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 01-Jul-2021 03:58:40 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08590/2_msa/P08590_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08590/3_mltree/P08590 --seed 2 --threads 4 --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 (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08590/2_msa/P08590_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 180 sites WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_E9H5Z2_E9H5Z2_DAPPU_6669 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and sp_P62152_CALM_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_B4HP77_B4HP77_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_B5DZG9_B5DZG9_DROPS_46245 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_B0XG51_B0XG51_CULQU_7176 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_K7IWY5_K7IWY5_NASVI_7425 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_A0A088AD88_A0A088AD88_APIME_7460 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_D6WB91_D6WB91_TRICA_7070 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_B4MY99_B4MY99_DROWI_7260 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_B3MC95_B3MC95_DROAN_7217 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_Q1ZZP3_Q1ZZP3_ACYPI_7029 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_B4G9V3_B4G9V3_DROPE_7234 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_B4LJR6_B4LJR6_DROVI_7244 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_Q1HQX3_Q1HQX3_AEDAE_7159 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_B4KTM1_B4KTM1_DROMO_7230 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_T1IQM0_T1IQM0_STRMM_126957 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_T1KBE7_T1KBE7_TETUR_32264 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_N6TLJ6_N6TLJ6_DENPD_77166 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_V4BWJ9_V4BWJ9_LOTGI_225164 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_A0A0L0C9L1_A0A0L0C9L1_LUCCU_7375 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_A0A0L8I9I4_A0A0L8I9I4_OCTBM_37653 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_A0A087UZS7_A0A087UZS7_9ARAC_407821 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_A0A0P6GHU6_A0A0P6GHU6_9CRUS_35525 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_A0A1S3H7Q1_A0A1S3H7Q1_LINUN_7574 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_A0A0M3QV58_A0A0M3QV58_DROBS_30019 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_A0A1D2N6J8_A0A1D2N6J8_ORCCI_48709 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_A0A1J1IW19_A0A1J1IW19_9DIPT_568069 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_A0A1W4UHE8_A0A1W4UHE8_DROFC_30025 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_A0A1W4X129_A0A1W4X129_AGRPL_224129 are exactly identical! WARNING: Sequences tr_B4QC96_B4QC96_DROSI_7240 and tr_A0A2J7QFD1_A0A2J7QFD1_9NEOP_105785 are exactly identical! WARNING: Sequences tr_B4R4Z9_B4R4Z9_DROSI_7240 and sp_P54357_MLC2_DROME_7227 are exactly identical! WARNING: Sequences tr_B4R4Z9_B4R4Z9_DROSI_7240 and tr_B4I0N0_B4I0N0_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4R4Z9_B4R4Z9_DROSI_7240 and tr_B4M793_B4M793_DROVI_7244 are exactly identical! WARNING: Sequences tr_B4R4Z9_B4R4Z9_DROSI_7240 and tr_B4L5Q5_B4L5Q5_DROMO_7230 are exactly identical! WARNING: Sequences tr_A0A2R8QP29_A0A2R8QP29_DANRE_7955 and tr_G1NDB0_G1NDB0_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A2R8QP29_A0A2R8QP29_DANRE_7955 and tr_F7BJZ4_F7BJZ4_HORSE_9796 are exactly identical! WARNING: Sequences tr_A0A2R8QP29_A0A2R8QP29_DANRE_7955 and tr_W5NZX8_W5NZX8_SHEEP_9940 are exactly identical! WARNING: Sequences tr_A0A2R8QP29_A0A2R8QP29_DANRE_7955 and tr_G7PXY7_G7PXY7_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2R8QP29_A0A2R8QP29_DANRE_7955 and tr_M3X5G8_M3X5G8_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2R8QP29_A0A2R8QP29_DANRE_7955 and tr_U3IK46_U3IK46_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A2R8QP29_A0A2R8QP29_DANRE_7955 and tr_A0A1S2ZZ76_A0A1S2ZZ76_ERIEU_9365 are exactly identical! WARNING: Sequences tr_Q4QHT2_Q4QHT2_LEIMA_5664 and tr_Q4CSZ2_Q4CSZ2_TRYCC_353153 are exactly identical! WARNING: Sequences tr_Q4QHT2_Q4QHT2_LEIMA_5664 and tr_Q4D139_Q4D139_TRYCC_353153 are exactly identical! WARNING: Sequences tr_Q4QHT2_Q4QHT2_LEIMA_5664 and tr_A4H5R9_A4H5R9_LEIBR_5660 are exactly identical! WARNING: Sequences tr_Q4QHT2_Q4QHT2_LEIMA_5664 and tr_A4HU13_A4HU13_LEIIN_5671 are exactly identical! WARNING: Sequences sp_Q60605_MYL6_MOUSE_10090 and tr_G1P7D7_G1P7D7_MYOLU_59463 are exactly identical! WARNING: Sequences sp_Q60605_MYL6_MOUSE_10090 and tr_G3HRQ4_G3HRQ4_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q60605_MYL6_MOUSE_10090 and sp_Q5R844_MYL6_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q60605_MYL6_MOUSE_10090 and tr_F7AX54_F7AX54_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q60605_MYL6_MOUSE_10090 and sp_P60660_MYL6_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q60605_MYL6_MOUSE_10090 and sp_P60662_MYL6_PIG_9823 are exactly identical! WARNING: Sequences sp_Q60605_MYL6_MOUSE_10090 and sp_P60661_MYL6_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q60605_MYL6_MOUSE_10090 and tr_A0A2Y9FRT9_A0A2Y9FRT9_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q60605_MYL6_MOUSE_10090 and tr_A0A384DU26_A0A384DU26_URSMA_29073 are exactly identical! WARNING: Sequences sp_Q60605_MYL6_MOUSE_10090 and tr_A0A383ZWY3_A0A383ZWY3_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3Y9L7_M3Y9L7_MUSPF_9669 and tr_F1Q3E5_F1Q3E5_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Y9L7_M3Y9L7_MUSPF_9669 and tr_G1M810_G1M810_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Y9L7_M3Y9L7_MUSPF_9669 and tr_M3W147_M3W147_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Y9L7_M3Y9L7_MUSPF_9669 and tr_A0A2Y9KRD4_A0A2Y9KRD4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3G9G0_A0A2I3G9G0_NOMLE_61853 and tr_G7N1I5_G7N1I5_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3G9G0_A0A2I3G9G0_NOMLE_61853 and tr_G7PE50_G7PE50_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3G9G0_A0A2I3G9G0_NOMLE_61853 and tr_A0A0D9SCH5_A0A0D9SCH5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3G9G0_A0A2I3G9G0_NOMLE_61853 and tr_A0A2K5L182_A0A2K5L182_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3G9G0_A0A2I3G9G0_NOMLE_61853 and tr_A0A2K5XKL7_A0A2K5XKL7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3GVX6_A0A2I3GVX6_NOMLE_61853 and tr_G7N8T7_G7N8T7_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GVX6_A0A2I3GVX6_NOMLE_61853 and tr_G7PLC0_G7PLC0_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3GVX6_A0A2I3GVX6_NOMLE_61853 and tr_A0A2K5P3H8_A0A2K5P3H8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GVX6_A0A2I3GVX6_NOMLE_61853 and tr_A0A2K6CST3_A0A2K6CST3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GVX6_A0A2I3GVX6_NOMLE_61853 and tr_A0A2K6A0W8_A0A2K6A0W8_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1R2V9_G1R2V9_NOMLE_61853 and tr_G3R2N7_G3R2N7_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R2V9_G1R2V9_NOMLE_61853 and tr_A0A2J8UZ69_A0A2J8UZ69_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R2V9_G1R2V9_NOMLE_61853 and sp_P12829_MYL4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R2V9_G1R2V9_NOMLE_61853 and tr_A0A0D9QUZ1_A0A0D9QUZ1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R2V9_G1R2V9_NOMLE_61853 and tr_A0A2K5ZRT5_A0A2K5ZRT5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1R2V9_G1R2V9_NOMLE_61853 and tr_A0A2R9AL56_A0A2R9AL56_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_G1NK53_G1NK53_MELGA_9103 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_G1KJS8_G1KJS8_ANOCA_28377 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_G1T1Q2_G1T1Q2_RABIT_9986 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_F7EEC4_F7EEC4_MONDO_13616 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_F6Z5C4_F6Z5C4_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_W5P5I7_W5P5I7_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_I3MRD3_I3MRD3_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_K7G387_K7G387_PELSI_13735 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_H0YWL0_H0YWL0_TAEGU_59729 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_G1LHZ6_G1LHZ6_AILME_9646 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_U3J8Q5_U3J8Q5_ANAPL_8839 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A087Y5M1_A0A087Y5M1_POEFO_48698 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A0P7UM01_A0A0P7UM01_9TELE_113540 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A091EDT5_A0A091EDT5_CORBR_85066 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A091IVH2_A0A091IVH2_EGRGA_188379 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A093Q9E8_A0A093Q9E8_9PASS_328815 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A091UMH1_A0A091UMH1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A087R516_A0A087R516_APTFO_9233 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A093H7A6_A0A093H7A6_STRCA_441894 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A091WA21_A0A091WA21_OPIHO_30419 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A099YXH8_A0A099YXH8_TINGU_94827 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A091G3J8_A0A091G3J8_9AVES_55661 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A0A0AH07_A0A0A0AH07_CHAVO_50402 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A093GU92_A0A093GU92_DRYPU_118200 are exactly identical! WARNING: Sequences tr_G1PG41_G1PG41_MYOLU_59463 and tr_A0A091HKG8_A0A091HKG8_CALAN_9244 are exactly identical! WARNING: Sequences tr_B0D6G4_B0D6G4_LACBS_486041 and tr_A8NMQ1_A8NMQ1_COPC7_240176 are exactly identical! WARNING: Sequences tr_B0D6G4_B0D6G4_LACBS_486041 and tr_A0A1M2VHI6_A0A1M2VHI6_TRAPU_154538 are exactly identical! WARNING: Sequences tr_B0D6G4_B0D6G4_LACBS_486041 and tr_A0A2G8S1A1_A0A2G8S1A1_9APHY_1077348 are exactly identical! WARNING: Sequences tr_B0D6G4_B0D6G4_LACBS_486041 and tr_A0A371DPS4_A0A371DPS4_9APHY_139420 are exactly identical! WARNING: Sequences tr_A0A2I2YJ43_A0A2I2YJ43_GORGO_9595 and tr_A0A2I3TKG0_A0A2I3TKG0_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Z4K8_A0A2I2Z4K8_GORGO_9595 and tr_A0A2I3RIC1_A0A2I3RIC1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Z4K8_A0A2I2Z4K8_GORGO_9595 and sp_P27482_CALL3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Z4K8_A0A2I2Z4K8_GORGO_9595 and tr_A0A2R8ZUK0_A0A2R8ZUK0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QJD8_G3QJD8_GORGO_9595 and sp_Q5R887_MYL3_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QJD8_G3QJD8_GORGO_9595 and sp_P08590_MYL3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QJD8_G3QJD8_GORGO_9595 and tr_A0A2R9BLR8_A0A2R9BLR8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R8I7_G3R8I7_GORGO_9595 and tr_H2QJC2_H2QJC2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R8I7_G3R8I7_GORGO_9595 and sp_P05976_MYL1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R8I7_G3R8I7_GORGO_9595 and tr_A0A2R9AVM1_A0A2R9AVM1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A4RRH9_A4RRH9_OSTLU_436017 and tr_A0A090M449_A0A090M449_OSTTA_70448 are exactly identical! WARNING: Sequences tr_A7RPI8_A7RPI8_NEMVE_45351 and tr_A0A1S3H6A4_A0A1S3H6A4_LINUN_7574 are exactly identical! WARNING: Sequences tr_A7RPI8_A7RPI8_NEMVE_45351 and tr_A0A2B4SHB2_A0A2B4SHB2_STYPI_50429 are exactly identical! WARNING: Sequences tr_H2NHN7_H2NHN7_PONAB_9601 and tr_G1TDK0_G1TDK0_RABIT_9986 are exactly identical! WARNING: Sequences tr_H2NHN7_H2NHN7_PONAB_9601 and tr_A0A286XZS1_A0A286XZS1_CAVPO_10141 are exactly identical! WARNING: Sequences tr_H2NHN7_H2NHN7_PONAB_9601 and tr_G5BB85_G5BB85_HETGA_10181 are exactly identical! WARNING: Sequences tr_H2NHN7_H2NHN7_PONAB_9601 and tr_A0A1S3ADI7_A0A1S3ADI7_ERIEU_9365 are exactly identical! WARNING: Sequences tr_H2NHN7_H2NHN7_PONAB_9601 and tr_A0A1S3FJF2_A0A1S3FJF2_DIPOR_10020 are exactly identical! WARNING: Sequences tr_H2NHN7_H2NHN7_PONAB_9601 and tr_A0A1U7SQ95_A0A1U7SQ95_TARSY_1868482 are exactly identical! WARNING: Sequences tr_H2NHN7_H2NHN7_PONAB_9601 and tr_A0A2K5NAD9_A0A2K5NAD9_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2NHN7_H2NHN7_PONAB_9601 and tr_A0A2Y9DRU3_A0A2Y9DRU3_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H2P8H0_H2P8H0_PONAB_9601 and tr_A0A0D9RBV5_A0A0D9RBV5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1MUW1_G1MUW1_MELGA_9103 and tr_A0A226NDH8_A0A226NDH8_CALSU_9009 are exactly identical! WARNING: Sequences tr_G1MUW1_G1MUW1_MELGA_9103 and tr_A0A226P1U4_A0A226P1U4_COLVI_9014 are exactly identical! WARNING: Sequences tr_B5DLM1_B5DLM1_DROPS_46245 and tr_B4GWC7_B4GWC7_DROPE_7234 are exactly identical! WARNING: Sequences tr_B9PR42_B9PR42_TOXGV_432359 and tr_A0A074T1R8_A0A074T1R8_HAMHA_99158 are exactly identical! WARNING: Sequences tr_E2R8F7_E2R8F7_CANLF_9615 and tr_G1M1P1_G1M1P1_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A2I3SBF1_A0A2I3SBF1_PANTR_9598 and tr_A0A2R9BLY4_A0A2R9BLY4_PANPA_9597 are exactly identical! WARNING: Sequences tr_G5AIM3_G5AIM3_PHYSP_1094619 and tr_H3G9K1_H3G9K1_PHYRM_164328 are exactly identical! WARNING: Sequences tr_G5AIM3_G5AIM3_PHYSP_1094619 and tr_D0N511_D0N511_PHYIT_403677 are exactly identical! WARNING: Sequences tr_G5AIM3_G5AIM3_PHYSP_1094619 and tr_W2PZM2_W2PZM2_PHYPN_761204 are exactly identical! WARNING: Sequences tr_G5AIM3_G5AIM3_PHYSP_1094619 and tr_K3XBA4_K3XBA4_PYTUL_431595 are exactly identical! WARNING: Sequences tr_G5AIM3_G5AIM3_PHYSP_1094619 and tr_A0A067CTC1_A0A067CTC1_SAPPC_695850 are exactly identical! WARNING: Sequences tr_G5AIM3_G5AIM3_PHYSP_1094619 and tr_T0QYM7_T0QYM7_9STRA_1156394 are exactly identical! WARNING: Sequences tr_G5AIM3_G5AIM3_PHYSP_1094619 and tr_A0A0W8CY15_A0A0W8CY15_PHYNI_4790 are exactly identical! WARNING: Sequences tr_G5AIM3_G5AIM3_PHYSP_1094619 and tr_W2N0W7_W2N0W7_PHYPR_4792 are exactly identical! WARNING: Sequences tr_G5AIM3_G5AIM3_PHYSP_1094619 and tr_A0A1V9YKD2_A0A1V9YKD2_9STRA_1202772 are exactly identical! WARNING: Sequences tr_G5AIM3_G5AIM3_PHYSP_1094619 and tr_A0A329SJQ3_A0A329SJQ3_9STRA_29920 are exactly identical! WARNING: Sequences tr_A0A3B5QQY7_A0A3B5QQY7_XIPMA_8083 and tr_A0A096LT44_A0A096LT44_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A088ASU4_A0A088ASU4_APIME_7460 and tr_A0A0M8ZRS7_A0A0M8ZRS7_9HYME_166423 are exactly identical! WARNING: Sequences tr_A0A088ASU4_A0A088ASU4_APIME_7460 and tr_A0A154P5F7_A0A154P5F7_9HYME_178035 are exactly identical! WARNING: Sequences tr_A0A158NNH2_A0A158NNH2_ATTCE_12957 and tr_F4WQG9_F4WQG9_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A180H0K4_A0A180H0K4_PUCT1_630390 and tr_E3KLJ3_E3KLJ3_PUCGT_418459 are exactly identical! WARNING: Sequences tr_A0A180H0K4_A0A180H0K4_PUCT1_630390 and tr_A0A0L0VM95_A0A0L0VM95_9BASI_1165861 are exactly identical! WARNING: Sequences tr_A0A180H0K4_A0A180H0K4_PUCT1_630390 and tr_A0A2N5UR53_A0A2N5UR53_9BASI_200324 are exactly identical! WARNING: Sequences tr_A0A1D5QK52_A0A1D5QK52_MACMU_9544 and tr_A0A096NFX6_A0A096NFX6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QK52_A0A1D5QK52_MACMU_9544 and tr_A0A0D9QYU5_A0A0D9QYU5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QK52_A0A1D5QK52_MACMU_9544 and tr_A0A2K5NFA3_A0A2K5NFA3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QK52_A0A1D5QK52_MACMU_9544 and tr_A0A2K6CE50_A0A2K6CE50_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QK52_A0A1D5QK52_MACMU_9544 and tr_A0A2K5Z3H4_A0A2K5Z3H4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1D5R0N5_A0A1D5R0N5_MACMU_9544 and tr_A0A2K5MIJ1_A0A2K5MIJ1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5R0N5_A0A1D5R0N5_MACMU_9544 and tr_A0A2K6CWD1_A0A2K6CWD1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5R0N5_A0A1D5R0N5_MACMU_9544 and tr_A0A2K6A4X3_A0A2K6A4X3_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6Y764_F6Y764_MACMU_9544 and tr_A0A096P690_A0A096P690_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6Y764_F6Y764_MACMU_9544 and tr_A0A2K5MLV9_A0A2K5MLV9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6Y764_F6Y764_MACMU_9544 and tr_A0A2K6DER9_A0A2K6DER9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7G4P0_F7G4P0_MACMU_9544 and tr_G7NXW8_G7NXW8_MACFA_9541 are exactly identical! WARNING: Sequences tr_H0ZMF4_H0ZMF4_TAEGU_59729 and tr_A0A218UML5_A0A218UML5_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A0P8Y748_A0A0P8Y748_DROAN_7217 and tr_A0A0M4F8T7_A0A0M4F8T7_DROBS_30019 are exactly identical! WARNING: Sequences tr_F8QB51_F8QB51_SERL3_936435 and tr_A0A0C3JRH8_A0A0C3JRH8_PISTI_870435 are exactly identical! WARNING: Sequences tr_F8QB51_F8QB51_SERL3_936435 and tr_A0A2H3E708_A0A2H3E708_ARMGA_47427 are exactly identical! WARNING: Sequences tr_F8QB51_F8QB51_SERL3_936435 and tr_A0A2H3BQN2_A0A2H3BQN2_9AGAR_1076256 are exactly identical! WARNING: Sequences tr_F8QB51_F8QB51_SERL3_936435 and tr_A0A284QY32_A0A284QY32_9AGAR_47428 are exactly identical! WARNING: Sequences tr_E3LYJ5_E3LYJ5_CAERE_31234 and tr_A8XS91_A8XS91_CAEBR_6238 are exactly identical! WARNING: Sequences tr_E3LYJ5_E3LYJ5_CAERE_31234 and tr_A0A1I7TLZ1_A0A1I7TLZ1_9PELO_1561998 are exactly identical! WARNING: Sequences tr_E3LZ12_E3LZ12_CAERE_31234 and tr_A0A261AVJ6_A0A261AVJ6_9PELO_1503980 are exactly identical! WARNING: Sequences tr_G1LEI9_G1LEI9_AILME_9646 and tr_A0A2U3WAN2_A0A2U3WAN2_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1LEI9_G1LEI9_AILME_9646 and tr_A0A2Y9J7K0_A0A2Y9J7K0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1LEI9_G1LEI9_AILME_9646 and tr_A0A384BU53_A0A384BU53_URSMA_29073 are exactly identical! WARNING: Sequences tr_G0QJK7_G0QJK7_ICHMG_857967 and tr_Q241P0_Q241P0_TETTS_312017 are exactly identical! WARNING: Sequences tr_B3S9B3_B3S9B3_TRIAD_10228 and tr_A0A369S0Z2_A0A369S0Z2_9METZ_287889 are exactly identical! WARNING: Sequences tr_I1CFG4_I1CFG4_RHIO9_246409 and tr_A0A367KY79_A0A367KY79_RHIST_4846 are exactly identical! WARNING: Sequences tr_S8EI27_S8EI27_FOMPI_743788 and tr_A0A165RD16_A0A165RD16_9APHY_1314783 are exactly identical! WARNING: Sequences tr_U3IDU0_U3IDU0_ANAPL_8839 and tr_A0A2I0MR83_A0A2I0MR83_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3IDU0_U3IDU0_ANAPL_8839 and tr_A0A1V4KDZ7_A0A1V4KDZ7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A015NDN8_A0A015NDN8_9GLOM_1432141 and tr_A0A2I1GNI1_A0A2I1GNI1_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015NDN8_A0A015NDN8_9GLOM_1432141 and tr_U9V8P2_U9V8P2_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044UQT6_A0A044UQT6_ONCVO_6282 and tr_A0A182E0T2_A0A182E0T2_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A074SXA4_A0A074SXA4_9HOMO_1423351 and tr_A0A0K6FY76_A0A0K6FY76_9HOMO_456999 are exactly identical! WARNING: Sequences tr_A0A2I3MLN6_A0A2I3MLN6_PAPAN_9555 and tr_A0A2K5LC03_A0A2K5LC03_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MLN6_A0A2I3MLN6_PAPAN_9555 and tr_A0A2K6E4S2_A0A2K6E4S2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3MLN6_A0A2I3MLN6_PAPAN_9555 and tr_A0A2K5XFF1_A0A2K5XFF1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0K0F6G7_A0A0K0F6G7_STRVS_75913 and tr_A0A0N5CEG9_A0A0N5CEG9_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A151LZL8_A0A151LZL8_ALLMI_8496 and tr_A0A1U7RZ50_A0A1U7RZ50_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151N6K4_A0A151N6K4_ALLMI_8496 and tr_A0A3Q0FLW7_A0A3Q0FLW7_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A183HAI3_A0A183HAI3_9BILA_387005 and tr_A0A1I7VH00_A0A1I7VH00_LOALO_7209 are exactly identical! WARNING: Sequences tr_A0A091IKL3_A0A091IKL3_EGRGA_188379 and tr_A0A087R5J0_A0A087R5J0_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IKL3_A0A091IKL3_EGRGA_188379 and tr_A0A091WNL9_A0A091WNL9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JBG1_A0A091JBG1_EGRGA_188379 and tr_A0A091W0M5_A0A091W0M5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JBG1_A0A091JBG1_EGRGA_188379 and tr_A0A0A0A698_A0A0A0A698_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0L0HNK3_A0A0L0HNK3_SPIPN_645134 and tr_A0A139AX67_A0A139AX67_GONPR_1344416 are exactly identical! WARNING: Sequences tr_A0A0L0HNK3_A0A0L0HNK3_SPIPN_645134 and tr_A0A177WMU9_A0A177WMU9_BATDE_403673 are exactly identical! WARNING: Sequences tr_A0A0N1PG10_A0A0N1PG10_PAPMA_76193 and tr_A0A194PVZ2_A0A194PVZ2_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A0V0RXP1_A0A0V0RXP1_9BILA_6336 and tr_A0A0V1D8T7_A0A0V1D8T7_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RXP1_A0A0V0RXP1_9BILA_6336 and tr_A0A0V0WT47_A0A0V0WT47_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RXP1_A0A0V0RXP1_9BILA_6336 and tr_A0A0V1KUR6_A0A0V1KUR6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0RXP1_A0A0V0RXP1_9BILA_6336 and tr_A0A0V0Z7Q2_A0A0V0Z7Q2_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0RXP1_A0A0V0RXP1_9BILA_6336 and tr_A0A0V1NZU7_A0A0V1NZU7_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0SDQ6_A0A0V0SDQ6_9BILA_6336 and tr_A0A0V0WKC3_A0A0V0WKC3_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0SDQ6_A0A0V0SDQ6_9BILA_6336 and tr_A0A0V0V4S3_A0A0V0V4S3_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0SDQ6_A0A0V0SDQ6_9BILA_6336 and tr_A0A0V1L2S1_A0A0V1L2S1_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0SDQ6_A0A0V0SDQ6_9BILA_6336 and tr_A0A0V1A9L7_A0A0V1A9L7_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0SDQ6_A0A0V0SDQ6_9BILA_6336 and tr_A0A0V1PN14_A0A0V1PN14_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0SDQ6_A0A0V0SDQ6_9BILA_6336 and tr_A0A0V0TE88_A0A0V0TE88_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1JJH7_A0A0V1JJH7_TRIPS_6337 and tr_A0A0V1MBD4_A0A0V1MBD4_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V1JJH7_A0A0V1JJH7_TRIPS_6337 and tr_A0A0V1I034_A0A0V1I034_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A0P1BS27_A0A0P1BS27_9BASI_401625 and tr_A0A316VVW9_A0A316VVW9_9BASI_1522189 are exactly identical! WARNING: Sequences tr_A0A151WWR2_A0A151WWR2_9HYME_64791 and tr_A0A195DLP2_A0A195DLP2_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A151WWR2_A0A151WWR2_9HYME_64791 and tr_A0A195B3J7_A0A195B3J7_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A151WWR2_A0A151WWR2_9HYME_64791 and tr_A0A195F763_A0A195F763_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A151WWR2_A0A151WWR2_9HYME_64791 and tr_A0A195D7G8_A0A195D7G8_9HYME_456900 are exactly identical! WARNING: Sequences tr_B5DGT2_B5DGT2_SALSA_8030 and tr_B5DGT3_B5DGT3_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1Y1V8L0_A0A1Y1V8L0_9FUNG_1754191 and tr_A0A1Y2D4X5_A0A1Y2D4X5_9FUNG_1754190 are exactly identical! WARNING: Sequences tr_A0A226NB08_A0A226NB08_CALSU_9009 and tr_A0A226PBZ9_A0A226PBZ9_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3DQ62_A0A2H3DQ62_ARMGA_47427 and tr_A0A2H3CHF1_A0A2H3CHF1_9AGAR_1076256 are exactly identical! WARNING: Sequences tr_A0A2H3DQ62_A0A2H3DQ62_ARMGA_47427 and tr_A0A284QWQ0_A0A284QWQ0_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2A2JE40_A0A2A2JE40_9BILA_2018661 and tr_A0A2A2LR76_A0A2A2LR76_9BILA_2018661 are exactly identical! WARNING: Sequences tr_A0A2U4C3A4_A0A2U4C3A4_TURTR_9739 and tr_A0A2Y9PCY3_A0A2Y9PCY3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3ZH38_A0A2U3ZH38_ODORO_9708 and tr_A0A2Y9N388_A0A2Y9N388_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A316YJX7_A0A316YJX7_9BASI_215250 and tr_A0A316VJD9_A0A316VJD9_9BASI_1280837 are exactly identical! WARNING: Sequences tr_A0A2Y9NRL8_A0A2Y9NRL8_DELLE_9749 and tr_A0A384CQ65_A0A384CQ65_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2Y9NRL8_A0A2Y9NRL8_DELLE_9749 and tr_A0A384ARW3_A0A384ARW3_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 226 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/P08590/3_mltree/P08590.raxml.reduced.phy Alignment comprises 1 partitions and 180 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 180 / 180 Gaps: 14.13 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08590/3_mltree/P08590.raxml.rba Parallelization scheme autoconfig: 4 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 / 180 / 14400 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -213350.914978] Initial branch length optimization [00:00:03 -175473.237880] Model parameter optimization (eps = 10.000000) [00:00:41 -174475.877645] AUTODETECT spr round 1 (radius: 5) [00:03:12 -105651.345846] AUTODETECT spr round 2 (radius: 10) [00:05:50 -68235.335526] AUTODETECT spr round 3 (radius: 15) [00:08:44 -51040.196646] AUTODETECT spr round 4 (radius: 20) [00:11:52 -47779.978070] AUTODETECT spr round 5 (radius: 25) [00:15:53 -45838.363952] SPR radius for FAST iterations: 25 (autodetect) [00:15:53 -45838.363952] Model parameter optimization (eps = 3.000000) [00:16:14 -45808.557938] FAST spr round 1 (radius: 25) [00:18:47 -39815.105828] FAST spr round 2 (radius: 25) [00:20:50 -38988.141691] FAST spr round 3 (radius: 25) [00:22:51 -38851.589476] FAST spr round 4 (radius: 25) [00:24:42 -38846.313422] FAST spr round 5 (radius: 25) [00:26:23 -38846.313338] Model parameter optimization (eps = 1.000000) [00:26:38 -38843.178485] SLOW spr round 1 (radius: 5) [00:28:47 -38835.473196] SLOW spr round 2 (radius: 5) [00:30:55 -38835.471283] SLOW spr round 3 (radius: 10) [00:33:05 -38834.965292] SLOW spr round 4 (radius: 5) [00:35:43 -38831.869867] SLOW spr round 5 (radius: 5) [00:38:04 -38831.869505] SLOW spr round 6 (radius: 10) [00:40:15 -38831.869398] SLOW spr round 7 (radius: 15) [00:43:17 -38831.177880] SLOW spr round 8 (radius: 5) [00:46:00 -38825.825713] SLOW spr round 9 (radius: 5) [00:48:26 -38825.825689] SLOW spr round 10 (radius: 10) [00:50:37 -38825.825672] SLOW spr round 11 (radius: 15) [00:53:36 -38825.825659] SLOW spr round 12 (radius: 20) [00:58:01 -38825.825647] SLOW spr round 13 (radius: 25) [01:04:28 -38825.825637] Model parameter optimization (eps = 0.100000) [01:04:38] [worker #0] ML tree search #1, logLikelihood: -38825.587287 [01:04:38 -216865.016056] Initial branch length optimization [01:04:41 -179417.654547] Model parameter optimization (eps = 10.000000) [01:05:20 -178348.011118] AUTODETECT spr round 1 (radius: 5) [01:07:08] [worker #1] ML tree search #2, logLikelihood: -38811.244932 [01:07:52 -105415.033392] AUTODETECT spr round 2 (radius: 10) [01:10:26 -68434.583367] AUTODETECT spr round 3 (radius: 15) [01:13:14 -55626.085581] AUTODETECT spr round 4 (radius: 20) [01:13:52] [worker #3] ML tree search #4, logLikelihood: -38824.555577 [01:16:34 -49290.701519] AUTODETECT spr round 5 (radius: 25) [01:19:21] [worker #2] ML tree search #3, logLikelihood: -38821.877177 [01:20:21 -47213.279886] SPR radius for FAST iterations: 25 (autodetect) [01:20:21 -47213.279886] Model parameter optimization (eps = 3.000000) [01:20:46 -47185.237713] FAST spr round 1 (radius: 25) [01:23:32 -39704.171418] FAST spr round 2 (radius: 25) [01:25:38 -38910.102331] FAST spr round 3 (radius: 25) [01:27:36 -38862.269540] FAST spr round 4 (radius: 25) [01:29:26 -38855.635080] FAST spr round 5 (radius: 25) [01:31:11 -38853.260013] FAST spr round 6 (radius: 25) [01:32:50 -38853.259968] Model parameter optimization (eps = 1.000000) [01:33:09 -38847.231624] SLOW spr round 1 (radius: 5) [01:35:18 -38830.852650] SLOW spr round 2 (radius: 5) [01:37:30 -38827.346356] SLOW spr round 3 (radius: 5) [01:39:39 -38820.717823] SLOW spr round 4 (radius: 5) [01:41:42 -38820.717803] SLOW spr round 5 (radius: 10) [01:43:53 -38819.457780] SLOW spr round 6 (radius: 5) [01:46:29 -38819.446628] SLOW spr round 7 (radius: 10) [01:48:46 -38819.446586] SLOW spr round 8 (radius: 15) [01:51:46 -38819.446546] SLOW spr round 9 (radius: 20) [01:56:08 -38819.446505] SLOW spr round 10 (radius: 25) [02:02:14 -38819.446459] Model parameter optimization (eps = 0.100000) [02:02:24] [worker #0] ML tree search #5, logLikelihood: -38819.282298 [02:02:24 -215193.800700] Initial branch length optimization [02:02:27 -177037.241506] Model parameter optimization (eps = 10.000000) [02:03:15 -176014.949194] AUTODETECT spr round 1 (radius: 5) [02:04:51] [worker #1] ML tree search #6, logLikelihood: -38800.199810 [02:05:44 -104409.935303] AUTODETECT spr round 2 (radius: 10) [02:08:19 -67810.869638] AUTODETECT spr round 3 (radius: 15) [02:11:16 -54276.945900] AUTODETECT spr round 4 (radius: 20) [02:13:39] [worker #3] ML tree search #8, logLikelihood: -38859.278561 [02:14:44 -48268.231825] AUTODETECT spr round 5 (radius: 25) [02:18:36 -47281.988637] SPR radius for FAST iterations: 25 (autodetect) [02:18:36 -47281.988637] Model parameter optimization (eps = 3.000000) [02:18:59 -47235.548580] FAST spr round 1 (radius: 25) [02:21:34 -39548.533124] FAST spr round 2 (radius: 25) [02:23:45 -38889.467740] FAST spr round 3 (radius: 25) [02:25:41 -38851.535750] FAST spr round 4 (radius: 25) [02:27:30 -38850.484637] FAST spr round 5 (radius: 25) [02:28:18] [worker #2] ML tree search #7, logLikelihood: -38900.129426 [02:29:12 -38850.481100] Model parameter optimization (eps = 1.000000) [02:29:27 -38847.562804] SLOW spr round 1 (radius: 5) [02:31:40 -38838.470598] SLOW spr round 2 (radius: 5) [02:33:51 -38838.438561] SLOW spr round 3 (radius: 10) [02:36:00 -38835.560287] SLOW spr round 4 (radius: 5) [02:38:35 -38835.559794] SLOW spr round 5 (radius: 10) [02:40:58 -38834.075472] SLOW spr round 6 (radius: 5) [02:43:34 -38822.423680] SLOW spr round 7 (radius: 5) [02:45:57 -38811.493588] SLOW spr round 8 (radius: 5) [02:48:11 -38811.448335] SLOW spr round 9 (radius: 10) [02:50:21 -38811.447761] SLOW spr round 10 (radius: 15) [02:53:22 -38811.447744] SLOW spr round 11 (radius: 20) [02:57:45 -38811.447728] SLOW spr round 12 (radius: 25) [03:04:03 -38811.447712] Model parameter optimization (eps = 0.100000) [03:04:09] [worker #0] ML tree search #9, logLikelihood: -38811.424187 [03:04:09 -214965.471807] Initial branch length optimization [03:04:12 -177418.036405] Model parameter optimization (eps = 10.000000) [03:05:15 -176399.238175] AUTODETECT spr round 1 (radius: 5) [03:07:48 -102071.265156] AUTODETECT spr round 2 (radius: 10) [03:10:21 -69385.725885] AUTODETECT spr round 3 (radius: 15) [03:13:19 -56328.093294] AUTODETECT spr round 4 (radius: 20) [03:16:45 -50672.037768] AUTODETECT spr round 5 (radius: 25) [03:20:37 -48470.769108] SPR radius for FAST iterations: 25 (autodetect) [03:20:38 -48470.769108] Model parameter optimization (eps = 3.000000) [03:20:58 -48414.189388] FAST spr round 1 (radius: 25) [03:22:19] [worker #3] ML tree search #12, logLikelihood: -38786.723462 [03:23:46 -39511.594520] FAST spr round 2 (radius: 25) [03:25:58 -38915.000166] FAST spr round 3 (radius: 25) [03:28:01 -38857.028633] FAST spr round 4 (radius: 25) [03:29:51 -38848.606118] FAST spr round 5 (radius: 25) [03:31:33 -38848.593463] Model parameter optimization (eps = 1.000000) [03:31:47 -38845.384247] SLOW spr round 1 (radius: 5) [03:33:56 -38834.715622] SLOW spr round 2 (radius: 5) [03:36:06 -38827.652118] SLOW spr round 3 (radius: 5) [03:38:14 -38822.043745] SLOW spr round 4 (radius: 5) [03:40:17 -38816.021764] SLOW spr round 5 (radius: 5) [03:42:20 -38816.021735] SLOW spr round 6 (radius: 10) [03:44:26 -38816.021728] SLOW spr round 7 (radius: 15) [03:46:29] [worker #2] ML tree search #11, logLikelihood: -39264.787132 [03:47:36 -38814.906282] SLOW spr round 8 (radius: 5) [03:50:24 -38814.903877] SLOW spr round 9 (radius: 10) [03:52:54 -38814.903229] SLOW spr round 10 (radius: 15) [03:55:52 -38814.903225] SLOW spr round 11 (radius: 20) [03:57:09] [worker #1] ML tree search #10, logLikelihood: -38819.729883 [04:00:34 -38814.903220] SLOW spr round 12 (radius: 25) [04:06:49 -38814.903216] Model parameter optimization (eps = 0.100000) [04:06:58] [worker #0] ML tree search #13, logLikelihood: -38814.682268 [04:06:58 -214340.368461] Initial branch length optimization [04:07:02 -176884.884991] Model parameter optimization (eps = 10.000000) [04:07:38 -175884.311172] AUTODETECT spr round 1 (radius: 5) [04:10:10 -104692.718387] AUTODETECT spr round 2 (radius: 10) [04:12:44 -70037.466308] AUTODETECT spr round 3 (radius: 15) [04:15:36 -57207.483446] AUTODETECT spr round 4 (radius: 20) [04:19:05 -49064.987421] AUTODETECT spr round 5 (radius: 25) [04:22:45 -45972.826265] SPR radius for FAST iterations: 25 (autodetect) [04:22:45 -45972.826265] Model parameter optimization (eps = 3.000000) [04:23:05 -45921.750405] FAST spr round 1 (radius: 25) [04:25:37 -39676.610776] FAST spr round 2 (radius: 25) [04:27:05] [worker #3] ML tree search #16, logLikelihood: -38834.128739 [04:27:44 -38953.674480] FAST spr round 3 (radius: 25) [04:29:41 -38847.575932] FAST spr round 4 (radius: 25) [04:31:31 -38836.742688] FAST spr round 5 (radius: 25) [04:33:14 -38836.742245] Model parameter optimization (eps = 1.000000) [04:33:26 -38835.676027] SLOW spr round 1 (radius: 5) [04:35:37 -38827.999184] SLOW spr round 2 (radius: 5) [04:37:46 -38827.144105] SLOW spr round 3 (radius: 5) [04:39:50 -38827.143165] SLOW spr round 4 (radius: 10) [04:42:03 -38813.882705] SLOW spr round 5 (radius: 5) [04:44:45 -38803.521143] SLOW spr round 6 (radius: 5) [04:46:11] [worker #2] ML tree search #15, logLikelihood: -38814.074049 [04:47:06 -38803.245054] SLOW spr round 7 (radius: 5) [04:47:42] [worker #1] ML tree search #14, logLikelihood: -38816.655136 [04:49:17 -38803.245025] SLOW spr round 8 (radius: 10) [04:51:27 -38803.245000] SLOW spr round 9 (radius: 15) [04:54:33 -38803.148103] SLOW spr round 10 (radius: 20) [04:58:50 -38803.147979] SLOW spr round 11 (radius: 25) [05:04:53 -38803.147972] Model parameter optimization (eps = 0.100000) [05:04:58] [worker #0] ML tree search #17, logLikelihood: -38803.136395 [05:29:40] [worker #3] ML tree search #20, logLikelihood: -38844.285454 [05:40:49] [worker #2] ML tree search #19, logLikelihood: -38828.436563 [05:42:29] [worker #1] ML tree search #18, logLikelihood: -38807.750279 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.219157,0.434311) (0.223139,0.536850) (0.340066,0.945813) (0.217639,2.129156) 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: -38786.723462 AIC score: 81583.446924 / AICc score: 8125643.446924 / BIC score: 87985.325410 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=180). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 374 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08590/3_mltree/P08590.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08590/3_mltree/P08590.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08590/3_mltree/P08590.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08590/3_mltree/P08590.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08590/3_mltree/P08590.raxml.log Analysis started: 01-Jul-2021 03:58:40 / finished: 01-Jul-2021 09:41:10 Elapsed time: 20549.609 seconds Consumed energy: 1721.169 Wh (= 9 km in an electric car, or 43 km with an e-scooter!)