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 08:08:55 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JU85/2_msa/Q5JU85_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JU85/3_mltree/Q5JU85 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JU85/2_msa/Q5JU85_trimmed_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 276 sites WARNING: Sequences tr_B4QJM8_B4QJM8_DROSI_7240 and tr_Q9VP80_Q9VP80_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QJM8_B4QJM8_DROSI_7240 and tr_B4IAJ4_B4IAJ4_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4QJM8_B4QJM8_DROSI_7240 and tr_A0A1W4V8U4_A0A1W4V8U4_DROFC_30025 are exactly identical! WARNING: Sequences tr_A0A1D5P3R1_A0A1D5P3R1_CHICK_9031 and tr_A0A093S8P2_A0A093S8P2_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A1D5P3R1_A0A1D5P3R1_CHICK_9031 and tr_A0A091VQA5_A0A091VQA5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1D5P3R1_A0A1D5P3R1_CHICK_9031 and tr_A0A087QX99_A0A087QX99_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1D5P3R1_A0A1D5P3R1_CHICK_9031 and tr_A0A093HXA3_A0A093HXA3_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A1D5P3R1_A0A1D5P3R1_CHICK_9031 and tr_A0A093GF11_A0A093GF11_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A1D5P3R1_A0A1D5P3R1_CHICK_9031 and tr_A0A091HZZ3_A0A091HZZ3_CALAN_9244 are exactly identical! WARNING: Sequences tr_F1NN93_F1NN93_CHICK_9031 and tr_A0A091EB76_A0A091EB76_CORBR_85066 are exactly identical! WARNING: Sequences tr_F1NN93_F1NN93_CHICK_9031 and tr_A0A2I0MKX8_A0A2I0MKX8_COLLI_8932 are exactly identical! WARNING: Sequences tr_F1NN93_F1NN93_CHICK_9031 and tr_A0A093IAK6_A0A093IAK6_DRYPU_118200 are exactly identical! WARNING: Sequences sp_P63034_CYH2_MOUSE_10090 and sp_P63035_CYH2_RAT_10116 are exactly identical! WARNING: Sequences sp_P63034_CYH2_MOUSE_10090 and tr_A0A1U7RD87_A0A1U7RD87_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_M3YE90_M3YE90_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_G3QXI3_G3QXI3_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_G1U774_G1U774_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_E2QZZ5_E2QZZ5_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_F6XU14_F6XU14_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A0G2JZX5_A0A0G2JZX5_RAT_10116 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A287DF26_A0A287DF26_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_H0WGP9_H0WGP9_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and sp_Q5JU85_IQEC2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A1D5QE91_A0A1D5QE91_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_G5BAY8_G5BAY8_HETGA_10181 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_F7I873_F7I873_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_F1RUI3_F1RUI3_PIG_9823 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A337SWN5_A0A337SWN5_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A096MR96_A0A096MR96_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A0D9RJG7_A0A0D9RJG7_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A1S3WLQ4_A0A1S3WLQ4_ERIEU_9365 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A1S3GSW9_A0A1S3GSW9_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A3Q0DPP6_A0A3Q0DPP6_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A3Q0CCN6_A0A3Q0CCN6_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A2K5NYF2_A0A2K5NYF2_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A2K6E2C2_A0A2K6E2C2_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A2K5XWY6_A0A2K5XWY6_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A2R9CBG8_A0A2R9CBG8_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A2U4C160_A0A2U4C160_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A2U3ZNG8_A0A2U3ZNG8_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A2U3Z0D3_A0A2U3Z0D3_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A2Y9E8D2_A0A2Y9E8D2_TRIMA_127582 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A2Y9IH11_A0A2Y9IH11_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A2Y9MY33_A0A2Y9MY33_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A2Y9F6P3_A0A2Y9F6P3_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q5DU25_IQEC2_MOUSE_10090 and tr_A0A384AA58_A0A384AA58_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q8R0S2_IQEC1_MOUSE_10090 and tr_G3GS04_G3GS04_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q8R0S2_IQEC1_MOUSE_10090 and tr_A0A0G2JUG7_A0A0G2JUG7_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8R0S2_IQEC1_MOUSE_10090 and tr_A0A1U8C214_A0A1U8C214_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q9QX11_CYH1_MOUSE_10090 and sp_P97694_CYH1_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XY13_M3XY13_MUSPF_9669 and tr_F1P6K1_F1P6K1_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3XY13_M3XY13_MUSPF_9669 and tr_A0A2U3YNX3_A0A2U3YNX3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XY13_M3XY13_MUSPF_9669 and tr_A0A2Y9LE19_A0A2Y9LE19_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z0R3_M3Z0R3_MUSPF_9669 and tr_G1SF84_G1SF84_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3Z0R3_M3Z0R3_MUSPF_9669 and tr_F1PUC7_F1PUC7_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z0R3_M3Z0R3_MUSPF_9669 and tr_F7FG08_F7FG08_MONDO_13616 are exactly identical! WARNING: Sequences tr_M3Z0R3_M3Z0R3_MUSPF_9669 and tr_F6YNZ3_F6YNZ3_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3Z0R3_M3Z0R3_MUSPF_9669 and tr_K7G9I1_K7G9I1_PELSI_13735 are exactly identical! WARNING: Sequences tr_M3Z0R3_M3Z0R3_MUSPF_9669 and tr_G3WZN6_G3WZN6_SARHA_9305 are exactly identical! WARNING: Sequences tr_M3Z0R3_M3Z0R3_MUSPF_9669 and tr_A0A151MZ71_A0A151MZ71_ALLMI_8496 are exactly identical! WARNING: Sequences tr_M3Z0R3_M3Z0R3_MUSPF_9669 and tr_A0A3Q0GLM0_A0A3Q0GLM0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_M3Z0R3_M3Z0R3_MUSPF_9669 and tr_A0A2U3ZB74_A0A2U3ZB74_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z0R3_M3Z0R3_MUSPF_9669 and tr_A0A2U3YUF7_A0A2U3YUF7_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Z0R3_M3Z0R3_MUSPF_9669 and tr_A0A2Y9RV05_A0A2Y9RV05_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A0A2I3GQR7_A0A2I3GQR7_NOMLE_61853 and tr_H2NZG5_H2NZG5_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3GQR7_A0A2I3GQR7_NOMLE_61853 and sp_Q99418_CYH2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GQR7_A0A2I3GQR7_NOMLE_61853 and tr_F7GGR0_F7GGR0_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GQR7_A0A2I3GQR7_NOMLE_61853 and tr_A0A0D9S2W3_A0A0D9S2W3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3GQR7_A0A2I3GQR7_NOMLE_61853 and tr_A0A1S3AKC2_A0A1S3AKC2_ERIEU_9365 are exactly identical! WARNING: Sequences tr_A0A2I3GQR7_A0A2I3GQR7_NOMLE_61853 and tr_A0A1S3G3T7_A0A1S3G3T7_DIPOR_10020 are exactly identical! WARNING: Sequences tr_A0A2I3GQR7_A0A2I3GQR7_NOMLE_61853 and tr_A0A3Q0DW12_A0A3Q0DW12_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A2I3GQR7_A0A2I3GQR7_NOMLE_61853 and tr_A0A2K5L818_A0A2K5L818_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GQR7_A0A2I3GQR7_NOMLE_61853 and tr_A0A2K6DW18_A0A2K6DW18_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GQR7_A0A2I3GQR7_NOMLE_61853 and tr_A0A2K5YTE2_A0A2K5YTE2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3GQR7_A0A2I3GQR7_NOMLE_61853 and tr_A0A2Y9DV91_A0A2Y9DV91_TRIMA_127582 are exactly identical! WARNING: Sequences tr_D8RRX5_D8RRX5_SELML_88036 and tr_D8SJM0_D8SJM0_SELML_88036 are exactly identical! WARNING: Sequences tr_G3QFC6_G3QFC6_GORGO_9595 and tr_A0A2I3RN99_A0A2I3RN99_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QFC6_G3QFC6_GORGO_9595 and tr_F7B954_F7B954_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QFC6_G3QFC6_GORGO_9595 and tr_G7NYG5_G7NYG5_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QFC6_G3QFC6_GORGO_9595 and tr_A0A0D9RAV2_A0A0D9RAV2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QFC6_G3QFC6_GORGO_9595 and tr_A0A2K5MVQ4_A0A2K5MVQ4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QFC6_G3QFC6_GORGO_9595 and tr_A0A2K6DSD5_A0A2K6DSD5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QFC6_G3QFC6_GORGO_9595 and tr_A0A2K5Z5H5_A0A2K5Z5H5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QFC6_G3QFC6_GORGO_9595 and tr_A0A2R9BER0_A0A2R9BER0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3S130_G3S130_GORGO_9595 and sp_Q9UPP2_IQEC3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S1P5_G3S1P5_GORGO_9595 and tr_H2NUW9_H2NUW9_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3S1P5_G3S1P5_GORGO_9595 and tr_F1PKP6_F1PKP6_CANLF_9615 are exactly identical! WARNING: Sequences tr_G3S1P5_G3S1P5_GORGO_9595 and tr_H0WV67_H0WV67_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G3S1P5_G3S1P5_GORGO_9595 and sp_Q15438_CYH1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S1P5_G3S1P5_GORGO_9595 and tr_A0A1D5QFG0_A0A1D5QFG0_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3S1P5_G3S1P5_GORGO_9595 and tr_A0A2I3MVV0_A0A2I3MVV0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3S1P5_G3S1P5_GORGO_9595 and tr_A0A0D9S481_A0A0D9S481_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3S1P5_G3S1P5_GORGO_9595 and tr_A0A1S3GYW7_A0A1S3GYW7_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G3S1P5_G3S1P5_GORGO_9595 and tr_A0A2K6EBL6_A0A2K6EBL6_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3S1P5_G3S1P5_GORGO_9595 and tr_A0A384CB04_A0A384CB04_URSMA_29073 are exactly identical! WARNING: Sequences tr_H2P9A8_H2P9A8_PONAB_9601 and tr_F6ZM78_F6ZM78_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1NKY8_G1NKY8_MELGA_9103 and tr_H0ZQZ2_H0ZQZ2_TAEGU_59729 are exactly identical! WARNING: Sequences tr_G1NKY8_G1NKY8_MELGA_9103 and tr_U3J5U2_U3J5U2_ANAPL_8839 are exactly identical! WARNING: Sequences tr_G1NKY8_G1NKY8_MELGA_9103 and tr_A0A151NID8_A0A151NID8_ALLMI_8496 are exactly identical! WARNING: Sequences tr_G1NKY8_G1NKY8_MELGA_9103 and tr_A0A091JDX2_A0A091JDX2_EGRGA_188379 are exactly identical! WARNING: Sequences tr_G1NKY8_G1NKY8_MELGA_9103 and tr_A0A091VW87_A0A091VW87_NIPNI_128390 are exactly identical! WARNING: Sequences tr_G1NKY8_G1NKY8_MELGA_9103 and tr_A0A087RJE5_A0A087RJE5_APTFO_9233 are exactly identical! WARNING: Sequences tr_G1NKY8_G1NKY8_MELGA_9103 and tr_A0A091W978_A0A091W978_OPIHO_30419 are exactly identical! WARNING: Sequences tr_G1NKY8_G1NKY8_MELGA_9103 and tr_A0A099YZH2_A0A099YZH2_TINGU_94827 are exactly identical! WARNING: Sequences tr_G1NKY8_G1NKY8_MELGA_9103 and tr_A0A091FT92_A0A091FT92_9AVES_55661 are exactly identical! WARNING: Sequences tr_G1NKY8_G1NKY8_MELGA_9103 and tr_A0A3Q0GZE3_A0A3Q0GZE3_ALLSI_38654 are exactly identical! WARNING: Sequences tr_G1NKY8_G1NKY8_MELGA_9103 and tr_A0A1V4K894_A0A1V4K894_PATFA_372326 are exactly identical! WARNING: Sequences tr_G1NKY8_G1NKY8_MELGA_9103 and tr_A0A218V920_A0A218V920_9PASE_299123 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_H2QW96_H2QW96_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_I3M9L7_I3M9L7_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_H0WTT2_H0WTT2_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and sp_Q9Y6D6_BIG1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_H0ZMA8_H0ZMA8_TAEGU_59729 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_U3BBV1_U3BBV1_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_G7PBZ4_G7PBZ4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_U3JS52_U3JS52_FICAL_59894 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A096MQ19_A0A096MQ19_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A0D9RND8_A0A0D9RND8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A151MN83_A0A151MN83_ALLMI_8496 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A091E8Q9_A0A091E8Q9_CORBR_85066 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A091IXT9_A0A091IXT9_EGRGA_188379 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A091VP85_A0A091VP85_NIPNI_128390 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A087QI37_A0A087QI37_APTFO_9233 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A093HEZ6_A0A093HEZ6_STRCA_441894 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A091WKI6_A0A091WKI6_OPIHO_30419 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A099Z9Y0_A0A099Z9Y0_TINGU_94827 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A091FKX7_A0A091FKX7_9AVES_55661 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A0A0B2M4_A0A0A0B2M4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A091IEG1_A0A091IEG1_CALAN_9244 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A1S3GMK1_A0A1S3GMK1_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A3Q0H1U3_A0A3Q0H1U3_ALLSI_38654 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A1V4KI76_A0A1V4KI76_PATFA_372326 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A218VBU1_A0A218VBU1_9PASE_299123 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A2K6E9P4_A0A2K6E9P4_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A2K6AG24_A0A2K6AG24_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1TAG2_G1TAG2_RABIT_9986 and tr_A0A2U3W2S4_A0A2U3W2S4_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I3SW02_A0A2I3SW02_PANTR_9598 and tr_A0A2R9BE08_A0A2R9BE08_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6RQA4_F6RQA4_ORNAN_9258 and tr_F6ZA19_F6ZA19_MONDO_13616 are exactly identical! WARNING: Sequences tr_F6RQA4_F6RQA4_ORNAN_9258 and tr_G3WHZ2_G3WHZ2_SARHA_9305 are exactly identical! WARNING: Sequences tr_W5P032_W5P032_SHEEP_9940 and tr_A0A2U4BMD8_A0A2U4BMD8_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5P032_W5P032_SHEEP_9940 and tr_A0A2Y9T6N2_A0A2Y9T6N2_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A3B5PVN1_A0A3B5PVN1_XIPMA_8083 and tr_A0A087YD38_A0A087YD38_POEFO_48698 are exactly identical! WARNING: Sequences tr_M3ZNX4_M3ZNX4_XIPMA_8083 and tr_A0A087YM63_A0A087YM63_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4A599_M4A599_XIPMA_8083 and tr_I3K9S1_I3K9S1_ORENI_8128 are exactly identical! WARNING: Sequences tr_M4A599_M4A599_XIPMA_8083 and tr_A0A087XDN7_A0A087XDN7_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4AD44_M4AD44_XIPMA_8083 and tr_A0A087XRS5_A0A087XRS5_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158P009_A0A158P009_ATTCE_12957 and tr_F4X3L9_F4X3L9_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158P009_A0A158P009_ATTCE_12957 and tr_A0A151XJR2_A0A151XJR2_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158P009_A0A158P009_ATTCE_12957 and tr_A0A195E0S9_A0A195E0S9_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158P009_A0A158P009_ATTCE_12957 and tr_A0A195BN26_A0A195BN26_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158P009_A0A158P009_ATTCE_12957 and tr_A0A195F306_A0A195F306_9HYME_34720 are exactly identical! WARNING: Sequences tr_H2RZJ3_H2RZJ3_TAKRU_31033 and tr_H3CPL4_H3CPL4_TETNG_99883 are exactly identical! WARNING: Sequences tr_A0A286XK88_A0A286XK88_CAVPO_10141 and tr_G5B887_G5B887_HETGA_10181 are exactly identical! WARNING: Sequences tr_A0A286XK88_A0A286XK88_CAVPO_10141 and tr_A0A091D715_A0A091D715_FUKDA_885580 are exactly identical! WARNING: Sequences tr_A0A0E0GJP3_A0A0E0GJP3_ORYNI_4536 and tr_B8AK12_B8AK12_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GJP3_A0A0E0GJP3_ORYNI_4536 and tr_I1P9F7_I1P9F7_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GJP3_A0A0E0GJP3_ORYNI_4536 and tr_A0A0E0NSE3_A0A0E0NSE3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GJP3_A0A0E0GJP3_ORYNI_4536 and tr_A0A0D3FG66_A0A0D3FG66_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0GJP3_A0A0E0GJP3_ORYNI_4536 and tr_A0A0D9Z4M3_A0A0D9Z4M3_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0HTM8_A0A0E0HTM8_ORYNI_4536 and tr_A0A0E0Q0A4_A0A0E0Q0A4_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0HTM8_A0A0E0HTM8_ORYNI_4536 and tr_A0A0D3GIR9_A0A0D3GIR9_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0HTM8_A0A0E0HTM8_ORYNI_4536 and tr_A0A0E0AC01_A0A0E0AC01_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F7FU66_F7FU66_MACMU_9544 and tr_A0A096MQ10_A0A096MQ10_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FU66_F7FU66_MACMU_9544 and tr_A0A2K5LYZ2_A0A2K5LYZ2_CERAT_9531 are exactly identical! WARNING: Sequences tr_E5S7R3_E5S7R3_TRISP_6334 and tr_A0A0V1CUH8_A0A0V1CUH8_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5S7R3_E5S7R3_TRISP_6334 and tr_A0A0V0U6N5_A0A0V0U6N5_9BILA_144512 are exactly identical! WARNING: Sequences tr_H3BWW0_H3BWW0_TETNG_99883 and tr_A0A2I4AQI2_A0A2I4AQI2_9TELE_52670 are exactly identical! WARNING: Sequences tr_G3NEM5_G3NEM5_GASAC_69293 and tr_A0A2U9CVH5_A0A2U9CVH5_SCOMX_52904 are exactly identical! WARNING: Sequences tr_H0Z0C4_H0Z0C4_TAEGU_59729 and tr_U3JB84_U3JB84_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0Z0C4_H0Z0C4_TAEGU_59729 and tr_A0A091GH38_A0A091GH38_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0Z0C4_H0Z0C4_TAEGU_59729 and tr_A0A218UCK7_A0A218UCK7_9PASE_299123 are exactly identical! WARNING: Sequences tr_B4N7K5_B4N7K5_DROWI_7260 and tr_B4GKP2_B4GKP2_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2R8PGP4_A0A2R8PGP4_CALJA_9483 and tr_A0A1S3WRX7_A0A1S3WRX7_ERIEU_9365 are exactly identical! WARNING: Sequences tr_A0A0Q9WG84_A0A0Q9WG84_DROVI_7244 and tr_A0A0Q9XGC9_A0A0Q9XGC9_DROMO_7230 are exactly identical! WARNING: Sequences tr_M7ZXZ3_M7ZXZ3_TRIUA_4572 and tr_A0A3B6HSC9_A0A3B6HSC9_WHEAT_4565 are exactly identical! WARNING: Sequences tr_M7ZXZ3_M7ZXZ3_TRIUA_4572 and tr_A0A3B6IVD2_A0A3B6IVD2_WHEAT_4565 are exactly identical! WARNING: Sequences tr_U3I799_U3I799_ANAPL_8839 and tr_A0A0Q3X395_A0A0Q3X395_AMAAE_12930 are exactly identical! WARNING: Sequences tr_U3I799_U3I799_ANAPL_8839 and tr_A0A226NJU9_A0A226NJU9_CALSU_9009 are exactly identical! WARNING: Sequences tr_U3J0W2_U3J0W2_ANAPL_8839 and tr_A0A226PSI6_A0A226PSI6_COLVI_9014 are exactly identical! WARNING: Sequences tr_U5GZC3_U5GZC3_USTV1_683840 and tr_A0A2X0NZN9_A0A2X0NZN9_9BASI_796604 are exactly identical! WARNING: Sequences tr_A0A3B6RN97_A0A3B6RN97_WHEAT_4565 and tr_A0A3B6SGY9_A0A3B6SGY9_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A3B6RN97_A0A3B6RN97_WHEAT_4565 and tr_A0A3B6TIJ0_A0A3B6TIJ0_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067H1X1_A0A067H1X1_CITSI_2711 and tr_V4U325_V4U325_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067H1X1_A0A067H1X1_CITSI_2711 and tr_A0A2H5NPI1_A0A2H5NPI1_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A096M825_A0A096M825_POEFO_48698 and tr_A0A096MFD8_A0A096MFD8_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A0D2MTF9_A0A0D2MTF9_GOSRA_29730 and tr_A0A1U8L294_A0A1U8L294_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0A1MQ22_A0A0A1MQ22_9FUNG_58291 and tr_A0A0A1NFA7_A0A0A1NFA7_9FUNG_58291 are exactly identical! WARNING: Sequences tr_A0A151MUP4_A0A151MUP4_ALLMI_8496 and tr_A0A3Q0FPE9_A0A3Q0FPE9_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091IZJ4_A0A091IZJ4_EGRGA_188379 and tr_A0A093Q832_A0A093Q832_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091IZJ4_A0A091IZJ4_EGRGA_188379 and tr_A0A091V1J7_A0A091V1J7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IZJ4_A0A091IZJ4_EGRGA_188379 and tr_A0A087R9Q8_A0A087R9Q8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IZJ4_A0A091IZJ4_EGRGA_188379 and tr_A0A091WKT3_A0A091WKT3_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091IZJ4_A0A091IZJ4_EGRGA_188379 and tr_A0A099Z0Y4_A0A099Z0Y4_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091IZJ4_A0A091IZJ4_EGRGA_188379 and tr_A0A0A0AUH9_A0A0A0AUH9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091IZJ4_A0A091IZJ4_EGRGA_188379 and tr_A0A2I0LTZ4_A0A2I0LTZ4_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091IZJ4_A0A091IZJ4_EGRGA_188379 and tr_A0A093GBD8_A0A093GBD8_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091IZJ4_A0A091IZJ4_EGRGA_188379 and tr_A0A091I885_A0A091I885_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091IZJ4_A0A091IZJ4_EGRGA_188379 and tr_A0A1V4JIE6_A0A1V4JIE6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0L9U3B3_A0A0L9U3B3_PHAAN_3914 and tr_A0A1S3T931_A0A1S3T931_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A0L9U3B3_A0A0L9U3B3_PHAAN_3914 and tr_A0A3Q0EMG4_A0A3Q0EMG4_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A194RH69_A0A194RH69_PAPMA_76193 and tr_A0A194QB74_A0A194QB74_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A0V1CVG3_A0A0V1CVG3_TRIBR_45882 and tr_A0A0V0W7F6_A0A0V0W7F6_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CVG3_A0A0V1CVG3_TRIBR_45882 and tr_A0A0V0VTZ4_A0A0V0VTZ4_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CVG3_A0A0V1CVG3_TRIBR_45882 and tr_A0A0V1LA46_A0A0V1LA46_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1L9Y4_A0A0V1L9Y4_9BILA_6335 and tr_A0A0V1A4Y8_A0A0V1A4Y8_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A151X9R4_A0A151X9R4_9HYME_64791 and tr_A0A151JNQ3_A0A151JNQ3_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A151X9R4_A0A151X9R4_9HYME_64791 and tr_A0A195CV07_A0A195CV07_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A1S3H1T5_A0A1S3H1T5_LINUN_7574 and tr_A0A1S3HZY5_A0A1S3HZY5_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3H1T5_A0A1S3H1T5_LINUN_7574 and tr_A0A1S3HZZ2_A0A1S3HZZ2_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3MFW3_A0A1S3MFW3_SALSA_8030 and tr_A0A060WVQ9_A0A060WVQ9_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3MLG5_A0A1S3MLG5_SALSA_8030 and tr_A0A060WS75_A0A060WS75_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3N6M2_A0A1S3N6M2_SALSA_8030 and tr_A0A1S3RY16_A0A1S3RY16_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3R1Z2_A0A1S3R1Z2_SALSA_8030 and tr_A0A060VNE5_A0A060VNE5_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A2D0SA88_A0A2D0SA88_ICTPU_7998 and tr_A0A2D0SB13_A0A2D0SB13_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SA88_A0A2D0SA88_ICTPU_7998 and tr_A0A2D0SBN6_A0A2D0SBN6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SL04_A0A2D0SL04_ICTPU_7998 and tr_A0A2D0SM81_A0A2D0SM81_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SQ37_A0A2D0SQ37_ICTPU_7998 and tr_W5UM42_W5UM42_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T2T5_A0A2D0T2T5_ICTPU_7998 and tr_A0A2D0T2T8_A0A2D0T2T8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2Y9PE76_A0A2Y9PE76_DELLE_9749 and tr_A0A2Y9F160_A0A2Y9F160_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 219 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/Q5JU85/3_mltree/Q5JU85.raxml.reduced.phy Alignment comprises 1 partitions and 276 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 276 / 276 Gaps: 3.37 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JU85/3_mltree/Q5JU85.raxml.rba Parallelization scheme autoconfig: 6 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 1000 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 276 / 22080 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -460181.875190] Initial branch length optimization [00:00:08 -371836.525808] Model parameter optimization (eps = 10.000000) [00:01:14 -370875.599376] AUTODETECT spr round 1 (radius: 5) [00:05:03 -200907.492917] AUTODETECT spr round 2 (radius: 10) [00:08:48 -138002.453835] AUTODETECT spr round 3 (radius: 15) [00:12:49 -108668.373929] AUTODETECT spr round 4 (radius: 20) [00:17:42 -92676.518713] AUTODETECT spr round 5 (radius: 25) [00:22:38 -82726.825456] SPR radius for FAST iterations: 25 (autodetect) [00:22:38 -82726.825456] Model parameter optimization (eps = 3.000000) [00:23:04 -82650.071345] FAST spr round 1 (radius: 25) [00:27:03 -67646.558772] FAST spr round 2 (radius: 25) [00:30:00 -66584.612775] FAST spr round 3 (radius: 25) [00:32:34 -66356.675728] FAST spr round 4 (radius: 25) [00:34:59 -66342.515021] FAST spr round 5 (radius: 25) [00:37:19 -66335.583537] FAST spr round 6 (radius: 25) [00:39:33 -66335.583420] Model parameter optimization (eps = 1.000000) [00:39:47 -66332.139007] SLOW spr round 1 (radius: 5) [00:42:34 -66319.128085] SLOW spr round 2 (radius: 5) [00:45:25 -66308.051995] SLOW spr round 3 (radius: 5) [00:48:16 -66308.050724] SLOW spr round 4 (radius: 10) [00:51:22 -66306.618050] SLOW spr round 5 (radius: 5) [00:54:58 -66306.617872] SLOW spr round 6 (radius: 10) [00:58:21 -66304.445769] SLOW spr round 7 (radius: 5) [01:01:54 -66304.445450] SLOW spr round 8 (radius: 10) [01:05:08 -66304.445399] SLOW spr round 9 (radius: 15) [01:09:22 -66304.445399] SLOW spr round 10 (radius: 20) [01:15:10 -66303.193711] SLOW spr round 11 (radius: 5) [01:19:03 -66303.193562] SLOW spr round 12 (radius: 10) [01:20:43] [worker #3] ML tree search #4, logLikelihood: -66312.284919 [01:22:38 -66301.172794] SLOW spr round 13 (radius: 5) [01:26:04 -66301.172762] SLOW spr round 14 (radius: 10) [01:29:17 -66301.172762] SLOW spr round 15 (radius: 15) [01:30:24] [worker #1] ML tree search #2, logLikelihood: -66318.522550 [01:33:30 -66301.172762] SLOW spr round 16 (radius: 20) [01:36:54] [worker #2] ML tree search #3, logLikelihood: -66316.004489 [01:39:15 -66301.172762] SLOW spr round 17 (radius: 25) [01:46:14 -66301.172762] Model parameter optimization (eps = 0.100000) [01:46:24] [worker #0] ML tree search #1, logLikelihood: -66300.861576 [01:46:24 -455457.023905] Initial branch length optimization [01:46:37 -368683.980399] Model parameter optimization (eps = 10.000000) [01:46:42] [worker #5] ML tree search #6, logLikelihood: -66318.428916 [01:47:52 -367794.366754] AUTODETECT spr round 1 (radius: 5) [01:51:43 -198833.276856] AUTODETECT spr round 2 (radius: 10) [01:55:25 -134967.760692] AUTODETECT spr round 3 (radius: 15) [01:59:32 -104921.229757] AUTODETECT spr round 4 (radius: 20) [02:04:03 -90839.355096] AUTODETECT spr round 5 (radius: 25) [02:09:06 -84655.517780] SPR radius for FAST iterations: 25 (autodetect) [02:09:06 -84655.517780] Model parameter optimization (eps = 3.000000) [02:09:14] [worker #4] ML tree search #5, logLikelihood: -66318.518434 [02:09:30 -84610.168067] FAST spr round 1 (radius: 25) [02:13:31 -67585.097563] FAST spr round 2 (radius: 25) [02:16:44 -66415.025070] FAST spr round 3 (radius: 25) [02:19:25 -66340.413595] FAST spr round 4 (radius: 25) [02:21:56 -66332.546880] FAST spr round 5 (radius: 25) [02:24:19 -66330.766605] FAST spr round 6 (radius: 25) [02:26:34 -66329.535057] FAST spr round 7 (radius: 25) [02:28:47 -66329.534992] Model parameter optimization (eps = 1.000000) [02:29:04 -66325.332880] SLOW spr round 1 (radius: 5) [02:31:59 -66316.323806] SLOW spr round 2 (radius: 5) [02:34:54 -66316.321999] SLOW spr round 3 (radius: 10) [02:38:04 -66315.256698] SLOW spr round 4 (radius: 5) [02:41:47 -66315.256231] SLOW spr round 5 (radius: 10) [02:45:18 -66314.334481] SLOW spr round 6 (radius: 5) [02:47:17] [worker #3] ML tree search #10, logLikelihood: -66318.637493 [02:48:48 -66314.334395] SLOW spr round 7 (radius: 10) [02:52:11 -66314.334308] SLOW spr round 8 (radius: 15) [02:56:23 -66314.334270] SLOW spr round 9 (radius: 20) [03:02:04 -66313.071843] SLOW spr round 10 (radius: 5) [03:05:59 -66313.071703] SLOW spr round 11 (radius: 10) [03:09:41 -66311.075821] SLOW spr round 12 (radius: 5) [03:13:08 -66311.075796] SLOW spr round 13 (radius: 10) [03:16:26 -66311.075796] SLOW spr round 14 (radius: 15) [03:20:37 -66311.075796] SLOW spr round 15 (radius: 20) [03:26:17 -66311.075796] SLOW spr round 16 (radius: 25) [03:33:13 -66311.075796] Model parameter optimization (eps = 0.100000) [03:33:20] [worker #0] ML tree search #7, logLikelihood: -66311.058553 [03:33:20 -459780.841265] Initial branch length optimization [03:33:27 -371636.761743] Model parameter optimization (eps = 10.000000) [03:34:38 -370645.372244] AUTODETECT spr round 1 (radius: 5) [03:37:32] [worker #1] ML tree search #8, logLikelihood: -66311.211612 [03:38:32 -195820.840724] AUTODETECT spr round 2 (radius: 10) [03:42:13 -132178.958840] AUTODETECT spr round 3 (radius: 15) [03:42:59] [worker #2] ML tree search #9, logLikelihood: -66313.831401 [03:46:20 -105687.153530] AUTODETECT spr round 4 (radius: 20) [03:50:41 -92056.161356] AUTODETECT spr round 5 (radius: 25) [03:55:07 -86422.990516] SPR radius for FAST iterations: 25 (autodetect) [03:55:07 -86422.990516] Model parameter optimization (eps = 3.000000) [03:55:39 -86249.679470] FAST spr round 1 (radius: 25) [03:59:23 -69154.168612] FAST spr round 2 (radius: 25) [04:02:17 -66629.708902] FAST spr round 3 (radius: 25) [04:04:01] [worker #3] ML tree search #16, logLikelihood: -66312.589686 [04:04:52 -66369.461533] FAST spr round 4 (radius: 25) [04:05:18] [worker #5] ML tree search #12, logLikelihood: -66321.412461 [04:07:17 -66347.933018] FAST spr round 5 (radius: 25) [04:09:36 -66345.344130] FAST spr round 6 (radius: 25) [04:11:45 -66345.344063] Model parameter optimization (eps = 1.000000) [04:12:01 -66343.666862] SLOW spr round 1 (radius: 5) [04:14:07] [worker #4] ML tree search #11, logLikelihood: -66319.099706 [04:14:53 -66332.337251] SLOW spr round 2 (radius: 5) [04:17:42 -66332.009270] SLOW spr round 3 (radius: 5) [04:20:30 -66330.148908] SLOW spr round 4 (radius: 5) [04:23:15 -66330.148820] SLOW spr round 5 (radius: 10) [04:26:14 -66329.183227] SLOW spr round 6 (radius: 5) [04:29:44 -66329.183216] SLOW spr round 7 (radius: 10) [04:33:03 -66329.183216] SLOW spr round 8 (radius: 15) [04:37:23 -66326.662456] SLOW spr round 9 (radius: 5) [04:41:07 -66324.653759] SLOW spr round 10 (radius: 5) [04:44:23 -66324.653757] SLOW spr round 11 (radius: 10) [04:47:32 -66324.653757] SLOW spr round 12 (radius: 15) [04:51:51 -66324.653757] SLOW spr round 13 (radius: 20) [04:57:16] [worker #1] ML tree search #14, logLikelihood: -66334.938841 [04:57:36 -66324.653757] SLOW spr round 14 (radius: 25) [05:04:48 -66324.653757] Model parameter optimization (eps = 0.100000) [05:05:03] [worker #0] ML tree search #13, logLikelihood: -66324.515538 [05:05:03 -460548.183679] Initial branch length optimization [05:05:10 -375460.561467] Model parameter optimization (eps = 10.000000) [05:06:16 -374505.969835] AUTODETECT spr round 1 (radius: 5) [05:10:12 -198343.148649] AUTODETECT spr round 2 (radius: 10) [05:13:56 -136428.721633] AUTODETECT spr round 3 (radius: 15) [05:17:57] [worker #2] ML tree search #15, logLikelihood: -66303.332291 [05:18:01 -111098.920088] AUTODETECT spr round 4 (radius: 20) [05:22:38 -89720.435212] AUTODETECT spr round 5 (radius: 25) [05:27:07] [worker #5] ML tree search #18, logLikelihood: -66307.160742 [05:27:14 -82041.820780] SPR radius for FAST iterations: 25 (autodetect) [05:27:14 -82041.820780] Model parameter optimization (eps = 3.000000) [05:27:38 -81975.103571] FAST spr round 1 (radius: 25) [05:31:27 -67859.028741] FAST spr round 2 (radius: 25) [05:34:18 -66549.139310] FAST spr round 3 (radius: 25) [05:36:56 -66373.259316] FAST spr round 4 (radius: 25) [05:39:25 -66360.276992] FAST spr round 5 (radius: 25) [05:41:44 -66357.475431] FAST spr round 6 (radius: 25) [05:43:54 -66357.475051] Model parameter optimization (eps = 1.000000) [05:44:13 -66356.377785] SLOW spr round 1 (radius: 5) [05:47:05 -66329.720885] SLOW spr round 2 (radius: 5) [05:49:53 -66326.790797] SLOW spr round 3 (radius: 5) [05:52:43 -66325.449907] SLOW spr round 4 (radius: 5) [05:55:28 -66325.449890] SLOW spr round 5 (radius: 10) [05:58:29 -66322.916601] SLOW spr round 6 (radius: 5) [06:02:01 -66322.916559] SLOW spr round 7 (radius: 10) [06:05:19 -66322.916555] SLOW spr round 8 (radius: 15) [06:09:38 -66322.224890] SLOW spr round 9 (radius: 5) [06:13:25 -66322.224888] SLOW spr round 10 (radius: 10) [06:16:53 -66322.224888] SLOW spr round 11 (radius: 15) [06:21:10 -66322.224888] SLOW spr round 12 (radius: 20) [06:27:05 -66320.398929] SLOW spr round 13 (radius: 5) [06:29:14] [worker #1] ML tree search #20, logLikelihood: -66303.204278 [06:30:57 -66318.344578] SLOW spr round 14 (radius: 5) [06:31:46] [worker #4] ML tree search #17, logLikelihood: -66305.240182 [06:34:16 -66318.344568] SLOW spr round 15 (radius: 10) [06:37:28 -66318.344567] SLOW spr round 16 (radius: 15) [06:41:47 -66318.344567] SLOW spr round 17 (radius: 20) [06:47:38 -66318.344567] SLOW spr round 18 (radius: 25) [06:54:25 -66318.344567] Model parameter optimization (eps = 0.100000) [06:54:35] [worker #0] ML tree search #19, logLikelihood: -66318.255147 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.195955,0.341518) (0.166994,0.405989) (0.391757,0.929581) (0.245294,2.042896) 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: -66300.861576 AIC score: 136607.723153 / AICc score: 8164631.723153 / BIC score: 143859.386087 Free parameters (model + branch lengths): 2003 WARNING: Number of free parameters (K=2003) is larger than alignment size (n=276). 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/Q5JU85/3_mltree/Q5JU85.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JU85/3_mltree/Q5JU85.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JU85/3_mltree/Q5JU85.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5JU85/3_mltree/Q5JU85.raxml.log Analysis started: 02-Jul-2021 08:08:55 / finished: 02-Jul-2021 15:03:31 Elapsed time: 24875.791 seconds Consumed energy: 2184.983 Wh (= 11 km in an electric car, or 55 km with an e-scooter!)