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 06-Jul-2021 05:36:36 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVW2/2_msa/Q9NVW2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVW2/3_mltree/Q9NVW2 --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/Q9NVW2/2_msa/Q9NVW2_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 134 sites WARNING: Sequences tr_B4QWL0_B4QWL0_DROSI_7240 and tr_B4HJY7_B4HJY7_DROSE_7238 are exactly identical! WARNING: Sequences tr_E2AFB3_E2AFB3_CAMFO_104421 and tr_F4X6B3_F4X6B3_ACREC_103372 are exactly identical! WARNING: Sequences tr_E2AFB3_E2AFB3_CAMFO_104421 and tr_A0A151WW22_A0A151WW22_9HYME_64791 are exactly identical! WARNING: Sequences tr_E2AFB3_E2AFB3_CAMFO_104421 and tr_A0A151IZD9_A0A151IZD9_9HYME_471704 are exactly identical! WARNING: Sequences tr_E2AFB3_E2AFB3_CAMFO_104421 and tr_A0A195AUE0_A0A195AUE0_9HYME_520822 are exactly identical! WARNING: Sequences tr_E2AFB3_E2AFB3_CAMFO_104421 and tr_A0A195FX84_A0A195FX84_9HYME_34720 are exactly identical! WARNING: Sequences tr_E2AFB3_E2AFB3_CAMFO_104421 and tr_A0A195CXG0_A0A195CXG0_9HYME_456900 are exactly identical! WARNING: Sequences tr_F1NRC6_F1NRC6_CHICK_9031 and tr_G1N2Q3_G1N2Q3_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NRC6_F1NRC6_CHICK_9031 and tr_U3IJU9_U3IJU9_ANAPL_8839 are exactly identical! WARNING: Sequences tr_F1NRC6_F1NRC6_CHICK_9031 and tr_A0A091J7D6_A0A091J7D6_EGRGA_188379 are exactly identical! WARNING: Sequences tr_F1NRC6_F1NRC6_CHICK_9031 and tr_A0A087QQT5_A0A087QQT5_APTFO_9233 are exactly identical! WARNING: Sequences tr_F1NRC6_F1NRC6_CHICK_9031 and tr_A0A093I487_A0A093I487_STRCA_441894 are exactly identical! WARNING: Sequences tr_F1NRC6_F1NRC6_CHICK_9031 and tr_A0A2I0MB69_A0A2I0MB69_COLLI_8932 are exactly identical! WARNING: Sequences tr_F1NRC6_F1NRC6_CHICK_9031 and tr_A0A226NJX3_A0A226NJX3_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NRC6_F1NRC6_CHICK_9031 and tr_A0A226P6T9_A0A226P6T9_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q90972_RNF13_CHICK_9031 and tr_A0A087RBR0_A0A087RBR0_APTFO_9233 are exactly identical! WARNING: Sequences sp_Q90972_RNF13_CHICK_9031 and tr_A0A091WP21_A0A091WP21_OPIHO_30419 are exactly identical! WARNING: Sequences tr_M3XTY6_M3XTY6_MUSPF_9669 and tr_D2HM63_D2HM63_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XTY6_M3XTY6_MUSPF_9669 and tr_A0A2U3XPC1_A0A2U3XPC1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XTY6_M3XTY6_MUSPF_9669 and tr_A0A2Y9JN45_A0A2Y9JN45_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XTY6_M3XTY6_MUSPF_9669 and tr_A0A384DEL1_A0A384DEL1_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_G1QUL9_G1QUL9_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A2I2YT34_A0A2I2YT34_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A2I3RCP0_A0A2I3RCP0_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_W5PPM5_W5PPM5_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_I3M5F5_I3M5F5_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_H0W9S5_H0W9S5_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and sp_Q9H0F5_RNF38_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_F6U3Y8_F6U3Y8_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_G3T5J1_G3T5J1_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_F6TTR7_F6TTR7_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A287BD76_A0A287BD76_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_G1LU07_G1LU07_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_G7PRX5_G7PRX5_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A337ST25_A0A337ST25_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A2I3NCK8_A0A2I3NCK8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A2K5MM52_A0A2K5MM52_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A2K6AW22_A0A2K6AW22_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A2K6A5M3_A0A2K6A5M3_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A2R9BFL4_A0A2R9BFL4_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A2U4CGE8_A0A2U4CGE8_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A2U3ZEZ2_A0A2U3ZEZ2_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A2Y9DCZ4_A0A2Y9DCZ4_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A2Y9JFH7_A0A2Y9JFH7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y3N1_M3Y3N1_MUSPF_9669 and tr_A0A2Y9QLD9_A0A2Y9QLD9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A3B3I8T3_A0A3B3I8T3_ORYLA_8090 and tr_A0A087X5N2_A0A087X5N2_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A3B3I8T3_A0A3B3I8T3_ORYLA_8090 and tr_A0A2U9C876_A0A2U9C876_SCOMX_52904 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_G3QW07_G3QW07_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_H2PBQ8_H2PBQ8_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and sp_Q5RCV8_RNF13_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_H2QNK4_H2QNK4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and sp_O43567_RNF13_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_H9ELX5_H9ELX5_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_G7NZM7_G7NZM7_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_A0A096MS08_A0A096MS08_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_A0A0D9RGK1_A0A0D9RGK1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_A0A2K6A6Z9_A0A2K6A6Z9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QSD2_G1QSD2_NOMLE_61853 and tr_A0A2R9BEY4_A0A2R9BEY4_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3IA73_G3IA73_CRIGR_10029 and sp_Q66HG0_RNF13_RAT_10116 are exactly identical! WARNING: Sequences tr_G3IA73_G3IA73_CRIGR_10029 and tr_A0A1U7QRX6_A0A1U7QRX6_MESAU_10036 are exactly identical! WARNING: Sequences tr_D8RRU9_D8RRU9_SELML_88036 and tr_D8SJQ6_D8SJQ6_SELML_88036 are exactly identical! WARNING: Sequences tr_G3QDA6_G3QDA6_GORGO_9595 and tr_H2QBZ2_H2QBZ2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QDA6_G3QDA6_GORGO_9595 and sp_Q9H6Y7_RN167_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QDA6_G3QDA6_GORGO_9595 and tr_F7EU71_F7EU71_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QDA6_G3QDA6_GORGO_9595 and tr_G7PT98_G7PT98_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QDA6_G3QDA6_GORGO_9595 and tr_A0A0D9RKH7_A0A0D9RKH7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QDA6_G3QDA6_GORGO_9595 and tr_A0A2K5LHF8_A0A2K5LHF8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QDA6_G3QDA6_GORGO_9595 and tr_A0A2K6CA94_A0A2K6CA94_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QDA6_G3QDA6_GORGO_9595 and tr_A0A2K5ZPG2_A0A2K5ZPG2_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QDA6_G3QDA6_GORGO_9595 and tr_A0A2R9BN69_A0A2R9BN69_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QF09_G3QF09_GORGO_9595 and tr_A0A2J8UT34_A0A2J8UT34_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QF09_G3QF09_GORGO_9595 and tr_H2QYT6_H2QYT6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QF09_G3QF09_GORGO_9595 and sp_Q9NVW2_RNF12_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QF09_G3QF09_GORGO_9595 and tr_F7H8F3_F7H8F3_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QF09_G3QF09_GORGO_9595 and tr_A0A0D9RF44_A0A0D9RF44_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QF09_G3QF09_GORGO_9595 and tr_A0A2K5L5D6_A0A2K5L5D6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QF09_G3QF09_GORGO_9595 and tr_A0A2K6AUK3_A0A2K6AUK3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QF09_G3QF09_GORGO_9595 and tr_A0A2K5ZMT5_A0A2K5ZMT5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QF09_G3QF09_GORGO_9595 and tr_A0A2R9A0I2_A0A2R9A0I2_PANPA_9597 are exactly identical! WARNING: Sequences tr_C3Y3H9_C3Y3H9_BRAFL_7739 and tr_C3ZXX3_C3ZXX3_BRAFL_7739 are exactly identical! WARNING: Sequences tr_A0A2J8T0C7_A0A2J8T0C7_PONAB_9601 and tr_F1PLL1_F1PLL1_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2J8T0C7_A0A2J8T0C7_PONAB_9601 and tr_F6XD79_F6XD79_HORSE_9796 are exactly identical! WARNING: Sequences tr_A0A2J8T0C7_A0A2J8T0C7_PONAB_9601 and tr_G5BZI4_G5BZI4_HETGA_10181 are exactly identical! WARNING: Sequences tr_A0A2J8T0C7_A0A2J8T0C7_PONAB_9601 and tr_Q3SZS9_Q3SZS9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A2J8T0C7_A0A2J8T0C7_PONAB_9601 and tr_A0A0D9REA2_A0A0D9REA2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2J8T0C7_A0A2J8T0C7_PONAB_9601 and tr_A0A1S2ZT45_A0A1S2ZT45_ERIEU_9365 are exactly identical! WARNING: Sequences tr_A0A2J8T0C7_A0A2J8T0C7_PONAB_9601 and tr_A0A2Y9FR51_A0A2Y9FR51_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2J8T0C7_A0A2J8T0C7_PONAB_9601 and tr_A0A384DGA1_A0A384DGA1_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1NER0_G1NER0_MELGA_9103 and tr_A0A226P162_A0A226P162_COLVI_9014 are exactly identical! WARNING: Sequences tr_H9G619_H9G619_ANOCA_28377 and tr_H3AIW7_H3AIW7_LATCH_7897 are exactly identical! WARNING: Sequences tr_H9G619_H9G619_ANOCA_28377 and tr_A0A151NDZ7_A0A151NDZ7_ALLMI_8496 are exactly identical! WARNING: Sequences tr_E2RSZ0_E2RSZ0_CANLF_9615 and tr_F6VTK5_F6VTK5_HORSE_9796 are exactly identical! WARNING: Sequences tr_E2RSZ0_E2RSZ0_CANLF_9615 and tr_L5KA69_L5KA69_PTEAL_9402 are exactly identical! WARNING: Sequences tr_E2RSZ0_E2RSZ0_CANLF_9615 and tr_A0A2U3XQM4_A0A2U3XQM4_LEPWE_9713 are exactly identical! WARNING: Sequences tr_F1P629_F1P629_CANLF_9615 and tr_A0A2Y9IN47_A0A2Y9IN47_ENHLU_391180 are exactly identical! WARNING: Sequences tr_H2Q7B4_H2Q7B4_PANTR_9598 and sp_Q9Y252_RNF6_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q7B4_H2Q7B4_PANTR_9598 and tr_A0A2R9B7B4_A0A2R9B7B4_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6PXA0_F6PXA0_MONDO_13616 and tr_G3WD20_G3WD20_SARHA_9305 are exactly identical! WARNING: Sequences tr_F6Y6Y8_F6Y6Y8_HORSE_9796 and sp_Q7L0R7_RNF44_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6Y6Y8_F6Y6Y8_HORSE_9796 and tr_A0A2U3YW72_A0A2U3YW72_LEPWE_9713 are exactly identical! WARNING: Sequences tr_F6Y6Y8_F6Y6Y8_HORSE_9796 and tr_A0A384C7W5_A0A384C7W5_URSMA_29073 are exactly identical! WARNING: Sequences tr_F6YDQ9_F6YDQ9_HORSE_9796 and tr_W5P6F7_W5P6F7_SHEEP_9940 are exactly identical! WARNING: Sequences tr_F6YDQ9_F6YDQ9_HORSE_9796 and tr_L5JZ26_L5JZ26_PTEAL_9402 are exactly identical! WARNING: Sequences tr_F6YDQ9_F6YDQ9_HORSE_9796 and tr_A0A2U3YHK6_A0A2U3YHK6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_W5P3L5_W5P3L5_SHEEP_9940 and sp_Q0VD51_RNF13_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5Q9J4_W5Q9J4_SHEEP_9940 and tr_E1BBI7_E1BBI7_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5Q9J4_W5Q9J4_SHEEP_9940 and tr_A0A2U4B3D3_A0A2U4B3D3_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5Q9J4_W5Q9J4_SHEEP_9940 and tr_A0A2Y9NRF4_A0A2Y9NRF4_DELLE_9749 are exactly identical! WARNING: Sequences tr_W5Q9J4_W5Q9J4_SHEEP_9940 and tr_A0A2Y9FKJ6_A0A2Y9FKJ6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_H2TVB8_H2TVB8_TAKRU_31033 and tr_H3CJ86_H3CJ86_TETNG_99883 are exactly identical! WARNING: Sequences tr_J3LDV1_J3LDV1_ORYBR_4533 and tr_A0A0E0G883_A0A0E0G883_ORYNI_4536 are exactly identical! WARNING: Sequences tr_J3LDV1_J3LDV1_ORYBR_4533 and tr_I1P1B2_I1P1B2_ORYGL_4538 are exactly identical! WARNING: Sequences tr_J3LDV1_J3LDV1_ORYBR_4533 and tr_A0A0E0CM03_A0A0E0CM03_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_J3LDV1_J3LDV1_ORYBR_4533 and tr_A0A0E0NGE5_A0A0E0NGE5_ORYRU_4529 are exactly identical! WARNING: Sequences tr_J3LDV1_J3LDV1_ORYBR_4533 and tr_A0A0D3F6F0_A0A0D3F6F0_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_J3LDV1_J3LDV1_ORYBR_4533 and tr_A0A0D9YTN9_A0A0D9YTN9_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_J3LDV1_J3LDV1_ORYBR_4533 and tr_A0A0E0K155_A0A0E0K155_ORYPU_4537 are exactly identical! WARNING: Sequences tr_J3LDV1_J3LDV1_ORYBR_4533 and tr_Q0E0D6_Q0E0D6_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0ICL7_A0A0E0ICL7_ORYNI_4536 and tr_A2YVP9_A2YVP9_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0ICL7_A0A0E0ICL7_ORYNI_4536 and tr_I1QJ34_I1QJ34_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0ICL7_A0A0E0ICL7_ORYNI_4536 and tr_A0A0E0EM38_A0A0E0EM38_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0ICL7_A0A0E0ICL7_ORYNI_4536 and tr_A0A0E0QJN3_A0A0E0QJN3_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0ICL7_A0A0E0ICL7_ORYNI_4536 and tr_A0A0D3H0T9_A0A0D3H0T9_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0ICL7_A0A0E0ICL7_ORYNI_4536 and tr_A0A0E0AW05_A0A0E0AW05_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F6XZY0_F6XZY0_MACMU_9544 and tr_G7PVW0_G7PVW0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6XZY0_F6XZY0_MACMU_9544 and tr_A0A2K5MHB0_A0A2K5MHB0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6XZY0_F6XZY0_MACMU_9544 and tr_A0A2K6AM15_A0A2K6AM15_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6XZY0_F6XZY0_MACMU_9544 and tr_A0A2K5ZLS0_A0A2K5ZLS0_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0YPA6_H0YPA6_TAEGU_59729 and tr_A0A218ULB7_A0A218ULB7_9PASE_299123 are exactly identical! WARNING: Sequences tr_F4WV10_F4WV10_ACREC_103372 and tr_A0A151J1N6_A0A151J1N6_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A287AZC7_A0A287AZC7_PIG_9823 and tr_A0A2U4B9L0_A0A2U4B9L0_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A287AZC7_A0A287AZC7_PIG_9823 and tr_A0A2Y9NTW9_A0A2Y9NTW9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A287AZC7_A0A287AZC7_PIG_9823 and tr_A0A384ALH4_A0A384ALH4_BALAS_310752 are exactly identical! WARNING: Sequences tr_F1RPK6_F1RPK6_PIG_9823 and tr_D2I1T1_D2I1T1_AILME_9646 are exactly identical! WARNING: Sequences tr_F1RPK6_F1RPK6_PIG_9823 and tr_M3VZS3_M3VZS3_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1RPK6_F1RPK6_PIG_9823 and tr_A0A2U3ZQY8_A0A2U3ZQY8_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1RPK6_F1RPK6_PIG_9823 and tr_A0A2Y9L145_A0A2Y9L145_ENHLU_391180 are exactly identical! WARNING: Sequences tr_F1RPK6_F1RPK6_PIG_9823 and tr_A0A384D3B3_A0A384D3B3_URSMA_29073 are exactly identical! WARNING: Sequences tr_F1S3A0_F1S3A0_PIG_9823 and tr_M3X156_M3X156_FELCA_9685 are exactly identical! WARNING: Sequences tr_B3RIX0_B3RIX0_TRIAD_10228 and tr_A0A369RVA2_A0A369RVA2_9METZ_287889 are exactly identical! WARNING: Sequences tr_B3S369_B3S369_TRIAD_10228 and tr_A0A369S2C0_A0A369S2C0_9METZ_287889 are exactly identical! WARNING: Sequences tr_U3JE14_U3JE14_FICAL_59894 and tr_A0A091V7N9_A0A091V7N9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_U3JE14_U3JE14_FICAL_59894 and tr_A0A2I0M698_A0A2I0M698_COLLI_8932 are exactly identical! WARNING: Sequences tr_W2QH31_W2QH31_PHYPN_761204 and tr_W2LK28_W2LK28_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A3B6KMZ5_A0A3B6KMZ5_WHEAT_4565 and tr_A0A3B6LS78_A0A3B6LS78_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A3B6NVJ2_A0A3B6NVJ2_WHEAT_4565 and tr_A0A3B6PS64_A0A3B6PS64_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A015KBJ0_A0A015KBJ0_9GLOM_1432141 and tr_A0A2H5T5L4_A0A2H5T5L4_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044TT14_A0A044TT14_ONCVO_6282 and tr_A0A182EDT5_A0A182EDT5_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A067FJH1_A0A067FJH1_CITSI_2711 and tr_V4UBU3_V4UBU3_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067FJH1_A0A067FJH1_CITSI_2711 and tr_A0A2H5P2W0_A0A2H5P2W0_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A067GS25_A0A067GS25_CITSI_2711 and tr_V4TPD6_V4TPD6_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067GS25_A0A067GS25_CITSI_2711 and tr_A0A2H5N8L0_A0A2H5N8L0_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A096MP75_A0A096MP75_PAPAN_9555 and tr_A0A2K6E9B4_A0A2K6E9B4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A078HEN4_A0A078HEN4_BRANA_3708 and tr_A0A0D3C041_A0A0D3C041_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0D2M3D2_A0A0D2M3D2_GOSRA_29730 and tr_A0A1U8P6L4_A0A1U8P6L4_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2M3D2_A0A0D2M3D2_GOSRA_29730 and tr_A0A1U8PF92_A0A1U8PF92_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2NKX6_A0A0D2NKX6_GOSRA_29730 and tr_A0A1U8I3L6_A0A1U8I3L6_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2RD44_A0A0D2RD44_GOSRA_29730 and tr_A0A1U8JUU5_A0A1U8JUU5_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2VAR7_A0A0D2VAR7_GOSRA_29730 and tr_A0A1U8IA44_A0A1U8IA44_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0N4TTD0_A0A0N4TTD0_BRUPA_6280 and tr_A0A0R3QZ08_A0A0R3QZ08_9BILA_42155 are exactly identical! WARNING: Sequences tr_A0A151NNM3_A0A151NNM3_ALLMI_8496 and tr_A0A1U7SLP7_A0A1U7SLP7_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0Q3PWS1_A0A0Q3PWS1_AMAAE_12930 and tr_A0A091W2B7_A0A091W2B7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A0Q3PWS1_A0A0Q3PWS1_AMAAE_12930 and tr_A0A2I0M1D7_A0A2I0M1D7_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A0L9V6W2_A0A0L9V6W2_PHAAN_3914 and tr_A0A1S3VN93_A0A1S3VN93_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A0L9VPW3_A0A0L9VPW3_PHAAN_3914 and tr_A0A1S3VGS0_A0A1S3VGS0_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A0A0AKU5_A0A0A0AKU5_CHAVO_50402 and tr_A0A1V4KZ07_A0A1V4KZ07_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3Y8G5_A0A1S3Y8G5_TOBAC_4097 and tr_A0A1S3ZU62_A0A1S3ZU62_TOBAC_4097 are exactly identical! WARNING: Sequences tr_A0A1S3Y8G5_A0A1S3Y8G5_TOBAC_4097 and tr_A0A1U7WQS1_A0A1U7WQS1_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4AAI4_A0A1S4AAI4_TOBAC_4097 and tr_A0A1U7XGI4_A0A1U7XGI4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4AH20_A0A1S4AH20_TOBAC_4097 and tr_A0A1U7VHE5_A0A1U7VHE5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4AK22_A0A1S4AK22_TOBAC_4097 and tr_A0A1J6HZS8_A0A1J6HZS8_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S4AK22_A0A1S4AK22_TOBAC_4097 and tr_A0A1U7UZS7_A0A1U7UZS7_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2U1L0I3_A0A2U1L0I3_ARTAN_35608 and tr_A0A2U1Q2G7_A0A2U1Q2G7_ARTAN_35608 are exactly identical! WARNING: Sequences tr_A0A2U3ZXM6_A0A2U3ZXM6_ODORO_9708 and tr_A0A2U3Z1R9_A0A2U3Z1R9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9MCV3_A0A2Y9MCV3_DELLE_9749 and tr_A0A2Y9EI22_A0A2Y9EI22_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 175 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/Q9NVW2/3_mltree/Q9NVW2.raxml.reduced.phy Alignment comprises 1 partitions and 134 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 134 / 134 Gaps: 10.01 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVW2/3_mltree/Q9NVW2.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 / 134 / 10720 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -231919.809601] Initial branch length optimization [00:00:03 -191450.342678] Model parameter optimization (eps = 10.000000) [00:00:39 -191180.133794] AUTODETECT spr round 1 (radius: 5) [00:03:21 -123950.741036] AUTODETECT spr round 2 (radius: 10) [00:06:06 -92076.069558] AUTODETECT spr round 3 (radius: 15) [00:09:08 -72529.740291] AUTODETECT spr round 4 (radius: 20) [00:12:13 -62456.219560] AUTODETECT spr round 5 (radius: 25) [00:15:30 -60538.757676] SPR radius for FAST iterations: 25 (autodetect) [00:15:30 -60538.757676] Model parameter optimization (eps = 3.000000) [00:15:56 -60504.941808] FAST spr round 1 (radius: 25) [00:19:11 -52676.230079] FAST spr round 2 (radius: 25) [00:21:38 -51947.374004] FAST spr round 3 (radius: 25) [00:23:49 -51885.167083] FAST spr round 4 (radius: 25) [00:25:54 -51875.431953] FAST spr round 5 (radius: 25) [00:27:49 -51875.316857] FAST spr round 6 (radius: 25) [00:29:43 -51875.316272] Model parameter optimization (eps = 1.000000) [00:30:05 -51867.069283] SLOW spr round 1 (radius: 5) [00:32:28 -51854.271847] SLOW spr round 2 (radius: 5) [00:34:51 -51853.843981] SLOW spr round 3 (radius: 5) [00:37:10 -51853.843670] SLOW spr round 4 (radius: 10) [00:39:31 -51852.496363] SLOW spr round 5 (radius: 5) [00:42:13 -51852.496117] SLOW spr round 6 (radius: 10) [00:44:47 -51852.496092] SLOW spr round 7 (radius: 15) [00:47:56 -51852.496089] SLOW spr round 8 (radius: 20) [00:52:09 -51852.496089] SLOW spr round 9 (radius: 25) [00:57:03 -51852.263898] SLOW spr round 10 (radius: 5) [00:59:57 -51852.263579] SLOW spr round 11 (radius: 10) [01:02:46 -51852.263550] SLOW spr round 12 (radius: 15) [01:05:52 -51852.263547] SLOW spr round 13 (radius: 20) [01:08:11] [worker #2] ML tree search #3, logLikelihood: -51847.444068 [01:10:04 -51852.263547] SLOW spr round 14 (radius: 25) [01:12:28] [worker #1] ML tree search #2, logLikelihood: -51840.653304 [01:14:57 -51852.263547] Model parameter optimization (eps = 0.100000) [01:15:04] [worker #0] ML tree search #1, logLikelihood: -51852.203578 [01:15:04 -232641.486318] Initial branch length optimization [01:15:07 -192687.258329] Model parameter optimization (eps = 10.000000) [01:15:46 -192386.910921] AUTODETECT spr round 1 (radius: 5) [01:18:25 -124679.948665] AUTODETECT spr round 2 (radius: 10) [01:21:07 -93783.605745] AUTODETECT spr round 3 (radius: 15) [01:23:58 -77055.961850] AUTODETECT spr round 4 (radius: 20) [01:27:09 -64562.754764] AUTODETECT spr round 5 (radius: 25) [01:30:14 -61798.061529] SPR radius for FAST iterations: 25 (autodetect) [01:30:14 -61798.061529] Model parameter optimization (eps = 3.000000) [01:30:36 -61758.888830] FAST spr round 1 (radius: 25) [01:33:37 -52850.101362] FAST spr round 2 (radius: 25) [01:36:01 -52246.784242] FAST spr round 3 (radius: 25) [01:38:16 -51982.731313] FAST spr round 4 (radius: 25) [01:40:21 -51859.546847] FAST spr round 5 (radius: 25) [01:42:22 -51854.131668] FAST spr round 6 (radius: 25) [01:44:17 -51854.007946] FAST spr round 7 (radius: 25) [01:46:12 -51854.007730] Model parameter optimization (eps = 1.000000) [01:46:23 -51853.112650] SLOW spr round 1 (radius: 5) [01:48:44 -51831.851832] SLOW spr round 2 (radius: 5) [01:51:06 -51831.057782] SLOW spr round 3 (radius: 5) [01:53:25 -51831.057159] SLOW spr round 4 (radius: 10) [01:55:46 -51830.422996] SLOW spr round 5 (radius: 5) [01:58:30 -51829.951009] SLOW spr round 6 (radius: 5) [02:00:59 -51829.950941] SLOW spr round 7 (radius: 10) [02:03:23 -51829.950935] SLOW spr round 8 (radius: 15) [02:06:39 -51829.803589] SLOW spr round 9 (radius: 5) [02:09:30 -51829.803562] SLOW spr round 10 (radius: 10) [02:10:56] [worker #1] ML tree search #5, logLikelihood: -51891.935537 [02:12:12 -51829.709286] SLOW spr round 11 (radius: 15) [02:15:21 -51828.571178] SLOW spr round 12 (radius: 5) [02:18:13 -51828.570986] SLOW spr round 13 (radius: 10) [02:19:58] [worker #2] ML tree search #6, logLikelihood: -52090.681440 [02:20:54 -51828.570986] SLOW spr round 14 (radius: 15) [02:24:04 -51827.936782] SLOW spr round 15 (radius: 5) [02:26:54 -51827.936779] SLOW spr round 16 (radius: 10) [02:29:36 -51827.936779] SLOW spr round 17 (radius: 15) [02:32:45 -51827.936779] SLOW spr round 18 (radius: 20) [02:36:56 -51827.936779] SLOW spr round 19 (radius: 25) [02:41:32 -51827.936779] Model parameter optimization (eps = 0.100000) [02:41:38] [worker #0] ML tree search #4, logLikelihood: -51827.925915 [02:41:38 -233120.397700] Initial branch length optimization [02:41:43 -192798.229729] Model parameter optimization (eps = 10.000000) [02:42:18 -192525.929470] AUTODETECT spr round 1 (radius: 5) [02:44:57 -129455.746227] AUTODETECT spr round 2 (radius: 10) [02:47:40 -91004.794201] AUTODETECT spr round 3 (radius: 15) [02:50:43 -70034.828779] AUTODETECT spr round 4 (radius: 20) [02:53:59 -63446.941886] AUTODETECT spr round 5 (radius: 25) [02:57:18 -60974.424775] SPR radius for FAST iterations: 25 (autodetect) [02:57:18 -60974.424775] Model parameter optimization (eps = 3.000000) [02:57:45 -60916.286263] FAST spr round 1 (radius: 25) [03:00:41 -52482.405140] FAST spr round 2 (radius: 25) [03:03:00 -51964.123974] FAST spr round 3 (radius: 25) [03:05:10 -51914.594012] FAST spr round 4 (radius: 25) [03:07:12 -51902.511833] FAST spr round 5 (radius: 25) [03:09:06 -51881.508067] FAST spr round 6 (radius: 25) [03:10:59 -51880.869366] FAST spr round 7 (radius: 25) [03:12:50 -51880.869138] Model parameter optimization (eps = 1.000000) [03:13:11 -51873.440186] SLOW spr round 1 (radius: 5) [03:15:31 -51863.857287] SLOW spr round 2 (radius: 5) [03:17:52 -51861.289627] SLOW spr round 3 (radius: 5) [03:20:10 -51859.651187] SLOW spr round 4 (radius: 5) [03:22:29 -51858.458127] SLOW spr round 5 (radius: 5) [03:24:45 -51857.791175] SLOW spr round 6 (radius: 5) [03:26:59 -51857.791162] SLOW spr round 7 (radius: 10) [03:29:18 -51856.828685] SLOW spr round 8 (radius: 5) [03:32:03 -51852.510002] SLOW spr round 9 (radius: 5) [03:32:32] [worker #1] ML tree search #8, logLikelihood: -51846.860935 [03:33:26] [worker #2] ML tree search #9, logLikelihood: -51836.532058 [03:34:31 -51851.360312] SLOW spr round 10 (radius: 5) [03:36:53 -51851.360310] SLOW spr round 11 (radius: 10) [03:39:14 -51851.360310] SLOW spr round 12 (radius: 15) [03:42:41 -51850.665332] SLOW spr round 13 (radius: 5) [03:45:29 -51850.665332] SLOW spr round 14 (radius: 10) [03:48:12 -51850.665332] SLOW spr round 15 (radius: 15) [03:51:26 -51849.494524] SLOW spr round 16 (radius: 5) [03:54:15 -51849.494523] SLOW spr round 17 (radius: 10) [03:56:59 -51849.494523] SLOW spr round 18 (radius: 15) [04:00:14 -51849.494523] SLOW spr round 19 (radius: 20) [04:05:02 -51849.494522] SLOW spr round 20 (radius: 25) [04:10:41 -51849.494522] Model parameter optimization (eps = 0.100000) [04:10:49] [worker #0] ML tree search #7, logLikelihood: -51849.461716 [04:10:49 -233985.090679] Initial branch length optimization [04:10:53 -194442.386142] Model parameter optimization (eps = 10.000000) [04:11:25 -194166.023075] AUTODETECT spr round 1 (radius: 5) [04:14:02 -126411.339084] AUTODETECT spr round 2 (radius: 10) [04:16:46 -94120.573951] AUTODETECT spr round 3 (radius: 15) [04:19:36 -76593.405746] AUTODETECT spr round 4 (radius: 20) [04:22:50 -66598.269906] AUTODETECT spr round 5 (radius: 25) [04:26:20 -63139.526672] SPR radius for FAST iterations: 25 (autodetect) [04:26:20 -63139.526672] Model parameter optimization (eps = 3.000000) [04:26:48 -63090.566068] FAST spr round 1 (radius: 25) [04:30:12 -52581.982168] FAST spr round 2 (radius: 25) [04:32:40 -52071.627734] FAST spr round 3 (radius: 25) [04:34:59 -51915.108475] FAST spr round 4 (radius: 25) [04:37:03 -51903.984640] FAST spr round 5 (radius: 25) [04:39:00 -51902.272758] FAST spr round 6 (radius: 25) [04:40:53 -51902.272414] Model parameter optimization (eps = 1.000000) [04:41:11 -51899.436281] SLOW spr round 1 (radius: 5) [04:42:27] [worker #1] ML tree search #11, logLikelihood: -51849.187757 [04:43:32 -51883.847144] SLOW spr round 2 (radius: 5) [04:45:54 -51883.357365] SLOW spr round 3 (radius: 5) [04:48:15 -51883.355362] SLOW spr round 4 (radius: 10) [04:50:06] [worker #2] ML tree search #12, logLikelihood: -52201.446960 [04:50:38 -51883.279127] SLOW spr round 5 (radius: 15) [04:53:57 -51866.128218] SLOW spr round 6 (radius: 5) [04:56:50 -51865.190435] SLOW spr round 7 (radius: 5) [04:59:25 -51864.069830] SLOW spr round 8 (radius: 5) [05:01:48 -51864.069781] SLOW spr round 9 (radius: 10) [05:04:11 -51864.069766] SLOW spr round 10 (radius: 15) [05:07:31 -51864.069765] SLOW spr round 11 (radius: 20) [05:11:48 -51864.069762] SLOW spr round 12 (radius: 25) [05:16:45 -51864.069760] Model parameter optimization (eps = 0.100000) [05:16:55] [worker #0] ML tree search #10, logLikelihood: -51863.695990 [05:16:55 -230947.403180] Initial branch length optimization [05:16:58 -190695.941523] Model parameter optimization (eps = 10.000000) [05:17:40 -190452.944540] AUTODETECT spr round 1 (radius: 5) [05:20:21 -124467.082697] AUTODETECT spr round 2 (radius: 10) [05:23:01 -92938.606369] AUTODETECT spr round 3 (radius: 15) [05:25:46 -76976.949111] AUTODETECT spr round 4 (radius: 20) [05:29:03 -65257.748945] AUTODETECT spr round 5 (radius: 25) [05:32:28 -61658.149773] SPR radius for FAST iterations: 25 (autodetect) [05:32:28 -61658.149773] Model parameter optimization (eps = 3.000000) [05:32:58 -61631.841676] FAST spr round 1 (radius: 25) [05:36:08 -52528.344640] FAST spr round 2 (radius: 25) [05:38:34 -51936.368378] FAST spr round 3 (radius: 25) [05:40:44 -51882.752445] FAST spr round 4 (radius: 25) [05:42:46 -51874.664432] FAST spr round 5 (radius: 25) [05:44:39 -51874.663919] Model parameter optimization (eps = 1.000000) [05:44:58 -51863.021260] SLOW spr round 1 (radius: 5) [05:47:20 -51856.192580] SLOW spr round 2 (radius: 5) [05:49:40 -51851.524677] SLOW spr round 3 (radius: 5) [05:52:02 -51850.035573] SLOW spr round 4 (radius: 5) [05:54:24 -51846.255028] SLOW spr round 5 (radius: 5) [05:56:44 -51846.182982] SLOW spr round 6 (radius: 10) [05:59:04 -51845.000474] SLOW spr round 7 (radius: 5) [06:01:46 -51845.000458] SLOW spr round 8 (radius: 10) [06:04:18 -51845.000456] SLOW spr round 9 (radius: 15) [06:07:33 -51844.541406] SLOW spr round 10 (radius: 5) [06:09:44] [worker #1] ML tree search #14, logLikelihood: -51844.042165 [06:10:22 -51844.541353] SLOW spr round 11 (radius: 10) [06:13:03 -51844.541353] SLOW spr round 12 (radius: 15) [06:14:16] [worker #2] ML tree search #15, logLikelihood: -51831.431618 [06:16:13 -51844.541353] SLOW spr round 13 (radius: 20) [06:20:36 -51844.541353] SLOW spr round 14 (radius: 25) [06:25:34 -51844.468909] Model parameter optimization (eps = 0.100000) [06:25:47] [worker #0] ML tree search #13, logLikelihood: -51844.114632 [06:25:47 -231666.260454] Initial branch length optimization [06:25:50 -190763.912316] Model parameter optimization (eps = 10.000000) [06:26:49 -190397.745296] AUTODETECT spr round 1 (radius: 5) [06:29:25 -121611.953112] AUTODETECT spr round 2 (radius: 10) [06:32:07 -93639.154760] AUTODETECT spr round 3 (radius: 15) [06:35:05 -79191.199691] AUTODETECT spr round 4 (radius: 20) [06:38:10 -70846.619712] AUTODETECT spr round 5 (radius: 25) [06:41:28 -64134.755714] SPR radius for FAST iterations: 25 (autodetect) [06:41:28 -64134.755714] Model parameter optimization (eps = 3.000000) [06:41:50 -64120.699764] FAST spr round 1 (radius: 25) [06:45:00 -52712.080645] FAST spr round 2 (radius: 25) [06:47:32 -52035.446826] FAST spr round 3 (radius: 25) [06:49:41 -51902.215806] FAST spr round 4 (radius: 25) [06:51:45 -51899.092140] FAST spr round 5 (radius: 25) [06:53:41 -51899.090901] Model parameter optimization (eps = 1.000000) [06:54:02 -51895.234545] SLOW spr round 1 (radius: 5) [06:56:32 -51865.809843] SLOW spr round 2 (radius: 5) [06:58:58 -51861.014451] SLOW spr round 3 (radius: 5) [07:01:16 -51860.999243] SLOW spr round 4 (radius: 10) [07:03:38 -51859.988231] SLOW spr round 5 (radius: 5) [07:06:22 -51859.857035] SLOW spr round 6 (radius: 5) [07:07:45] [worker #1] ML tree search #17, logLikelihood: -51837.703981 [07:08:52 -51859.855848] SLOW spr round 7 (radius: 10) [07:11:11] [worker #2] ML tree search #18, logLikelihood: -51836.799693 [07:11:17 -51859.855785] SLOW spr round 8 (radius: 15) [07:14:26 -51859.855782] SLOW spr round 9 (radius: 20) [07:18:15 -51859.855782] SLOW spr round 10 (radius: 25) [07:22:37 -51858.708576] SLOW spr round 11 (radius: 5) [07:25:30 -51858.708419] SLOW spr round 12 (radius: 10) [07:28:17 -51858.708417] SLOW spr round 13 (radius: 15) [07:31:20 -51858.708417] SLOW spr round 14 (radius: 20) [07:35:14 -51855.773023] SLOW spr round 15 (radius: 5) [07:38:06 -51854.481366] SLOW spr round 16 (radius: 5) [07:40:40 -51854.481286] SLOW spr round 17 (radius: 10) [07:43:07 -51854.481285] SLOW spr round 18 (radius: 15) [07:46:14 -51854.481285] SLOW spr round 19 (radius: 20) [07:50:05 -51854.481285] SLOW spr round 20 (radius: 25) [07:54:29 -51854.481284] Model parameter optimization (eps = 0.100000) [07:54:39] [worker #0] ML tree search #16, logLikelihood: -51854.328978 [07:54:39 -233702.288786] Initial branch length optimization [07:54:42 -193595.897908] Model parameter optimization (eps = 10.000000) [07:55:19 -193301.970238] AUTODETECT spr round 1 (radius: 5) [07:57:58 -125917.120649] AUTODETECT spr round 2 (radius: 10) [08:00:38 -95370.135084] AUTODETECT spr round 3 (radius: 15) [08:03:33 -75578.533179] AUTODETECT spr round 4 (radius: 20) [08:06:41 -65766.258074] AUTODETECT spr round 5 (radius: 25) [08:09:57 -63081.447501] SPR radius for FAST iterations: 25 (autodetect) [08:09:57 -63081.447501] Model parameter optimization (eps = 3.000000) [08:10:23 -63040.324850] FAST spr round 1 (radius: 25) [08:13:35 -53147.689003] FAST spr round 2 (radius: 25) [08:16:08 -51926.895737] FAST spr round 3 (radius: 25) [08:18:22 -51883.889719] FAST spr round 4 (radius: 25) [08:20:21 -51879.206804] FAST spr round 5 (radius: 25) [08:22:16 -51878.117330] FAST spr round 6 (radius: 25) [08:24:08 -51878.116986] Model parameter optimization (eps = 1.000000) [08:24:21] [worker #1] ML tree search #20, logLikelihood: -51846.559732 [08:24:30 -51874.076890] SLOW spr round 1 (radius: 5) [08:26:52 -51859.165478] SLOW spr round 2 (radius: 5) [08:29:13 -51857.769926] SLOW spr round 3 (radius: 5) [08:31:28 -51857.769180] SLOW spr round 4 (radius: 10) [08:33:47 -51854.044880] SLOW spr round 5 (radius: 5) [08:36:30 -51850.737124] SLOW spr round 6 (radius: 5) [08:38:59 -51849.600598] SLOW spr round 7 (radius: 5) [08:41:20 -51848.755567] SLOW spr round 8 (radius: 5) [08:43:37 -51848.755297] SLOW spr round 9 (radius: 10) [08:45:54 -51848.755066] SLOW spr round 10 (radius: 15) [08:49:01 -51848.399213] SLOW spr round 11 (radius: 5) [08:51:51 -51847.338395] SLOW spr round 12 (radius: 5) [08:54:21 -51847.338371] SLOW spr round 13 (radius: 10) [08:56:46 -51847.338357] SLOW spr round 14 (radius: 15) [08:59:48 -51847.338345] SLOW spr round 15 (radius: 20) [09:03:34 -51847.338335] SLOW spr round 16 (radius: 25) [09:07:47 -51847.338327] Model parameter optimization (eps = 0.100000) [09:07:59] [worker #0] ML tree search #19, logLikelihood: -51847.029912 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.155750,0.211307) (0.099718,0.293426) (0.386220,0.973270) (0.358312,1.568277) 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: -51827.925915 AIC score: 107665.851830 / AICc score: 8151725.851830 / BIC score: 113476.020629 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=134). 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/Q9NVW2/3_mltree/Q9NVW2.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVW2/3_mltree/Q9NVW2.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVW2/3_mltree/Q9NVW2.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9NVW2/3_mltree/Q9NVW2.raxml.log Analysis started: 06-Jul-2021 05:36:36 / finished: 06-Jul-2021 14:44:35 Elapsed time: 32879.679 seconds Consumed energy: 2020.174 Wh (= 10 km in an electric car, or 51 km with an e-scooter!)