RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 01-Jul-2021 23:16:52 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/2_msa/Q9HCH5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/3_mltree/Q9HCH5 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/2_msa/Q9HCH5_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 131 sites WARNING: Sequences tr_B4QZR2_B4QZR2_DROSI_7240 and tr_A0A0B4K657_A0A0B4K657_DROME_7227 are exactly identical! WARNING: Sequences tr_A0A2R8QSP1_A0A2R8QSP1_DANRE_7955 and tr_Q1L913_Q1L913_DANRE_7955 are exactly identical! WARNING: Sequences tr_A0A1D5P3K5_A0A1D5P3K5_CHICK_9031 and tr_A0A091F0Z0_A0A091F0Z0_CORBR_85066 are exactly identical! WARNING: Sequences tr_A0A1D5P3K5_A0A1D5P3K5_CHICK_9031 and tr_A0A091G0E4_A0A091G0E4_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1D5P3K5_A0A1D5P3K5_CHICK_9031 and tr_A0A2I0LZU1_A0A2I0LZU1_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1D5P3K5_A0A1D5P3K5_CHICK_9031 and tr_A0A093GCF9_A0A093GCF9_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A1D5P3K5_A0A1D5P3K5_CHICK_9031 and tr_A0A1V4KG22_A0A1V4KG22_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1D5P3K5_A0A1D5P3K5_CHICK_9031 and tr_A0A226NHV1_A0A226NHV1_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5P3K5_A0A1D5P3K5_CHICK_9031 and tr_A0A226NXR2_A0A226NXR2_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A1D5PAQ9_A0A1D5PAQ9_CHICK_9031 and tr_G1N1J7_G1N1J7_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5PAQ9_A0A1D5PAQ9_CHICK_9031 and tr_A0A226N661_A0A226N661_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5PAQ9_A0A1D5PAQ9_CHICK_9031 and tr_A0A226PAY6_A0A226PAY6_COLVI_9014 are exactly identical! WARNING: Sequences tr_E1C1G0_E1C1G0_CHICK_9031 and tr_G1N4Y9_G1N4Y9_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1C1G0_E1C1G0_CHICK_9031 and tr_U3JDF0_U3JDF0_FICAL_59894 are exactly identical! WARNING: Sequences tr_E1C1G0_E1C1G0_CHICK_9031 and tr_A0A218UTP4_A0A218UTP4_9PASE_299123 are exactly identical! WARNING: Sequences tr_F1NUG3_F1NUG3_CHICK_9031 and tr_G1NP53_G1NP53_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NUG3_F1NUG3_CHICK_9031 and tr_A0A226PIG0_A0A226PIG0_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q9R0Q1_SYTL4_MOUSE_10090 and sp_Q8VHQ7_SYTL4_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Y8J1_M3Y8J1_MUSPF_9669 and tr_A0A2Y9IHN5_A0A2Y9IHN5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YEZ5_M3YEZ5_MUSPF_9669 and tr_A0A2U3ZIT4_A0A2U3ZIT4_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YEZ5_M3YEZ5_MUSPF_9669 and tr_A0A2U3XQ86_A0A2U3XQ86_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YEZ5_M3YEZ5_MUSPF_9669 and tr_A0A2Y9K7R6_A0A2Y9K7R6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YMC2_M3YMC2_MUSPF_9669 and tr_F1RXS2_F1RXS2_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Z3L7_M3Z3L7_MUSPF_9669 and tr_G1ME65_G1ME65_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z3L7_M3Z3L7_MUSPF_9669 and tr_A0A337SB45_A0A337SB45_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z3L7_M3Z3L7_MUSPF_9669 and tr_A0A2U3VG26_A0A2U3VG26_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z3L7_M3Z3L7_MUSPF_9669 and tr_A0A2U3X6R7_A0A2U3X6R7_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Z3L7_M3Z3L7_MUSPF_9669 and tr_A0A2Y9KPN0_A0A2Y9KPN0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z3L7_M3Z3L7_MUSPF_9669 and tr_A0A384BPK5_A0A384BPK5_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3G2E9_A0A2I3G2E9_NOMLE_61853 and tr_W5Q2N6_W5Q2N6_SHEEP_9940 are exactly identical! WARNING: Sequences tr_A0A2I3G2E9_A0A2I3G2E9_NOMLE_61853 and tr_H0VEH4_H0VEH4_CAVPO_10141 are exactly identical! WARNING: Sequences tr_A0A2I3G2E9_A0A2I3G2E9_NOMLE_61853 and tr_A0A2I3NI95_A0A2I3NI95_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3G2E9_A0A2I3G2E9_NOMLE_61853 and tr_A0A3Q0E4S4_A0A3Q0E4S4_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A2I3G2E9_A0A2I3G2E9_NOMLE_61853 and tr_A0A2K5YD37_A0A2K5YD37_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QK05_G1QK05_NOMLE_61853 and tr_A0A1D5QQD6_A0A1D5QQD6_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QK05_G1QK05_NOMLE_61853 and tr_G7Q2I2_G7Q2I2_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QK05_G1QK05_NOMLE_61853 and tr_A0A2I3MZL1_A0A2I3MZL1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QK05_G1QK05_NOMLE_61853 and tr_A0A2K6CGW5_A0A2K6CGW5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QK05_G1QK05_NOMLE_61853 and tr_A0A2K5YC48_A0A2K5YC48_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_G3RRS8_G3RRS8_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and sp_O00443_P3C2A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_A0A1D5QJY6_A0A1D5QJY6_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_F7ILS1_F7ILS1_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_I3LLX2_I3LLX2_PIG_9823 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_D2HRK9_D2HRK9_AILME_9646 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_G7PQM7_G7PQM7_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_A0A2I3NGB5_A0A2I3NGB5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_A0A2K5KPN9_A0A2K5KPN9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_A0A2K6BX54_A0A2K6BX54_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_A0A2K5ZTD5_A0A2K5ZTD5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_A0A2R9BSX3_A0A2R9BSX3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_A0A2U3X0X7_A0A2U3X0X7_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_A0A2Y9RIE6_A0A2Y9RIE6_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_A0A2Y9JRR9_A0A2Y9JRR9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1S7M5_G1S7M5_NOMLE_61853 and tr_A0A384DJC8_A0A384DJC8_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1P8L0_G1P8L0_MYOLU_59463 and tr_F6U9E2_F6U9E2_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1P8L0_G1P8L0_MYOLU_59463 and tr_H0WK36_H0WK36_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G1P8L0_G1P8L0_MYOLU_59463 and tr_A0A2I2UT47_A0A2I2UT47_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1P8L0_G1P8L0_MYOLU_59463 and tr_A0A1U7UJN6_A0A1U7UJN6_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1PQI8_G1PQI8_MYOLU_59463 and tr_W5QAV3_W5QAV3_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1QEV8_G1QEV8_MYOLU_59463 and tr_I3N8S4_I3N8S4_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1QEV8_G1QEV8_MYOLU_59463 and tr_H0WNJ4_H0WNJ4_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G1QEV8_G1QEV8_MYOLU_59463 and tr_F7HKA9_F7HKA9_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QEV8_G1QEV8_MYOLU_59463 and tr_G3SW14_G3SW14_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G1QEV8_G1QEV8_MYOLU_59463 and tr_F7GR19_F7GR19_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1QEV8_G1QEV8_MYOLU_59463 and tr_F1SBX0_F1SBX0_PIG_9823 are exactly identical! WARNING: Sequences tr_G1QEV8_G1QEV8_MYOLU_59463 and tr_A0A0D9RIF1_A0A0D9RIF1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QEV8_G1QEV8_MYOLU_59463 and tr_A0A1S3FY38_A0A1S3FY38_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G1QEV8_G1QEV8_MYOLU_59463 and tr_A0A2K5M541_A0A2K5M541_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QEV8_G1QEV8_MYOLU_59463 and tr_A0A2K6C4Y9_A0A2K6C4Y9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QCU4_G3QCU4_GORGO_9595 and sp_Q8IYJ3_SYTL1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QCU4_G3QCU4_GORGO_9595 and tr_A0A2R8ZG42_A0A2R8ZG42_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QFR4_G3QFR4_GORGO_9595 and tr_K7D3C4_K7D3C4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QFR4_G3QFR4_GORGO_9595 and sp_Q96C24_SYTL4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QFR4_G3QFR4_GORGO_9595 and tr_A0A2R8ZUW0_A0A2R8ZUW0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QHH5_G3QHH5_GORGO_9595 and tr_H2R2J0_H2R2J0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QHH5_G3QHH5_GORGO_9595 and sp_Q9HCH5_SYTL2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QHH5_G3QHH5_GORGO_9595 and tr_A0A2R9AIM2_A0A2R9AIM2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QIY7_G3QIY7_GORGO_9595 and tr_H2RHT3_H2RHT3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QIY7_G3QIY7_GORGO_9595 and sp_Q8TDW5_SYTL5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QIY7_G3QIY7_GORGO_9595 and tr_A0A2R9CC23_A0A2R9CC23_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R0Z1_G3R0Z1_GORGO_9595 and tr_A0A2J8IWZ5_A0A2J8IWZ5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R0Z1_G3R0Z1_GORGO_9595 and sp_O00445_SYT5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NE05_H2NE05_PONAB_9601 and sp_Q5RAY1_P3C2A_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1SUU0_G1SUU0_RABIT_9986 and tr_A0A2I2UAK1_A0A2I2UAK1_FELCA_9685 are exactly identical! WARNING: Sequences tr_B5DVF9_B5DVF9_DROPS_46245 and tr_B4G6E6_B4G6E6_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2I3RIW3_A0A2I3RIW3_PANTR_9598 and sp_Q9Y6V0_PCLO_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TMY3_A0A2I3TMY3_PANTR_9598 and tr_A0A2R9CKB6_A0A2R9CKB6_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q9JKS6_PCLO_RAT_10116 and tr_A0A1U8CAR3_A0A1U8CAR3_MESAU_10036 are exactly identical! WARNING: Sequences tr_M4ABX5_M4ABX5_XIPMA_8083 and tr_A0A096LYX2_A0A096LYX2_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A088AKZ2_A0A088AKZ2_APIME_7460 and tr_A0A0M8ZQ56_A0A0M8ZQ56_9HYME_166423 are exactly identical! WARNING: Sequences tr_A0A088AKZ2_A0A088AKZ2_APIME_7460 and tr_A0A2A3EB21_A0A2A3EB21_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NW14_A0A158NW14_ATTCE_12957 and tr_F4X0A8_F4X0A8_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NW14_A0A158NW14_ATTCE_12957 and tr_A0A151X5Q4_A0A151X5Q4_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NW14_A0A158NW14_ATTCE_12957 and tr_A0A151J4H8_A0A151J4H8_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NW14_A0A158NW14_ATTCE_12957 and tr_A0A151JW47_A0A151JW47_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A158NW14_A0A158NW14_ATTCE_12957 and tr_A0A195D2Z6_A0A195D2Z6_9HYME_456900 are exactly identical! WARNING: Sequences tr_F7FK83_F7FK83_MACMU_9544 and tr_G7PND6_G7PND6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GMC4_F7GMC4_MACMU_9544 and tr_A0A0D9S829_A0A0D9S829_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GMC4_F7GMC4_MACMU_9544 and tr_A0A2K5P1U4_A0A2K5P1U4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GMC4_F7GMC4_MACMU_9544 and tr_A0A2K6D1J0_A0A2K6D1J0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GWJ4_F7GWJ4_MACMU_9544 and tr_G7Q379_G7Q379_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GWJ4_F7GWJ4_MACMU_9544 and tr_A0A096MNV2_A0A096MNV2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GWJ4_F7GWJ4_MACMU_9544 and tr_A0A0D9RDA9_A0A0D9RDA9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GWJ4_F7GWJ4_MACMU_9544 and tr_A0A2K5MV24_A0A2K5MV24_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GWJ4_F7GWJ4_MACMU_9544 and tr_A0A2K6D1C1_A0A2K6D1C1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GWJ4_F7GWJ4_MACMU_9544 and tr_A0A2K5ZRI6_A0A2K5ZRI6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3SSF4_G3SSF4_LOXAF_9785 and tr_A0A287BAW8_A0A287BAW8_PIG_9823 are exactly identical! WARNING: Sequences tr_E3LD22_E3LD22_CAERE_31234 and tr_A0A261CRD4_A0A261CRD4_9PELO_1503980 are exactly identical! WARNING: Sequences tr_G1LA08_G1LA08_AILME_9646 and tr_A0A2U3W9U1_A0A2U3W9U1_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1LA08_G1LA08_AILME_9646 and tr_A0A2U3Z1K3_A0A2U3Z1K3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1LA08_G1LA08_AILME_9646 and tr_A0A384DMJ3_A0A384DMJ3_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1LL15_G1LL15_AILME_9646 and tr_A0A384CIP4_A0A384CIP4_URSMA_29073 are exactly identical! WARNING: Sequences sp_A6QP06_SYTL2_BOVIN_9913 and tr_F1MY23_F1MY23_BOVIN_9913 are exactly identical! WARNING: Sequences tr_U3J4J5_U3J4J5_ANAPL_8839 and tr_A0A091F4V4_A0A091F4V4_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3J4J5_U3J4J5_ANAPL_8839 and tr_A0A093PBB5_A0A093PBB5_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3J4J5_U3J4J5_ANAPL_8839 and tr_A0A091VLE4_A0A091VLE4_OPIHO_30419 are exactly identical! WARNING: Sequences tr_U3J4J5_U3J4J5_ANAPL_8839 and tr_A0A091G7C7_A0A091G7C7_9AVES_55661 are exactly identical! WARNING: Sequences tr_U3J4J5_U3J4J5_ANAPL_8839 and tr_A0A2I0MB66_A0A2I0MB66_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3J4J5_U3J4J5_ANAPL_8839 and tr_A0A1V4KZV7_A0A1V4KZV7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A096N149_A0A096N149_PAPAN_9555 and tr_A0A2K5M1G0_A0A2K5M1G0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096N149_A0A096N149_PAPAN_9555 and tr_A0A2K6DX18_A0A2K6DX18_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096N149_A0A096N149_PAPAN_9555 and tr_A0A2K5Z8I8_A0A2K5Z8I8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0MWK6_A0A0A0MWK6_PAPAN_9555 and tr_A0A2K5MDX8_A0A2K5MDX8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0A0MWK6_A0A0A0MWK6_PAPAN_9555 and tr_A0A2K6DYL4_A0A2K6DYL4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0A0MWK6_A0A0A0MWK6_PAPAN_9555 and tr_A0A2K5XLY6_A0A2K5XLY6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3NEC8_A0A2I3NEC8_PAPAN_9555 and tr_A0A0D9QUK2_A0A0D9QUK2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3NEC8_A0A2I3NEC8_PAPAN_9555 and tr_A0A2K5LS28_A0A2K5LS28_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3NEC8_A0A2I3NEC8_PAPAN_9555 and tr_A0A2K5YKB6_A0A2K5YKB6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151MC58_A0A151MC58_ALLMI_8496 and tr_A0A3Q0GPU0_A0A3Q0GPU0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151N685_A0A151N685_ALLMI_8496 and tr_A0A3Q0H868_A0A3Q0H868_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151N8Z6_A0A151N8Z6_ALLMI_8496 and tr_A0A1U7S2D1_A0A1U7S2D1_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NNA0_A0A151NNA0_ALLMI_8496 and tr_A0A1U7S9G3_A0A1U7S9G3_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NPC8_A0A151NPC8_ALLMI_8496 and tr_A0A3Q0GHV5_A0A3Q0GHV5_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091EAP5_A0A091EAP5_CORBR_85066 and tr_A0A0A0A983_A0A0A0A983_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JEB8_A0A091JEB8_EGRGA_188379 and tr_A0A091UKI5_A0A091UKI5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JEB8_A0A091JEB8_EGRGA_188379 and tr_A0A087QUD4_A0A087QUD4_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JEB8_A0A091JEB8_EGRGA_188379 and tr_A0A093GIP3_A0A093GIP3_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091JLU4_A0A091JLU4_EGRGA_188379 and tr_A0A0A0ABU8_A0A0A0ABU8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091VL87_A0A091VL87_OPIHO_30419 and tr_A0A0A0APX9_A0A0A0APX9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0MB15_A0A2I0MB15_COLLI_8932 and tr_A0A1V4KYW0_A0A1V4KYW0_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MHU2_A0A2I0MHU2_COLLI_8932 and tr_A0A1V4JNR7_A0A1V4JNR7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1C9U4_A0A0V1C9U4_TRIBR_45882 and tr_A0A0V1PG66_A0A0V1PG66_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0V3G0_A0A0V0V3G0_9BILA_181606 and tr_A0A0V1M5Z1_A0A0V1M5Z1_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V1LEG4_A0A0V1LEG4_9BILA_6335 and tr_A0A0V0TF41_A0A0V0TF41_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1PA79_A0A0V1PA79_9BILA_92180 and tr_A0A0V0UA16_A0A0V0UA16_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S2Z9D8_A0A1S2Z9D8_ERIEU_9365 and tr_A0A2U4CEL9_A0A2U4CEL9_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A1S2Z9D8_A0A1S2Z9D8_ERIEU_9365 and tr_A0A2Y9LWU4_A0A2Y9LWU4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A1S2Z9D8_A0A1S2Z9D8_ERIEU_9365 and tr_A0A2Y9ELY2_A0A2Y9ELY2_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A1S2Z9D8_A0A1S2Z9D8_ERIEU_9365 and tr_A0A383ZIK8_A0A383ZIK8_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A1S3HI94_A0A1S3HI94_LINUN_7574 and tr_A0A2R2MR48_A0A2R2MR48_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3J3D0_A0A1S3J3D0_LINUN_7574 and tr_A0A1S3JPN9_A0A1S3JPN9_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1I7TWK1_A0A1I7TWK1_9PELO_1561998 and tr_A0A1I7TWK2_A0A1I7TWK2_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1L8GEH2_A0A1L8GEH2_XENLA_8355 and tr_A0A1L8GIB5_A0A1L8GIB5_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A226MY05_A0A226MY05_CALSU_9009 and tr_A0A226PIF3_A0A226PIF3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NJU1_A0A226NJU1_CALSU_9009 and tr_A0A226P7R5_A0A226P7R5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PXQ0_A0A2D0PXQ0_ICTPU_7998 and tr_A0A2D0PZE0_A0A2D0PZE0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R629_A0A2D0R629_ICTPU_7998 and tr_W5UA52_W5UA52_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RH67_A0A2D0RH67_ICTPU_7998 and tr_W5U824_W5U824_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RN21_A0A2D0RN21_ICTPU_7998 and tr_A0A2D0RPM3_A0A2D0RPM3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3V3F1_A0A2U3V3F1_TURTR_9739 and tr_A0A2Y9PGD2_A0A2Y9PGD2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CFY5_A0A2U4CFY5_TURTR_9739 and tr_A0A2Y9PX21_A0A2Y9PX21_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CFY5_A0A2U4CFY5_TURTR_9739 and tr_A0A2Y9FLK5_A0A2Y9FLK5_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 163 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/Q9HCH5/3_mltree/Q9HCH5.raxml.reduced.phy Alignment comprises 1 partitions and 131 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 131 / 131 Gaps: 5.59 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/3_mltree/Q9HCH5.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 131 / 10480 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -245840.993860] Initial branch length optimization [00:00:03 -206484.207432] Model parameter optimization (eps = 10.000000) [00:00:49 -205942.139303] AUTODETECT spr round 1 (radius: 5) [00:03:01 -126332.315717] AUTODETECT spr round 2 (radius: 10) [00:05:20 -86762.483294] AUTODETECT spr round 3 (radius: 15) [00:07:45 -71875.715209] AUTODETECT spr round 4 (radius: 20) [00:10:28 -67297.943764] AUTODETECT spr round 5 (radius: 25) [00:13:37 -61301.575810] SPR radius for FAST iterations: 25 (autodetect) [00:13:37 -61301.575810] Model parameter optimization (eps = 3.000000) [00:14:00 -60970.376462] FAST spr round 1 (radius: 25) [00:16:26 -49960.855154] FAST spr round 2 (radius: 25) [00:18:35 -48440.082085] FAST spr round 3 (radius: 25) [00:20:18 -47071.875267] FAST spr round 4 (radius: 25) [00:22:00 -46916.184819] FAST spr round 5 (radius: 25) [00:23:41 -46890.848914] FAST spr round 6 (radius: 25) [00:25:15 -46890.848750] Model parameter optimization (eps = 1.000000) [00:25:31 -46876.468465] SLOW spr round 1 (radius: 5) [00:27:26 -46863.539827] SLOW spr round 2 (radius: 5) [00:29:13 -46863.274162] SLOW spr round 3 (radius: 5) [00:31:00 -46863.273889] SLOW spr round 4 (radius: 10) [00:32:58 -46857.219200] SLOW spr round 5 (radius: 5) [00:35:14 -46854.718602] SLOW spr round 6 (radius: 5) [00:37:27 -46854.442905] SLOW spr round 7 (radius: 5) [00:39:35 -46852.575649] SLOW spr round 8 (radius: 5) [00:41:35 -46852.396082] SLOW spr round 9 (radius: 5) [00:43:24 -46852.395283] SLOW spr round 10 (radius: 10) [00:45:14 -46852.395256] SLOW spr round 11 (radius: 15) [00:47:58 -46852.203582] SLOW spr round 12 (radius: 5) [00:50:21 -46852.203571] SLOW spr round 13 (radius: 10) [00:52:31 -46849.387250] SLOW spr round 14 (radius: 5) [00:54:41 -46849.009974] SLOW spr round 15 (radius: 5) [00:56:38 -46849.008493] SLOW spr round 16 (radius: 10) [00:58:37 -46849.008075] SLOW spr round 17 (radius: 15) [01:01:06] [worker #1] ML tree search #2, logLikelihood: -46847.365051 [01:01:14 -46849.007947] SLOW spr round 18 (radius: 20) [01:05:20 -46848.193485] SLOW spr round 19 (radius: 5) [01:07:52 -46848.193244] SLOW spr round 20 (radius: 10) [01:09:39] [worker #2] ML tree search #3, logLikelihood: -46868.553547 [01:09:59 -46848.193199] SLOW spr round 21 (radius: 15) [01:12:33 -46848.193183] SLOW spr round 22 (radius: 20) [01:16:23 -46848.193177] SLOW spr round 23 (radius: 25) [01:21:15 -46848.193173] Model parameter optimization (eps = 0.100000) [01:21:34] [worker #0] ML tree search #1, logLikelihood: -46847.606660 [01:21:34 -244356.794327] Initial branch length optimization [01:21:38 -205703.099465] Model parameter optimization (eps = 10.000000) [01:22:09 -205155.532145] AUTODETECT spr round 1 (radius: 5) [01:24:23 -125992.072490] AUTODETECT spr round 2 (radius: 10) [01:26:41 -84545.623018] AUTODETECT spr round 3 (radius: 15) [01:29:21 -69208.093598] AUTODETECT spr round 4 (radius: 20) [01:32:04 -58723.318322] AUTODETECT spr round 5 (radius: 25) [01:35:14 -57473.636537] SPR radius for FAST iterations: 25 (autodetect) [01:35:15 -57473.636537] Model parameter optimization (eps = 3.000000) [01:35:34 -57133.845435] FAST spr round 1 (radius: 25) [01:37:59 -48770.260619] FAST spr round 2 (radius: 25) [01:39:53 -48223.772955] FAST spr round 3 (radius: 25) [01:41:40 -47227.994716] FAST spr round 4 (radius: 25) [01:43:19 -46980.610631] FAST spr round 5 (radius: 25) [01:44:56 -46900.614589] FAST spr round 6 (radius: 25) [01:46:34 -46891.105466] FAST spr round 7 (radius: 25) [01:48:10 -46886.298436] FAST spr round 8 (radius: 25) [01:49:45 -46883.261847] FAST spr round 9 (radius: 25) [01:51:12 -46883.245152] Model parameter optimization (eps = 1.000000) [01:51:20 -46882.012761] SLOW spr round 1 (radius: 5) [01:53:28 -46874.714677] SLOW spr round 2 (radius: 5) [01:55:29 -46872.588930] SLOW spr round 3 (radius: 5) [01:57:26 -46872.588768] SLOW spr round 4 (radius: 10) [01:59:19 -46871.245131] SLOW spr round 5 (radius: 5) [02:01:29 -46871.245113] SLOW spr round 6 (radius: 10) [02:03:34 -46871.245112] SLOW spr round 7 (radius: 15) [02:06:06 -46871.061649] SLOW spr round 8 (radius: 5) [02:08:24 -46871.061649] SLOW spr round 9 (radius: 10) [02:10:27 -46871.061649] SLOW spr round 10 (radius: 15) [02:12:55 -46871.061649] SLOW spr round 11 (radius: 20) [02:14:39] [worker #1] ML tree search #5, logLikelihood: -46851.639961 [02:16:22 -46870.636501] SLOW spr round 12 (radius: 5) [02:18:51 -46870.234026] SLOW spr round 13 (radius: 5) [02:21:09 -46870.233545] SLOW spr round 14 (radius: 10) [02:23:13 -46870.233544] SLOW spr round 15 (radius: 15) [02:23:38] [worker #2] ML tree search #6, logLikelihood: -46860.199282 [02:25:41 -46870.233544] SLOW spr round 16 (radius: 20) [02:29:08 -46870.233544] SLOW spr round 17 (radius: 25) [02:33:46 -46865.999617] SLOW spr round 18 (radius: 5) [02:36:10 -46864.349719] SLOW spr round 19 (radius: 5) [02:38:17 -46863.879941] SLOW spr round 20 (radius: 5) [02:40:19 -46863.879665] SLOW spr round 21 (radius: 10) [02:42:16 -46860.706768] SLOW spr round 22 (radius: 5) [02:44:42 -46858.642675] SLOW spr round 23 (radius: 5) [02:46:56 -46858.409191] SLOW spr round 24 (radius: 5) [02:48:57 -46858.409161] SLOW spr round 25 (radius: 10) [02:50:50 -46858.409161] SLOW spr round 26 (radius: 15) [02:53:24 -46858.409159] SLOW spr round 27 (radius: 20) [02:57:02 -46858.409158] SLOW spr round 28 (radius: 25) [03:01:49 -46858.409158] Model parameter optimization (eps = 0.100000) [03:01:56] [worker #0] ML tree search #4, logLikelihood: -46858.278947 [03:01:56 -244451.619272] Initial branch length optimization [03:01:59 -205347.858023] Model parameter optimization (eps = 10.000000) [03:02:38 -204827.740405] AUTODETECT spr round 1 (radius: 5) [03:04:47 -125221.387079] AUTODETECT spr round 2 (radius: 10) [03:07:14 -86238.487328] AUTODETECT spr round 3 (radius: 15) [03:09:46 -66355.379720] AUTODETECT spr round 4 (radius: 20) [03:12:48 -57729.989248] AUTODETECT spr round 5 (radius: 25) [03:16:29 -56011.984171] SPR radius for FAST iterations: 25 (autodetect) [03:16:29 -56011.984171] Model parameter optimization (eps = 3.000000) [03:16:47 -55697.709567] FAST spr round 1 (radius: 25) [03:19:05 -47706.477401] FAST spr round 2 (radius: 25) [03:21:03 -47215.641053] FAST spr round 3 (radius: 25) [03:22:00] [worker #1] ML tree search #8, logLikelihood: -46841.202512 [03:22:50 -46891.057308] FAST spr round 4 (radius: 25) [03:24:24 -46885.714854] FAST spr round 5 (radius: 25) [03:25:52 -46884.204866] FAST spr round 6 (radius: 25) [03:27:20 -46884.202885] Model parameter optimization (eps = 1.000000) [03:27:33 -46882.471874] SLOW spr round 1 (radius: 5) [03:29:28 -46868.154134] SLOW spr round 2 (radius: 5) [03:31:22 -46861.188857] SLOW spr round 3 (radius: 5) [03:33:09 -46857.104250] SLOW spr round 4 (radius: 5) [03:35:16 -46856.883827] SLOW spr round 5 (radius: 5) [03:35:38] [worker #2] ML tree search #9, logLikelihood: -46859.681815 [03:37:09 -46856.880159] SLOW spr round 6 (radius: 10) [03:39:13 -46855.537231] SLOW spr round 7 (radius: 5) [03:41:23 -46853.891844] SLOW spr round 8 (radius: 5) [03:43:26 -46853.890855] SLOW spr round 9 (radius: 10) [03:45:24 -46853.890248] SLOW spr round 10 (radius: 15) [03:48:07 -46852.874762] SLOW spr round 11 (radius: 5) [03:50:25 -46852.582141] SLOW spr round 12 (radius: 5) [03:52:29 -46852.582007] SLOW spr round 13 (radius: 10) [03:54:29 -46852.581947] SLOW spr round 14 (radius: 15) [03:57:06 -46852.581907] SLOW spr round 15 (radius: 20) [04:01:08 -46852.581884] SLOW spr round 16 (radius: 25) [04:06:12 -46852.581870] Model parameter optimization (eps = 0.100000) [04:06:23] [worker #0] ML tree search #7, logLikelihood: -46851.783949 [04:06:23 -243699.069618] Initial branch length optimization [04:06:27 -205596.206174] Model parameter optimization (eps = 10.000000) [04:07:03 -204892.277179] AUTODETECT spr round 1 (radius: 5) [04:09:17 -125629.506302] AUTODETECT spr round 2 (radius: 10) [04:11:36 -85090.352568] AUTODETECT spr round 3 (radius: 15) [04:14:02 -67690.509000] AUTODETECT spr round 4 (radius: 20) [04:16:51 -59735.544631] AUTODETECT spr round 5 (radius: 25) [04:20:26 -57049.100092] SPR radius for FAST iterations: 25 (autodetect) [04:20:26 -57049.100092] Model parameter optimization (eps = 3.000000) [04:20:51 -56697.591819] FAST spr round 1 (radius: 25) [04:23:12 -47665.114584] FAST spr round 2 (radius: 25) [04:25:15 -46937.529411] FAST spr round 3 (radius: 25) [04:27:00 -46889.847470] FAST spr round 4 (radius: 25) [04:28:45 -46885.360200] FAST spr round 5 (radius: 25) [04:30:16 -46882.079855] FAST spr round 6 (radius: 25) [04:31:41 -46882.079830] Model parameter optimization (eps = 1.000000) [04:31:50 -46880.876644] SLOW spr round 1 (radius: 5) [04:33:30] [worker #1] ML tree search #11, logLikelihood: -46870.690949 [04:33:43 -46870.427364] SLOW spr round 2 (radius: 5) [04:35:34 -46869.405010] SLOW spr round 3 (radius: 5) [04:37:23 -46869.404859] SLOW spr round 4 (radius: 10) [04:38:29] [worker #2] ML tree search #12, logLikelihood: -46849.054222 [04:39:15 -46866.491865] SLOW spr round 5 (radius: 5) [04:41:26 -46865.580409] SLOW spr round 6 (radius: 5) [04:43:24 -46865.580383] SLOW spr round 7 (radius: 10) [04:45:24 -46865.580368] SLOW spr round 8 (radius: 15) [04:48:00 -46861.696354] SLOW spr round 9 (radius: 5) [04:50:40 -46861.485732] SLOW spr round 10 (radius: 5) [04:52:55 -46860.174487] SLOW spr round 11 (radius: 5) [04:54:54 -46859.272297] SLOW spr round 12 (radius: 5) [04:56:42 -46859.271949] SLOW spr round 13 (radius: 10) [04:58:33 -46859.271832] SLOW spr round 14 (radius: 15) [05:01:22 -46859.271709] SLOW spr round 15 (radius: 20) [05:05:18 -46859.046337] SLOW spr round 16 (radius: 5) [05:07:39 -46858.787727] SLOW spr round 17 (radius: 5) [05:09:45 -46858.787432] SLOW spr round 18 (radius: 10) [05:11:41 -46858.787287] SLOW spr round 19 (radius: 15) [05:14:23 -46858.787285] SLOW spr round 20 (radius: 20) [05:18:38 -46858.787284] SLOW spr round 21 (radius: 25) [05:23:45 -46858.787284] Model parameter optimization (eps = 0.100000) [05:23:56] [worker #0] ML tree search #10, logLikelihood: -46858.782943 [05:23:56 -244752.940689] Initial branch length optimization [05:24:00 -204378.644411] Model parameter optimization (eps = 10.000000) [05:24:41 -203805.279188] AUTODETECT spr round 1 (radius: 5) [05:26:52 -128316.421330] AUTODETECT spr round 2 (radius: 10) [05:29:13 -86103.888839] AUTODETECT spr round 3 (radius: 15) [05:31:31 -68982.227016] AUTODETECT spr round 4 (radius: 20) [05:34:27 -59492.377372] AUTODETECT spr round 5 (radius: 25) [05:37:52 -56459.038991] SPR radius for FAST iterations: 25 (autodetect) [05:37:52 -56459.038991] Model parameter optimization (eps = 3.000000) [05:38:10 -56152.724590] FAST spr round 1 (radius: 25) [05:40:21] [worker #1] ML tree search #14, logLikelihood: -46856.231292 [05:40:41 -47341.668760] FAST spr round 2 (radius: 25) [05:42:40 -46952.369120] FAST spr round 3 (radius: 25) [05:44:31 -46903.903044] FAST spr round 4 (radius: 25) [05:46:06 -46896.476690] FAST spr round 5 (radius: 25) [05:47:34 -46893.909587] FAST spr round 6 (radius: 25) [05:49:03 -46893.520002] FAST spr round 7 (radius: 25) [05:50:33 -46893.519949] Model parameter optimization (eps = 1.000000) [05:50:49 -46887.137605] SLOW spr round 1 (radius: 5) [05:52:40 -46874.154802] SLOW spr round 2 (radius: 5) [05:54:31 -46873.378967] SLOW spr round 3 (radius: 5) [05:56:17 -46872.124933] SLOW spr round 4 (radius: 5) [05:58:10 -46871.342995] SLOW spr round 5 (radius: 5) [05:58:42] [worker #2] ML tree search #15, logLikelihood: -46869.756041 [06:00:01 -46871.342573] SLOW spr round 6 (radius: 10) [06:01:55 -46870.056871] SLOW spr round 7 (radius: 5) [06:04:10 -46868.435741] SLOW spr round 8 (radius: 5) [06:06:27 -46866.454415] SLOW spr round 9 (radius: 5) [06:08:29 -46866.454362] SLOW spr round 10 (radius: 10) [06:10:25 -46862.418916] SLOW spr round 11 (radius: 5) [06:12:36 -46861.111033] SLOW spr round 12 (radius: 5) [06:14:40 -46860.770882] SLOW spr round 13 (radius: 5) [06:16:34 -46859.697100] SLOW spr round 14 (radius: 5) [06:18:25 -46859.695707] SLOW spr round 15 (radius: 10) [06:20:16 -46859.695625] SLOW spr round 16 (radius: 15) [06:22:46 -46859.503588] SLOW spr round 17 (radius: 5) [06:25:05 -46859.503586] SLOW spr round 18 (radius: 10) [06:27:10 -46859.503585] SLOW spr round 19 (radius: 15) [06:29:49 -46859.503584] SLOW spr round 20 (radius: 20) [06:33:31 -46858.879280] SLOW spr round 21 (radius: 5) [06:35:52 -46858.879245] SLOW spr round 22 (radius: 10) [06:37:59 -46858.879231] SLOW spr round 23 (radius: 15) [06:40:30 -46858.879223] SLOW spr round 24 (radius: 20) [06:43:54 -46858.714508] SLOW spr round 25 (radius: 5) [06:46:14 -46858.395097] SLOW spr round 26 (radius: 5) [06:48:18 -46858.394867] SLOW spr round 27 (radius: 10) [06:50:19 -46858.394867] SLOW spr round 28 (radius: 15) [06:52:13] [worker #1] ML tree search #17, logLikelihood: -46862.172658 [06:52:47 -46858.394867] SLOW spr round 29 (radius: 20) [06:56:26 -46858.394867] SLOW spr round 30 (radius: 25) [07:01:04 -46858.394865] Model parameter optimization (eps = 0.100000) [07:01:13] [worker #0] ML tree search #13, logLikelihood: -46857.280868 [07:01:13 -243219.055087] Initial branch length optimization [07:01:16 -203506.550679] Model parameter optimization (eps = 10.000000) [07:01:55 -202930.389743] AUTODETECT spr round 1 (radius: 5) [07:04:09 -126891.446377] AUTODETECT spr round 2 (radius: 10) [07:06:32 -89687.841445] AUTODETECT spr round 3 (radius: 15) [07:09:01 -71494.274130] AUTODETECT spr round 4 (radius: 20) [07:11:55 -62993.387573] AUTODETECT spr round 5 (radius: 25) [07:13:27] [worker #2] ML tree search #18, logLikelihood: -46872.169884 [07:15:27 -58803.976331] SPR radius for FAST iterations: 25 (autodetect) [07:15:27 -58803.976331] Model parameter optimization (eps = 3.000000) [07:15:46 -58448.968471] FAST spr round 1 (radius: 25) [07:18:08 -47803.903003] FAST spr round 2 (radius: 25) [07:20:12 -47213.140357] FAST spr round 3 (radius: 25) [07:21:59 -47144.776325] FAST spr round 4 (radius: 25) [07:23:34 -47132.135477] FAST spr round 5 (radius: 25) [07:25:01 -47132.134734] Model parameter optimization (eps = 1.000000) [07:25:12 -47130.457929] SLOW spr round 1 (radius: 5) [07:27:05 -47111.941159] SLOW spr round 2 (radius: 5) [07:28:58 -47108.760311] SLOW spr round 3 (radius: 5) [07:30:51 -47108.627799] SLOW spr round 4 (radius: 5) [07:32:38 -47108.627514] SLOW spr round 5 (radius: 10) [07:34:28 -47108.097801] SLOW spr round 6 (radius: 5) [07:36:39 -47108.097694] SLOW spr round 7 (radius: 10) [07:38:43 -47108.097643] SLOW spr round 8 (radius: 15) [07:41:04 -47107.832875] SLOW spr round 9 (radius: 5) [07:43:41 -47107.832839] SLOW spr round 10 (radius: 10) [07:45:51 -47107.092829] SLOW spr round 11 (radius: 5) [07:48:02 -47107.092803] SLOW spr round 12 (radius: 10) [07:49:57 -47107.092782] SLOW spr round 13 (radius: 15) [07:52:25 -47107.092764] SLOW spr round 14 (radius: 20) [07:55:38 -47106.471624] SLOW spr round 15 (radius: 5) [07:57:59 -47106.471447] SLOW spr round 16 (radius: 10) [08:00:07 -47106.471430] SLOW spr round 17 (radius: 15) [08:02:34 -47106.471419] SLOW spr round 18 (radius: 20) [08:05:40 -47106.471410] SLOW spr round 19 (radius: 25) [08:05:53] [worker #1] ML tree search #20, logLikelihood: -46854.964143 [08:09:43 -47106.022981] SLOW spr round 20 (radius: 5) [08:12:08 -47106.022971] SLOW spr round 21 (radius: 10) [08:14:12 -47106.022930] SLOW spr round 22 (radius: 15) [08:16:37 -47106.022926] SLOW spr round 23 (radius: 20) [08:19:49 -47106.022922] SLOW spr round 24 (radius: 25) [08:23:35 -47106.022919] Model parameter optimization (eps = 0.100000) [08:23:47] [worker #0] ML tree search #16, logLikelihood: -47105.767934 [08:23:47 -244326.024149] Initial branch length optimization [08:23:50 -204778.836262] Model parameter optimization (eps = 10.000000) [08:24:44 -204141.183558] AUTODETECT spr round 1 (radius: 5) [08:26:56 -128372.420059] AUTODETECT spr round 2 (radius: 10) [08:29:11 -86876.694925] AUTODETECT spr round 3 (radius: 15) [08:31:48 -67654.377623] AUTODETECT spr round 4 (radius: 20) [08:34:38 -59915.102266] AUTODETECT spr round 5 (radius: 25) [08:38:02 -57025.668336] SPR radius for FAST iterations: 25 (autodetect) [08:38:02 -57025.668336] Model parameter optimization (eps = 3.000000) [08:38:28 -56742.718022] FAST spr round 1 (radius: 25) [08:40:46 -47738.915556] FAST spr round 2 (radius: 25) [08:42:40 -47376.715794] FAST spr round 3 (radius: 25) [08:44:26 -46893.322350] FAST spr round 4 (radius: 25) [08:46:01 -46885.372801] FAST spr round 5 (radius: 25) [08:47:29 -46884.082598] FAST spr round 6 (radius: 25) [08:48:57 -46880.144486] FAST spr round 7 (radius: 25) [08:50:28 -46880.144417] Model parameter optimization (eps = 1.000000) [08:50:38 -46878.969615] SLOW spr round 1 (radius: 5) [08:52:21 -46870.998498] SLOW spr round 2 (radius: 5) [08:54:21 -46869.917069] SLOW spr round 3 (radius: 5) [08:56:15 -46869.864599] SLOW spr round 4 (radius: 10) [08:58:08 -46869.417100] SLOW spr round 5 (radius: 5) [09:00:17 -46869.417071] SLOW spr round 6 (radius: 10) [09:02:16 -46869.417067] SLOW spr round 7 (radius: 15) [09:04:50 -46869.128122] SLOW spr round 8 (radius: 5) [09:07:11 -46869.128119] SLOW spr round 9 (radius: 10) [09:09:17 -46868.412386] SLOW spr round 10 (radius: 5) [09:11:23 -46868.412382] SLOW spr round 11 (radius: 10) [09:13:22 -46868.412379] SLOW spr round 12 (radius: 15) [09:15:44 -46868.412376] SLOW spr round 13 (radius: 20) [09:19:01 -46867.811063] SLOW spr round 14 (radius: 5) [09:21:08 -46867.793696] SLOW spr round 15 (radius: 10) [09:23:04 -46867.793530] SLOW spr round 16 (radius: 15) [09:25:19 -46867.793525] SLOW spr round 17 (radius: 20) [09:28:41 -46867.676604] SLOW spr round 18 (radius: 5) [09:31:00 -46867.676541] SLOW spr round 19 (radius: 10) [09:33:08 -46867.676531] SLOW spr round 20 (radius: 15) [09:35:35 -46867.676525] SLOW spr round 21 (radius: 20) [09:39:11 -46867.676520] SLOW spr round 22 (radius: 25) [09:43:59 -46866.751755] SLOW spr round 23 (radius: 5) [09:46:23 -46866.751749] SLOW spr round 24 (radius: 10) [09:48:30 -46866.751745] SLOW spr round 25 (radius: 15) [09:51:00 -46866.751741] SLOW spr round 26 (radius: 20) [09:54:40 -46866.751737] SLOW spr round 27 (radius: 25) [09:59:20 -46866.751733] Model parameter optimization (eps = 0.100000) [09:59:27] [worker #0] ML tree search #19, logLikelihood: -46866.736507 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.198547,0.585911) (0.181547,0.906233) (0.420927,0.893098) (0.198979,1.724885) 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: -46841.202512 AIC score: 97692.405023 / AICc score: 8141752.405023 / BIC score: 103457.175656 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=131). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/3_mltree/Q9HCH5.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/3_mltree/Q9HCH5.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/3_mltree/Q9HCH5.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCH5/3_mltree/Q9HCH5.raxml.log Analysis started: 01-Jul-2021 23:16:52 / finished: 02-Jul-2021 09:16:20 Elapsed time: 35967.786 seconds Consumed energy: 3007.825 Wh (= 15 km in an electric car, or 75 km with an e-scooter!)