345321 [02:23:28 -191942.418151] Model parameter optimization (eps = 10.000000) [02:24:11 -191365.549029] AUTODETECT spr round 1 (radius: 5) [02:27:09 -106234.821771] AUTODETECT spr round 2 (radius: 10) [02:29:56 -76134.554382] AUTODETECT spr round 3 (radius: 15) [02:33:14 -63459.362047] AUTODETECT spr round 4 (radius: 20) [02:33:26] [worker #3] ML tree search #9, logLikelihood: -44987.869915 [02:37:04 -58285.598049] AUTODETECT spr round 5 (radius: 25) [02:41:44 -55020.870269] SPR radius for FAST iterations: 25 (autodetect) [02:41:44 -55020.870269] Model parameter optimization (eps = 3.000000) [02:42:00 -55000.104525] FAST spr round 1 (radius: 25) [02:45:07 -45803.839237] FAST spr round 2 (radius: 25) [02:47:21 -45082.591961] FAST spr round 3 (radius: 25) [02:48:08] [worker #2] ML tree search #8, logLikelihood: -44995.390657 [02:49:23 -45060.566305] FAST spr round 4 (radius: 25) [02:51:20 -45046.832496] FAST spr round 5 (radius: 25) [02:53:06 -45045.767205] FAST spr round 6 (radius: 25) [02:54:47 -45045.767006] Model parameter optimization (eps = 1.000000) [02:55:02 -45030.003617] SLOW spr round 1 (radius: 5) [02:57:17 -45017.579116] SLOW spr round 2 (radius: 5) [02:59:32 -45016.465507] SLOW spr round 3 (radius: 5) [03:01:52 -45016.462862] SLOW spr round 4 (radius: 10) [03:04:23 -45011.033215] SLOW spr round 5 (radius: 5) [03:07:36 -45011.032839] SLOW spr round 6 (radius: 10) [03:10:28 -45009.071876] SLOW spr round 7 (radius: 5) [03:13:31 -45009.071527] SLOW spr round 8 (radius: 10) [03:16:14 -45009.071466] SLOW spr round 9 (radius: 15) [03:19:55 -45007.911540] SLOW spr round 10 (radius: 5) [03:23:14 -45007.906869] SLOW spr round 11 (radius: 10) [03:26:07 -45007.906845] SLOW spr round 12 (radius: 15) [03:29:47 -45007.906805] SLOW spr round 13 (radius: 20) [03:35:29 -45007.906790] SLOW spr round 14 (radius: 25) [03:36:06] [worker #4] ML tree search #15, logLikelihood: -45002.550309 [03:42:42 -45007.906776] Model parameter optimization (eps = 0.100000) [03:42:52] [worker #0] ML tree search #11, logLikelihood: -45007.432699 [03:42:52 -223907.237535] Initial branch length optimization [03:43:01 -193692.061329] Model parameter optimization (eps = 10.000000) [03:43:41 -193043.831452] AUTODETECT spr round 1 (radius: 5) [03:46:38 -107803.133551] AUTODETECT spr round 2 (radius: 10) [03:49:27 -72328.808654] AUTODETECT spr round 3 (radius: 15) [03:50:11] [worker #1] ML tree search #12, logLikelihood: -45011.401650 [03:52:34 -62440.883026] AUTODETECT spr round 4 (radius: 20) [03:56:10 -55237.504257] AUTODETECT spr round 5 (radius: 25) [03:56:13] [worker #2] ML tree search #13, logLikelihood: -45020.611277 [03:58:49] [worker #3] ML tree search #14, logLikelihood: -44995.447161 [04:00:30 -53715.506169] SPR radius for FAST iterations: 25 (autodetect) [04:00:30 -53715.506169] Model parameter optimization (eps = 3.000000) [04:00:50 -53704.038699] FAST spr round 1 (radius: 25) [04:03:56 -45299.533903] FAST spr round 2 (radius: 25) [04:06:23 -45048.750525] FAST spr round 3 (radius: 25) [04:08:23 -45035.801382] FAST spr round 4 (radius: 25) [04:10:13 -45032.284535] FAST spr round 5 (radius: 25) [04:11:58 -45031.145671] FAST spr round 6 (radius: 25) [04:13:39 -45031.145610] Model parameter optimization (eps = 1.000000) [04:13:54 -45020.022064] SLOW spr round 1 (radius: 5) [04:16:15 -45009.413120] SLOW spr round 2 (radius: 5) [04:18:37 -45006.153985] SLOW spr round 3 (radius: 5) [04:21:00 -45004.445825] SLOW spr round 4 (radius: 5) [04:23:22 -45004.445420] SLOW spr round 5 (radius: 10) [04:25:53 -45004.445248] SLOW spr round 6 (radius: 15) [04:29:46 -45004.445108] SLOW spr round 7 (radius: 20) [04:35:01 -45003.828599] SLOW spr round 8 (radius: 5) [04:38:28 -45003.828392] SLOW spr round 9 (radius: 10) [04:41:27 -45003.828325] SLOW spr round 10 (radius: 15) [04:44:59 -45003.828306] SLOW spr round 11 (radius: 20) [04:50:19 -45003.828287] SLOW spr round 12 (radius: 25) [04:56:33 -45003.828269] Model parameter optimization (eps = 0.100000) [04:56:45] [worker #0] ML tree search #16, logLikelihood: -45003.321988 [04:57:46] [worker #4] ML tree search #20, logLikelihood: -44992.491955 [04:58:56] [worker #1] ML tree search #17, logLikelihood: -44980.653751 [05:03:12] [worker #3] ML tree search #19, logLikelihood: -45020.872530 [05:36:33] [worker #2] ML tree search #18, logLikelihood: -44986.787737 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.325683,0.325209) (0.386476,0.724303) (0.155668,1.235476) (0.132173,3.191533) 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: -44980.653751 AIC score: 93971.307502 / AICc score: 8138031.307502 / BIC score: 101520.515663 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=319). 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/P68400/3_mltree/P68400.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P68400/3_mltree/P68400.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P68400/3_mltree/P68400.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P68400/3_mltree/P68400.raxml.log Analysis started: 05-Jul-2021 03:09:33 / finished: 05-Jul-2021 08:46:07 Elapsed time: 20193.878 seconds Consumed energy: 1210.815 Wh (= 6 km in an electric car, or 30 km with an e-scooter!)