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 04-Jul-2021 00:15:11 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43424/2_msa/O43424_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43424/3_mltree/O43424 --seed 2 --threads 2 --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 (2 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43424/2_msa/O43424_trimmed_msa.fasta [00:00:00] Loaded alignment with 841 taxa and 108 sites WARNING: Sequences tr_B4QMR2_B4QMR2_DROSI_7240 and tr_M9PHV5_M9PHV5_DROME_7227 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_G1MUQ7_G1MUQ7_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_K7G8S0_K7G8S0_PELSI_13735 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_H0Z5G4_H0Z5G4_TAEGU_59729 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_U3JVW5_U3JVW5_FICAL_59894 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_U3J5C6_U3J5C6_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_A0A151MTD9_A0A151MTD9_ALLMI_8496 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_A0A0Q3PEC0_A0A0Q3PEC0_AMAAE_12930 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_A0A093PGR6_A0A093PGR6_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_A0A087QH89_A0A087QH89_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_A0A091XCP2_A0A091XCP2_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_A0A099ZQ43_A0A099ZQ43_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_A0A091FMC5_A0A091FMC5_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_A0A0A0B1L5_A0A0A0B1L5_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_A0A2I0MFA0_A0A2I0MFA0_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_A0A091HRA1_A0A091HRA1_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_A0A1U8D2H5_A0A1U8D2H5_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_A0A1V4KJP3_A0A1V4KJP3_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1D5PEE9_A0A1D5PEE9_CHICK_9031 and tr_A0A218UJC3_A0A218UJC3_9PASE_299123 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_G1N1N6_G1N1N6_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_K7FV51_K7FV51_PELSI_13735 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_H0YY37_H0YY37_TAEGU_59729 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_U3JU91_U3JU91_FICAL_59894 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_R0JL74_R0JL74_ANAPL_8839 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_A0A0Q3SYI5_A0A0Q3SYI5_AMAAE_12930 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_A0A091F8M5_A0A091F8M5_CORBR_85066 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_A0A093QE44_A0A093QE44_9PASS_328815 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_A0A091W1I4_A0A091W1I4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_A0A093HEI7_A0A093HEI7_STRCA_441894 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_A0A091G6G2_A0A091G6G2_9AVES_55661 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_A0A099ZZZ0_A0A099ZZZ0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_A0A2I0M935_A0A2I0M935_COLLI_8932 are exactly identical! WARNING: Sequences tr_F1NAD5_F1NAD5_CHICK_9031 and tr_A0A218V288_A0A218V288_9PASE_299123 are exactly identical! WARNING: Sequences tr_F1NAK2_F1NAK2_CHICK_9031 and tr_A0A0Q3M9L7_A0A0Q3M9L7_AMAAE_12930 are exactly identical! WARNING: Sequences tr_F1NAK2_F1NAK2_CHICK_9031 and tr_A0A091WB77_A0A091WB77_OPIHO_30419 are exactly identical! WARNING: Sequences tr_F1NAK2_F1NAK2_CHICK_9031 and tr_A0A099Z3K4_A0A099Z3K4_TINGU_94827 are exactly identical! WARNING: Sequences tr_F1NAK2_F1NAK2_CHICK_9031 and tr_A0A226NIP3_A0A226NIP3_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q61625_GRID2_MOUSE_10090 and sp_Q63226_GRID2_RAT_10116 are exactly identical! WARNING: Sequences sp_Q61625_GRID2_MOUSE_10090 and tr_A0A1U7QWD2_A0A1U7QWD2_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_M3Y7I1_M3Y7I1_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A2I3G2U3_A0A2I3G2U3_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_G1PQJ0_G1PQJ0_MYOLU_59463 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_G3RCT9_G3RCT9_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_H2NYZ6_H2NYZ6_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_G1TIJ4_G1TIJ4_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_E2RFB5_E2RFB5_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A2I3S1J9_A0A2I3S1J9_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_F7DSG0_F7DSG0_ORNAN_9258 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_H9H7B2_H9H7B2_MONDO_13616 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_F7A380_F7A380_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and sp_Q63273_GRIK5_RAT_10116 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_I3MID5_I3MID5_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_H0XD91_H0XD91_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_H0W7U9_H0W7U9_CAVPO_10141 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and sp_Q16478_GRIK5_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_F7HPP3_F7HPP3_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_G5AZQ7_G5AZQ7_HETGA_10181 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_G3W359_G3W359_SARHA_9305 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_U3EFN9_U3EFN9_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_F1RGG5_F1RGG5_PIG_9823 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_G1LDT5_G1LDT5_AILME_9646 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_G7PXQ4_G7PXQ4_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_L5L7K9_L5L7K9_PTEAL_9402 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A337SHA5_A0A337SHA5_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A2I3MDR0_A0A2I3MDR0_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A091DNC7_A0A091DNC7_FUKDA_885580 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A0D9S128_A0A0D9S128_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A1S3GGY2_A0A1S3GGY2_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A3Q0EDE4_A0A3Q0EDE4_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A1U8CZZ1_A0A1U8CZZ1_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A2K5LH50_A0A2K5LH50_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A2K6DP98_A0A2K6DP98_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A2K5Z8I3_A0A2K5Z8I3_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A2R9B7D6_A0A2R9B7D6_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A2U3ZNN9_A0A2U3ZNN9_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A2Y9IFW6_A0A2Y9IFW6_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A2Y9P2D8_A0A2Y9P2D8_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A2Y9TBU9_A0A2Y9TBU9_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q61626_GRIK5_MOUSE_10090 and tr_A0A383YZV6_A0A383YZV6_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q61627_GRID1_MOUSE_10090 and tr_A0A091DSD1_A0A091DSD1_FUKDA_885580 are exactly identical! WARNING: Sequences sp_Q8BMF5_GRIK4_MOUSE_10090 and tr_G3IAU4_G3IAU4_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q8BMF5_GRIK4_MOUSE_10090 and tr_G1SI38_G1SI38_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q8BMF5_GRIK4_MOUSE_10090 and tr_F6SKB7_F6SKB7_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q8BMF5_GRIK4_MOUSE_10090 and sp_Q01812_GRIK4_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8BMF5_GRIK4_MOUSE_10090 and tr_A0A1U8BYV7_A0A1U8BYV7_MESAU_10036 are exactly identical! WARNING: Sequences tr_W5JDY0_W5JDY0_ANODA_43151 and tr_B0WHP1_B0WHP1_CULQU_7176 are exactly identical! WARNING: Sequences tr_W5JDY0_W5JDY0_ANODA_43151 and tr_Q17HY9_Q17HY9_AEDAE_7159 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_G1PNN5_G1PNN5_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_F1PEI5_F1PEI5_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_W5QA32_W5QA32_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_I3MD23_I3MD23_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_H0WQZ2_H0WQZ2_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_G5C882_G5C882_HETGA_10181 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_G3T9I4_G3T9I4_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_I3L7T2_I3L7T2_PIG_9823 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_L5KQN4_L5KQN4_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_A0A337SF47_A0A337SF47_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_A0A2U4AMU0_A0A2U4AMU0_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_A0A2U3X6X9_A0A2U3X6X9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_A0A2Y9KCQ6_A0A2Y9KCQ6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_A0A2Y9NVJ2_A0A2Y9NVJ2_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_A0A384DEE7_A0A384DEE7_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3XSP9_M3XSP9_MUSPF_9669 and tr_A0A384AA03_A0A384AA03_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_G3RT89_G3RT89_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_H2NFM0_H2NFM0_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_F1PHA8_F1PHA8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and sp_Q5IS46_GRIK4_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_F7FB74_F7FB74_MONDO_13616 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_W5Q939_W5Q939_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_I3MQJ2_I3MQJ2_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_H0WIU0_H0WIU0_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and sp_Q16099_GRIK4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A1D5R2U8_A0A1D5R2U8_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_G5APF2_G5APF2_HETGA_10181 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_G3TIJ1_G3TIJ1_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_F6PKN4_F6PKN4_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_F1S9S0_F1S9S0_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_G1LNH0_G1LNH0_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_G7PPC1_G7PPC1_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_F1MCW8_F1MCW8_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_L5JPY5_L5JPY5_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_M3W072_M3W072_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A096NFJ7_A0A096NFJ7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A0D9S3Z6_A0A0D9S3Z6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A1S2ZRX8_A0A1S2ZRX8_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A3Q0DUH5_A0A3Q0DUH5_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A2K5MDA2_A0A2K5MDA2_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A2K6BYM9_A0A2K6BYM9_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A2K5XRZ2_A0A2K5XRZ2_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A2R9ADN4_A0A2R9ADN4_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A2U4BWG9_A0A2U4BWG9_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A2U3X533_A0A2U3X533_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A2U3XSF6_A0A2U3XSF6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A2Y9K6Q2_A0A2Y9K6Q2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A2Y9M247_A0A2Y9M247_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A2Y9FFF8_A0A2Y9FFF8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3Y2P0_M3Y2P0_MUSPF_9669 and tr_A0A384BAP9_A0A384BAP9_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3YB28_M3YB28_MUSPF_9669 and tr_A0A2Y9JCT5_A0A2Y9JCT5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_A0A2I3HEG0_A0A2I3HEG0_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_G1PSP9_G1PSP9_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_G3R0C0_G3R0C0_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_A0A2J8S084_A0A2J8S084_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_H2RB88_H2RB88_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and sp_Q5IS45_NMDE1_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_F6TCK9_F6TCK9_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and sp_Q12879_NMDE1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_A0A1D5QE40_A0A1D5QE40_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_G5BWG2_G5BWG2_HETGA_10181 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_F1MLZ9_F1MLZ9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_L5KP13_L5KP13_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_A0A096NLM9_A0A096NLM9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_A0A0D9R862_A0A0D9R862_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_A0A2K6D391_A0A2K6D391_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YTD1_M3YTD1_MUSPF_9669 and tr_A0A2R9AYV3_A0A2R9AYV3_PANPA_9597 are exactly identical! WARNING: Sequences tr_B4J091_B4J091_DROGR_7222 and tr_B4LHH3_B4LHH3_DROVI_7244 are exactly identical! WARNING: Sequences tr_G1RVW9_G1RVW9_NOMLE_61853 and tr_G3QDP7_G3QDP7_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RVW9_G1RVW9_NOMLE_61853 and tr_H2PDX0_H2PDX0_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RVW9_G1RVW9_NOMLE_61853 and tr_C7G3M0_C7G3M0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RVW9_G1RVW9_NOMLE_61853 and sp_O43424_GRID2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RVW9_G1RVW9_NOMLE_61853 and tr_F7BZZ7_F7BZZ7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RVW9_G1RVW9_NOMLE_61853 and tr_F7E4U9_F7E4U9_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RVW9_G1RVW9_NOMLE_61853 and tr_G7P5X5_G7P5X5_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RVW9_G1RVW9_NOMLE_61853 and tr_A0A2I3LQV6_A0A2I3LQV6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RVW9_G1RVW9_NOMLE_61853 and tr_A0A0D9QW21_A0A0D9QW21_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RVW9_G1RVW9_NOMLE_61853 and tr_A0A2K5M3C5_A0A2K5M3C5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RVW9_G1RVW9_NOMLE_61853 and tr_A0A2K6AWA2_A0A2K6AWA2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RVW9_G1RVW9_NOMLE_61853 and tr_A0A2R9A3M3_A0A2R9A3M3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3HPN5_G3HPN5_CRIGR_10029 and tr_A0A2U3YQT3_A0A2U3YQT3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and tr_H2NAD9_H2NAD9_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and tr_H2Q269_H2Q269_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and tr_I3MQN3_I3MQN3_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and sp_Q9ULK0_GRID1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and tr_F7HBB4_F7HBB4_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and tr_U3EE85_U3EE85_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and tr_G7PEW2_G7PEW2_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and tr_A0A096P4D8_A0A096P4D8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and tr_A0A0D9RB87_A0A0D9RB87_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and tr_A0A1U7SWS6_A0A1U7SWS6_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and tr_A0A2K5MBC2_A0A2K5MBC2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and tr_A0A2K6CX08_A0A2K6CX08_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and tr_A0A2K5YIE9_A0A2K5YIE9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3R9C0_G3R9C0_GORGO_9595 and tr_A0A2R9AC14_A0A2R9AC14_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PJW8_H2PJW8_PONAB_9601 and tr_G7P442_G7P442_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1MTI0_G1MTI0_MELGA_9103 and tr_U3JTX2_U3JTX2_FICAL_59894 are exactly identical! WARNING: Sequences tr_G1MTI0_G1MTI0_MELGA_9103 and tr_A0A091EXD8_A0A091EXD8_CORBR_85066 are exactly identical! WARNING: Sequences tr_G1MTI0_G1MTI0_MELGA_9103 and tr_A0A218UDF0_A0A218UDF0_9PASE_299123 are exactly identical! WARNING: Sequences tr_G3US54_G3US54_MELGA_9103 and tr_A0A3Q0DRI4_A0A3Q0DRI4_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3US54_G3US54_MELGA_9103 and tr_A0A2U3YW61_A0A2U3YW61_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1T1A9_G1T1A9_RABIT_9986 and tr_H0VJM3_H0VJM3_CAVPO_10141 are exactly identical! WARNING: Sequences tr_Q17697_Q17697_CAEEL_6239 and tr_A0A2H2I5Z1_A0A2H2I5Z1_CAEJA_281687 are exactly identical! WARNING: Sequences tr_K7E4Y6_K7E4Y6_MONDO_13616 and tr_A0A226MIV3_A0A226MIV3_CALSU_9009 are exactly identical! WARNING: Sequences tr_W5NQK0_W5NQK0_SHEEP_9940 and tr_F1N6E6_F1N6E6_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A3B5PXL8_A0A3B5PXL8_XIPMA_8083 and tr_A0A087YMF8_A0A087YMF8_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A3B5QA27_A0A3B5QA27_XIPMA_8083 and tr_G3P604_G3P604_GASAC_69293 are exactly identical! WARNING: Sequences tr_A0A3B5R3F4_A0A3B5R3F4_XIPMA_8083 and tr_A0A087XEB2_A0A087XEB2_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A088ADP1_A0A088ADP1_APIME_7460 and tr_A0A0M8ZVL9_A0A0M8ZVL9_9HYME_166423 are exactly identical! WARNING: Sequences tr_A0A088AND7_A0A088AND7_APIME_7460 and tr_A0A0L7RH80_A0A0L7RH80_9HYME_597456 are exactly identical! WARNING: Sequences tr_A0A088AND7_A0A088AND7_APIME_7460 and tr_A0A2A3EFD6_A0A2A3EFD6_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NYN4_A0A158NYN4_ATTCE_12957 and tr_E2C3M5_E2C3M5_HARSA_610380 are exactly identical! WARNING: Sequences tr_A0A158NYN4_A0A158NYN4_ATTCE_12957 and tr_A0A195DE06_A0A195DE06_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NZ96_A0A158NZ96_ATTCE_12957 and tr_A0A151J8G6_A0A151J8G6_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NZ96_A0A158NZ96_ATTCE_12957 and tr_A0A195B155_A0A195B155_9HYME_520822 are exactly identical! WARNING: Sequences tr_I3J7U1_I3J7U1_ORENI_8128 and tr_A0A087XJW8_A0A087XJW8_POEFO_48698 are exactly identical! WARNING: Sequences tr_H0WIA2_H0WIA2_OTOGA_30611 and tr_F1SEP5_F1SEP5_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A2H2IWP2_A0A2H2IWP2_CAEJA_281687 and tr_K7HUH2_K7HUH2_CAEJA_281687 are exactly identical! WARNING: Sequences tr_K7H424_K7H424_CAEJA_281687 and tr_E3NI25_E3NI25_CAERE_31234 are exactly identical! WARNING: Sequences tr_E5SFC8_E5SFC8_TRISP_6334 and tr_A0A0V1D3B5_A0A0V1D3B5_TRIBR_45882 are exactly identical! WARNING: Sequences tr_G3U243_G3U243_LOXAF_9785 and tr_L5KBZ4_L5KBZ4_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G3U243_G3U243_LOXAF_9785 and tr_A0A1S3G8X7_A0A1S3G8X7_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G3WAY2_G3WAY2_SARHA_9305 and tr_G1ML63_G1ML63_AILME_9646 are exactly identical! WARNING: Sequences tr_G0N5N1_G0N5N1_CAEBE_135651 and tr_A0A261BSZ2_A0A261BSZ2_9PELO_1503980 are exactly identical! WARNING: Sequences tr_G0P2D6_G0P2D6_CAEBE_135651 and tr_G0PK10_G0PK10_CAEBE_135651 are exactly identical! WARNING: Sequences tr_G0P2D6_G0P2D6_CAEBE_135651 and tr_E3MN25_E3MN25_CAERE_31234 are exactly identical! WARNING: Sequences tr_G0P2D6_G0P2D6_CAEBE_135651 and tr_A8XGR3_A8XGR3_CAEBR_6238 are exactly identical! WARNING: Sequences tr_G0P2D6_G0P2D6_CAEBE_135651 and tr_A0A1I7T4S8_A0A1I7T4S8_9PELO_1561998 are exactly identical! WARNING: Sequences tr_G0P2D6_G0P2D6_CAEBE_135651 and tr_A0A1I7T4S9_A0A1I7T4S9_9PELO_1561998 are exactly identical! WARNING: Sequences tr_G0P2D6_G0P2D6_CAEBE_135651 and tr_A0A261C7W0_A0A261C7W0_9PELO_1503980 are exactly identical! WARNING: Sequences tr_G0P2D6_G0P2D6_CAEBE_135651 and tr_A0A2G5V0Y0_A0A2G5V0Y0_9PELO_1611254 are exactly identical! WARNING: Sequences tr_F7DEY7_F7DEY7_XENTR_8364 and tr_A0A1L8FFY4_A0A1L8FFY4_XENLA_8355 are exactly identical! WARNING: Sequences tr_F7DEY7_F7DEY7_XENTR_8364 and tr_A0A1L8FLD0_A0A1L8FLD0_XENLA_8355 are exactly identical! WARNING: Sequences tr_F7E4G4_F7E4G4_XENTR_8364 and tr_A0A1L8FK36_A0A1L8FK36_XENLA_8355 are exactly identical! WARNING: Sequences tr_A8XPK4_A8XPK4_CAEBR_6238 and tr_A0A2G5UFY4_A0A2G5UFY4_9PELO_1611254 are exactly identical! WARNING: Sequences tr_D2H1B6_D2H1B6_AILME_9646 and tr_G3MZJ2_G3MZJ2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1LTK0_G1LTK0_AILME_9646 and tr_M3WEE4_M3WEE4_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1LTK0_G1LTK0_AILME_9646 and tr_A0A384CI47_A0A384CI47_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1MC55_G1MC55_AILME_9646 and tr_A0A2K5XBC1_A0A2K5XBC1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3N1N5_G3N1N5_BOVIN_9913 and tr_A0A384AYE4_A0A384AYE4_BALAS_310752 are exactly identical! WARNING: Sequences tr_U3J2Z4_U3J2Z4_ANAPL_8839 and tr_A0A151NQC1_A0A151NQC1_ALLMI_8496 are exactly identical! WARNING: Sequences tr_U3J2Z4_U3J2Z4_ANAPL_8839 and tr_A0A093JQ91_A0A093JQ91_STRCA_441894 are exactly identical! WARNING: Sequences tr_U3J2Z4_U3J2Z4_ANAPL_8839 and tr_A0A099Z9C4_A0A099Z9C4_TINGU_94827 are exactly identical! WARNING: Sequences tr_U3J2Z4_U3J2Z4_ANAPL_8839 and tr_A0A2I0LS96_A0A2I0LS96_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3J2Z4_U3J2Z4_ANAPL_8839 and tr_A0A091HLP2_A0A091HLP2_CALAN_9244 are exactly identical! WARNING: Sequences tr_U3J2Z4_U3J2Z4_ANAPL_8839 and tr_A0A1U7RWT3_A0A1U7RWT3_ALLSI_38654 are exactly identical! WARNING: Sequences tr_U3J2Z4_U3J2Z4_ANAPL_8839 and tr_A0A1V4J7L2_A0A1V4J7L2_PATFA_372326 are exactly identical! WARNING: Sequences tr_U3J2Z4_U3J2Z4_ANAPL_8839 and tr_A0A226NDX9_A0A226NDX9_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A0D9RA34_A0A0D9RA34_CHLSB_60711 and tr_A0A226MYK3_A0A226MYK3_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A0D9RA34_A0A0D9RA34_CHLSB_60711 and tr_A0A226PJA2_A0A226PJA2_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A0N8K2F6_A0A0N8K2F6_9TELE_113540 and tr_A0A1S3SXN7_A0A1S3SXN7_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A0P7URF4_A0A0P7URF4_9TELE_113540 and tr_A0A060Z1U6_A0A060Z1U6_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A0K0EWW1_A0A0K0EWW1_STRVS_75913 and tr_A0A0N5C5R2_A0A0N5C5R2_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A151NML4_A0A151NML4_ALLMI_8496 and tr_A0A3Q0G768_A0A3Q0G768_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091J3R0_A0A091J3R0_EGRGA_188379 and tr_A0A091WK57_A0A091WK57_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A0V0YEN8_A0A0V0YEN8_TRIPS_6337 and tr_A0A0V1N0V6_A0A0V1N0V6_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A151X914_A0A151X914_9HYME_64791 and tr_A0A195FT20_A0A195FT20_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A1S3QFH6_A0A1S3QFH6_SALSA_8030 and tr_A0A1S3RZ66_A0A1S3RZ66_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3RMZ7_A0A1S3RMZ7_SALSA_8030 and tr_A0A060X4U7_A0A060X4U7_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A0M3QW67_A0A0M3QW67_DROBS_30019 and tr_A0A0M4ENP8_A0A0M4ENP8_DROBS_30019 are exactly identical! WARNING: Sequences tr_A0A1I7SYX1_A0A1I7SYX1_9PELO_1561998 and tr_A0A1I7SYX2_A0A1I7SYX2_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1L8FGX2_A0A1L8FGX2_XENLA_8355 and tr_A0A1L8FN24_A0A1L8FN24_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A3Q0DUR1_A0A3Q0DUR1_TARSY_1868482 and tr_A0A2U4ACF1_A0A2U4ACF1_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A1U8D3F5_A0A1U8D3F5_MESAU_10036 and tr_A0A2U3XKP1_A0A2U3XKP1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A226MDQ2_A0A226MDQ2_CALSU_9009 and tr_A0A226PEI5_A0A226PEI5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MJ56_A0A226MJ56_CALSU_9009 and tr_A0A226P6W1_A0A226P6W1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MJ56_A0A226MJ56_CALSU_9009 and tr_A0A2U3YY35_A0A2U3YY35_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2A2JL68_A0A2A2JL68_9BILA_2018661 and tr_A0A2A2LTL3_A0A2A2LTL3_9BILA_2018661 are exactly identical! WARNING: Sequences tr_A0A2G8JQ35_A0A2G8JQ35_STIJA_307972 and tr_A0A2G8JT87_A0A2G8JT87_STIJA_307972 are exactly identical! WARNING: Sequences tr_A0A2U4AK69_A0A2U4AK69_TURTR_9739 and tr_A0A2Y9MLU8_A0A2Y9MLU8_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4AK69_A0A2U4AK69_TURTR_9739 and tr_A0A2Y9TGC0_A0A2Y9TGC0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4AK69_A0A2U4AK69_TURTR_9739 and tr_A0A383ZIE8_A0A383ZIE8_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 259 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/O43424/3_mltree/O43424.raxml.reduced.phy Alignment comprises 1 partitions and 108 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 108 / 108 Gaps: 12.00 % Invariant sites: 0.93 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43424/3_mltree/O43424.raxml.rba Parallelization scheme autoconfig: 2 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 841 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 108 / 8640 [00:00:00] Data distribution: max. searches per worker: 10 Starting ML tree search with 20 distinct starting trees [00:00:00 -124600.563819] Initial branch length optimization [00:00:02 -99869.420975] Model parameter optimization (eps = 10.000000) [00:00:29 -99352.111046] AUTODETECT spr round 1 (radius: 5) [00:01:44 -65941.259698] AUTODETECT spr round 2 (radius: 10) [00:03:07 -48206.844474] AUTODETECT spr round 3 (radius: 15) [00:04:33 -39337.093734] AUTODETECT spr round 4 (radius: 20) [00:06:17 -35176.206138] AUTODETECT spr round 5 (radius: 25) [00:08:05 -33884.167388] SPR radius for FAST iterations: 25 (autodetect) [00:08:05 -33884.167388] Model parameter optimization (eps = 3.000000) [00:08:27 -33710.221874] FAST spr round 1 (radius: 25) [00:09:57 -29748.849042] FAST spr round 2 (radius: 25) [00:11:12 -29492.277694] FAST spr round 3 (radius: 25) [00:12:22 -29474.035669] FAST spr round 4 (radius: 25) [00:13:27 -29469.795897] FAST spr round 5 (radius: 25) [00:14:26 -29469.734460] Model parameter optimization (eps = 1.000000) [00:14:45 -29456.604331] SLOW spr round 1 (radius: 5) [00:15:52 -29447.236745] SLOW spr round 2 (radius: 5) [00:17:00 -29443.905218] SLOW spr round 3 (radius: 5) [00:18:08 -29443.904398] SLOW spr round 4 (radius: 10) [00:19:23 -29442.691263] SLOW spr round 5 (radius: 5) [00:20:48 -29440.622219] SLOW spr round 6 (radius: 5) [00:22:06 -29438.178635] SLOW spr round 7 (radius: 5) [00:23:21 -29425.937675] SLOW spr round 8 (radius: 5) [00:24:30 -29424.313298] SLOW spr round 9 (radius: 5) [00:25:36 -29424.295538] SLOW spr round 10 (radius: 10) [00:26:51 -29416.021494] SLOW spr round 11 (radius: 5) [00:28:14 -29414.421939] SLOW spr round 12 (radius: 5) [00:29:24 -29414.419087] SLOW spr round 13 (radius: 10) [00:30:36 -29414.417931] SLOW spr round 14 (radius: 15) [00:32:16 -29413.374838] SLOW spr round 15 (radius: 5) [00:33:38 -29413.374634] SLOW spr round 16 (radius: 10) [00:34:56 -29413.374575] SLOW spr round 17 (radius: 15) [00:36:33 -29413.374558] SLOW spr round 18 (radius: 20) [00:38:48 -29412.955759] SLOW spr round 19 (radius: 5) [00:40:12 -29412.955678] SLOW spr round 20 (radius: 10) [00:41:33 -29412.178128] SLOW spr round 21 (radius: 5) [00:42:53 -29412.178092] SLOW spr round 22 (radius: 10) [00:44:09 -29412.178076] SLOW spr round 23 (radius: 15) [00:45:49 -29412.178075] SLOW spr round 24 (radius: 20) [00:48:06 -29412.178075] SLOW spr round 25 (radius: 25) [00:50:49 -29411.732143] SLOW spr round 26 (radius: 5) [00:52:10] [worker #1] ML tree search #2, logLikelihood: -29515.364440 [00:52:13 -29411.730996] SLOW spr round 27 (radius: 10) [00:53:35 -29411.730935] SLOW spr round 28 (radius: 15) [00:55:15 -29410.673163] SLOW spr round 29 (radius: 5) [00:56:37 -29410.619722] SLOW spr round 30 (radius: 10) [00:57:56 -29410.619428] SLOW spr round 31 (radius: 15) [00:59:35 -29410.619174] SLOW spr round 32 (radius: 20) [01:01:51 -29410.618912] SLOW spr round 33 (radius: 25) [01:04:33 -29410.618654] Model parameter optimization (eps = 0.100000) [01:04:44] [worker #0] ML tree search #1, logLikelihood: -29409.860866 [01:04:44 -124548.759947] Initial branch length optimization [01:04:45 -99446.880025] Model parameter optimization (eps = 10.000000) [01:05:09 -98796.703137] AUTODETECT spr round 1 (radius: 5) [01:06:22 -68284.643419] AUTODETECT spr round 2 (radius: 10) [01:07:45 -49677.995258] AUTODETECT spr round 3 (radius: 15) [01:09:10 -40099.948405] AUTODETECT spr round 4 (radius: 20) [01:10:46 -35173.377796] AUTODETECT spr round 5 (radius: 25) [01:12:32 -33836.530708] SPR radius for FAST iterations: 25 (autodetect) [01:12:32 -33836.530708] Model parameter optimization (eps = 3.000000) [01:12:52 -33644.324586] FAST spr round 1 (radius: 25) [01:14:22 -29750.876977] FAST spr round 2 (radius: 25) [01:15:38 -29472.538562] FAST spr round 3 (radius: 25) [01:16:44 -29448.106721] FAST spr round 4 (radius: 25) [01:17:45 -29445.545692] FAST spr round 5 (radius: 25) [01:18:41 -29445.531793] Model parameter optimization (eps = 1.000000) [01:18:54 -29440.104555] SLOW spr round 1 (radius: 5) [01:19:59 -29430.479192] SLOW spr round 2 (radius: 5) [01:21:03 -29426.844618] SLOW spr round 3 (radius: 5) [01:22:08 -29426.608185] SLOW spr round 4 (radius: 5) [01:23:13 -29426.607446] SLOW spr round 5 (radius: 10) [01:24:23 -29425.804816] SLOW spr round 6 (radius: 5) [01:25:43 -29417.307011] SLOW spr round 7 (radius: 5) [01:26:55 -29417.306074] SLOW spr round 8 (radius: 10) [01:28:09 -29416.569194] SLOW spr round 9 (radius: 5) [01:29:28 -29416.568830] SLOW spr round 10 (radius: 10) [01:30:44 -29416.568735] SLOW spr round 11 (radius: 15) [01:32:24 -29413.291881] SLOW spr round 12 (radius: 5) [01:33:48 -29411.755731] SLOW spr round 13 (radius: 5) [01:35:03 -29411.754475] SLOW spr round 14 (radius: 10) [01:36:16 -29409.647704] SLOW spr round 15 (radius: 5) [01:37:36 -29408.634137] SLOW spr round 16 (radius: 5) [01:38:47 -29408.633800] SLOW spr round 17 (radius: 10) [01:39:59 -29408.633731] SLOW spr round 18 (radius: 15) [01:41:42 -29408.446021] SLOW spr round 19 (radius: 5) [01:43:08 -29408.445927] SLOW spr round 20 (radius: 10) [01:44:30 -29408.445859] SLOW spr round 21 (radius: 15) [01:46:14 -29408.445795] SLOW spr round 22 (radius: 20) [01:48:42 -29408.445726] SLOW spr round 23 (radius: 25) [01:51:41 -29407.992761] SLOW spr round 24 (radius: 5) [01:51:46] [worker #1] ML tree search #4, logLikelihood: -29416.200023 [01:53:11 -29407.991390] SLOW spr round 25 (radius: 10) [01:54:37 -29407.991364] SLOW spr round 26 (radius: 15) [01:56:22 -29407.458253] SLOW spr round 27 (radius: 5) [01:57:48 -29407.458230] SLOW spr round 28 (radius: 10) [01:59:11 -29407.458212] SLOW spr round 29 (radius: 15) [02:00:55 -29407.458192] SLOW spr round 30 (radius: 20) [02:03:18 -29407.458177] SLOW spr round 31 (radius: 25) [02:06:15 -29407.458162] Model parameter optimization (eps = 0.100000) [02:06:26] [worker #0] ML tree search #3, logLikelihood: -29405.888199 [02:06:26 -125682.122870] Initial branch length optimization [02:06:28 -100065.138985] Model parameter optimization (eps = 10.000000) [02:06:55 -99550.554168] AUTODETECT spr round 1 (radius: 5) [02:08:09 -68178.978361] AUTODETECT spr round 2 (radius: 10) [02:09:38 -49099.601878] AUTODETECT spr round 3 (radius: 15) [02:11:09 -40060.266678] AUTODETECT spr round 4 (radius: 20) [02:12:55 -35134.573034] AUTODETECT spr round 5 (radius: 25) [02:14:51 -34252.027146] SPR radius for FAST iterations: 25 (autodetect) [02:14:51 -34252.027146] Model parameter optimization (eps = 3.000000) [02:15:11 -34030.136530] FAST spr round 1 (radius: 25) [02:16:42 -29775.807877] FAST spr round 2 (radius: 25) [02:17:59 -29506.540858] FAST spr round 3 (radius: 25) [02:19:07 -29468.884511] FAST spr round 4 (radius: 25) [02:20:11 -29454.031482] FAST spr round 5 (radius: 25) [02:21:11 -29453.536783] FAST spr round 6 (radius: 25) [02:22:10 -29453.535962] Model parameter optimization (eps = 1.000000) [02:22:25 -29436.025157] SLOW spr round 1 (radius: 5) [02:23:31 -29421.910668] SLOW spr round 2 (radius: 5) [02:24:35 -29416.968062] SLOW spr round 3 (radius: 5) [02:25:39 -29416.967111] SLOW spr round 4 (radius: 10) [02:26:48 -29416.559264] SLOW spr round 5 (radius: 5) [02:28:08 -29414.991047] SLOW spr round 6 (radius: 5) [02:29:20 -29414.967758] SLOW spr round 7 (radius: 10) [02:30:34 -29414.870399] SLOW spr round 8 (radius: 15) [02:32:11 -29414.041648] SLOW spr round 9 (radius: 5) [02:33:33 -29414.040821] SLOW spr round 10 (radius: 10) [02:34:53 -29414.040458] SLOW spr round 11 (radius: 15) [02:36:27 -29414.040150] SLOW spr round 12 (radius: 20) [02:38:37 -29411.285155] SLOW spr round 13 (radius: 5) [02:40:00 -29411.099153] SLOW spr round 14 (radius: 5) [02:41:17 -29411.099111] SLOW spr round 15 (radius: 10) [02:42:32 -29411.099095] SLOW spr round 16 (radius: 15) [02:44:13 -29411.099095] SLOW spr round 17 (radius: 20) [02:46:33 -29411.099095] SLOW spr round 18 (radius: 25) [02:49:33 -29410.544687] SLOW spr round 19 (radius: 5) [02:51:02 -29410.533376] SLOW spr round 20 (radius: 10) [02:52:30 -29410.531873] SLOW spr round 21 (radius: 15) [02:53:05] [worker #1] ML tree search #6, logLikelihood: -29463.938403 [02:54:12 -29410.531691] SLOW spr round 22 (radius: 20) [02:56:28 -29410.531669] SLOW spr round 23 (radius: 25) [02:59:27 -29409.768766] SLOW spr round 24 (radius: 5) [03:00:57 -29409.764988] SLOW spr round 25 (radius: 10) [03:02:23 -29409.570532] SLOW spr round 26 (radius: 5) [03:03:43 -29409.570388] SLOW spr round 27 (radius: 10) [03:05:02 -29409.570380] SLOW spr round 28 (radius: 15) [03:06:43 -29409.570380] SLOW spr round 29 (radius: 20) [03:09:03 -29408.437258] SLOW spr round 30 (radius: 5) [03:10:32 -29408.435385] SLOW spr round 31 (radius: 10) [03:11:58 -29408.435152] SLOW spr round 32 (radius: 15) [03:13:38 -29408.435123] SLOW spr round 33 (radius: 20) [03:15:56 -29408.435119] SLOW spr round 34 (radius: 25) [03:18:57 -29407.837281] SLOW spr round 35 (radius: 5) [03:20:26 -29407.837280] SLOW spr round 36 (radius: 10) [03:21:53 -29407.837280] SLOW spr round 37 (radius: 15) [03:23:33 -29407.837280] SLOW spr round 38 (radius: 20) [03:25:50 -29407.837280] SLOW spr round 39 (radius: 25) [03:28:51 -29407.837280] Model parameter optimization (eps = 0.100000) [03:29:01] [worker #0] ML tree search #5, logLikelihood: -29407.342748 [03:29:01 -124868.532229] Initial branch length optimization [03:29:03 -99414.072016] Model parameter optimization (eps = 10.000000) [03:29:25 -98848.522237] AUTODETECT spr round 1 (radius: 5) [03:30:39 -67209.090519] AUTODETECT spr round 2 (radius: 10) [03:32:02 -49413.751078] AUTODETECT spr round 3 (radius: 15) [03:33:27 -39394.918316] AUTODETECT spr round 4 (radius: 20) [03:35:11 -34671.827129] AUTODETECT spr round 5 (radius: 25) [03:37:10 -33871.241081] SPR radius for FAST iterations: 25 (autodetect) [03:37:10 -33871.241081] Model parameter optimization (eps = 3.000000) [03:37:34 -33634.278699] FAST spr round 1 (radius: 25) [03:39:03 -29837.720090] FAST spr round 2 (radius: 25) [03:40:20 -29498.682508] FAST spr round 3 (radius: 25) [03:41:28 -29464.571403] FAST spr round 4 (radius: 25) [03:42:31 -29458.255879] FAST spr round 5 (radius: 25) [03:43:30 -29458.255110] Model parameter optimization (eps = 1.000000) [03:43:45 -29450.803791] SLOW spr round 1 (radius: 5) [03:44:49 -29436.051736] SLOW spr round 2 (radius: 5) [03:45:53 -29435.302415] SLOW spr round 3 (radius: 5) [03:46:58 -29435.301922] SLOW spr round 4 (radius: 10) [03:48:07 -29435.215152] SLOW spr round 5 (radius: 15) [03:49:49 -29433.142995] SLOW spr round 6 (radius: 5) [03:51:14 -29432.280149] SLOW spr round 7 (radius: 5) [03:52:29 -29432.279830] SLOW spr round 8 (radius: 10) [03:53:44 -29431.204673] SLOW spr round 9 (radius: 5) [03:55:04 -29428.586328] SLOW spr round 10 (radius: 5) [03:56:15 -29428.481559] SLOW spr round 11 (radius: 5) [03:57:21 -29428.481499] SLOW spr round 12 (radius: 10) [03:58:25] [worker #1] ML tree search #8, logLikelihood: -29437.902243 [03:58:31 -29428.481426] SLOW spr round 13 (radius: 15) [04:00:11 -29428.481404] SLOW spr round 14 (radius: 20) [04:02:23 -29428.481388] SLOW spr round 15 (radius: 25) [04:04:57 -29428.170517] SLOW spr round 16 (radius: 5) [04:06:23 -29428.169306] SLOW spr round 17 (radius: 10) [04:07:45 -29422.596655] SLOW spr round 18 (radius: 5) [04:09:05 -29417.823808] SLOW spr round 19 (radius: 5) [04:10:17 -29417.117855] SLOW spr round 20 (radius: 5) [04:11:26 -29416.410609] SLOW spr round 21 (radius: 5) [04:12:31 -29416.408658] SLOW spr round 22 (radius: 10) [04:13:40 -29416.408351] SLOW spr round 23 (radius: 15) [04:15:21 -29415.187909] SLOW spr round 24 (radius: 5) [04:16:44 -29415.187341] SLOW spr round 25 (radius: 10) [04:18:03 -29415.187093] SLOW spr round 26 (radius: 15) [04:19:39 -29415.186879] SLOW spr round 27 (radius: 20) [04:21:52 -29415.186684] SLOW spr round 28 (radius: 25) [04:24:23 -29415.186505] Model parameter optimization (eps = 0.100000) [04:24:31] [worker #0] ML tree search #7, logLikelihood: -29413.831818 [04:24:31 -124328.125107] Initial branch length optimization [04:24:32 -99763.670227] Model parameter optimization (eps = 10.000000) [04:24:55 -99177.492420] AUTODETECT spr round 1 (radius: 5) [04:26:06 -66434.004296] AUTODETECT spr round 2 (radius: 10) [04:27:27 -48059.433481] AUTODETECT spr round 3 (radius: 15) [04:28:49 -40773.922661] AUTODETECT spr round 4 (radius: 20) [04:30:30 -36797.697590] AUTODETECT spr round 5 (radius: 25) [04:32:28 -34486.826324] SPR radius for FAST iterations: 25 (autodetect) [04:32:28 -34486.826324] Model parameter optimization (eps = 3.000000) [04:32:44 -34293.399734] FAST spr round 1 (radius: 25) [04:34:12 -29767.618206] FAST spr round 2 (radius: 25) [04:35:23 -29495.923821] FAST spr round 3 (radius: 25) [04:36:28 -29453.460640] FAST spr round 4 (radius: 25) [04:37:29 -29438.868366] FAST spr round 5 (radius: 25) [04:38:29 -29432.165343] FAST spr round 6 (radius: 25) [04:39:27 -29429.310718] FAST spr round 7 (radius: 25) [04:40:22 -29429.308502] Model parameter optimization (eps = 1.000000) [04:40:37 -29421.893329] SLOW spr round 1 (radius: 5) [04:41:41 -29411.024917] SLOW spr round 2 (radius: 5) [04:42:45 -29409.360109] SLOW spr round 3 (radius: 5) [04:43:48 -29409.359135] SLOW spr round 4 (radius: 10) [04:44:57 -29408.457667] SLOW spr round 5 (radius: 5) [04:46:17 -29407.270258] SLOW spr round 6 (radius: 5) [04:47:27 -29407.269570] SLOW spr round 7 (radius: 10) [04:48:38 -29406.202373] SLOW spr round 8 (radius: 5) [04:49:25] [worker #1] ML tree search #10, logLikelihood: -29492.004987 [04:49:58 -29401.070298] SLOW spr round 9 (radius: 5) [04:51:09 -29401.068729] SLOW spr round 10 (radius: 10) [04:52:22 -29399.094843] SLOW spr round 11 (radius: 5) [04:53:39 -29398.785381] SLOW spr round 12 (radius: 5) [04:54:49 -29398.785240] SLOW spr round 13 (radius: 10) [04:56:01 -29398.785205] SLOW spr round 14 (radius: 15) [04:57:41 -29396.209301] SLOW spr round 15 (radius: 5) [04:59:03 -29396.189883] SLOW spr round 16 (radius: 10) [05:00:22 -29395.723402] SLOW spr round 17 (radius: 5) [05:01:38 -29394.432068] SLOW spr round 18 (radius: 5) [05:02:47 -29394.431722] SLOW spr round 19 (radius: 10) [05:03:58 -29394.431699] SLOW spr round 20 (radius: 15) [05:05:38 -29394.048237] SLOW spr round 21 (radius: 5) [05:07:02 -29394.044923] SLOW spr round 22 (radius: 10) [05:08:23 -29394.044753] SLOW spr round 23 (radius: 15) [05:10:07 -29394.044662] SLOW spr round 24 (radius: 20) [05:12:29 -29393.885991] SLOW spr round 25 (radius: 5) [05:13:57 -29393.885871] SLOW spr round 26 (radius: 10) [05:15:21 -29393.885802] SLOW spr round 27 (radius: 15) [05:17:05 -29393.885709] SLOW spr round 28 (radius: 20) [05:19:28 -29393.629385] SLOW spr round 29 (radius: 5) [05:20:57 -29393.627135] SLOW spr round 30 (radius: 10) [05:22:21 -29393.627113] SLOW spr round 31 (radius: 15) [05:24:03 -29393.627107] SLOW spr round 32 (radius: 20) [05:26:26 -29393.627105] SLOW spr round 33 (radius: 25) [05:29:30 -29392.862853] SLOW spr round 34 (radius: 5) [05:30:59 -29392.862127] SLOW spr round 35 (radius: 10) [05:32:25 -29390.832439] SLOW spr round 36 (radius: 5) [05:33:45 -29390.832256] SLOW spr round 37 (radius: 10) [05:35:03 -29390.832210] SLOW spr round 38 (radius: 15) [05:36:46 -29390.832191] SLOW spr round 39 (radius: 20) [05:39:09 -29389.830842] SLOW spr round 40 (radius: 5) [05:40:37 -29389.830836] SLOW spr round 41 (radius: 10) [05:42:00 -29389.830834] SLOW spr round 42 (radius: 15) [05:43:38 -29389.830833] SLOW spr round 43 (radius: 20) [05:45:53 -29389.830832] SLOW spr round 44 (radius: 25) [05:48:02] [worker #1] ML tree search #12, logLikelihood: -29418.372943 [05:48:48 -29389.830832] Model parameter optimization (eps = 0.100000) [05:48:56] [worker #0] ML tree search #9, logLikelihood: -29388.677472 [05:48:56 -124668.597130] Initial branch length optimization [05:48:59 -99397.725787] Model parameter optimization (eps = 10.000000) [05:49:25 -98855.218823] AUTODETECT spr round 1 (radius: 5) [05:50:40 -67005.634020] AUTODETECT spr round 2 (radius: 10) [05:52:02 -48224.932184] AUTODETECT spr round 3 (radius: 15) [05:53:25 -39748.465106] AUTODETECT spr round 4 (radius: 20) [05:55:17 -36197.164269] AUTODETECT spr round 5 (radius: 25) [05:57:14 -34894.307088] SPR radius for FAST iterations: 25 (autodetect) [05:57:14 -34894.307088] Model parameter optimization (eps = 3.000000) [05:57:40 -34740.038840] FAST spr round 1 (radius: 25) [05:59:07 -29793.324227] FAST spr round 2 (radius: 25) [06:00:20 -29520.866164] FAST spr round 3 (radius: 25) [06:01:25 -29487.859666] FAST spr round 4 (radius: 25) [06:02:24 -29487.061432] FAST spr round 5 (radius: 25) [06:03:20 -29487.059968] Model parameter optimization (eps = 1.000000) [06:03:31 -29479.170965] SLOW spr round 1 (radius: 5) [06:04:36 -29464.245021] SLOW spr round 2 (radius: 5) [06:05:41 -29464.232366] SLOW spr round 3 (radius: 10) [06:06:49 -29464.122668] SLOW spr round 4 (radius: 5) [06:08:09 -29464.121916] SLOW spr round 5 (radius: 10) [06:09:24 -29464.121276] SLOW spr round 6 (radius: 15) [06:11:05 -29462.931623] SLOW spr round 7 (radius: 5) [06:12:28 -29462.930618] SLOW spr round 8 (radius: 10) [06:13:45 -29462.930457] SLOW spr round 9 (radius: 15) [06:15:24 -29462.930397] SLOW spr round 10 (radius: 20) [06:17:41 -29462.226075] SLOW spr round 11 (radius: 5) [06:19:05 -29462.209426] SLOW spr round 12 (radius: 10) [06:20:25 -29461.684756] SLOW spr round 13 (radius: 5) [06:21:40 -29461.684755] SLOW spr round 14 (radius: 10) [06:22:54 -29461.684056] SLOW spr round 15 (radius: 15) [06:24:34 -29461.684056] SLOW spr round 16 (radius: 20) [06:26:48 -29461.684056] SLOW spr round 17 (radius: 25) [06:29:29 -29461.027549] SLOW spr round 18 (radius: 5) [06:30:53 -29460.667804] SLOW spr round 19 (radius: 5) [06:32:07 -29460.667804] SLOW spr round 20 (radius: 10) [06:33:20 -29460.271988] SLOW spr round 21 (radius: 5) [06:34:36 -29460.270484] SLOW spr round 22 (radius: 10) [06:35:50 -29460.269840] SLOW spr round 23 (radius: 15) [06:37:31 -29457.955504] SLOW spr round 24 (radius: 5) [06:38:53 -29457.955471] SLOW spr round 25 (radius: 10) [06:40:10 -29457.955470] SLOW spr round 26 (radius: 15) [06:41:50 -29457.955469] SLOW spr round 27 (radius: 20) [06:44:06 -29457.955469] SLOW spr round 28 (radius: 25) [06:46:12] [worker #1] ML tree search #14, logLikelihood: -29398.551598 [06:46:46 -29457.955469] Model parameter optimization (eps = 0.100000) [06:46:49] [worker #0] ML tree search #11, logLikelihood: -29457.949155 [06:46:49 -124029.240743] Initial branch length optimization [06:46:51 -99338.305509] Model parameter optimization (eps = 10.000000) [06:47:16 -98747.468914] AUTODETECT spr round 1 (radius: 5) [06:48:28 -66263.893311] AUTODETECT spr round 2 (radius: 10) [06:49:46 -48026.460112] AUTODETECT spr round 3 (radius: 15) [06:51:05 -40957.043752] AUTODETECT spr round 4 (radius: 20) [06:52:48 -36306.183448] AUTODETECT spr round 5 (radius: 25) [06:54:39 -34249.103662] SPR radius for FAST iterations: 25 (autodetect) [06:54:39 -34249.103662] Model parameter optimization (eps = 3.000000) [06:54:58 -34074.045397] FAST spr round 1 (radius: 25) [06:56:29 -29768.929024] FAST spr round 2 (radius: 25) [06:57:44 -29554.671355] FAST spr round 3 (radius: 25) [06:58:48 -29496.193865] FAST spr round 4 (radius: 25) [06:59:48 -29485.707626] FAST spr round 5 (radius: 25) [07:00:45 -29482.747968] FAST spr round 6 (radius: 25) [07:01:41 -29482.747371] Model parameter optimization (eps = 1.000000) [07:01:51 -29474.871094] SLOW spr round 1 (radius: 5) [07:02:55 -29470.748292] SLOW spr round 2 (radius: 5) [07:03:59 -29467.231774] SLOW spr round 3 (radius: 5) [07:05:03 -29467.026636] SLOW spr round 4 (radius: 5) [07:06:06 -29467.026072] SLOW spr round 5 (radius: 10) [07:07:15 -29459.261089] SLOW spr round 6 (radius: 5) [07:08:36 -29443.553698] SLOW spr round 7 (radius: 5) [07:09:48 -29441.716635] SLOW spr round 8 (radius: 5) [07:10:55 -29439.953246] SLOW spr round 9 (radius: 5) [07:11:59 -29439.953204] SLOW spr round 10 (radius: 10) [07:13:07 -29439.953163] SLOW spr round 11 (radius: 15) [07:14:45 -29439.420767] SLOW spr round 12 (radius: 5) [07:16:07 -29439.419561] SLOW spr round 13 (radius: 10) [07:17:25 -29439.419500] SLOW spr round 14 (radius: 15) [07:19:00 -29439.419455] SLOW spr round 15 (radius: 20) [07:21:15 -29439.019550] SLOW spr round 16 (radius: 5) [07:22:40 -29436.847868] SLOW spr round 17 (radius: 5) [07:23:56 -29435.303256] SLOW spr round 18 (radius: 5) [07:25:06 -29434.070209] SLOW spr round 19 (radius: 5) [07:26:12 -29433.644434] SLOW spr round 20 (radius: 5) [07:27:15 -29433.643377] SLOW spr round 21 (radius: 10) [07:28:23 -29433.643311] SLOW spr round 22 (radius: 15) [07:30:01 -29433.643072] SLOW spr round 23 (radius: 20) [07:30:27] [worker #1] ML tree search #16, logLikelihood: -29402.913375 [07:32:13 -29433.643034] SLOW spr round 24 (radius: 25) [07:35:03 -29433.642840] Model parameter optimization (eps = 0.100000) [07:35:11] [worker #0] ML tree search #13, logLikelihood: -29432.641052 [07:35:11 -125053.865485] Initial branch length optimization [07:35:13 -99659.651186] Model parameter optimization (eps = 10.000000) [07:35:34 -99140.103853] AUTODETECT spr round 1 (radius: 5) [07:36:45 -65948.122629] AUTODETECT spr round 2 (radius: 10) [07:38:04 -47074.182333] AUTODETECT spr round 3 (radius: 15) [07:39:25 -38483.686088] AUTODETECT spr round 4 (radius: 20) [07:41:19 -34229.941573] AUTODETECT spr round 5 (radius: 25) [07:43:11 -33798.482502] SPR radius for FAST iterations: 25 (autodetect) [07:43:11 -33798.482502] Model parameter optimization (eps = 3.000000) [07:43:27 -33610.973408] FAST spr round 1 (radius: 25) [07:44:57 -29799.496978] FAST spr round 2 (radius: 25) [07:46:11 -29493.036116] FAST spr round 3 (radius: 25) [07:47:17 -29460.786494] FAST spr round 4 (radius: 25) [07:48:19 -29460.022777] FAST spr round 5 (radius: 25) [07:49:18 -29460.022041] Model parameter optimization (eps = 1.000000) [07:49:28 -29454.782659] SLOW spr round 1 (radius: 5) [07:50:36 -29446.922472] SLOW spr round 2 (radius: 5) [07:51:45 -29446.774575] SLOW spr round 3 (radius: 5) [07:52:53 -29446.760967] SLOW spr round 4 (radius: 10) [07:54:07 -29446.759562] SLOW spr round 5 (radius: 15) [07:55:56 -29446.498632] SLOW spr round 6 (radius: 5) [07:57:25 -29445.607108] SLOW spr round 7 (radius: 5) [07:58:44 -29445.424334] SLOW spr round 8 (radius: 5) [07:59:56 -29445.423845] SLOW spr round 9 (radius: 10) [08:01:12 -29444.615880] SLOW spr round 10 (radius: 5) [08:02:35 -29444.615273] SLOW spr round 11 (radius: 10) [08:03:54 -29444.614814] SLOW spr round 12 (radius: 15) [08:05:36 -29444.614339] SLOW spr round 13 (radius: 20) [08:07:59 -29440.861968] SLOW spr round 14 (radius: 5) [08:09:28 -29440.861922] SLOW spr round 15 (radius: 10) [08:10:52 -29440.861895] SLOW spr round 16 (radius: 15) [08:12:34 -29440.556695] SLOW spr round 17 (radius: 5) [08:14:01 -29440.556679] SLOW spr round 18 (radius: 10) [08:15:23 -29440.556665] SLOW spr round 19 (radius: 15) [08:17:05 -29440.556654] SLOW spr round 20 (radius: 20) [08:19:28 -29440.556643] SLOW spr round 21 (radius: 25) [08:21:33] [worker #1] ML tree search #18, logLikelihood: -29442.197988 [08:22:18 -29439.701078] SLOW spr round 22 (radius: 5) [08:23:47 -29439.701034] SLOW spr round 23 (radius: 10) [08:25:13 -29439.371288] SLOW spr round 24 (radius: 5) [08:26:33 -29439.371283] SLOW spr round 25 (radius: 10) [08:27:51 -29439.371278] SLOW spr round 26 (radius: 15) [08:29:34 -29439.371278] SLOW spr round 27 (radius: 20) [08:31:56 -29439.371278] SLOW spr round 28 (radius: 25) [08:34:44 -29439.371278] Model parameter optimization (eps = 0.100000) [08:34:48] [worker #0] ML tree search #15, logLikelihood: -29439.357655 [08:34:48 -123759.808992] Initial branch length optimization [08:34:50 -99015.487208] Model parameter optimization (eps = 10.000000) [08:35:12 -98446.836932] AUTODETECT spr round 1 (radius: 5) [08:36:26 -65918.576195] AUTODETECT spr round 2 (radius: 10) [08:37:49 -48381.117228] AUTODETECT spr round 3 (radius: 15) [08:39:16 -41225.666796] AUTODETECT spr round 4 (radius: 20) [08:41:02 -39700.819535] AUTODETECT spr round 5 (radius: 25) [08:42:55 -36230.325555] SPR radius for FAST iterations: 25 (autodetect) [08:42:55 -36230.325555] Model parameter optimization (eps = 3.000000) [08:43:15 -36054.082525] FAST spr round 1 (radius: 25) [08:44:45 -30677.772955] FAST spr round 2 (radius: 25) [08:46:00 -29972.957167] FAST spr round 3 (radius: 25) [08:47:11 -29590.785067] FAST spr round 4 (radius: 25) [08:48:17 -29537.358209] FAST spr round 5 (radius: 25) [08:49:18 -29535.515644] FAST spr round 6 (radius: 25) [08:50:18 -29535.512818] Model parameter optimization (eps = 1.000000) [08:50:30 -29525.668021] SLOW spr round 1 (radius: 5) [08:51:38 -29516.378356] SLOW spr round 2 (radius: 5) [08:52:43 -29515.827434] SLOW spr round 3 (radius: 5) [08:53:49 -29515.826600] SLOW spr round 4 (radius: 10) [08:55:00 -29512.394132] SLOW spr round 5 (radius: 5) [08:56:21 -29512.386499] SLOW spr round 6 (radius: 10) [08:57:40 -29509.108181] SLOW spr round 7 (radius: 5) [08:58:59 -29499.248986] SLOW spr round 8 (radius: 5) [09:00:11 -29499.182491] SLOW spr round 9 (radius: 10) [09:01:25 -29497.869057] SLOW spr round 10 (radius: 5) [09:02:44 -29497.819003] SLOW spr round 11 (radius: 10) [09:04:02 -29497.818032] SLOW spr round 12 (radius: 15) [09:05:50 -29496.502233] SLOW spr round 13 (radius: 5) [09:06:16] [worker #1] ML tree search #20, logLikelihood: -29433.033585 [09:07:17 -29496.500703] SLOW spr round 14 (radius: 10) [09:08:40 -29494.631623] SLOW spr round 15 (radius: 5) [09:10:01 -29494.485265] SLOW spr round 16 (radius: 5) [09:11:14 -29494.482389] SLOW spr round 17 (radius: 10) [09:12:29 -29494.481157] SLOW spr round 18 (radius: 15) [09:14:17 -29494.480558] SLOW spr round 19 (radius: 20) [09:16:45 -29493.974063] SLOW spr round 20 (radius: 5) [09:18:13 -29493.973906] SLOW spr round 21 (radius: 10) [09:19:37 -29493.973889] SLOW spr round 22 (radius: 15) [09:21:23 -29493.973874] SLOW spr round 23 (radius: 20) [09:23:51 -29493.973853] SLOW spr round 24 (radius: 25) [09:26:39 -29485.013526] SLOW spr round 25 (radius: 5) [09:28:09 -29485.008143] SLOW spr round 26 (radius: 10) [09:29:33 -29479.340143] SLOW spr round 27 (radius: 5) [09:30:53 -29479.338657] SLOW spr round 28 (radius: 10) [09:32:11 -29479.338624] SLOW spr round 29 (radius: 15) [09:33:57 -29479.278871] SLOW spr round 30 (radius: 20) [09:36:24 -29479.276869] SLOW spr round 31 (radius: 25) [09:39:11 -29479.145547] SLOW spr round 32 (radius: 5) [09:40:40 -29479.143260] SLOW spr round 33 (radius: 10) [09:42:04 -29479.142360] SLOW spr round 34 (radius: 15) [09:43:51 -29479.142032] SLOW spr round 35 (radius: 20) [09:46:18 -29479.141919] SLOW spr round 36 (radius: 25) [09:49:06 -29479.140185] Model parameter optimization (eps = 0.100000) [09:49:13] [worker #0] ML tree search #17, logLikelihood: -29478.803121 [09:49:13 -124650.528354] Initial branch length optimization [09:49:15 -98747.745795] Model parameter optimization (eps = 10.000000) [09:49:44 -98138.820559] AUTODETECT spr round 1 (radius: 5) [09:51:01 -68326.176363] AUTODETECT spr round 2 (radius: 10) [09:52:27 -49007.453750] AUTODETECT spr round 3 (radius: 15) [09:53:54 -41072.622291] AUTODETECT spr round 4 (radius: 20) [09:55:36 -36052.072982] AUTODETECT spr round 5 (radius: 25) [09:57:42 -34417.981931] SPR radius for FAST iterations: 25 (autodetect) [09:57:42 -34417.981931] Model parameter optimization (eps = 3.000000) [09:58:02 -34189.543115] FAST spr round 1 (radius: 25) [09:59:36 -30342.199994] FAST spr round 2 (radius: 25) [10:00:55 -29976.579043] FAST spr round 3 (radius: 25) [10:02:04 -29856.393882] FAST spr round 4 (radius: 25) [10:03:07 -29846.532764] FAST spr round 5 (radius: 25) [10:04:09 -29842.761963] FAST spr round 6 (radius: 25) [10:05:09 -29842.761039] Model parameter optimization (eps = 1.000000) [10:05:20 -29833.721618] SLOW spr round 1 (radius: 5) [10:06:27 -29821.888640] SLOW spr round 2 (radius: 5) [10:07:33 -29818.186455] SLOW spr round 3 (radius: 5) [10:08:37 -29818.186155] SLOW spr round 4 (radius: 10) [10:09:51 -29684.216929] SLOW spr round 5 (radius: 5) [10:11:17 -29529.024155] SLOW spr round 6 (radius: 5) [10:12:35 -29482.506256] SLOW spr round 7 (radius: 5) [10:13:46 -29482.247367] SLOW spr round 8 (radius: 5) [10:14:53 -29481.487258] SLOW spr round 9 (radius: 5) [10:15:58 -29481.485882] SLOW spr round 10 (radius: 10) [10:17:11 -29452.113638] SLOW spr round 11 (radius: 5) [10:18:35 -29447.962629] SLOW spr round 12 (radius: 5) [10:19:49 -29447.959903] SLOW spr round 13 (radius: 10) [10:21:03 -29447.956517] SLOW spr round 14 (radius: 15) [10:22:50 -29447.955933] SLOW spr round 15 (radius: 20) [10:25:20 -29446.090934] SLOW spr round 16 (radius: 5) [10:26:47 -29446.090680] SLOW spr round 17 (radius: 10) [10:28:10 -29446.090558] SLOW spr round 18 (radius: 15) [10:29:55 -29445.482097] SLOW spr round 19 (radius: 5) [10:31:21 -29445.476171] SLOW spr round 20 (radius: 10) [10:32:43 -29445.472341] SLOW spr round 21 (radius: 15) [10:34:28 -29445.472271] SLOW spr round 22 (radius: 20) [10:36:58 -29445.472006] SLOW spr round 23 (radius: 25) [10:40:07 -29445.362827] SLOW spr round 24 (radius: 5) [10:41:35 -29445.362498] SLOW spr round 25 (radius: 10) [10:42:59 -29445.362431] SLOW spr round 26 (radius: 15) [10:44:45 -29445.362365] SLOW spr round 27 (radius: 20) [10:47:16 -29445.362299] SLOW spr round 28 (radius: 25) [10:50:25 -29445.362233] Model parameter optimization (eps = 0.100000) [10:50:33] [worker #0] ML tree search #19, logLikelihood: -29444.991545 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.224297,0.423222) (0.202253,0.593768) (0.331444,0.801265) (0.242006,2.146258) 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: -29388.677472 AIC score: 62147.354945 / AICc score: 5743967.354945 / BIC score: 66666.746062 Free parameters (model + branch lengths): 1685 WARNING: Number of free parameters (K=1685) is larger than alignment size (n=108). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 2 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43424/3_mltree/O43424.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43424/3_mltree/O43424.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43424/3_mltree/O43424.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43424/3_mltree/O43424.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O43424/3_mltree/O43424.raxml.log Analysis started: 04-Jul-2021 00:15:11 / finished: 04-Jul-2021 11:05:45 Elapsed time: 39033.720 seconds Consumed energy: 3234.646 Wh (= 16 km in an electric car, or 81 km with an e-scooter!)