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 6258R CPU @ 2.70GHz, 56 cores, 187 GB RAM RAxML-NG was called at 04-Jun-2021 03:53:17 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92834/2_msa/Q92834_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92834/3_mltree/Q92834 --seed 2 --threads 5 --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 (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92834/2_msa/Q92834_trimmed_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 309 sites WARNING: Sequences tr_A0A1D5PJF8_A0A1D5PJF8_CHICK_9031 and tr_G1MXY8_G1MXY8_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1C4H7_E1C4H7_CHICK_9031 and tr_A0A1V4JD09_A0A1V4JD09_PATFA_372326 are exactly identical! WARNING: Sequences tr_F1NBC5_F1NBC5_CHICK_9031 and tr_G1N136_G1N136_MELGA_9103 are exactly identical! WARNING: Sequences tr_A6H6S0_A6H6S0_MOUSE_10090 and tr_D3ZPP6_D3ZPP6_RAT_10116 are exactly identical! WARNING: Sequences tr_E9PZP8_E9PZP8_MOUSE_10090 and tr_W5QHY1_W5QHY1_SHEEP_9940 are exactly identical! WARNING: Sequences tr_E9PZP8_E9PZP8_MOUSE_10090 and tr_A0A0G2JTT6_A0A0G2JTT6_RAT_10116 are exactly identical! WARNING: Sequences tr_E9PZP8_E9PZP8_MOUSE_10090 and tr_A0A287A377_A0A287A377_PIG_9823 are exactly identical! WARNING: Sequences tr_E9PZP8_E9PZP8_MOUSE_10090 and tr_F1MNS0_F1MNS0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_E9PZP8_E9PZP8_MOUSE_10090 and tr_L5K194_L5K194_PTEAL_9402 are exactly identical! WARNING: Sequences tr_E9PZP8_E9PZP8_MOUSE_10090 and tr_M3WAL2_M3WAL2_FELCA_9685 are exactly identical! WARNING: Sequences tr_E9PZP8_E9PZP8_MOUSE_10090 and tr_A0A1S3EN48_A0A1S3EN48_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3XNF5_M3XNF5_MUSPF_9669 and tr_A0A2Y9K3C0_A0A2Y9K3C0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XST9_M3XST9_MUSPF_9669 and tr_G1PK60_G1PK60_MYOLU_59463 are exactly identical! WARNING: Sequences tr_M3XST9_M3XST9_MUSPF_9669 and tr_D2GX49_D2GX49_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XST9_M3XST9_MUSPF_9669 and tr_A0A2U3VAU9_A0A2U3VAU9_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XST9_M3XST9_MUSPF_9669 and tr_A0A384DEC4_A0A384DEC4_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3G8M1_A0A2I3G8M1_NOMLE_61853 and tr_G3QXR3_G3QXR3_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3G8M1_A0A2I3G8M1_NOMLE_61853 and sp_Q5RCZ7_RCBT2_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3G8M1_A0A2I3G8M1_NOMLE_61853 and tr_A0A2I3S6F1_A0A2I3S6F1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3G8M1_A0A2I3G8M1_NOMLE_61853 and sp_O95199_RCBT2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3G8M1_A0A2I3G8M1_NOMLE_61853 and tr_A0A2R9BS25_A0A2R9BS25_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RF95_G1RF95_NOMLE_61853 and tr_G3R1P2_G3R1P2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RF95_G1RF95_NOMLE_61853 and tr_K7C830_K7C830_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RF95_G1RF95_NOMLE_61853 and sp_Q15034_HERC3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RF95_G1RF95_NOMLE_61853 and tr_F6QY96_F6QY96_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RF95_G1RF95_NOMLE_61853 and tr_F7GTC6_F7GTC6_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RF95_G1RF95_NOMLE_61853 and tr_G7P5W8_G7P5W8_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RF95_G1RF95_NOMLE_61853 and tr_A0A096NH35_A0A096NH35_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RF95_G1RF95_NOMLE_61853 and tr_A0A0D9QW53_A0A0D9QW53_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RF95_G1RF95_NOMLE_61853 and tr_A0A2K6EAZ6_A0A2K6EAZ6_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RF95_G1RF95_NOMLE_61853 and tr_A0A2K5Z0M8_A0A2K5Z0M8_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RF95_G1RF95_NOMLE_61853 and tr_A0A2R9A1G0_A0A2R9A1G0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2Y4U1_A0A2I2Y4U1_GORGO_9595 and tr_H2Q9K1_H2Q9K1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Y4U1_A0A2I2Y4U1_GORGO_9595 and sp_Q15751_HERC1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Y4U1_A0A2I2Y4U1_GORGO_9595 and tr_H9EUE9_H9EUE9_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2Y4U1_A0A2I2Y4U1_GORGO_9595 and tr_G7P8U0_G7P8U0_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I2Y4U1_A0A2I2Y4U1_GORGO_9595 and tr_A0A096NMA9_A0A096NMA9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2Y4U1_A0A2I2Y4U1_GORGO_9595 and tr_A0A0D9RIZ5_A0A0D9RIZ5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2Y4U1_A0A2I2Y4U1_GORGO_9595 and tr_A0A2K6DT69_A0A2K6DT69_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2Y4U1_A0A2I2Y4U1_GORGO_9595 and tr_A0A2K5YQA7_A0A2K5YQA7_MANLE_9568 are exactly identical! WARNING: Sequences tr_E2QYQ5_E2QYQ5_CANLF_9615 and tr_G1L6L1_G1L6L1_AILME_9646 are exactly identical! WARNING: Sequences tr_E2QYQ5_E2QYQ5_CANLF_9615 and tr_A0A2Y9NN35_A0A2Y9NN35_DELLE_9749 are exactly identical! WARNING: Sequences tr_E2QYQ5_E2QYQ5_CANLF_9615 and tr_A0A2Y9T2C9_A0A2Y9T2C9_PHYCD_9755 are exactly identical! WARNING: Sequences tr_E2QYQ5_E2QYQ5_CANLF_9615 and tr_A0A384DJ82_A0A384DJ82_URSMA_29073 are exactly identical! WARNING: Sequences tr_E2RFV1_E2RFV1_CANLF_9615 and tr_D2GXJ6_D2GXJ6_AILME_9646 are exactly identical! WARNING: Sequences tr_E2RFV1_E2RFV1_CANLF_9615 and tr_A0A337SJ34_A0A337SJ34_FELCA_9685 are exactly identical! WARNING: Sequences tr_E2RFV1_E2RFV1_CANLF_9615 and tr_A0A2U4BEW1_A0A2U4BEW1_TURTR_9739 are exactly identical! WARNING: Sequences tr_E2RFV1_E2RFV1_CANLF_9615 and tr_A0A2U3VG86_A0A2U3VG86_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2RFV1_E2RFV1_CANLF_9615 and tr_A0A2U3XBT7_A0A2U3XBT7_LEPWE_9713 are exactly identical! WARNING: Sequences tr_E2RFV1_E2RFV1_CANLF_9615 and tr_A0A2Y9PTV6_A0A2Y9PTV6_DELLE_9749 are exactly identical! WARNING: Sequences tr_J9NWI5_J9NWI5_CANLF_9615 and sp_Q9N1T2_RPGR_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3RKF0_A0A2I3RKF0_PANTR_9598 and tr_A0A2I3SRD1_A0A2I3SRD1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3RKF0_A0A2I3RKF0_PANTR_9598 and sp_Q92834_RPGR_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3RKF0_A0A2I3RKF0_PANTR_9598 and tr_A0A2R8ZAF4_A0A2R8ZAF4_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7B173_K7B173_PANTR_9598 and tr_A0A2R9BDZ0_A0A2R9BDZ0_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7BYI8_K7BYI8_PANTR_9598 and sp_P18754_RCC1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7BYI8_K7BYI8_PANTR_9598 and tr_A0A2R9AKL9_A0A2R9AKL9_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6VZU8_F6VZU8_HORSE_9796 and tr_H0X8G0_H0X8G0_OTOGA_30611 are exactly identical! WARNING: Sequences tr_F6VZU8_F6VZU8_HORSE_9796 and tr_A0A1U7QK67_A0A1U7QK67_MESAU_10036 are exactly identical! WARNING: Sequences tr_B0X7X1_B0X7X1_CULQU_7176 and tr_B0XB49_B0XB49_CULQU_7176 are exactly identical! WARNING: Sequences tr_A0A088A9B2_A0A088A9B2_APIME_7460 and tr_A0A2A3EG75_A0A2A3EG75_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NRC6_A0A158NRC6_ATTCE_12957 and tr_A0A195BFI9_A0A195BFI9_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0E0G846_A0A0E0G846_ORYNI_4536 and tr_B8AJF0_B8AJF0_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0G846_A0A0E0G846_ORYNI_4536 and tr_A0A0E0NGC0_A0A0E0NGC0_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0G846_A0A0E0G846_ORYNI_4536 and tr_A0A0D9YTK1_A0A0D9YTK1_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0G846_A0A0E0G846_ORYNI_4536 and tr_Q69SU2_Q69SU2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0H131_A0A0E0H131_ORYNI_4536 and tr_I1PLG0_I1PLG0_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0H131_A0A0E0H131_ORYNI_4536 and tr_A0A0E0DEH4_A0A0E0DEH4_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0H131_A0A0E0H131_ORYNI_4536 and tr_A0A0D3FW31_A0A0D3FW31_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0H131_A0A0E0H131_ORYNI_4536 and tr_A0A0D9ZL03_A0A0D9ZL03_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A1D5RIY0_A0A1D5RIY0_MACMU_9544 and tr_G7PVE3_G7PVE3_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5RIY0_A0A1D5RIY0_MACMU_9544 and tr_A0A2I3ND45_A0A2I3ND45_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5RIY0_A0A1D5RIY0_MACMU_9544 and tr_A0A2K5M3E4_A0A2K5M3E4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5RIY0_A0A1D5RIY0_MACMU_9544 and tr_A0A2K6EBB7_A0A2K6EBB7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5RIY0_A0A1D5RIY0_MACMU_9544 and tr_A0A2K5YY25_A0A2K5YY25_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7FBK1_F7FBK1_MACMU_9544 and tr_G7PDD3_G7PDD3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FBK1_F7FBK1_MACMU_9544 and tr_A0A096P537_A0A096P537_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FBK1_F7FBK1_MACMU_9544 and tr_A0A0D9R593_A0A0D9R593_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7FBK1_F7FBK1_MACMU_9544 and tr_A0A2K5MP27_A0A2K5MP27_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FBK1_F7FBK1_MACMU_9544 and tr_A0A2K6C0X7_A0A2K6C0X7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FBK1_F7FBK1_MACMU_9544 and tr_A0A2K5YV13_A0A2K5YV13_MANLE_9568 are exactly identical! WARNING: Sequences tr_A2XTP3_A2XTP3_ORYSI_39946 and tr_A0A0E0P9F4_A0A0E0P9F4_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2XTP3_A2XTP3_ORYSI_39946 and tr_Q7XRB6_Q7XRB6_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B8BKY9_B8BKY9_ORYSI_39946 and tr_B9GB42_B9GB42_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1P185_I1P185_ORYGL_4538 and tr_A0A0D3F6C1_A0A0D3F6C1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_H0YXW6_H0YXW6_TAEGU_59729 and tr_U3JU48_U3JU48_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0YXW6_H0YXW6_TAEGU_59729 and tr_A0A091F6Q0_A0A091F6Q0_CORBR_85066 are exactly identical! WARNING: Sequences tr_M3WIT1_M3WIT1_FELCA_9685 and tr_A0A384CD35_A0A384CD35_URSMA_29073 are exactly identical! WARNING: Sequences tr_R0JV21_R0JV21_ANAPL_8839 and tr_A0A091HXY8_A0A091HXY8_CALAN_9244 are exactly identical! WARNING: Sequences tr_W2PS24_W2PS24_PHYPN_761204 and tr_A0A0W8C445_A0A0W8C445_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PS24_W2PS24_PHYPN_761204 and tr_W2ICR4_W2ICR4_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2PYJ9_W2PYJ9_PHYPN_761204 and tr_A0A0W8BX49_A0A0W8BX49_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PYJ9_W2PYJ9_PHYPN_761204 and tr_A0A0W8DBN8_A0A0W8DBN8_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PYJ9_W2PYJ9_PHYPN_761204 and tr_W2KQK4_W2KQK4_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QDQ6_W2QDQ6_PHYPN_761204 and tr_A0A0W8AXK3_A0A0W8AXK3_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QDQ6_W2QDQ6_PHYPN_761204 and tr_W2JCZ3_W2JCZ3_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QDQ6_W2QDQ6_PHYPN_761204 and tr_A0A329RIN8_A0A329RIN8_9STRA_29920 are exactly identical! WARNING: Sequences tr_W2QKT7_W2QKT7_PHYPN_761204 and tr_W2LQQ9_W2LQQ9_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2R339_W2R339_PHYPN_761204 and tr_A0A0W8DIE4_A0A0W8DIE4_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2R339_W2R339_PHYPN_761204 and tr_W2KL56_W2KL56_PHYPR_4792 are exactly identical! WARNING: Sequences tr_V4TF07_V4TF07_9ROSI_85681 and tr_A0A2H5N9Y2_A0A2H5N9Y2_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0L0BSC7_A0A0L0BSC7_LUCCU_7375 and tr_A0A0L0BXE6_A0A0L0BXE6_LUCCU_7375 are exactly identical! WARNING: Sequences tr_A0A151MA00_A0A151MA00_ALLMI_8496 and tr_A0A1U7RWS7_A0A1U7RWS7_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0W8C8L5_A0A0W8C8L5_PHYNI_4790 and tr_A0A0W8DWH4_A0A0W8DWH4_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A0W8DY86_A0A0W8DY86_PHYNI_4790 and tr_W2KNN0_W2KNN0_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0L9UCH3_A0A0L9UCH3_PHAAN_3914 and tr_A0A1S3U5L6_A0A1S3U5L6_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A087QXX0_A0A087QXX0_APTFO_9233 and tr_A0A0A0A2J7_A0A0A0A2J7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1D7X2_A0A0V1D7X2_TRIBR_45882 and tr_A0A0V0VFE0_A0A0V0VFE0_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DEL0_A0A0V1DEL0_TRIBR_45882 and tr_A0A0V1A7U5_A0A0V1A7U5_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0WUA8_A0A0V0WUA8_9BILA_92179 and tr_A0A0V0VTA8_A0A0V0VTA8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0WUA8_A0A0V0WUA8_9BILA_92179 and tr_A0A0V1LE23_A0A0V1LE23_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0WUA8_A0A0V0WUA8_9BILA_92179 and tr_A0A0V0U5H4_A0A0V0U5H4_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0XAE9_A0A0V0XAE9_9BILA_92179 and tr_A0A0V1NQF3_A0A0V1NQF3_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S3YIX1_A0A1S3YIX1_TOBAC_4097 and tr_A0A1U7VWV0_A0A1U7VWV0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3RE08_A0A1S3RE08_SALSA_8030 and tr_A0A1S3SL20_A0A1S3SL20_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1U8I0F6_A0A1U8I0F6_GOSHI_3635 and tr_A0A1U8I6A4_A0A1U8I6A4_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A1U8C822_A0A1U8C822_MESAU_10036 and sp_P23800_RCC1_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A226MGY4_A0A226MGY4_CALSU_9009 and tr_A0A226PCU2_A0A226PCU2_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QL78_A0A2D0QL78_ICTPU_7998 and tr_A0A2D0QN40_A0A2D0QN40_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4ALX7_A0A2U4ALX7_TURTR_9739 and tr_A0A2Y9P728_A0A2Y9P728_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BG03_A0A2U4BG03_TURTR_9739 and tr_A0A2Y9NGC4_A0A2Y9NGC4_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 121 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92834/3_mltree/Q92834.raxml.reduced.phy Alignment comprises 1 partitions and 309 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 309 / 309 Gaps: 4.65 % Invariant sites: 1.29 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92834/3_mltree/Q92834.raxml.rba Parallelization scheme autoconfig: 5 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 1000 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 309 / 24720 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -609255.420570] Initial branch length optimization [00:00:18 -511657.692103] Model parameter optimization (eps = 10.000000) [00:01:34 -506984.172502] AUTODETECT spr round 1 (radius: 5) [00:06:19 -350790.335000] AUTODETECT spr round 2 (radius: 10) [00:11:08 -258389.208024] AUTODETECT spr round 3 (radius: 15) [00:16:01 -216872.379466] AUTODETECT spr round 4 (radius: 20) [00:21:41 -194485.699328] AUTODETECT spr round 5 (radius: 25) [00:29:21 -173193.559911] SPR radius for FAST iterations: 25 (autodetect) [00:29:21 -173193.559911] Model parameter optimization (eps = 3.000000) [00:29:50 -173150.466995] FAST spr round 1 (radius: 25) [00:35:10 -144114.982063] FAST spr round 2 (radius: 25) [00:38:47 -143205.774486] FAST spr round 3 (radius: 25) [00:41:55 -143134.528394] FAST spr round 4 (radius: 25) [00:44:45 -143116.388769] FAST spr round 5 (radius: 25) [00:47:28 -143109.977432] FAST spr round 6 (radius: 25) [00:49:59 -143109.971678] Model parameter optimization (eps = 1.000000) [00:50:19 -143108.087299] SLOW spr round 1 (radius: 5) [00:54:01 -143071.103836] SLOW spr round 2 (radius: 5) [00:57:34 -143066.372202] SLOW spr round 3 (radius: 5) [01:00:59 -143062.957679] SLOW spr round 4 (radius: 5) [01:04:18 -143062.957278] SLOW spr round 5 (radius: 10) [01:07:49 -143062.478374] SLOW spr round 6 (radius: 5) [01:12:00 -143062.478266] SLOW spr round 7 (radius: 10) [01:15:54 -143062.478264] SLOW spr round 8 (radius: 15) [01:21:23 -143062.478264] SLOW spr round 9 (radius: 20) [01:28:22] [worker #4] ML tree search #5, logLikelihood: -143088.400321 [01:30:21 -143062.478264] SLOW spr round 10 (radius: 25) [01:32:36] [worker #2] ML tree search #3, logLikelihood: -143034.261490 [01:41:47 -143062.478264] Model parameter optimization (eps = 0.100000) [01:41:59] [worker #0] ML tree search #1, logLikelihood: -143062.408256 [01:41:59 -605093.489949] Initial branch length optimization [01:42:10 -506754.761989] Model parameter optimization (eps = 10.000000) [01:43:26 -502306.286019] AUTODETECT spr round 1 (radius: 5) [01:47:53 -336075.023349] AUTODETECT spr round 2 (radius: 10) [01:52:38 -241444.027157] AUTODETECT spr round 3 (radius: 15) [01:57:26 -193261.522396] AUTODETECT spr round 4 (radius: 20) [02:02:53 -173540.140423] AUTODETECT spr round 5 (radius: 25) [02:06:22] [worker #1] ML tree search #2, logLikelihood: -143064.847105 [02:09:09 -167133.015816] SPR radius for FAST iterations: 25 (autodetect) [02:09:09 -167133.015816] Model parameter optimization (eps = 3.000000) [02:09:40 -167003.428103] FAST spr round 1 (radius: 25) [02:13:45] [worker #3] ML tree search #4, logLikelihood: -143061.296826 [02:15:03 -144023.514019] FAST spr round 2 (radius: 25) [02:18:57 -143171.244988] FAST spr round 3 (radius: 25) [02:22:07 -143113.520927] FAST spr round 4 (radius: 25) [02:24:56 -143106.165041] FAST spr round 5 (radius: 25) [02:27:35 -143104.897472] FAST spr round 6 (radius: 25) [02:30:07 -143104.897321] Model parameter optimization (eps = 1.000000) [02:30:27 -143101.834917] SLOW spr round 1 (radius: 5) [02:34:16 -143054.929968] SLOW spr round 2 (radius: 5) [02:37:49 -143048.749419] SLOW spr round 3 (radius: 5) [02:41:25 -143044.030185] SLOW spr round 4 (radius: 5) [02:44:54 -143043.404503] SLOW spr round 5 (radius: 5) [02:48:22 -143042.645134] SLOW spr round 6 (radius: 5) [02:51:49 -143042.418041] SLOW spr round 7 (radius: 5) [02:55:12 -143042.416957] SLOW spr round 8 (radius: 10) [02:58:37 -143042.416933] SLOW spr round 9 (radius: 15) [03:04:25 -143041.948339] SLOW spr round 10 (radius: 5) [03:08:52 -143041.948335] SLOW spr round 11 (radius: 10) [03:12:59 -143041.948334] SLOW spr round 12 (radius: 15) [03:16:47] [worker #4] ML tree search #10, logLikelihood: -143067.552555 [03:18:20 -143041.948334] SLOW spr round 13 (radius: 20) [03:27:23 -143041.948334] SLOW spr round 14 (radius: 25) [03:38:31 -143041.948334] Model parameter optimization (eps = 0.100000) [03:38:46] [worker #0] ML tree search #6, logLikelihood: -143041.394593 [03:38:46 -610465.153083] Initial branch length optimization [03:38:55 -513420.690574] Model parameter optimization (eps = 10.000000) [03:40:16 -509025.889151] AUTODETECT spr round 1 (radius: 5) [03:44:44 -339288.790979] AUTODETECT spr round 2 (radius: 10) [03:46:55] [worker #2] ML tree search #8, logLikelihood: -143065.945701 [03:49:35 -262016.200440] AUTODETECT spr round 3 (radius: 15) [03:54:33 -206021.451171] AUTODETECT spr round 4 (radius: 20) [04:00:28 -188235.237178] AUTODETECT spr round 5 (radius: 25) [04:06:24] [worker #1] ML tree search #7, logLikelihood: -143047.957421 [04:06:48 -172949.015064] SPR radius for FAST iterations: 25 (autodetect) [04:06:48 -172949.015064] Model parameter optimization (eps = 3.000000) [04:07:21 -172891.235740] FAST spr round 1 (radius: 25) [04:12:33 -144637.319743] FAST spr round 2 (radius: 25) [04:16:29 -143189.897526] FAST spr round 3 (radius: 25) [04:19:37 -143124.826565] FAST spr round 4 (radius: 25) [04:22:17 -143122.051948] FAST spr round 5 (radius: 25) [04:24:50 -143122.049889] Model parameter optimization (eps = 1.000000) [04:25:16 -143113.268477] SLOW spr round 1 (radius: 5) [04:28:58 -143074.053055] SLOW spr round 2 (radius: 5) [04:32:35 -143061.188265] SLOW spr round 3 (radius: 5) [04:36:07 -143060.803325] SLOW spr round 4 (radius: 5) [04:39:31 -143060.803276] SLOW spr round 5 (radius: 10) [04:43:00 -143060.803145] SLOW spr round 6 (radius: 15) [04:48:41 -143060.333808] SLOW spr round 7 (radius: 5) [04:53:10 -143060.333751] SLOW spr round 8 (radius: 10) [04:57:17 -143060.333751] SLOW spr round 9 (radius: 15) [04:59:21] [worker #3] ML tree search #9, logLikelihood: -143047.261677 [05:02:33 -143060.333751] SLOW spr round 10 (radius: 20) [05:11:17 -143060.333751] SLOW spr round 11 (radius: 25) [05:13:38] [worker #4] ML tree search #15, logLikelihood: -143057.476500 [05:13:40] [worker #2] ML tree search #13, logLikelihood: -143033.649338 [05:22:09 -143060.333751] Model parameter optimization (eps = 0.100000) [05:22:17] [worker #0] ML tree search #11, logLikelihood: -143060.261255 [05:22:17 -607631.831274] Initial branch length optimization [05:22:30 -512543.651921] Model parameter optimization (eps = 10.000000) [05:23:58 -508168.385164] AUTODETECT spr round 1 (radius: 5) [05:28:22 -341835.842904] AUTODETECT spr round 2 (radius: 10) [05:33:09 -249395.126438] AUTODETECT spr round 3 (radius: 15) [05:38:25 -187257.096195] AUTODETECT spr round 4 (radius: 20) [05:44:19 -166156.474822] AUTODETECT spr round 5 (radius: 25) [05:51:23 -163683.223646] SPR radius for FAST iterations: 25 (autodetect) [05:51:23 -163683.223646] Model parameter optimization (eps = 3.000000) [05:51:54 -163562.849813] FAST spr round 1 (radius: 25) [05:54:36] [worker #1] ML tree search #12, logLikelihood: -143040.387044 [05:56:58 -144158.197925] FAST spr round 2 (radius: 25) [06:00:30 -143190.292692] FAST spr round 3 (radius: 25) [06:03:30 -143109.906626] FAST spr round 4 (radius: 25) [06:06:10 -143105.112299] FAST spr round 5 (radius: 25) [06:08:43 -143103.228996] FAST spr round 6 (radius: 25) [06:11:12 -143103.228914] Model parameter optimization (eps = 1.000000) [06:11:24 -143102.385266] SLOW spr round 1 (radius: 5) [06:14:56 -143074.729336] SLOW spr round 2 (radius: 5) [06:18:28 -143073.848604] SLOW spr round 3 (radius: 5) [06:21:58 -143072.510282] SLOW spr round 4 (radius: 5) [06:25:25 -143071.911891] SLOW spr round 5 (radius: 5) [06:28:46 -143071.911690] SLOW spr round 6 (radius: 10) [06:32:14 -143070.203729] SLOW spr round 7 (radius: 5) [06:36:26 -143069.797125] SLOW spr round 8 (radius: 5) [06:40:11 -143068.323243] SLOW spr round 9 (radius: 5) [06:43:40 -143068.323210] SLOW spr round 10 (radius: 10) [06:47:09 -143068.323207] SLOW spr round 11 (radius: 15) [06:52:55 -143067.329586] SLOW spr round 12 (radius: 5) [06:55:24] [worker #2] ML tree search #18, logLikelihood: -143067.680652 [06:57:25 -143062.841939] SLOW spr round 13 (radius: 5) [07:01:14 -143062.841669] SLOW spr round 14 (radius: 10) [07:04:52 -143062.841662] SLOW spr round 15 (radius: 15) [07:10:23 -143062.841661] SLOW spr round 16 (radius: 20) [07:15:58] [worker #3] ML tree search #14, logLikelihood: -143068.989767 [07:19:32 -143062.841661] SLOW spr round 17 (radius: 25) [07:26:11] [worker #4] ML tree search #20, logLikelihood: -143066.273418 [07:31:16 -143062.841661] Model parameter optimization (eps = 0.100000) [07:31:29] [worker #0] ML tree search #16, logLikelihood: -143062.568869 [07:50:41] [worker #1] ML tree search #17, logLikelihood: -143072.856736 [08:57:27] [worker #3] ML tree search #19, logLikelihood: -143054.172455 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.149528,0.526280) (0.306599,0.493386) (0.375420,1.232307) (0.168453,1.824853) 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: -143033.649338 AIC score: 290073.298676 / AICc score: 8318097.298676 / BIC score: 297551.181254 Free parameters (model + branch lengths): 2003 WARNING: Number of free parameters (K=2003) is larger than alignment size (n=309). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92834/3_mltree/Q92834.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92834/3_mltree/Q92834.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92834/3_mltree/Q92834.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92834/3_mltree/Q92834.raxml.log Analysis started: 04-Jun-2021 03:53:17 / finished: 04-Jun-2021 12:50:44 Elapsed time: 32247.795 seconds Consumed energy: 3035.995 Wh (= 15 km in an electric car, or 76 km with an e-scooter!)