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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 03-Jun-2021 15:05:55 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15918/2_msa/P15918_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15918/3_mltree/P15918 --seed 2 --threads 1 --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), NONE/sequential [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15918/2_msa/P15918_trimmed_msa.fasta [00:00:00] Loaded alignment with 549 taxa and 36 sites WARNING: Sequences tr_E7FEA4_E7FEA4_DANRE_7955 and tr_W5KUP3_W5KUP3_ASTMX_7994 are exactly identical! WARNING: Sequences tr_F1NAX4_F1NAX4_CHICK_9031 and sp_Q5F3B2_RN166_CHICK_9031 are exactly identical! WARNING: Sequences tr_F1NAX4_F1NAX4_CHICK_9031 and tr_A0A1V4K2Z5_A0A1V4K2Z5_PATFA_372326 are exactly identical! WARNING: Sequences tr_F1NAX4_F1NAX4_CHICK_9031 and tr_A0A226NC54_A0A226NC54_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NAX4_F1NAX4_CHICK_9031 and tr_A0A226PEB3_A0A226PEB3_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q3U9F6_RN166_MOUSE_10090 and tr_F1PHC6_F1PHC6_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q3U9F6_RN166_MOUSE_10090 and tr_W5PUL0_W5PUL0_SHEEP_9940 are exactly identical! WARNING: Sequences sp_Q3U9F6_RN166_MOUSE_10090 and sp_Q6J1I7_RN166_RAT_10116 are exactly identical! WARNING: Sequences sp_Q3U9F6_RN166_MOUSE_10090 and tr_H0UX27_H0UX27_CAVPO_10141 are exactly identical! WARNING: Sequences sp_Q3U9F6_RN166_MOUSE_10090 and tr_G3SVL3_G3SVL3_LOXAF_9785 are exactly identical! WARNING: Sequences sp_Q3U9F6_RN166_MOUSE_10090 and tr_A6H736_A6H736_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q3U9F6_RN166_MOUSE_10090 and tr_A0A1S3A993_A0A1S3A993_ERIEU_9365 are exactly identical! WARNING: Sequences sp_Q3U9F6_RN166_MOUSE_10090 and tr_A0A2U3VCA4_A0A2U3VCA4_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q3U9F6_RN166_MOUSE_10090 and tr_A0A2Y9DN84_A0A2Y9DN84_TRIMA_127582 are exactly identical! WARNING: Sequences sp_Q3U9F6_RN166_MOUSE_10090 and tr_A0A2Y9K2Q8_A0A2Y9K2Q8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G9KLD4_G9KLD4_MUSPF_9669 and tr_J9PBI0_J9PBI0_CANLF_9615 are exactly identical! WARNING: Sequences tr_G9KLD4_G9KLD4_MUSPF_9669 and tr_F6V3R9_F6V3R9_HORSE_9796 are exactly identical! WARNING: Sequences tr_G9KLD4_G9KLD4_MUSPF_9669 and tr_I3NGP2_I3NGP2_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G9KLD4_G9KLD4_MUSPF_9669 and tr_H0WI65_H0WI65_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G9KLD4_G9KLD4_MUSPF_9669 and tr_G3T2M2_G3T2M2_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G9KLD4_G9KLD4_MUSPF_9669 and tr_D2HQL7_D2HQL7_AILME_9646 are exactly identical! WARNING: Sequences tr_G9KLD4_G9KLD4_MUSPF_9669 and tr_M3X3H3_M3X3H3_FELCA_9685 are exactly identical! WARNING: Sequences tr_G9KLD4_G9KLD4_MUSPF_9669 and tr_A0A2U3WU92_A0A2U3WU92_ODORO_9708 are exactly identical! WARNING: Sequences tr_G9KLD4_G9KLD4_MUSPF_9669 and tr_A0A2Y9RTL9_A0A2Y9RTL9_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G9KLD4_G9KLD4_MUSPF_9669 and tr_A0A384C474_A0A384C474_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YZZ2_M3YZZ2_MUSPF_9669 and tr_A0A2I3G2Y6_A0A2I3G2Y6_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3YZZ2_M3YZZ2_MUSPF_9669 and tr_A0A2Y9J2M5_A0A2Y9J2M5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z8B8_M3Z8B8_MUSPF_9669 and tr_D2HV49_D2HV49_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z8B8_M3Z8B8_MUSPF_9669 and tr_A0A2Y9JV89_A0A2Y9JV89_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z8B8_M3Z8B8_MUSPF_9669 and tr_A0A384BR25_A0A384BR25_URSMA_29073 are exactly identical! WARNING: Sequences tr_B6HRK7_B6HRK7_PENRW_500485 and tr_A0A0A2L9Y9_A0A0A2L9Y9_PENIT_40296 are exactly identical! WARNING: Sequences tr_B6HRK7_B6HRK7_PENRW_500485 and tr_A0A1V6Y2V6_A0A1V6Y2V6_PENNA_60175 are exactly identical! WARNING: Sequences tr_E3RZZ4_E3RZZ4_PYRTT_861557 and tr_B2WF21_B2WF21_PYRTR_426418 are exactly identical! WARNING: Sequences tr_E3RZZ4_E3RZZ4_PYRTT_861557 and tr_R0ICB3_R0ICB3_SETT2_671987 are exactly identical! WARNING: Sequences tr_E3RZZ4_E3RZZ4_PYRTT_861557 and tr_A0A177DVV1_A0A177DVV1_ALTAL_5599 are exactly identical! WARNING: Sequences tr_E3RZZ4_E3RZZ4_PYRTT_861557 and tr_A0A2W1H1X4_A0A2W1H1X4_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G1NTJ5_G1NTJ5_MYOLU_59463 and tr_G5B131_G5B131_HETGA_10181 are exactly identical! WARNING: Sequences tr_G1NTJ5_G1NTJ5_MYOLU_59463 and tr_L5KYG5_L5KYG5_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1PCJ2_G1PCJ2_MYOLU_59463 and tr_F6Q5Y4_F6Q5Y4_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1PCJ2_G1PCJ2_MYOLU_59463 and tr_G7PZY8_G7PZY8_MACFA_9541 are exactly identical! WARNING: Sequences tr_J3K2E2_J3K2E2_COCIM_246410 and tr_E9D1F5_E9D1F5_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3K2E2_J3K2E2_COCIM_246410 and tr_A0A0J6YQ57_A0A0J6YQ57_COCIT_404692 are exactly identical! WARNING: Sequences tr_Q8I5Z0_Q8I5Z0_PLAF7_36329 and tr_A5K0F4_A5K0F4_PLAVS_126793 are exactly identical! WARNING: Sequences tr_Q8I5Z0_Q8I5Z0_PLAF7_36329 and tr_Q7RNQ0_Q7RNQ0_PLAYO_73239 are exactly identical! WARNING: Sequences tr_Q8I5Z0_Q8I5Z0_PLAF7_36329 and tr_A0A384KUE5_A0A384KUE5_PLAKH_5851 are exactly identical! WARNING: Sequences tr_Q8I5Z0_Q8I5Z0_PLAF7_36329 and tr_A0A077X7D5_A0A077X7D5_PLABA_5823 are exactly identical! WARNING: Sequences tr_A0A2I2ZGP8_A0A2I2ZGP8_GORGO_9595 and tr_A0A2I3RIF0_A0A2I3RIF0_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZGP8_A0A2I2ZGP8_GORGO_9595 and sp_P15918_RAG1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZGP8_A0A2I2ZGP8_GORGO_9595 and tr_A0A2R9CSL6_A0A2R9CSL6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R284_G3R284_GORGO_9595 and tr_H2QQE1_H2QQE1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R284_G3R284_GORGO_9595 and tr_A0A2R8ZHI6_A0A2R8ZHI6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and tr_H2QBQ3_H2QBQ3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and sp_Q96A37_RN166_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and tr_A0A1D5Q476_A0A1D5Q476_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and tr_U3DQK0_U3DQK0_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and tr_A0A096N2Q9_A0A096N2Q9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and tr_A0A0D9S2C6_A0A0D9S2C6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and tr_A0A2K5KVC0_A0A2K5KVC0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RA09_G3RA09_GORGO_9595 and tr_A0A2K6E6Q7_A0A2K6E6Q7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3JSS6_G3JSS6_CORMM_983644 and tr_J5JCB9_J5JCB9_BEAB2_655819 are exactly identical! WARNING: Sequences tr_G3JSS6_G3JSS6_CORMM_983644 and tr_A0A0A2VFD5_A0A0A2VFD5_BEABA_1245745 are exactly identical! WARNING: Sequences tr_G3JSS6_G3JSS6_CORMM_983644 and tr_A0A167EKW3_A0A167EKW3_9HYPO_1081107 are exactly identical! WARNING: Sequences tr_G3JSS6_G3JSS6_CORMM_983644 and tr_A0A2N6P2V5_A0A2N6P2V5_BEABA_176275 are exactly identical! WARNING: Sequences tr_G1TU62_G1TU62_RABIT_9986 and sp_P34088_RAG1_RABIT_9986 are exactly identical! WARNING: Sequences tr_B8NPX5_B8NPX5_ASPFN_332952 and tr_A0A0L1JCR6_A0A0L1JCR6_ASPNO_1509407 are exactly identical! WARNING: Sequences tr_F6WSB4_F6WSB4_HORSE_9796 and tr_I3MY25_I3MY25_ICTTR_43179 are exactly identical! WARNING: Sequences tr_F6WSB4_F6WSB4_HORSE_9796 and tr_A0A1U8C9P5_A0A1U8C9P5_MESAU_10036 are exactly identical! WARNING: Sequences tr_F6WSB4_F6WSB4_HORSE_9796 and tr_A0A2Y9D8H7_A0A2Y9D8H7_TRIMA_127582 are exactly identical! WARNING: Sequences tr_F6WSB4_F6WSB4_HORSE_9796 and tr_A0A2Y9P7L1_A0A2Y9P7L1_DELLE_9749 are exactly identical! WARNING: Sequences tr_F6WSB4_F6WSB4_HORSE_9796 and tr_A0A2Y9EQ27_A0A2Y9EQ27_PHYCD_9755 are exactly identical! WARNING: Sequences tr_F6WSB4_F6WSB4_HORSE_9796 and tr_A0A384A1T6_A0A384A1T6_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A3B5QSB9_A0A3B5QSB9_XIPMA_8083 and tr_A0A087XVF8_A0A087XVF8_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A3B5RF18_A0A3B5RF18_XIPMA_8083 and tr_A0A087YCG0_A0A087YCG0_POEFO_48698 are exactly identical! WARNING: Sequences tr_I3N033_I3N033_ICTTR_43179 and tr_M3WFN8_M3WFN8_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A3B5K2J8_A0A3B5K2J8_TAKRU_31033 and tr_H3CFP4_H3CFP4_TETNG_99883 are exactly identical! WARNING: Sequences tr_A0A3B5KQ33_A0A3B5KQ33_TAKRU_31033 and tr_H3DKX7_H3DKX7_TETNG_99883 are exactly identical! WARNING: Sequences tr_A0A3B5KQ33_A0A3B5KQ33_TAKRU_31033 and tr_A0A1S3S1U1_A0A1S3S1U1_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A3B5KQ33_A0A3B5KQ33_TAKRU_31033 and tr_A0A1S3S219_A0A1S3S219_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A3B5KQ33_A0A3B5KQ33_TAKRU_31033 and tr_A0A1S3S229_A0A1S3S229_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A3B5KQ33_A0A3B5KQ33_TAKRU_31033 and tr_B5X7W6_B5X7W6_SALSA_8030 are exactly identical! WARNING: Sequences sp_Q96EQ8_RN125_HUMAN_9606 and tr_A0A096NB50_A0A096NB50_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q96EQ8_RN125_HUMAN_9606 and tr_A0A2K6D0Z3_A0A2K6D0Z3_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q96EQ8_RN125_HUMAN_9606 and tr_A0A2R8ZZB0_A0A2R8ZZB0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G7NDK1_G7NDK1_MACMU_9544 and tr_G7PQD9_G7PQD9_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7NDK1_G7NDK1_MACMU_9544 and tr_A0A096N450_A0A096N450_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NDK1_G7NDK1_MACMU_9544 and tr_A0A0D9QZL1_A0A0D9QZL1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7NDK1_G7NDK1_MACMU_9544 and tr_A0A2K5LZS8_A0A2K5LZS8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7NDK1_G7NDK1_MACMU_9544 and tr_A0A2K6ARB2_A0A2K6ARB2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NDK1_G7NDK1_MACMU_9544 and tr_A0A2K5XFH0_A0A2K5XFH0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K1XA28_A0A2K1XA28_POPTR_3694 and tr_A0A2K1XA42_A0A2K1XA42_POPTR_3694 are exactly identical! WARNING: Sequences tr_G7XVL7_G7XVL7_ASPKW_1033177 and tr_Q0CVM3_Q0CVM3_ASPTN_341663 are exactly identical! WARNING: Sequences tr_G7XVL7_G7XVL7_ASPKW_1033177 and tr_V5HR72_V5HR72_BYSSN_1356009 are exactly identical! WARNING: Sequences tr_G7XVL7_G7XVL7_ASPKW_1033177 and tr_A0A135LUR5_A0A135LUR5_PENPA_5078 are exactly identical! WARNING: Sequences tr_G7XVL7_G7XVL7_ASPKW_1033177 and tr_A0A146FLG2_A0A146FLG2_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XVL7_G7XVL7_ASPKW_1033177 and tr_A0A1F5LPV6_A0A1F5LPV6_9EURO_1835702 are exactly identical! WARNING: Sequences tr_G7XVL7_G7XVL7_ASPKW_1033177 and tr_A0A1R3RV60_A0A1R3RV60_ASPC5_602072 are exactly identical! WARNING: Sequences tr_G7XVL7_G7XVL7_ASPKW_1033177 and tr_A0A2I2GEE4_A0A2I2GEE4_9EURO_1392250 are exactly identical! WARNING: Sequences tr_G7XVL7_G7XVL7_ASPKW_1033177 and tr_A0A2I2FIU8_A0A2I2FIU8_9EURO_41067 are exactly identical! WARNING: Sequences tr_G7XVL7_G7XVL7_ASPKW_1033177 and tr_A0A2J5HPM9_A0A2J5HPM9_9EURO_482145 are exactly identical! WARNING: Sequences tr_K2R3C5_K2R3C5_MACPH_1126212 and tr_A0A1J9S7X3_A0A1J9S7X3_9PEZI_236234 are exactly identical! WARNING: Sequences tr_K7F953_K7F953_PELSI_13735 and tr_G3VYV6_G3VYV6_SARHA_9305 are exactly identical! WARNING: Sequences tr_K7F953_K7F953_PELSI_13735 and tr_A0A091J7P1_A0A091J7P1_EGRGA_188379 are exactly identical! WARNING: Sequences tr_K7F953_K7F953_PELSI_13735 and tr_A0A091URR8_A0A091URR8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_K7F953_K7F953_PELSI_13735 and tr_A0A087QQ40_A0A087QQ40_APTFO_9233 are exactly identical! WARNING: Sequences tr_K7F953_K7F953_PELSI_13735 and tr_A0A093HKQ5_A0A093HKQ5_STRCA_441894 are exactly identical! WARNING: Sequences tr_K7F953_K7F953_PELSI_13735 and tr_A0A099YW13_A0A099YW13_TINGU_94827 are exactly identical! WARNING: Sequences tr_K7F953_K7F953_PELSI_13735 and tr_A0A091GUV7_A0A091GUV7_9AVES_55661 are exactly identical! WARNING: Sequences tr_K7F953_K7F953_PELSI_13735 and tr_A0A0A0AUQ8_A0A0A0AUQ8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_K7F953_K7F953_PELSI_13735 and tr_A0A2I0LIV8_A0A2I0LIV8_COLLI_8932 are exactly identical! WARNING: Sequences tr_K7F953_K7F953_PELSI_13735 and tr_A0A093GM77_A0A093GM77_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H6BP32_H6BP32_EXODN_858893 and tr_A0A072P1J8_A0A072P1J8_9EURO_1182545 are exactly identical! WARNING: Sequences tr_H6BP32_H6BP32_EXODN_858893 and tr_A0A0D2EVV1_A0A0D2EVV1_9EURO_348802 are exactly identical! WARNING: Sequences tr_H0ZBK3_H0ZBK3_TAEGU_59729 and tr_A0A091F434_A0A091F434_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZBK3_H0ZBK3_TAEGU_59729 and tr_A0A093QC98_A0A093QC98_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZBK3_H0ZBK3_TAEGU_59729 and tr_A0A091HIG3_A0A091HIG3_CALAN_9244 are exactly identical! WARNING: Sequences tr_H0ZIP6_H0ZIP6_TAEGU_59729 and tr_U3KIY3_U3KIY3_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZIP6_H0ZIP6_TAEGU_59729 and tr_A0A091F4N0_A0A091F4N0_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZIP6_H0ZIP6_TAEGU_59729 and tr_A0A218UYR9_A0A218UYR9_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A1X7SL45_A0A1X7SL45_AMPQE_400682 and tr_A0A1X7SNW0_A0A1X7SNW0_AMPQE_400682 are exactly identical! WARNING: Sequences tr_A0A1X7SL45_A0A1X7SL45_AMPQE_400682 and tr_A0A1X7SS07_A0A1X7SS07_AMPQE_400682 are exactly identical! WARNING: Sequences tr_A0A1X7SL45_A0A1X7SL45_AMPQE_400682 and tr_A0A1X7TNN2_A0A1X7TNN2_AMPQE_400682 are exactly identical! WARNING: Sequences tr_A0A1X7TRU7_A0A1X7TRU7_AMPQE_400682 and tr_A0A1X7TS91_A0A1X7TS91_AMPQE_400682 are exactly identical! WARNING: Sequences tr_I3L7X1_I3L7X1_PIG_9823 and sp_Q867B5_RAG1_PIG_9823 are exactly identical! WARNING: Sequences tr_C9SPX9_C9SPX9_VERA1_526221 and tr_E3QR20_E3QR20_COLGM_645133 are exactly identical! WARNING: Sequences tr_C9SPX9_C9SPX9_VERA1_526221 and tr_L2GH20_L2GH20_COLFN_1213859 are exactly identical! WARNING: Sequences tr_C9SPX9_C9SPX9_VERA1_526221 and tr_A0A066XFK6_A0A066XFK6_COLSU_1173701 are exactly identical! WARNING: Sequences tr_E3QIL0_E3QIL0_COLGM_645133 and tr_A0A010S0J8_A0A010S0J8_9PEZI_1445577 are exactly identical! WARNING: Sequences tr_E3QIL0_E3QIL0_COLGM_645133 and tr_A0A135UIC0_A0A135UIC0_9PEZI_1209931 are exactly identical! WARNING: Sequences tr_E3QIL0_E3QIL0_COLGM_645133 and tr_A0A166T5G8_A0A166T5G8_9PEZI_708197 are exactly identical! WARNING: Sequences tr_E3QIL0_E3QIL0_COLGM_645133 and tr_A0A161W7G0_A0A161W7G0_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_F2SCH4_F2SCH4_TRIRC_559305 and tr_A0A178EVA9_A0A178EVA9_TRIRU_5551 are exactly identical! WARNING: Sequences tr_F2SRW3_F2SRW3_TRIRC_559305 and tr_D4B472_D4B472_ARTBC_663331 are exactly identical! WARNING: Sequences tr_F2SRW3_F2SRW3_TRIRC_559305 and tr_F2PQU3_F2PQU3_TRIEC_559882 are exactly identical! WARNING: Sequences tr_F2SRW3_F2SRW3_TRIRC_559305 and tr_A0A059JBP3_A0A059JBP3_9EURO_1215338 are exactly identical! WARNING: Sequences tr_F2SRW3_F2SRW3_TRIRC_559305 and tr_A0A178EY63_A0A178EY63_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G0RLF8_G0RLF8_HYPJQ_431241 and tr_A0A2P4Z8Y1_A0A2P4Z8Y1_9HYPO_398673 are exactly identical! WARNING: Sequences tr_G0RLF8_G0RLF8_HYPJQ_431241 and tr_A0A2T3Z5J2_A0A2T3Z5J2_9HYPO_1042311 are exactly identical! WARNING: Sequences tr_G0RLF8_G0RLF8_HYPJQ_431241 and tr_A0A2T4BVC1_A0A2T4BVC1_TRILO_983965 are exactly identical! WARNING: Sequences tr_R0LZS8_R0LZS8_ANAPL_8839 and tr_A0A091JRA9_A0A091JRA9_EGRGA_188379 are exactly identical! WARNING: Sequences tr_R0LZS8_R0LZS8_ANAPL_8839 and tr_A0A093PU14_A0A093PU14_9PASS_328815 are exactly identical! WARNING: Sequences tr_R0LZS8_R0LZS8_ANAPL_8839 and tr_A0A093I8M0_A0A093I8M0_STRCA_441894 are exactly identical! WARNING: Sequences tr_R0LZS8_R0LZS8_ANAPL_8839 and tr_A0A091W6F9_A0A091W6F9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_R0LZS8_R0LZS8_ANAPL_8839 and tr_A0A0A0A5Z8_A0A0A0A5Z8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_R0LZS8_R0LZS8_ANAPL_8839 and tr_A0A2I0MPH0_A0A2I0MPH0_COLLI_8932 are exactly identical! WARNING: Sequences tr_R0LZS8_R0LZS8_ANAPL_8839 and tr_A0A091I8R8_A0A091I8R8_CALAN_9244 are exactly identical! WARNING: Sequences tr_S0EBS2_S0EBS2_GIBF5_1279085 and tr_A0A2H3GSF6_A0A2H3GSF6_FUSOX_327505 are exactly identical! WARNING: Sequences tr_V2XA04_V2XA04_MONRO_1381753 and tr_A0A0W0FJX1_A0A0W0FJX1_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2QXD7_W2QXD7_PHYPN_761204 and tr_W2I0L5_W2I0L5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QXD7_W2QXD7_PHYPN_761204 and tr_A0A329T2T9_A0A329T2T9_9STRA_29920 are exactly identical! WARNING: Sequences tr_A0A015JUW3_A0A015JUW3_9GLOM_1432141 and tr_A0A2I1FUU1_A0A2I1FUU1_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015JUW3_A0A015JUW3_9GLOM_1432141 and tr_A0A2H5U8E4_A0A2H5U8E4_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015JUW3_A0A015JUW3_9GLOM_1432141 and tr_A0A2Z6Q1C2_A0A2Z6Q1C2_9GLOM_94130 are exactly identical! WARNING: Sequences tr_A0A067GLK3_A0A067GLK3_CITSI_2711 and tr_V4SXV8_V4SXV8_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067GLK3_A0A067GLK3_CITSI_2711 and tr_A0A2H5NGI4_A0A2H5NGI4_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A067JRF7_A0A067JRF7_JATCU_180498 and tr_A0A2C9WI22_A0A2C9WI22_MANES_3983 are exactly identical! WARNING: Sequences tr_A0A094F8E5_A0A094F8E5_9PEZI_1420912 and tr_A0A1B8GBI7_A0A1B8GBI7_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0A2J5Z0_A0A0A2J5Z0_PENEN_27334 and tr_A0A0M8NYN5_A0A0M8NYN5_9EURO_229535 are exactly identical! WARNING: Sequences tr_A0A0A2J5Z0_A0A0A2J5Z0_PENEN_27334 and tr_A0A101MCJ3_A0A101MCJ3_9EURO_48697 are exactly identical! WARNING: Sequences tr_A0A0A2J5Z0_A0A0A2J5Z0_PENEN_27334 and tr_A0A1V6R799_A0A1V6R799_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A0L0NBU8_A0A0L0NBU8_9HYPO_1163406 and tr_A0A179H0N2_A0A179H0N2_9HYPO_33203 are exactly identical! WARNING: Sequences tr_A0A0L0NBU8_A0A0L0NBU8_9HYPO_1163406 and tr_A0A2C5Y1L0_A0A2C5Y1L0_9HYPO_1399860 are exactly identical! WARNING: Sequences tr_A0A0L0NBU8_A0A0L0NBU8_9HYPO_1163406 and tr_A0A2K3Q7J0_A0A2K3Q7J0_9HYPO_45235 are exactly identical! WARNING: Sequences tr_A0A0L0NBU8_A0A0L0NBU8_9HYPO_1163406 and tr_A0A2S4KQA5_A0A2S4KQA5_9HYPO_94208 are exactly identical! WARNING: Sequences tr_A0A0L0NJI2_A0A0L0NJI2_9HYPO_1163406 and tr_A0A2S4KWI6_A0A2S4KWI6_9HYPO_94208 are exactly identical! WARNING: Sequences tr_A0A151MBE1_A0A151MBE1_ALLMI_8496 and tr_A0A1U7SWQ0_A0A1U7SWQ0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0D2BDZ3_A0A0D2BDZ3_9EURO_91928 and tr_A0A0D2CD51_A0A0D2CD51_9EURO_215243 are exactly identical! WARNING: Sequences tr_A0A0D2BDZ3_A0A0D2BDZ3_9EURO_91928 and tr_A0A0D2D408_A0A0D2D408_9EURO_348802 are exactly identical! WARNING: Sequences tr_A0A0D2BSY6_A0A0D2BSY6_9EURO_91928 and tr_A0A0D2BMU7_A0A0D2BMU7_9EURO_215243 are exactly identical! WARNING: Sequences tr_A0A1S3XJS4_A0A1S3XJS4_TOBAC_4097 and tr_A0A1U7YCD9_A0A1U7YCD9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3KPD4_A0A1S3KPD4_SALSA_8030 and tr_A0A060YFU9_A0A060YFU9_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3N9T5_A0A1S3N9T5_SALSA_8030 and tr_B5X2U3_B5X2U3_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3N9T5_A0A1S3N9T5_SALSA_8030 and tr_A0A060YXE3_A0A060YXE3_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1B8AJV2_A0A1B8AJV2_FUSPO_36050 and tr_A0A2T4GKA7_A0A2T4GKA7_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A1B8AJV2_A0A1B8AJV2_FUSPO_36050 and tr_A0A2L2TEH0_A0A2L2TEH0_9HYPO_56646 are exactly identical! WARNING: Sequences tr_A0A1B8C4W1_A0A1B8C4W1_9PEZI_1622147 and tr_A0A1B8EM44_A0A1B8EM44_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_A0A1L8EMY0_A0A1L8EMY0_XENLA_8355 and tr_A0A1L8EUJ3_A0A1L8EUJ3_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A1Q5UP17_A0A1Q5UP17_9EURO_1316194 and tr_A0A1V6TZZ5_A0A1V6TZZ5_9EURO_303698 are exactly identical! WARNING: Sequences tr_A0A226MQZ7_A0A226MQZ7_CALSU_9009 and tr_A0A226PQ49_A0A226PQ49_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3BFH6_A0A2H3BFH6_9AGAR_1076256 and tr_A0A284QZY5_A0A284QZY5_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2D0Q113_A0A2D0Q113_ICTPU_7998 and tr_A0A2D0QLK1_A0A2D0QLK1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QID7_A0A2D0QID7_ICTPU_7998 and tr_A0A2D0RAL5_A0A2D0RAL5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QID7_A0A2D0QID7_ICTPU_7998 and tr_A0A2D0RBS4_A0A2D0RBS4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QID7_A0A2D0QID7_ICTPU_7998 and tr_A0A2D0RBT2_A0A2D0RBT2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QID7_A0A2D0QID7_ICTPU_7998 and tr_A0A2D0RBU0_A0A2D0RBU0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QID7_A0A2D0QID7_ICTPU_7998 and tr_A0A2D0RDQ1_A0A2D0RDQ1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RLK1_A0A2D0RLK1_ICTPU_7998 and tr_A0A2D0RLK8_A0A2D0RLK8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2I2FAW5_A0A2I2FAW5_9EURO_41067 and tr_A0A2J5HR28_A0A2J5HR28_9EURO_482145 are exactly identical! WARNING: Sequences tr_A0A103Y6G6_A0A103Y6G6_CYNCS_59895 and tr_A0A103Y6H6_A0A103Y6H6_CYNCS_59895 are exactly identical! WARNING: Sequences tr_A0A2U3V981_A0A2U3V981_TURTR_9739 and tr_A0A2Y9P676_A0A2Y9P676_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A319CL27_A0A319CL27_9EURO_1448315 and tr_A0A2V5IB38_A0A2V5IB38_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A319CL27_A0A319CL27_9EURO_1448315 and tr_A0A2V5HEZ5_A0A2V5HEZ5_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 191 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15918/3_mltree/P15918.raxml.reduced.phy Alignment comprises 1 partitions and 36 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 36 / 36 Gaps: 2.59 % Invariant sites: 2.78 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15918/3_mltree/P15918.raxml.rba Parallelization scheme autoconfig: 1 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 549 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 36 / 2880 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -33949.681174] Initial branch length optimization [00:00:00 -28557.727971] Model parameter optimization (eps = 10.000000) [00:00:13 -28115.739085] AUTODETECT spr round 1 (radius: 5) [00:00:35 -20927.612317] AUTODETECT spr round 2 (radius: 10) [00:01:03 -15790.751363] AUTODETECT spr round 3 (radius: 15) [00:01:33 -12002.378859] AUTODETECT spr round 4 (radius: 20) [00:02:13 -11069.575471] AUTODETECT spr round 5 (radius: 25) [00:02:55 -10913.070600] SPR radius for FAST iterations: 25 (autodetect) [00:02:55 -10913.070600] Model parameter optimization (eps = 3.000000) [00:03:04 -10863.953012] FAST spr round 1 (radius: 25) [00:03:29 -9602.038205] FAST spr round 2 (radius: 25) [00:03:51 -9548.440067] FAST spr round 3 (radius: 25) [00:04:12 -9544.348812] FAST spr round 4 (radius: 25) [00:04:33 -9518.730813] FAST spr round 5 (radius: 25) [00:04:52 -9518.729151] Model parameter optimization (eps = 1.000000) [00:04:55 -9518.195770] SLOW spr round 1 (radius: 5) [00:05:22 -9512.325134] SLOW spr round 2 (radius: 5) [00:05:48 -9507.145719] SLOW spr round 3 (radius: 5) [00:06:12 -9506.454679] SLOW spr round 4 (radius: 5) [00:06:36 -9506.454425] SLOW spr round 5 (radius: 10) [00:07:01 -9504.932681] SLOW spr round 6 (radius: 5) [00:07:32 -9504.932391] SLOW spr round 7 (radius: 10) [00:07:59 -9504.932345] SLOW spr round 8 (radius: 15) [00:08:35 -9503.533473] SLOW spr round 9 (radius: 5) [00:09:09 -9499.769830] SLOW spr round 10 (radius: 5) [00:09:37 -9496.919772] SLOW spr round 11 (radius: 5) [00:10:03 -9496.919452] SLOW spr round 12 (radius: 10) 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 03-Jun-2021 15:19:21 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15918/2_msa/P15918_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15918/3_mltree/P15918 --seed 2 --threads 1 --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), NONE/sequential WARNING: The model you specified on the command line (LG4X) will be ignored since the binary MSA file already contains a model definition. If you want to change the model, please re-run RAxML-NG with the original PHYLIP/FASTA alignment and --redo option. [00:00:00] Loading binary alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15918/3_mltree/P15918.raxml.rba [00:00:00] Alignment comprises 549 taxa, 1 partitions and 36 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 36 / 36 Gaps: 2.59 % Invariant sites: 2.78 % Parallelization scheme autoconfig: 1 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] NOTE: Resuming execution from checkpoint (logLH: -9496.92, ML trees: 0, bootstraps: 0) [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 36 / 2880 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -9496.919452] SPR radius for FAST iterations: 25 (autodetect) [00:00:00 -9496.919452] SLOW spr round 12 (radius: 10) [00:00:20 -9496.919398] SLOW spr round 13 (radius: 15) [00:00:51 -9496.720066] SLOW spr round 14 (radius: 5) [00:01:16 -9496.720063] SLOW spr round 15 (radius: 10) [00:01:38 -9496.720063] SLOW spr round 16 (radius: 15) [00:02:07 -9496.267293] SLOW spr round 17 (radius: 5) [00:02:32 -9496.267154] SLOW spr round 18 (radius: 10) [00:02:54 -9496.267154] SLOW spr round 19 (radius: 15) [00:03:22 -9496.267154] SLOW spr round 20 (radius: 20) [00:04:04 -9455.573506] SLOW spr round 21 (radius: 5) [00:04:31 -9424.804193] SLOW spr round 22 (radius: 5) [00:04:54 -9422.007121] SLOW spr round 23 (radius: 5) [00:05:15 -9422.007111] SLOW spr round 24 (radius: 10) [00:05:35 -9422.007111] SLOW spr round 25 (radius: 15) [00:06:05 -9422.007111] SLOW spr round 26 (radius: 20) [00:06:45 -9422.007111] SLOW spr round 27 (radius: 25) [00:07:35 -9422.007111] Model parameter optimization (eps = 0.100000) [00:07:38] ML tree search #1, logLikelihood: -9421.931949 [00:07:38 -34009.849855] Initial branch length optimization [00:07:38 -28574.186763] Model parameter optimization (eps = 10.000000) [00:07:46 -28173.486336] AUTODETECT spr round 1 (radius: 5) [00:08:04 -20726.307922] AUTODETECT spr round 2 (radius: 10) [00:08:26 -16088.097050] AUTODETECT spr round 3 (radius: 15) [00:08:50 -13079.057922] AUTODETECT spr round 4 (radius: 20) [00:09:21 -11114.546454] AUTODETECT spr round 5 (radius: 25) [00:09:50 -10965.112654] SPR radius for FAST iterations: 25 (autodetect) [00:09:50 -10965.112654] Model parameter optimization (eps = 3.000000) [00:09:58 -10932.156109] FAST spr round 1 (radius: 25) [00:10:17 -9624.826541] FAST spr round 2 (radius: 25) [00:10:35 -9515.189657] FAST spr round 3 (radius: 25) [00:10:52 -9479.500321] FAST spr round 4 (radius: 25) [00:11:09 -9475.603807] FAST spr round 5 (radius: 25) [00:11:26 -9474.804883] FAST spr round 6 (radius: 25) [00:11:42 -9474.562294] FAST spr round 7 (radius: 25) [00:11:58 -9474.562075] Model parameter optimization (eps = 1.000000) [00:12:05 -9471.935959] SLOW spr round 1 (radius: 5) [00:12:27 -9470.774051] SLOW spr round 2 (radius: 5) [00:12:47 -9470.773680] SLOW spr round 3 (radius: 10) [00:13:07 -9469.982059] SLOW spr round 4 (radius: 5) [00:13:32 -9469.981979] SLOW spr round 5 (radius: 10) [00:13:53 -9469.915316] SLOW spr round 6 (radius: 15) [00:14:19 -9468.606212] SLOW spr round 7 (radius: 5) [00:14:45 -9465.635601] SLOW spr round 8 (radius: 5) [00:15:08 -9460.060714] SLOW spr round 9 (radius: 5) [00:15:30 -9458.048494] SLOW spr round 10 (radius: 5) [00:15:51 -9455.926887] SLOW spr round 11 (radius: 5) [00:16:10 -9455.925998] SLOW spr round 12 (radius: 10) [00:16:29 -9455.925830] SLOW spr round 13 (radius: 15) [00:16:56 -9448.906793] SLOW spr round 14 (radius: 5) [00:17:21 -9448.904845] SLOW spr round 15 (radius: 10) [00:17:43 -9445.441724] SLOW spr round 16 (radius: 5) [00:18:07 -9445.439162] SLOW spr round 17 (radius: 10) [00:18:28 -9445.438822] SLOW spr round 18 (radius: 15) [00:18:54 -9443.064109] SLOW spr round 19 (radius: 5) [00:19:20 -9442.926149] SLOW spr round 20 (radius: 5) [00:19:42 -9442.925973] SLOW spr round 21 (radius: 10) [00:20:02 -9442.925973] SLOW spr round 22 (radius: 15) [00:20:27 -9442.925973] SLOW spr round 23 (radius: 20) [00:20:58 -9442.275300] SLOW spr round 24 (radius: 5) [00:21:25 -9442.007742] SLOW spr round 25 (radius: 5) [00:21:48 -9442.007638] SLOW spr round 26 (radius: 10) [00:22:08 -9442.007637] SLOW spr round 27 (radius: 15) [00:22:34 -9442.007637] SLOW spr round 28 (radius: 20) [00:23:06 -9440.265965] SLOW spr round 29 (radius: 5) [00:23:32 -9440.265965] SLOW spr round 30 (radius: 10) [00:23:54 -9440.265965] SLOW spr round 31 (radius: 15) [00:24:19 -9440.265965] SLOW spr round 32 (radius: 20) [00:24:49 -9439.659568] SLOW spr round 33 (radius: 5) [00:25:16 -9437.595694] SLOW spr round 34 (radius: 5) [00:25:39 -9437.594839] SLOW spr round 35 (radius: 10) [00:26:00 -9437.594657] SLOW spr round 36 (radius: 15) [00:26:26 -9437.594612] SLOW spr round 37 (radius: 20) [00:26:56 -9437.569096] SLOW spr round 38 (radius: 25) [00:27:32 -9437.569065] Model parameter optimization (eps = 0.100000) [00:27:42] ML tree search #2, logLikelihood: -9361.774655 [00:27:42 -34148.140139] Initial branch length optimization [00:27:42 -28778.657546] Model parameter optimization (eps = 10.000000) [00:27:54 -28371.649288] AUTODETECT spr round 1 (radius: 5) [00:28:11 -20264.430817] AUTODETECT spr round 2 (radius: 10) [00:28:32 -14794.095460] AUTODETECT spr round 3 (radius: 15) [00:28:55 -11910.497431] AUTODETECT spr round 4 (radius: 20) [00:29:19 -11251.735278] AUTODETECT spr round 5 (radius: 25) [00:29:48 -10945.656702] SPR radius for FAST iterations: 25 (autodetect) [00:29:48 -10945.656702] Model parameter optimization (eps = 3.000000) [00:29:55 -10906.429654] FAST spr round 1 (radius: 25) [00:30:14 -9742.171675] FAST spr round 2 (radius: 25) [00:30:32 -9605.804502] FAST spr round 3 (radius: 25) [00:30:49 -9573.953988] FAST spr round 4 (radius: 25) [00:31:05 -9571.596995] FAST spr round 5 (radius: 25) [00:31:21 -9571.595451] Model parameter optimization (eps = 1.000000) [00:31:26 -9570.428985] SLOW spr round 1 (radius: 5) [00:31:47 -9569.353405] SLOW spr round 2 (radius: 5) [00:32:07 -9569.340594] SLOW spr round 3 (radius: 10) [00:32:25 -9569.340356] SLOW spr round 4 (radius: 15) [00:32:53 -9512.620620] SLOW spr round 5 (radius: 5) [00:33:18 -9497.081533] SLOW spr round 6 (radius: 5) [00:33:40 -9497.075415] SLOW spr round 7 (radius: 10) [00:34:00 -9494.661400] SLOW spr round 8 (radius: 5) [00:34:24 -9494.205786] SLOW spr round 9 (radius: 5) [00:34:45 -9494.204209] SLOW spr round 10 (radius: 10) [00:35:04 -9494.204037] SLOW spr round 11 (radius: 15) [00:35:31 -9490.578181] SLOW spr round 12 (radius: 5) [00:35:56 -9489.223506] SLOW spr round 13 (radius: 5) [00:36:17 -9489.132840] SLOW spr round 14 (radius: 10) [00:36:37 -9488.728134] SLOW spr round 15 (radius: 5) [00:37:00 -9488.700983] SLOW spr round 16 (radius: 10) [00:37:20 -9488.700461] SLOW spr round 17 (radius: 15) [00:37:45 -9488.043359] SLOW spr round 18 (radius: 5) [00:38:09 -9487.665197] SLOW spr round 19 (radius: 5) [00:38:31 -9487.665170] SLOW spr round 20 (radius: 10) [00:38:50 -9487.665170] SLOW spr round 21 (radius: 15) [00:39:16 -9487.665170] SLOW spr round 22 (radius: 20) [00:39:48 -9485.787496] SLOW spr round 23 (radius: 5) [00:40:14 -9484.687148] SLOW spr round 24 (radius: 5) [00:40:36 -9483.741541] SLOW spr round 25 (radius: 5) [00:40:57 -9483.352742] SLOW spr round 26 (radius: 5) [00:41:16 -9483.352725] SLOW spr round 27 (radius: 10) [00:41:35 -9483.352725] SLOW spr round 28 (radius: 15) [00:42:04 -9433.827979] SLOW spr round 29 (radius: 5) [00:42:31 -9430.267248] SLOW spr round 30 (radius: 5) [00:42:53 -9430.267030] SLOW spr round 31 (radius: 10) [00:43:13 -9429.530096] SLOW spr round 32 (radius: 5) [00:43:38 -9428.472412] SLOW spr round 33 (radius: 5) [00:44:00 -9428.472357] SLOW spr round 34 (radius: 10) [00:44:19 -9428.472357] SLOW spr round 35 (radius: 15) [00:44:48 -9428.159459] SLOW spr round 36 (radius: 5) [00:45:13 -9428.158867] SLOW spr round 37 (radius: 10) [00:45:35 -9428.158851] SLOW spr round 38 (radius: 15) [00:46:02 -9428.158850] SLOW spr round 39 (radius: 20) [00:46:37 -9427.475026] SLOW spr round 40 (radius: 5) [00:47:03 -9427.474932] SLOW spr round 41 (radius: 10) [00:47:24 -9427.474931] SLOW spr round 42 (radius: 15) [00:47:51 -9427.474931] SLOW spr round 43 (radius: 20) [00:48:26 -9427.474931] SLOW spr round 44 (radius: 25) [00:49:09 -9402.797580] SLOW spr round 45 (radius: 5) [00:49:36 -9394.942637] SLOW spr round 46 (radius: 5) [00:49:58 -9394.941351] SLOW spr round 47 (radius: 10) [00:50:18 -9369.082730] SLOW spr round 48 (radius: 5) [00:50:43 -9368.840235] SLOW spr round 49 (radius: 5) [00:51:04 -9368.840216] SLOW spr round 50 (radius: 10) [00:51:24 -9368.840216] SLOW spr round 51 (radius: 15) [00:51:52 -9368.350354] SLOW spr round 52 (radius: 5) [00:52:17 -9367.121999] SLOW spr round 53 (radius: 5) [00:52:39 -9367.121966] SLOW spr round 54 (radius: 10) [00:52:59 -9367.121966] SLOW spr round 55 (radius: 15) [00:53:26 -9367.121966] SLOW spr round 56 (radius: 20) [00:53:59 -9367.121966] SLOW spr round 57 (radius: 25) [00:54:38 -9365.584338] SLOW spr round 58 (radius: 5) [00:55:04 -9364.457076] SLOW spr round 59 (radius: 5) [00:55:27 -9364.109951] SLOW spr round 60 (radius: 5) [00:55:47 -9364.109932] SLOW spr round 61 (radius: 10) [00:56:06 -9364.109932] SLOW spr round 62 (radius: 15) [00:56:34 -9364.109932] SLOW spr round 63 (radius: 20) [00:57:06 -9364.109932] SLOW spr round 64 (radius: 25) [00:57:43 -9364.109932] Model parameter optimization (eps = 0.100000) [00:57:51] ML tree search #3, logLikelihood: -9361.146410 [00:57:51 -34105.632860] Initial branch length optimization [00:57:51 -28714.440264] Model parameter optimization (eps = 10.000000) [00:58:03 -28341.288048] AUTODETECT spr round 1 (radius: 5) [00:58:20 -20190.691401] AUTODETECT spr round 2 (radius: 10) [00:58:43 -15030.722146] AUTODETECT spr round 3 (radius: 15) [00:59:07 -11924.405892] AUTODETECT spr round 4 (radius: 20) [00:59:31 -11022.840009] AUTODETECT spr round 5 (radius: 25) [00:59:58 -10744.220975] SPR radius for FAST iterations: 25 (autodetect) [00:59:58 -10744.220975] Model parameter optimization (eps = 3.000000) [01:00:05 -10703.881474] FAST spr round 1 (radius: 25) [01:00:24 -9696.343847] FAST spr round 2 (radius: 25) [01:00:42 -9583.955779] FAST spr round 3 (radius: 25) [01:00:59 -9457.999646] FAST spr round 4 (radius: 25) [01:01:15 -9388.955121] FAST spr round 5 (radius: 25) [01:01:30 -9386.621113] FAST spr round 6 (radius: 25) [01:01:45 -9386.621082] Model parameter optimization (eps = 1.000000) [01:01:53 -9381.798636] SLOW spr round 1 (radius: 5) [01:02:11 -9379.029938] SLOW spr round 2 (radius: 5) [01:02:30 -9377.841383] SLOW spr round 3 (radius: 5) [01:02:48 -9377.712220] SLOW spr round 4 (radius: 5) [01:03:06 -9377.712203] SLOW spr round 5 (radius: 10) [01:03:24 -9377.712193] SLOW spr round 6 (radius: 15) [01:03:51 -9371.951101] SLOW spr round 7 (radius: 5) [01:04:14 -9371.769625] SLOW spr round 8 (radius: 5) [01:04:34 -9371.769602] SLOW spr round 9 (radius: 10) [01:04:53 -9371.033548] SLOW spr round 10 (radius: 5) [01:05:15 -9371.033543] SLOW spr round 11 (radius: 10) [01:05:34 -9371.033533] SLOW spr round 12 (radius: 15) [01:05:59 -9371.033522] SLOW spr round 13 (radius: 20) [01:06:30 -9369.886483] SLOW spr round 14 (radius: 5) [01:06:54 -9369.885050] SLOW spr round 15 (radius: 10) [01:07:14 -9369.884623] SLOW spr round 16 (radius: 15) [01:07:38 -9369.884432] SLOW spr round 17 (radius: 20) [01:08:09 -9369.411751] SLOW spr round 18 (radius: 5) [01:08:32 -9367.128050] SLOW spr round 19 (radius: 5) [01:08:53 -9367.127644] SLOW spr round 20 (radius: 10) [01:09:11 -9367.127632] SLOW spr round 21 (radius: 15) [01:09:36 -9367.127630] SLOW spr round 22 (radius: 20) [01:10:06 -9367.127630] SLOW spr round 23 (radius: 25) [01:10:44 -9362.839059] SLOW spr round 24 (radius: 5) [01:11:08 -9362.836827] SLOW spr round 25 (radius: 10) [01:11:28 -9362.836023] SLOW spr round 26 (radius: 15) [01:11:51 -9362.835616] SLOW spr round 27 (radius: 20) [01:12:22 -9362.835382] SLOW spr round 28 (radius: 25) [01:12:59 -9362.835240] Model parameter optimization (eps = 0.100000) [01:13:03] ML tree search #4, logLikelihood: -9362.649238 [01:13:03 -34118.994960] Initial branch length optimization [01:13:04 -28650.965110] Model parameter optimization (eps = 10.000000) [01:13:16 -28285.769912] AUTODETECT spr round 1 (radius: 5) [01:13:32 -20453.130164] AUTODETECT spr round 2 (radius: 10) [01:13:56 -14870.772587] AUTODETECT spr round 3 (radius: 15) [01:14:18 -12975.150845] AUTODETECT spr round 4 (radius: 20) [01:14:42 -12146.137991] AUTODETECT spr round 5 (radius: 25) [01:15:11 -11209.631003] SPR radius for FAST iterations: 25 (autodetect) [01:15:11 -11209.631003] Model parameter optimization (eps = 3.000000) [01:15:21 -11164.853861] FAST spr round 1 (radius: 25) [01:15:41 -9644.278089] FAST spr round 2 (radius: 25) [01:15:59 -9464.799491] FAST spr round 3 (radius: 25) [01:16:16 -9451.860650] FAST spr round 4 (radius: 25) [01:16:31 -9451.523130] FAST spr round 5 (radius: 25) [01:16:46 -9451.522989] Model parameter optimization (eps = 1.000000) [01:16:51 -9450.178570] SLOW spr round 1 (radius: 5) [01:17:11 -9448.368229] SLOW spr round 2 (radius: 5) [01:17:30 -9447.380888] SLOW spr round 3 (radius: 5) [01:17:49 -9447.380859] SLOW spr round 4 (radius: 10) [01:18:08 -9447.380852] SLOW spr round 5 (radius: 15) [01:18:38 -9446.162296] SLOW spr round 6 (radius: 5) [01:19:04 -9377.490481] SLOW spr round 7 (radius: 5) [01:19:27 -9377.417593] SLOW spr round 8 (radius: 10) [01:19:48 -9376.289739] SLOW spr round 9 (radius: 5) [01:20:12 -9374.621731] SLOW spr round 10 (radius: 5) [01:20:34 -9374.621157] SLOW spr round 11 (radius: 10) [01:20:54 -9374.620778] SLOW spr round 12 (radius: 15) [01:21:22 -9374.620526] SLOW spr round 13 (radius: 20) [01:21:59 -9373.898544] SLOW spr round 14 (radius: 5) [01:22:26 -9372.008581] SLOW spr round 15 (radius: 5) [01:22:48 -9372.007709] SLOW spr round 16 (radius: 10) [01:23:09 -9372.007542] SLOW spr round 17 (radius: 15) [01:23:38 -9372.007509] SLOW spr round 18 (radius: 20) [01:24:15 -9370.981993] SLOW spr round 19 (radius: 5) [01:24:41 -9370.955426] SLOW spr round 20 (radius: 10) [01:25:03 -9370.954009] SLOW spr round 21 (radius: 15) [01:25:30 -9370.953191] SLOW spr round 22 (radius: 20) [01:26:06 -9370.612023] SLOW spr round 23 (radius: 5) [01:26:33 -9369.708744] SLOW spr round 24 (radius: 5) [01:26:56 -9369.706895] SLOW spr round 25 (radius: 10) [01:27:17 -9368.182584] SLOW spr round 26 (radius: 5) [01:27:42 -9367.215162] SLOW spr round 27 (radius: 5) [01:28:04 -9366.880631] SLOW spr round 28 (radius: 5) [01:28:24 -9366.880586] SLOW spr round 29 (radius: 10) [01:28:44 -9366.880583] SLOW spr round 30 (radius: 15) [01:29:13 -9366.880583] SLOW spr round 31 (radius: 20) [01:29:50 -9366.722766] SLOW spr round 32 (radius: 5) [01:30:16 -9366.703442] SLOW spr round 33 (radius: 10) [01:30:39 -9366.702482] SLOW spr round 34 (radius: 15) [01:31:06 -9366.702055] SLOW spr round 35 (radius: 20) [01:31:44 -9366.701865] SLOW spr round 36 (radius: 25) [01:32:30 -9366.403532] SLOW spr round 37 (radius: 5) [01:32:56 -9366.403484] SLOW spr round 38 (radius: 10) [01:33:19 -9366.403466] SLOW spr round 39 (radius: 15) [01:33:47 -9366.403458] SLOW spr round 40 (radius: 20) [01:34:24 -9366.403454] SLOW spr round 41 (radius: 25) [01:35:10 -9366.403453] Model parameter optimization (eps = 0.100000) [01:35:16] ML tree search #5, logLikelihood: -9364.744471 [01:35:16 -34082.443178] Initial branch length optimization [01:35:17 -28699.959032] Model parameter optimization (eps = 10.000000) [01:35:26 -28481.324304] AUTODETECT spr round 1 (radius: 5) [01:35:44 -19507.330357] AUTODETECT spr round 2 (radius: 10) [01:36:04 -14758.311669] AUTODETECT spr round 3 (radius: 15) [01:36:32 -12073.061133] AUTODETECT spr round 4 (radius: 20) [01:37:00 -11380.047881] AUTODETECT spr round 5 (radius: 25) [01:37:30 -11188.998234] SPR radius for FAST iterations: 25 (autodetect) [01:37:30 -11188.998234] Model parameter optimization (eps = 3.000000) [01:37:37 -11183.377414] FAST spr round 1 (radius: 25) [01:37:56 -9712.074896] FAST spr round 2 (radius: 25) [01:38:14 -9473.795077] FAST spr round 3 (radius: 25) [01:38:30 -9384.073250] FAST spr round 4 (radius: 25) [01:38:46 -9378.997535] FAST spr round 5 (radius: 25) [01:39:02 -9375.615355] FAST spr round 6 (radius: 25) [01:39:17 -9375.614894] Model parameter optimization (eps = 1.000000) [01:39:21 -9374.693119] SLOW spr round 1 (radius: 5) [01:39:41 -9371.146804] SLOW spr round 2 (radius: 5) [01:40:00 -9369.377683] SLOW spr round 3 (radius: 5) [01:40:19 -9369.209279] SLOW spr round 4 (radius: 5) [01:40:37 -9369.209063] SLOW spr round 5 (radius: 10) [01:40:55 -9369.209051] SLOW spr round 6 (radius: 15) [01:41:23 -9369.209037] SLOW spr round 7 (radius: 20) [01:41:58 -9369.209023] SLOW spr round 8 (radius: 25) [01:42:40 -9367.253174] SLOW spr round 9 (radius: 5) [01:43:04 -9367.253174] SLOW spr round 10 (radius: 10) [01:43:26 -9367.253174] SLOW spr round 11 (radius: 15) [01:43:53 -9367.253174] SLOW spr round 12 (radius: 20) [01:44:29 -9367.253174] SLOW spr round 13 (radius: 25) [01:45:12 -9367.253174] Model parameter optimization (eps = 0.100000) [01:45:14] ML tree search #6, logLikelihood: -9367.213494 [01:45:14 -33913.687848] Initial branch length optimization [01:45:14 -28580.452527] Model parameter optimization (eps = 10.000000) [01:45:22 -28435.738724] AUTODETECT spr round 1 (radius: 5) [01:45:39 -19552.583503] AUTODETECT spr round 2 (radius: 10) [01:45:59 -13912.168945] AUTODETECT spr round 3 (radius: 15) [01:46:27 -11953.726226] AUTODETECT spr round 4 (radius: 20) [01:46:53 -11399.049067] AUTODETECT spr round 5 (radius: 25) [01:47:27 -11154.743402] SPR radius for FAST iterations: 25 (autodetect) [01:47:27 -11154.743402] Model parameter optimization (eps = 3.000000) [01:47:35 -11136.160066] FAST spr round 1 (radius: 25) [01:47:54 -9699.373130] FAST spr round 2 (radius: 25) [01:48:11 -9396.892228] FAST spr round 3 (radius: 25) [01:48:28 -9367.599121] FAST spr round 4 (radius: 25) [01:48:43 -9364.259662] FAST spr round 5 (radius: 25) [01:48:58 -9364.258857] Model parameter optimization (eps = 1.000000) [01:49:03 -9362.697992] SLOW spr round 1 (radius: 5) [01:49:21 -9361.266788] SLOW spr round 2 (radius: 5) [01:49:40 -9360.999659] SLOW spr round 3 (radius: 5) [01:49:58 -9360.999575] SLOW spr round 4 (radius: 10) [01:50:16 -9360.999566] SLOW spr round 5 (radius: 15) [01:50:42 -9360.812786] SLOW spr round 6 (radius: 5) [01:51:06 -9356.926886] SLOW spr round 7 (radius: 5) [01:51:27 -9356.925991] SLOW spr round 8 (radius: 10) [01:51:46 -9356.068416] SLOW spr round 9 (radius: 5) [01:52:08 -9356.068087] SLOW spr round 10 (radius: 10) [01:52:27 -9356.068034] SLOW spr round 11 (radius: 15) [01:52:52 -9356.040051] SLOW spr round 12 (radius: 20) [01:53:23 -9355.015311] SLOW spr round 13 (radius: 5) [01:53:47 -9354.185237] SLOW spr round 14 (radius: 5) [01:54:09 -9351.809037] SLOW spr round 15 (radius: 5) [01:54:28 -9351.560975] SLOW spr round 16 (radius: 5) [01:54:46 -9351.560341] SLOW spr round 17 (radius: 10) [01:55:04 -9351.560339] SLOW spr round 18 (radius: 15) [01:55:31 -9351.560319] SLOW spr round 19 (radius: 20) [01:56:02 -9351.560319] SLOW spr round 20 (radius: 25) [01:56:41 -9351.349802] SLOW spr round 21 (radius: 5) [01:57:04 -9351.274409] SLOW spr round 22 (radius: 10) [01:57:24 -9351.274234] SLOW spr round 23 (radius: 15) [01:57:49 -9351.274234] SLOW spr round 24 (radius: 20) [01:58:21 -9351.274234] SLOW spr round 25 (radius: 25) [01:58:59 -9351.267210] Model parameter optimization (eps = 0.100000) [01:59:01] ML tree search #7, logLikelihood: -9351.261122 [01:59:01 -34315.224449] Initial branch length optimization [01:59:01 -28806.685915] Model parameter optimization (eps = 10.000000) [01:59:12 -28347.129522] AUTODETECT spr round 1 (radius: 5) [01:59:29 -20537.632599] AUTODETECT spr round 2 (radius: 10) [01:59:50 -15186.316467] AUTODETECT spr round 3 (radius: 15) [02:00:11 -13384.963303] AUTODETECT spr round 4 (radius: 20) [02:00:37 -11830.313806] AUTODETECT spr round 5 (radius: 25) [02:01:06 -11339.215836] SPR radius for FAST iterations: 25 (autodetect) [02:01:06 -11339.215836] Model parameter optimization (eps = 3.000000) [02:01:15 -11293.956639] FAST spr round 1 (radius: 25) [02:01:33 -9646.651938] FAST spr round 2 (radius: 25) [02:01:51 -9523.302912] FAST spr round 3 (radius: 25) [02:02:07 -9469.846327] FAST spr round 4 (radius: 25) [02:02:22 -9468.540432] FAST spr round 5 (radius: 25) [02:02:37 -9468.539573] Model parameter optimization (eps = 1.000000) [02:02:42 -9466.591074] SLOW spr round 1 (radius: 5) [02:03:02 -9458.556445] SLOW spr round 2 (radius: 5) [02:03:21 -9456.525122] SLOW spr round 3 (radius: 5) [02:03:40 -9456.524169] SLOW spr round 4 (radius: 10) [02:03:58 -9455.277962] SLOW spr round 5 (radius: 5) [02:04:22 -9455.277357] SLOW spr round 6 (radius: 10) [02:04:42 -9455.187481] SLOW spr round 7 (radius: 15) [02:05:10 -9433.160270] SLOW spr round 8 (radius: 5) [02:05:35 -9430.207295] SLOW spr round 9 (radius: 5) [02:05:56 -9430.194111] SLOW spr round 10 (radius: 10) [02:06:15 -9430.166150] SLOW spr round 11 (radius: 15) [02:06:41 -9430.164890] SLOW spr round 12 (radius: 20) [02:07:16 -9430.164333] SLOW spr round 13 (radius: 25) [02:08:00 -9398.538716] SLOW spr round 14 (radius: 5) [02:08:26 -9370.073573] SLOW spr round 15 (radius: 5) [02:08:49 -9367.070067] SLOW spr round 16 (radius: 5) [02:09:09 -9367.069728] SLOW spr round 17 (radius: 10) [02:09:28 -9363.498325] SLOW spr round 18 (radius: 5) [02:09:53 -9360.621776] SLOW spr round 19 (radius: 5) [02:10:15 -9360.616890] SLOW spr round 20 (radius: 10) [02:10:35 -9360.615103] SLOW spr round 21 (radius: 15) [02:11:02 -9360.614129] SLOW spr round 22 (radius: 20) [02:11:37 -9360.613588] SLOW spr round 23 (radius: 25) [02:12:21 -9360.372608] SLOW spr round 24 (radius: 5) [02:12:47 -9360.099400] SLOW spr round 25 (radius: 5) [02:13:09 -9360.099280] SLOW spr round 26 (radius: 10) [02:13:29 -9359.510425] SLOW spr round 27 (radius: 5) [02:13:53 -9359.508858] SLOW spr round 28 (radius: 10) [02:14:13 -9359.508592] SLOW spr round 29 (radius: 15) [02:14:39 -9359.508523] SLOW spr round 30 (radius: 20) [02:15:14 -9359.508498] SLOW spr round 31 (radius: 25) [02:15:56 -9359.508488] Model parameter optimization (eps = 0.100000) [02:16:02] ML tree search #8, logLikelihood: -9357.765721 [02:16:02 -33859.801754] Initial branch length optimization [02:16:03 -28535.477641] Model parameter optimization (eps = 10.000000) [02:16:14 -28204.481977] AUTODETECT spr round 1 (radius: 5) [02:16:32 -20049.877945] AUTODETECT spr round 2 (radius: 10) [02:16:51 -15307.627539] AUTODETECT spr round 3 (radius: 15) [02:17:15 -13085.584976] AUTODETECT spr round 4 (radius: 20) [02:17:38 -11832.354484] AUTODETECT spr round 5 (radius: 25) [02:18:05 -11289.905891] SPR radius for FAST iterations: 25 (autodetect) [02:18:05 -11289.905891] Model parameter optimization (eps = 3.000000) [02:18:15 -11267.570214] FAST spr round 1 (radius: 25) [02:18:34 -9639.482419] FAST spr round 2 (radius: 25) [02:18:51 -9528.556239] FAST spr round 3 (radius: 25) [02:19:08 -9494.303318] FAST spr round 4 (radius: 25) [02:19:24 -9490.141732] FAST spr round 5 (radius: 25) [02:19:39 -9489.765148] FAST spr round 6 (radius: 25) [02:19:54 -9489.732760] Model parameter optimization (eps = 1.000000) [02:20:01 -9482.489429] SLOW spr round 1 (radius: 5) [02:20:21 -9478.415478] SLOW spr round 2 (radius: 5) [02:20:41 -9478.068170] SLOW spr round 3 (radius: 5) [02:20:59 -9478.068170] SLOW spr round 4 (radius: 10) [02:21:18 -9475.141793] SLOW spr round 5 (radius: 5) [02:21:44 -9474.999381] SLOW spr round 6 (radius: 5) [02:22:05 -9474.998942] SLOW spr round 7 (radius: 10) [02:22:25 -9474.969982] SLOW spr round 8 (radius: 15) [02:22:53 -9470.189831] SLOW spr round 9 (radius: 5) [02:23:19 -9414.291239] SLOW spr round 10 (radius: 5) [02:23:41 -9399.106616] SLOW spr round 11 (radius: 5) [02:24:01 -9399.106590] SLOW spr round 12 (radius: 10) [02:24:21 -9399.106588] SLOW spr round 13 (radius: 15) [02:24:50 -9398.593625] SLOW spr round 14 (radius: 5) [02:25:15 -9398.593610] SLOW spr round 15 (radius: 10) [02:25:38 -9395.111244] SLOW spr round 16 (radius: 5) [02:26:03 -9394.140697] SLOW spr round 17 (radius: 5) [02:26:24 -9393.952055] SLOW spr round 18 (radius: 5) [02:26:44 -9393.951222] SLOW spr round 19 (radius: 10) [02:27:03 -9393.950670] SLOW spr round 20 (radius: 15) [02:27:31 -9393.950290] SLOW spr round 21 (radius: 20) [02:28:05 -9393.136559] SLOW spr round 22 (radius: 5) [02:28:31 -9393.134122] SLOW spr round 23 (radius: 10) [02:28:53 -9392.899773] SLOW spr round 24 (radius: 5) [02:29:17 -9392.898558] SLOW spr round 25 (radius: 10) [02:29:38 -9392.898163] SLOW spr round 26 (radius: 15) [02:30:04 -9392.898000] SLOW spr round 27 (radius: 20) [02:30:39 -9392.897929] SLOW spr round 28 (radius: 25) [02:31:23 -9380.139302] SLOW spr round 29 (radius: 5) [02:31:50 -9374.489207] SLOW spr round 30 (radius: 5) [02:32:14 -9373.307258] SLOW spr round 31 (radius: 5) [02:32:35 -9373.160084] SLOW spr round 32 (radius: 5) [02:32:55 -9373.159708] SLOW spr round 33 (radius: 10) [02:33:14 -9372.442528] SLOW spr round 34 (radius: 5) [02:33:39 -9372.246859] SLOW spr round 35 (radius: 5) [02:34:01 -9372.246772] SLOW spr round 36 (radius: 10) [02:34:21 -9372.246772] SLOW spr round 37 (radius: 15) [02:34:50 -9371.559149] SLOW spr round 38 (radius: 5) [02:35:17 -9369.520076] SLOW spr round 39 (radius: 5) [02:35:40 -9368.024335] SLOW spr round 40 (radius: 5) [02:36:01 -9368.023664] SLOW spr round 41 (radius: 10) [02:36:20 -9368.023593] SLOW spr round 42 (radius: 15) [02:36:51 -9368.023552] SLOW spr round 43 (radius: 20) [02:37:27 -9368.023520] SLOW spr round 44 (radius: 25) [02:38:13 -9368.023494] Model parameter optimization (eps = 0.100000) [02:38:21] ML tree search #9, logLikelihood: -9366.222007 [02:38:21 -34076.193231] Initial branch length optimization [02:38:21 -28777.010418] Model parameter optimization (eps = 10.000000) [02:38:30 -28626.982426] AUTODETECT spr round 1 (radius: 5) [02:38:46 -19451.137471] AUTODETECT spr round 2 (radius: 10) [02:39:05 -15341.616656] AUTODETECT spr round 3 (radius: 15) [02:39:34 -12403.854212] AUTODETECT spr round 4 (radius: 20) [02:40:01 -11179.861911] AUTODETECT spr round 5 (radius: 25) [02:40:31 -11040.334031] SPR radius for FAST iterations: 25 (autodetect) [02:40:31 -11040.334031] Model parameter optimization (eps = 3.000000) [02:40:39 -11021.947337] FAST spr round 1 (radius: 25) [02:40:59 -9541.846958] FAST spr round 2 (radius: 25) [02:41:16 -9460.534072] FAST spr round 3 (radius: 25) [02:41:32 -9455.306231] FAST spr round 4 (radius: 25) [02:41:47 -9452.396291] FAST spr round 5 (radius: 25) [02:42:02 -9451.898287] FAST spr round 6 (radius: 25) [02:42:17 -9451.897643] Model parameter optimization (eps = 1.000000) [02:42:20 -9451.133570] SLOW spr round 1 (radius: 5) [02:42:40 -9447.854788] SLOW spr round 2 (radius: 5) [02:42:58 -9447.852140] SLOW spr round 3 (radius: 10) [02:43:17 -9443.514667] SLOW spr round 4 (radius: 5) [02:43:41 -9440.680940] SLOW spr round 5 (radius: 5) [02:44:03 -9439.462617] SLOW spr round 6 (radius: 5) [02:44:23 -9439.137820] SLOW spr round 7 (radius: 5) [02:44:42 -9439.137011] SLOW spr round 8 (radius: 10) [02:45:00 -9435.951201] SLOW spr round 9 (radius: 5) [02:45:24 -9435.950272] SLOW spr round 10 (radius: 10) [02:45:44 -9435.950184] SLOW spr round 11 (radius: 15) [02:46:08 -9435.950166] SLOW spr round 12 (radius: 20) [02:46:40 -9435.950155] SLOW spr round 13 (radius: 25) [02:47:18 -9435.783512] SLOW spr round 14 (radius: 5) [02:47:43 -9434.582023] SLOW spr round 15 (radius: 5) [02:48:05 -9434.581804] SLOW spr round 16 (radius: 10) [02:48:24 -9434.581786] SLOW spr round 17 (radius: 15) [02:48:49 -9434.581773] SLOW spr round 18 (radius: 20) [02:49:20 -9434.581762] SLOW spr round 19 (radius: 25) [02:49:57 -9434.365861] SLOW spr round 20 (radius: 5) [02:50:22 -9434.365635] SLOW spr round 21 (radius: 10) [02:50:43 -9434.365608] SLOW spr round 22 (radius: 15) [02:51:07 -9434.365605] SLOW spr round 23 (radius: 20) [02:51:39 -9434.365604] SLOW spr round 24 (radius: 25) [02:52:16 -9434.365604] Model parameter optimization (eps = 0.100000) [02:52:18] ML tree search #10, logLikelihood: -9434.293422 [02:52:18 -34248.092450] Initial branch length optimization [02:52:19 -28832.377344] Model parameter optimization (eps = 10.000000) [02:52:30 -28393.134565] AUTODETECT spr round 1 (radius: 5) [02:52:47 -20295.720797] AUTODETECT spr round 2 (radius: 10) [02:53:07 -15393.284851] AUTODETECT spr round 3 (radius: 15) [02:53:30 -13216.263070] AUTODETECT spr round 4 (radius: 20) [02:53:54 -11750.952324] AUTODETECT spr round 5 (radius: 25) [02:54:20 -11358.836052] SPR radius for FAST iterations: 25 (autodetect) [02:54:20 -11358.836052] Model parameter optimization (eps = 3.000000) [02:54:28 -11309.929395] FAST spr round 1 (radius: 25) [02:54:47 -9677.868447] FAST spr round 2 (radius: 25) [02:55:04 -9565.889605] FAST spr round 3 (radius: 25) [02:55:21 -9503.627545] FAST spr round 4 (radius: 25) [02:55:36 -9503.617189] Model parameter optimization (eps = 1.000000) [02:55:43 -9501.632190] SLOW spr round 1 (radius: 5) [02:56:04 -9463.864404] SLOW spr round 2 (radius: 5) [02:56:23 -9449.025846] SLOW spr round 3 (radius: 5) [02:56:43 -9423.029509] SLOW spr round 4 (radius: 5) [02:57:03 -9422.114020] SLOW spr round 5 (radius: 5) [02:57:22 -9422.113846] SLOW spr round 6 (radius: 10) [02:57:41 -9421.717482] SLOW spr round 7 (radius: 5) [02:58:05 -9421.716245] SLOW spr round 8 (radius: 10) [02:58:26 -9421.716181] SLOW spr round 9 (radius: 15) [02:58:54 -9420.959174] SLOW spr round 10 (radius: 5) [02:59:20 -9420.850769] SLOW spr round 11 (radius: 5) [02:59:42 -9420.849395] SLOW spr round 12 (radius: 10) [03:00:02 -9420.753523] SLOW spr round 13 (radius: 15) [03:00:31 -9420.753298] SLOW spr round 14 (radius: 20) [03:01:08 -9397.348800] SLOW spr round 15 (radius: 5) [03:01:35 -9367.654003] SLOW spr round 16 (radius: 5) [03:01:58 -9367.448827] SLOW spr round 17 (radius: 5) [03:02:19 -9367.447502] SLOW spr round 18 (radius: 10) [03:02:38 -9367.447133] SLOW spr round 19 (radius: 15) [03:03:10 -9367.447016] SLOW spr round 20 (radius: 20) [03:03:47 -9367.446985] SLOW spr round 21 (radius: 25) [03:04:31 -9367.446964] Model parameter optimization (eps = 0.100000) [03:04:40] ML tree search #11, logLikelihood: -9365.349559 [03:04:40 -34127.932445] Initial branch length optimization [03:04:40 -28793.017595] Model parameter optimization (eps = 10.000000) [03:04:49 -28468.974136] AUTODETECT spr round 1 (radius: 5) [03:05:06 -20286.610731] AUTODETECT spr round 2 (radius: 10) [03:05:27 -15001.349397] AUTODETECT spr round 3 (radius: 15) [03:05:49 -12508.340024] AUTODETECT spr round 4 (radius: 20) [03:06:11 -11465.257972] AUTODETECT spr round 5 (radius: 25) [03:06:34 -11309.982256] SPR radius for FAST iterations: 25 (autodetect) [03:06:34 -11309.982256] Model parameter optimization (eps = 3.000000) [03:06:42 -11257.992432] FAST spr round 1 (radius: 25) [03:07:01 -9669.373181] FAST spr round 2 (radius: 25) [03:07:19 -9563.658363] FAST spr round 3 (radius: 25) [03:07:35 -9541.157917] FAST spr round 4 (radius: 25) [03:07:51 -9478.831272] FAST spr round 5 (radius: 25) [03:08:05 -9478.830474] Model parameter optimization (eps = 1.000000) [03:08:10 -9476.297245] SLOW spr round 1 (radius: 5) [03:08:30 -9475.496863] SLOW spr round 2 (radius: 5) [03:08:49 -9475.496547] SLOW spr round 3 (radius: 10) [03:09:07 -9471.406490] SLOW spr round 4 (radius: 5) [03:09:31 -9471.405352] SLOW spr round 5 (radius: 10) [03:09:50 -9471.405244] SLOW spr round 6 (radius: 15) [03:10:15 -9471.405224] SLOW spr round 7 (radius: 20) [03:10:49 -9471.405223] SLOW spr round 8 (radius: 25) [03:11:29 -9456.944829] SLOW spr round 9 (radius: 5) [03:11:55 -9439.246708] SLOW spr round 10 (radius: 5) [03:12:17 -9438.442527] SLOW spr round 11 (radius: 5) [03:12:37 -9438.442493] SLOW spr round 12 (radius: 10) [03:12:56 -9437.767779] SLOW spr round 13 (radius: 5) [03:13:20 -9437.766329] SLOW spr round 14 (radius: 10) [03:13:39 -9437.766177] SLOW spr round 15 (radius: 15) [03:14:04 -9437.766140] SLOW spr round 16 (radius: 20) [03:14:35 -9437.766135] SLOW spr round 17 (radius: 25) [03:15:11 -9437.766134] Model parameter optimization (eps = 0.100000) [03:15:13] ML tree search #12, logLikelihood: -9437.684414 [03:15:13 -33985.373168] Initial branch length optimization [03:15:14 -28585.956304] Model parameter optimization (eps = 10.000000) [03:15:22 -28392.541038] AUTODETECT spr round 1 (radius: 5) [03:15:39 -19399.064099] AUTODETECT spr round 2 (radius: 10) [03:16:00 -13165.490717] AUTODETECT spr round 3 (radius: 15) [03:16:20 -11208.571582] AUTODETECT spr round 4 (radius: 20) [03:16:46 -10813.772732] AUTODETECT spr round 5 (radius: 25) [03:17:15 -10777.566376] SPR radius for FAST iterations: 25 (autodetect) [03:17:15 -10777.566376] Model parameter optimization (eps = 3.000000) [03:17:23 -10768.596359] FAST spr round 1 (radius: 25) [03:17:42 -9637.202768] FAST spr round 2 (radius: 25) [03:18:00 -9491.892407] FAST spr round 3 (radius: 25) [03:18:16 -9455.739844] FAST spr round 4 (radius: 25) [03:18:32 -9455.688604] Model parameter optimization (eps = 1.000000) [03:18:34 -9455.455118] SLOW spr round 1 (radius: 5) [03:18:53 -9452.119367] SLOW spr round 2 (radius: 5) [03:19:12 -9452.111147] SLOW spr round 3 (radius: 10) [03:19:30 -9452.107057] SLOW spr round 4 (radius: 15) [03:19:58 -9451.819661] SLOW spr round 5 (radius: 5) [03:20:22 -9451.608260] SLOW spr round 6 (radius: 5) [03:20:43 -9451.608253] SLOW spr round 7 (radius: 10) [03:21:02 -9451.608249] SLOW spr round 8 (radius: 15) [03:21:29 -9451.608247] SLOW spr round 9 (radius: 20) [03:22:04 -9451.608246] SLOW spr round 10 (radius: 25) [03:22:45 -9451.608245] Model parameter optimization (eps = 0.100000) [03:22:47] ML tree search #13, logLikelihood: -9451.592460 [03:22:47 -34050.354075] Initial branch length optimization [03:22:47 -28806.239020] Model parameter optimization (eps = 10.000000) [03:22:56 -28574.171051] AUTODETECT spr round 1 (radius: 5) [03:23:13 -19639.721961] AUTODETECT spr round 2 (radius: 10) [03:23:33 -14840.661454] AUTODETECT spr round 3 (radius: 15) [03:23:54 -11687.073665] AUTODETECT spr round 4 (radius: 20) [03:24:23 -10965.664359] AUTODETECT spr round 5 (radius: 25) [03:24:51 -10867.274513] SPR radius for FAST iterations: 25 (autodetect) [03:24:51 -10867.274513] Model parameter optimization (eps = 3.000000) [03:24:59 -10860.121269] FAST spr round 1 (radius: 25) [03:25:19 -9645.988395] FAST spr round 2 (radius: 25) [03:25:37 -9536.510082] FAST spr round 3 (radius: 25) [03:25:53 -9524.920429] FAST spr round 4 (radius: 25) [03:26:08 -9524.052461] FAST spr round 5 (radius: 25) [03:26:23 -9524.050463] Model parameter optimization (eps = 1.000000) [03:26:27 -9523.283430] SLOW spr round 1 (radius: 5) [03:26:46 -9520.359630] SLOW spr round 2 (radius: 5) [03:27:05 -9520.020995] SLOW spr round 3 (radius: 5) [03:27:22 -9520.020233] SLOW spr round 4 (radius: 10) [03:27:41 -9509.741620] SLOW spr round 5 (radius: 5) [03:28:05 -9500.434643] SLOW spr round 6 (radius: 5) [03:28:27 -9500.059945] SLOW spr round 7 (radius: 5) [03:28:47 -9499.705911] SLOW spr round 8 (radius: 5) [03:29:06 -9499.700831] SLOW spr round 9 (radius: 10) [03:29:25 -9499.163861] SLOW spr round 10 (radius: 5) [03:29:49 -9498.869001] SLOW spr round 11 (radius: 5) [03:30:10 -9498.861114] SLOW spr round 12 (radius: 10) [03:30:29 -9498.859601] SLOW spr round 13 (radius: 15) [03:30:56 -9496.570629] SLOW spr round 14 (radius: 5) [03:31:20 -9496.570080] SLOW spr round 15 (radius: 10) [03:31:41 -9496.570060] SLOW spr round 16 (radius: 15) [03:32:07 -9496.281406] SLOW spr round 17 (radius: 5) [03:32:31 -9496.281381] SLOW spr round 18 (radius: 10) [03:32:52 -9496.281380] SLOW spr round 19 (radius: 15) [03:33:18 -9496.281379] SLOW spr round 20 (radius: 20) [03:33:55 -9464.150161] SLOW spr round 21 (radius: 5) [03:34:21 -9455.528952] SLOW spr round 22 (radius: 5) [03:34:42 -9455.528732] SLOW spr round 23 (radius: 10) [03:35:01 -9455.528730] SLOW spr round 24 (radius: 15) [03:35:28 -9455.528730] SLOW spr round 25 (radius: 20) [03:36:04 -9455.528730] SLOW spr round 26 (radius: 25) [03:36:48 -9455.528730] Model parameter optimization (eps = 0.100000) [03:36:52] ML tree search #14, logLikelihood: -9455.403510 [03:36:52 -34167.125107] Initial branch length optimization [03:36:53 -28734.289769] Model parameter optimization (eps = 10.000000) [03:37:01 -28545.586629] AUTODETECT spr round 1 (radius: 5) [03:37:19 -19940.646078] AUTODETECT spr round 2 (radius: 10) [03:37:38 -14780.432940] AUTODETECT spr round 3 (radius: 15) [03:37:59 -12720.061667] AUTODETECT spr round 4 (radius: 20) [03:38:23 -11556.965669] AUTODETECT spr round 5 (radius: 25) [03:38:55 -11407.795534] SPR radius for FAST iterations: 25 (autodetect) [03:38:55 -11407.795534] Model parameter optimization (eps = 3.000000) [03:39:01 -11400.254615] FAST spr round 1 (radius: 25) [03:39:20 -9763.382473] FAST spr round 2 (radius: 25) [03:39:38 -9549.577769] FAST spr round 3 (radius: 25) [03:39:54 -9439.975224] FAST spr round 4 (radius: 25) [03:40:11 -9429.892396] FAST spr round 5 (radius: 25) [03:40:26 -9428.460132] FAST spr round 6 (radius: 25) [03:40:41 -9428.460132] Model parameter optimization (eps = 1.000000) [03:40:47 -9427.108890] SLOW spr round 1 (radius: 5) [03:41:07 -9426.003818] SLOW spr round 2 (radius: 5) [03:41:26 -9425.953947] SLOW spr round 3 (radius: 10) [03:41:45 -9425.953942] SLOW spr round 4 (radius: 15) [03:42:12 -9425.621752] SLOW spr round 5 (radius: 5) [03:42:37 -9425.621678] SLOW spr round 6 (radius: 10) [03:42:58 -9425.621660] SLOW spr round 7 (radius: 15) [03:43:23 -9370.530480] SLOW spr round 8 (radius: 5) [03:43:49 -9353.982220] SLOW spr round 9 (radius: 5) [03:44:11 -9353.982203] SLOW spr round 10 (radius: 10) [03:44:31 -9353.982199] SLOW spr round 11 (radius: 15) [03:44:58 -9353.982198] SLOW spr round 12 (radius: 20) [03:45:30 -9353.982197] SLOW spr round 13 (radius: 25) [03:46:09 -9353.982197] Model parameter optimization (eps = 0.100000) [03:46:15] ML tree search #15, logLikelihood: -9352.380848 [03:46:15 -33959.932325] Initial branch length optimization [03:46:15 -28480.032814] Model parameter optimization (eps = 10.000000) [03:46:25 -28245.784631] AUTODETECT spr round 1 (radius: 5) [03:46:43 -19469.605400] AUTODETECT spr round 2 (radius: 10) [03:47:03 -15836.443420] AUTODETECT spr round 3 (radius: 15) [03:47:31 -13880.991628] AUTODETECT spr round 4 (radius: 20) [03:47:56 -11930.689650] AUTODETECT spr round 5 (radius: 25) [03:48:22 -11757.570138] SPR radius for FAST iterations: 25 (autodetect) [03:48:22 -11757.570138] Model parameter optimization (eps = 3.000000) [03:48:31 -11671.495934] FAST spr round 1 (radius: 25) [03:48:51 -10089.036866] FAST spr round 2 (radius: 25) [03:49:09 -9713.701935] FAST spr round 3 (radius: 25) [03:49:27 -9460.156612] FAST spr round 4 (radius: 25) [03:49:44 -9439.100480] FAST spr round 5 (radius: 25) [03:50:00 -9434.276901] FAST spr round 6 (radius: 25) [03:50:16 -9432.774311] FAST spr round 7 (radius: 25) [03:50:31 -9432.772764] Model parameter optimization (eps = 1.000000) [03:50:36 -9430.611457] SLOW spr round 1 (radius: 5) [03:50:56 -9428.304876] SLOW spr round 2 (radius: 5) [03:51:14 -9428.304644] SLOW spr round 3 (radius: 10) [03:51:32 -9427.040029] SLOW spr round 4 (radius: 5) [03:51:55 -9426.803283] SLOW spr round 5 (radius: 5) [03:52:16 -9426.803122] SLOW spr round 6 (radius: 10) [03:52:35 -9425.407470] SLOW spr round 7 (radius: 5) [03:52:57 -9424.213578] SLOW spr round 8 (radius: 5) [03:53:17 -9424.213578] SLOW spr round 9 (radius: 10) [03:53:36 -9424.213578] SLOW spr round 10 (radius: 15) [03:54:01 -9420.985741] SLOW spr round 11 (radius: 5) [03:54:25 -9420.985569] SLOW spr round 12 (radius: 10) [03:54:45 -9420.985489] SLOW spr round 13 (radius: 15) [03:55:10 -9420.985446] SLOW spr round 14 (radius: 20) [03:55:42 -9412.932162] SLOW spr round 15 (radius: 5) [03:56:06 -9361.973134] SLOW spr round 16 (radius: 5) [03:56:27 -9361.688737] SLOW spr round 17 (radius: 5) [03:56:46 -9361.688504] SLOW spr round 18 (radius: 10) [03:57:05 -9361.688404] SLOW spr round 19 (radius: 15) [03:57:31 -9361.688355] SLOW spr round 20 (radius: 20) [03:58:02 -9361.688329] SLOW spr round 21 (radius: 25) [03:58:38 -9354.078279] SLOW spr round 22 (radius: 5) [03:59:03 -9352.094271] SLOW spr round 23 (radius: 5) [03:59:25 -9351.677107] SLOW spr round 24 (radius: 5) [03:59:44 -9351.205041] SLOW spr round 25 (radius: 5) [04:00:02 -9351.155926] SLOW spr round 26 (radius: 10) [04:00:20 -9351.155922] SLOW spr round 27 (radius: 15) [04:00:47 -9351.155922] SLOW spr round 28 (radius: 20) [04:01:19 -9351.155922] SLOW spr round 29 (radius: 25) [04:01:56 -9351.155922] Model parameter optimization (eps = 0.100000) [04:01:59] ML tree search #16, logLikelihood: -9351.076523 [04:01:59 -33923.350291] Initial branch length optimization [04:01:59 -28484.326463] Model parameter optimization (eps = 10.000000) [04:02:06 -28096.421775] AUTODETECT spr round 1 (radius: 5) [04:02:23 -20165.330175] AUTODETECT spr round 2 (radius: 10) [04:02:49 -14555.951481] AUTODETECT spr round 3 (radius: 15) [04:03:15 -12311.465909] AUTODETECT spr round 4 (radius: 20) [04:03:38 -11705.779182] AUTODETECT spr round 5 (radius: 25) [04:04:04 -11580.199848] SPR radius for FAST iterations: 25 (autodetect) [04:04:04 -11580.199848] Model parameter optimization (eps = 3.000000) [04:04:11 -11554.436225] FAST spr round 1 (radius: 25) [04:04:32 -9933.715243] FAST spr round 2 (radius: 25) [04:04:50 -9706.571269] FAST spr round 3 (radius: 25) [04:05:06 -9439.362825] FAST spr round 4 (radius: 25) [04:05:23 -9427.217342] FAST spr round 5 (radius: 25) [04:05:38 -9425.529487] FAST spr round 6 (radius: 25) [04:05:52 -9425.529454] Model parameter optimization (eps = 1.000000) [04:06:00 -9416.444961] SLOW spr round 1 (radius: 5) [04:06:20 -9399.725254] SLOW spr round 2 (radius: 5) [04:06:40 -9397.969750] SLOW spr round 3 (radius: 5) [04:06:59 -9397.960241] SLOW spr round 4 (radius: 10) [04:07:18 -9395.566372] SLOW spr round 5 (radius: 5) [04:07:41 -9390.324069] SLOW spr round 6 (radius: 5) [04:08:03 -9387.574236] SLOW spr round 7 (radius: 5) [04:08:22 -9387.573933] SLOW spr round 8 (radius: 10) [04:08:40 -9387.487511] SLOW spr round 9 (radius: 15) [04:09:10 -9371.029206] SLOW spr round 10 (radius: 5) [04:09:35 -9368.652661] SLOW spr round 11 (radius: 5) [04:09:56 -9368.652620] SLOW spr round 12 (radius: 10) [04:10:15 -9368.652612] SLOW spr round 13 (radius: 15) [04:10:42 -9368.652611] SLOW spr round 14 (radius: 20) [04:11:17 -9368.652598] SLOW spr round 15 (radius: 25) [04:11:55 -9368.021801] SLOW spr round 16 (radius: 5) [04:12:20 -9368.020723] SLOW spr round 17 (radius: 10) [04:12:41 -9368.020672] SLOW spr round 18 (radius: 15) [04:13:07 -9368.020664] SLOW spr round 19 (radius: 20) [04:13:43 -9368.020650] SLOW spr round 20 (radius: 25) [04:14:21 -9367.337369] SLOW spr round 21 (radius: 5) [04:14:46 -9367.336844] SLOW spr round 22 (radius: 10) [04:15:07 -9367.336835] SLOW spr round 23 (radius: 15) [04:15:33 -9367.336834] SLOW spr round 24 (radius: 20) [04:16:09 -9367.336834] SLOW spr round 25 (radius: 25) [04:16:47 -9367.336834] Model parameter optimization (eps = 0.100000) [04:16:52] ML tree search #17, logLikelihood: -9366.515749 [04:16:52 -34105.014989] Initial branch length optimization [04:16:52 -28836.981418] Model parameter optimization (eps = 10.000000) [04:17:06 -28413.368200] AUTODETECT spr round 1 (radius: 5) [04:17:22 -20606.322544] AUTODETECT spr round 2 (radius: 10) [04:17:46 -15279.452632] AUTODETECT spr round 3 (radius: 15) [04:18:10 -11847.500201] AUTODETECT spr round 4 (radius: 20) [04:18:35 -11272.729862] AUTODETECT spr round 5 (radius: 25) [04:19:04 -11029.804306] SPR radius for FAST iterations: 25 (autodetect) [04:19:04 -11029.804306] Model parameter optimization (eps = 3.000000) [04:19:11 -10978.667663] FAST spr round 1 (radius: 25) [04:19:30 -9669.514611] FAST spr round 2 (radius: 25) [04:19:46 -9459.469189] FAST spr round 3 (radius: 25) [04:20:03 -9454.778424] FAST spr round 4 (radius: 25) [04:20:18 -9454.300457] FAST spr round 5 (radius: 25) [04:20:33 -9452.994033] FAST spr round 6 (radius: 25) [04:20:48 -9452.993819] Model parameter optimization (eps = 1.000000) [04:20:55 -9450.740834] SLOW spr round 1 (radius: 5) [04:21:15 -9447.128217] SLOW spr round 2 (radius: 5) [04:21:35 -9444.780379] SLOW spr round 3 (radius: 5) [04:21:55 -9442.878365] SLOW spr round 4 (radius: 5) [04:22:14 -9442.541145] SLOW spr round 5 (radius: 5) [04:22:33 -9441.824830] SLOW spr round 6 (radius: 5) [04:22:52 -9441.821891] SLOW spr round 7 (radius: 10) [04:23:11 -9436.139326] SLOW spr round 8 (radius: 5) [04:23:36 -9434.956911] SLOW spr round 9 (radius: 5) [04:23:57 -9434.951022] SLOW spr round 10 (radius: 10) [04:24:16 -9434.951002] SLOW spr round 11 (radius: 15) [04:24:46 -9395.478876] SLOW spr round 12 (radius: 5) [04:25:12 -9365.398524] SLOW spr round 13 (radius: 5) [04:25:35 -9364.079754] SLOW spr round 14 (radius: 5) [04:25:55 -9363.643038] SLOW spr round 15 (radius: 5) [04:26:14 -9363.639936] SLOW spr round 16 (radius: 10) [04:26:33 -9359.447767] SLOW spr round 17 (radius: 5) [04:26:58 -9356.415141] SLOW spr round 18 (radius: 5) [04:27:20 -9356.414189] SLOW spr round 19 (radius: 10) [04:27:39 -9356.414080] SLOW spr round 20 (radius: 15) [04:28:08 -9356.358267] SLOW spr round 21 (radius: 20) [04:28:44 -9356.358243] SLOW spr round 22 (radius: 25) [04:29:25 -9356.358243] Model parameter optimization (eps = 0.100000) [04:29:34] ML tree search #18, logLikelihood: -9353.810050 [04:29:34 -34041.920634] Initial branch length optimization [04:29:34 -28648.672952] Model parameter optimization (eps = 10.000000) [04:29:43 -28284.402823] AUTODETECT spr round 1 (radius: 5) [04:30:00 -20168.335200] AUTODETECT spr round 2 (radius: 10) [04:30:20 -15138.182413] AUTODETECT spr round 3 (radius: 15) [04:30:43 -12604.961295] AUTODETECT spr round 4 (radius: 20) [04:31:07 -11065.542662] AUTODETECT spr round 5 (radius: 25) [04:31:38 -10796.330822] SPR radius for FAST iterations: 25 (autodetect) [04:31:38 -10796.330822] Model parameter optimization (eps = 3.000000) [04:31:47 -10766.942423] FAST spr round 1 (radius: 25) [04:32:06 -9522.478829] FAST spr round 2 (radius: 25) [04:32:24 -9459.514246] FAST spr round 3 (radius: 25) [04:32:41 -9442.837016] FAST spr round 4 (radius: 25) [04:32:56 -9441.443985] FAST spr round 5 (radius: 25) [04:33:11 -9441.428048] Model parameter optimization (eps = 1.000000) [04:33:15 -9440.812605] SLOW spr round 1 (radius: 5) [04:33:35 -9439.118707] SLOW spr round 2 (radius: 5) [04:33:54 -9437.065166] SLOW spr round 3 (radius: 5) [04:34:13 -9437.064265] SLOW spr round 4 (radius: 10) [04:34:34 -9429.395545] SLOW spr round 5 (radius: 5) [04:35:00 -9428.887860] SLOW spr round 6 (radius: 5) [04:35:22 -9428.887509] SLOW spr round 7 (radius: 10) [04:35:42 -9427.996122] SLOW spr round 8 (radius: 5) [04:36:08 -9427.995882] SLOW spr round 9 (radius: 10) [04:36:29 -9427.995869] SLOW spr round 10 (radius: 15) [04:37:00 -9372.030380] SLOW spr round 11 (radius: 5) [04:37:27 -9356.867755] SLOW spr round 12 (radius: 5) [04:37:50 -9356.806348] SLOW spr round 13 (radius: 10) [04:38:11 -9354.811775] SLOW spr round 14 (radius: 5) [04:38:37 -9354.811611] SLOW spr round 15 (radius: 10) [04:38:59 -9354.811577] SLOW spr round 16 (radius: 15) [04:39:29 -9354.811563] SLOW spr round 17 (radius: 20) [04:40:13 -9354.089445] SLOW spr round 18 (radius: 5) [04:40:41 -9354.089358] SLOW spr round 19 (radius: 10) [04:41:04 -9354.089346] SLOW spr round 20 (radius: 15) [04:41:34 -9354.089336] SLOW spr round 21 (radius: 20) [04:42:18 -9354.089336] SLOW spr round 22 (radius: 25) [04:43:13 -9352.671084] SLOW spr round 23 (radius: 5) [04:43:41 -9352.669526] SLOW spr round 24 (radius: 10) [04:44:05 -9352.669455] SLOW spr round 25 (radius: 15) [04:44:35 -9352.669453] SLOW spr round 26 (radius: 20) [04:45:19 -9352.669453] SLOW spr round 27 (radius: 25) [04:46:14 -9352.669453] Model parameter optimization (eps = 0.100000) [04:46:21] ML tree search #19, logLikelihood: -9350.400095 [04:46:21 -34035.018367] Initial branch length optimization [04:46:21 -28869.601431] Model parameter optimization (eps = 10.000000) [04:46:33 -28429.860345] AUTODETECT spr round 1 (radius: 5) [04:46:49 -19621.149670] AUTODETECT spr round 2 (radius: 10) [04:47:11 -15025.850955] AUTODETECT spr round 3 (radius: 15) [04:47:33 -12501.666201] AUTODETECT spr round 4 (radius: 20) [04:47:58 -11176.143411] AUTODETECT spr round 5 (radius: 25) [04:48:24 -10898.194308] SPR radius for FAST iterations: 25 (autodetect) [04:48:24 -10898.194308] Model parameter optimization (eps = 3.000000) [04:48:31 -10868.180118] FAST spr round 1 (radius: 25) [04:48:51 -9624.659479] FAST spr round 2 (radius: 25) [04:49:08 -9474.070741] FAST spr round 3 (radius: 25) [04:49:25 -9452.546749] FAST spr round 4 (radius: 25) [04:49:40 -9449.410078] FAST spr round 5 (radius: 25) [04:49:54 -9449.410060] Model parameter optimization (eps = 1.000000) [04:50:01 -9447.428679] SLOW spr round 1 (radius: 5) [04:50:21 -9441.289888] SLOW spr round 2 (radius: 5) [04:50:40 -9441.284623] SLOW spr round 3 (radius: 10) [04:50:59 -9437.911105] SLOW spr round 4 (radius: 5) [04:51:24 -9433.097696] SLOW spr round 5 (radius: 5) [04:51:47 -9431.480229] SLOW spr round 6 (radius: 5) [04:52:07 -9430.787764] SLOW spr round 7 (radius: 5) [04:52:26 -9430.786571] SLOW spr round 8 (radius: 10) [04:52:45 -9430.786241] SLOW spr round 9 (radius: 15) [04:53:15 -9366.826768] SLOW spr round 10 (radius: 5) [04:53:42 -9346.997366] SLOW spr round 11 (radius: 5) [04:54:03 -9346.997322] SLOW spr round 12 (radius: 10) [04:54:23 -9346.997312] SLOW spr round 13 (radius: 15) [04:54:52 -9346.997308] SLOW spr round 14 (radius: 20) [04:55:30 -9345.969938] SLOW spr round 15 (radius: 5) [04:55:55 -9345.969938] SLOW spr round 16 (radius: 10) [04:56:17 -9345.969938] SLOW spr round 17 (radius: 15) [04:56:45 -9345.969938] SLOW spr round 18 (radius: 20) [04:57:24 -9345.969938] SLOW spr round 19 (radius: 25) [04:58:08 -9345.969938] Model parameter optimization (eps = 0.100000) [04:58:15] ML tree search #20, logLikelihood: -9343.782438 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.229179,0.036066) (0.106109,0.290957) (0.386987,0.943802) (0.277725,2.144644) 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: -9343.782438 AIC score: 20889.564876 / AICc score: 2447493.564876 / BIC score: 22633.019227 Free parameters (model + branch lengths): 1101 WARNING: Number of free parameters (K=1101) is larger than alignment size (n=36). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15918/3_mltree/P15918.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15918/3_mltree/P15918.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15918/3_mltree/P15918.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P15918/3_mltree/P15918.raxml.log Analysis started: 03-Jun-2021 15:19:21 / finished: 03-Jun-2021 20:17:36 Elapsed time: 17895.220 seconds (this run) / 18498.530 seconds (total with restarts) Consumed energy: 1369.973 Wh (= 7 km in an electric car, or 34 km with an e-scooter!)