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 06:50:28 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/2_msa/Q6AWC2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/3_mltree/Q6AWC2 --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/300621_run/phylogeny-snakemake/results/Q6AWC2/2_msa/Q6AWC2_trimmed_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 341 sites WARNING: Sequences tr_B4QFM5_B4QFM5_DROSI_7240 and tr_B4I7K2_B4I7K2_DROSE_7238 are exactly identical! WARNING: Sequences sp_Q9WVQ1_MAGI2_MOUSE_10090 and tr_M3Z3K7_M3Z3K7_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q9WVQ1_MAGI2_MOUSE_10090 and tr_A0A2Y9KPG0_A0A2Y9KPG0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y1M8_M3Y1M8_MUSPF_9669 and tr_A0A2Y9IW45_A0A2Y9IW45_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YZS4_M3YZS4_MUSPF_9669 and tr_F6Y537_F6Y537_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YZS4_M3YZS4_MUSPF_9669 and tr_W5PM45_W5PM45_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3YZS4_M3YZS4_MUSPF_9669 and tr_A0A287B5P8_A0A287B5P8_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YZS4_M3YZS4_MUSPF_9669 and tr_G1M7Z3_G1M7Z3_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YZS4_M3YZS4_MUSPF_9669 and tr_E1B7V9_E1B7V9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YZS4_M3YZS4_MUSPF_9669 and tr_M3WB91_M3WB91_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YZS4_M3YZS4_MUSPF_9669 and tr_A0A2U3WP62_A0A2U3WP62_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I3GGT0_A0A2I3GGT0_NOMLE_61853 and sp_Q5TCQ9_MAGI3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GGT0_A0A2I3GGT0_NOMLE_61853 and tr_A0A096N7W8_A0A096N7W8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3GGT0_A0A2I3GGT0_NOMLE_61853 and tr_A0A2K5NEQ5_A0A2K5NEQ5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GGT0_A0A2I3GGT0_NOMLE_61853 and tr_A0A2K6C8V3_A0A2K6C8V3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GGT0_A0A2I3GGT0_NOMLE_61853 and tr_A0A2K5YKF4_A0A2K5YKF4_MANLE_9568 are exactly identical! WARNING: Sequences tr_J3K9N9_J3K9N9_COCIM_246410 and tr_E9CRR5_E9CRR5_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3K9N9_J3K9N9_COCIM_246410 and tr_A0A0J6YB63_A0A0J6YB63_COCIT_404692 are exactly identical! WARNING: Sequences tr_A0A2I2ZL88_A0A2I2ZL88_GORGO_9595 and tr_H2PAB7_H2PAB7_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2ZL88_A0A2I2ZL88_GORGO_9595 and sp_Q96QZ7_MAGI1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZL88_A0A2I2ZL88_GORGO_9595 and tr_F7HE96_F7HE96_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3QG32_G3QG32_GORGO_9595 and tr_H2QUU4_H2QUU4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QG32_G3QG32_GORGO_9595 and sp_Q86UL8_MAGI2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QG32_G3QG32_GORGO_9595 and tr_A0A2R9BL89_A0A2R9BL89_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RYD7_G3RYD7_GORGO_9595 and tr_H2QRY9_H2QRY9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RYD7_G3RYD7_GORGO_9595 and sp_Q8IX03_KIBRA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S284_G3S284_GORGO_9595 and tr_A0A2R9BXN5_A0A2R9BXN5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PN21_H2PN21_PONAB_9601 and tr_I3LZJ7_I3LZJ7_ICTTR_43179 are exactly identical! WARNING: Sequences tr_H2PN21_H2PN21_PONAB_9601 and tr_H0WXE4_H0WXE4_OTOGA_30611 are exactly identical! WARNING: Sequences tr_H2PN21_H2PN21_PONAB_9601 and tr_A0A287AC12_A0A287AC12_PIG_9823 are exactly identical! WARNING: Sequences tr_H2PN21_H2PN21_PONAB_9601 and tr_G1M2A1_G1M2A1_AILME_9646 are exactly identical! WARNING: Sequences tr_H2PN21_H2PN21_PONAB_9601 and tr_A0A337SIQ5_A0A337SIQ5_FELCA_9685 are exactly identical! WARNING: Sequences tr_H2PN21_H2PN21_PONAB_9601 and tr_A0A2U3VG29_A0A2U3VG29_ODORO_9708 are exactly identical! WARNING: Sequences tr_H2PN21_H2PN21_PONAB_9601 and tr_A0A2Y9EAJ0_A0A2Y9EAJ0_TRIMA_127582 are exactly identical! WARNING: Sequences tr_C0NMQ2_C0NMQ2_AJECG_447093 and tr_C6H2E0_C6H2E0_AJECH_544712 are exactly identical! WARNING: Sequences tr_C0NMQ2_C0NMQ2_AJECG_447093 and tr_F0U541_F0U541_AJEC8_544711 are exactly identical! WARNING: Sequences tr_G3URX0_G3URX0_MELGA_9103 and tr_A0A226MMD9_A0A226MMD9_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A179UHY6_A0A179UHY6_BLAGS_559298 and tr_C5GFJ5_C5GFJ5_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A3B5QT24_A0A3B5QT24_XIPMA_8083 and tr_A0A087Y4B2_A0A087Y4B2_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NRT0_A0A158NRT0_ATTCE_12957 and tr_F4WQS8_F4WQS8_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A1D5QV36_A0A1D5QV36_MACMU_9544 and tr_G7P1X6_G7P1X6_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QV36_A0A1D5QV36_MACMU_9544 and tr_A0A2I3MW62_A0A2I3MW62_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QV36_A0A1D5QV36_MACMU_9544 and tr_A0A2K6DEX0_A0A2K6DEX0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QV36_A0A1D5QV36_MACMU_9544 and tr_A0A2K5YU87_A0A2K5YU87_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6SW62_F6SW62_MACMU_9544 and tr_A0A0D9RCV2_A0A0D9RCV2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6SW62_F6SW62_MACMU_9544 and tr_A0A2K5LF08_A0A2K5LF08_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6SW62_F6SW62_MACMU_9544 and tr_A0A2K6B5K5_A0A2K6B5K5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6V3H6_F6V3H6_MACMU_9544 and tr_A0A0D9RH82_A0A0D9RH82_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6V3H6_F6V3H6_MACMU_9544 and tr_A0A2K6BVS0_A0A2K6BVS0_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0YWU2_H0YWU2_TAEGU_59729 and tr_A0A091F943_A0A091F943_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0YWU2_H0YWU2_TAEGU_59729 and tr_A0A091W0K0_A0A091W0K0_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0YWU2_H0YWU2_TAEGU_59729 and tr_A0A091WQ79_A0A091WQ79_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0YWU2_H0YWU2_TAEGU_59729 and tr_A0A091GQT8_A0A091GQT8_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0YWU2_H0YWU2_TAEGU_59729 and tr_A0A0A0ADL1_A0A0A0ADL1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0YWU2_H0YWU2_TAEGU_59729 and tr_A0A2I0MHG5_A0A2I0MHG5_COLLI_8932 are exactly identical! WARNING: Sequences tr_H0YWU2_H0YWU2_TAEGU_59729 and tr_A0A1V4K1N3_A0A1V4K1N3_PATFA_372326 are exactly identical! WARNING: Sequences tr_H0YWU2_H0YWU2_TAEGU_59729 and tr_A0A218US26_A0A218US26_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZH11_H0ZH11_TAEGU_59729 and tr_A0A091EWX9_A0A091EWX9_CORBR_85066 are exactly identical! WARNING: Sequences tr_H1A4I8_H1A4I8_TAEGU_59729 and tr_A0A091EZA2_A0A091EZA2_CORBR_85066 are exactly identical! WARNING: Sequences tr_F9XPD8_F9XPD8_ZYMTI_336722 and tr_A0A1X7S762_A0A1X7S762_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G0MM60_G0MM60_CAEBE_135651 and tr_G0NV82_G0NV82_CAEBE_135651 are exactly identical! WARNING: Sequences tr_A0A287AK47_A0A287AK47_PIG_9823 and tr_A0A2Y9PBC6_A0A2Y9PBC6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A8WZ81_A8WZ81_CAEBR_6238 and tr_A0A2G5VT08_A0A2G5VT08_9PELO_1611254 are exactly identical! WARNING: Sequences tr_U3IY82_U3IY82_ANAPL_8839 and tr_A0A091JAN7_A0A091JAN7_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3IY82_U3IY82_ANAPL_8839 and tr_A0A091HYN7_A0A091HYN7_CALAN_9244 are exactly identical! WARNING: Sequences tr_M2Z2Z1_M2Z2Z1_PSEFD_383855 and tr_A0A139HWE0_A0A139HWE0_9PEZI_321146 are exactly identical! WARNING: Sequences tr_U5HEL7_U5HEL7_USTV1_683840 and tr_A0A2X0P4T2_A0A2X0P4T2_9BASI_796604 are exactly identical! WARNING: Sequences tr_U5HEL7_U5HEL7_USTV1_683840 and tr_A0A2X0LLM8_A0A2X0LLM8_9BASI_289078 are exactly identical! WARNING: Sequences tr_V2WZL5_V2WZL5_MONRO_1381753 and tr_A0A0W0F231_A0A0W0F231_9AGAR_221103 are exactly identical! WARNING: Sequences tr_V2X9P0_V2X9P0_MONRO_1381753 and tr_A0A0W0G149_A0A0W0G149_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W9WJC3_W9WJC3_9EURO_1182544 and tr_A0A1C1CSV9_A0A1C1CSV9_9EURO_86049 are exactly identical! WARNING: Sequences tr_A0A096NG20_A0A096NG20_PAPAN_9555 and tr_A0A2K5LC48_A0A2K5LC48_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NG20_A0A096NG20_PAPAN_9555 and tr_A0A2K5Z3N5_A0A2K5Z3N5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NH40_A0A096NH40_PAPAN_9555 and tr_A0A2K6AVV7_A0A2K6AVV7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A151MTP6_A0A151MTP6_ALLMI_8496 and tr_A0A3Q0HK64_A0A3Q0HK64_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A093Q1B7_A0A093Q1B7_9PASS_328815 and tr_A0A0A0ADY1_A0A0A0ADY1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A093Q1B7_A0A093Q1B7_9PASS_328815 and tr_A0A093G7J6_A0A093G7J6_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091UPZ5_A0A091UPZ5_NIPNI_128390 and tr_A0A087RII8_A0A087RII8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UPZ5_A0A091UPZ5_NIPNI_128390 and tr_A0A0A0AIV3_A0A0A0AIV3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0L0RZ82_A0A0L0RZ82_ALLMA_578462 and tr_A0A0L0S7E5_A0A0L0S7E5_ALLMA_578462 are exactly identical! WARNING: Sequences tr_A0A0V1CYJ0_A0A0V1CYJ0_TRIBR_45882 and tr_A0A0V0TTT6_A0A0V0TTT6_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1ACI1_A0A0V1ACI1_9BILA_990121 and tr_A0A0V1NX84_A0A0V1NX84_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A167NMY3_A0A167NMY3_9BASI_1330018 and tr_A0A165IET5_A0A165IET5_9BASI_1353952 are exactly identical! WARNING: Sequences tr_A0A1B7N8Y7_A0A1B7N8Y7_9HOMO_1314800 and tr_A0A1J8PMS3_A0A1J8PMS3_9HOMO_180088 are exactly identical! WARNING: Sequences tr_A0A1I7UEW2_A0A1I7UEW2_9PELO_1561998 and tr_A0A1I7UEW3_A0A1I7UEW3_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A2H3DN70_A0A2H3DN70_ARMGA_47427 and tr_A0A2H3C4G0_A0A2H3C4G0_9AGAR_1076256 are exactly identical! WARNING: Sequences tr_A0A2H3DN70_A0A2H3DN70_ARMGA_47427 and tr_A0A284QUR2_A0A284QUR2_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2H3DQQ8_A0A2H3DQQ8_ARMGA_47427 and tr_A0A2H3BZE7_A0A2H3BZE7_9AGAR_1076256 are exactly identical! WARNING: Sequences tr_A0A2H3DQQ8_A0A2H3DQQ8_ARMGA_47427 and tr_A0A284RFW1_A0A284RFW1_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2D0PIM1_A0A2D0PIM1_ICTPU_7998 and tr_A0A2D0PIP5_A0A2D0PIP5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PIM1_A0A2D0PIM1_ICTPU_7998 and tr_A0A2D0PL20_A0A2D0PL20_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QYS8_A0A2D0QYS8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QYT2_A0A2D0QYT2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QYT3_A0A2D0QYT3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QYT7_A0A2D0QYT7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QYT9_A0A2D0QYT9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QYU4_A0A2D0QYU4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QYU5_A0A2D0QYU5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QYU8_A0A2D0QYU8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QZ12_A0A2D0QZ12_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QZ17_A0A2D0QZ17_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QZ23_A0A2D0QZ23_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QZ28_A0A2D0QZ28_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R0K1_A0A2D0R0K1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R0K7_A0A2D0R0K7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R0L3_A0A2D0R0L3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R0L9_A0A2D0R0L9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R1A2_A0A2D0R1A2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R1A8_A0A2D0R1A8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R1B5_A0A2D0R1B5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R1C3_A0A2D0R1C3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RZG4_A0A2D0RZG4_ICTPU_7998 and tr_A0A2D0RZH2_A0A2D0RZH2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RZG4_A0A2D0RZG4_ICTPU_7998 and tr_A0A2D0RZH3_A0A2D0RZH3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RZG4_A0A2D0RZG4_ICTPU_7998 and tr_A0A2D0S108_A0A2D0S108_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4CC88_A0A2U4CC88_TURTR_9739 and tr_A0A2Y9NGA4_A0A2Y9NGA4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CC88_A0A2U4CC88_TURTR_9739 and tr_A0A2Y9SMK8_A0A2Y9SMK8_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 116 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/Q6AWC2/3_mltree/Q6AWC2.raxml.reduced.phy Alignment comprises 1 partitions and 341 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 341 / 341 Gaps: 12.95 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/3_mltree/Q6AWC2.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 999 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 341 / 27280 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -591976.313332] Initial branch length optimization [00:00:10 -481032.614413] Model parameter optimization (eps = 10.000000) [00:01:51 -477518.617465] AUTODETECT spr round 1 (radius: 5) [00:06:03 -269427.542332] AUTODETECT spr round 2 (radius: 10) [00:10:09 -183302.715490] AUTODETECT spr round 3 (radius: 15) [00:14:35 -139650.923984] AUTODETECT spr round 4 (radius: 20) [00:19:43 -127079.555184] AUTODETECT spr round 5 (radius: 25) [00:26:30 -116421.011904] SPR radius for FAST iterations: 25 (autodetect) [00:26:30 -116421.011904] Model parameter optimization (eps = 3.000000) [00:27:12 -116012.403387] FAST spr round 1 (radius: 25) [00:31:56 -92354.038973] FAST spr round 2 (radius: 25) [00:35:28 -91169.096774] FAST spr round 3 (radius: 25) [00:38:16 -91101.892166] FAST spr round 4 (radius: 25) [00:40:54 -91091.964271] FAST spr round 5 (radius: 25) [00:43:15 -91091.961458] Model parameter optimization (eps = 1.000000) [00:43:50 -91086.922069] SLOW spr round 1 (radius: 5) [00:46:56 -91072.781856] SLOW spr round 2 (radius: 5) [00:50:04 -91071.608846] SLOW spr round 3 (radius: 5) [00:53:05 -91071.608683] SLOW spr round 4 (radius: 10) [00:56:21 -91062.332014] SLOW spr round 5 (radius: 5) [01:00:35 -91062.328525] SLOW spr round 6 (radius: 10) [01:04:23 -91062.328447] SLOW spr round 7 (radius: 15) [01:09:32 -91061.982816] SLOW spr round 8 (radius: 5) [01:14:00 -91061.972891] SLOW spr round 9 (radius: 10) [01:17:52 -91061.971130] SLOW spr round 10 (radius: 15) [01:22:53 -91061.970712] SLOW spr round 11 (radius: 20) [01:30:03 -91061.970601] SLOW spr round 12 (radius: 25) [01:34:28] [worker #2] ML tree search #3, logLikelihood: -91111.598453 [01:36:00] [worker #1] ML tree search #2, logLikelihood: -91079.412852 [01:36:01] [worker #3] ML tree search #4, logLikelihood: -91066.851967 [01:38:40 -91061.970562] Model parameter optimization (eps = 0.100000) [01:39:00] [worker #0] ML tree search #1, logLikelihood: -91061.163264 [01:39:00 -584179.863040] Initial branch length optimization [01:39:07 -471366.092421] Model parameter optimization (eps = 10.000000) [01:40:07 -467712.728925] AUTODETECT spr round 1 (radius: 5) [01:43:56 -261412.036993] AUTODETECT spr round 2 (radius: 10) [01:47:44 -176241.662825] AUTODETECT spr round 3 (radius: 15) [01:51:51 -137635.412422] AUTODETECT spr round 4 (radius: 20) [01:56:13 -115017.003385] AUTODETECT spr round 5 (radius: 25) [01:58:02] [worker #4] ML tree search #5, logLikelihood: -91302.328401 [02:01:15 -107977.977672] SPR radius for FAST iterations: 25 (autodetect) [02:01:15 -107977.977672] Model parameter optimization (eps = 3.000000) [02:02:00 -107592.922636] FAST spr round 1 (radius: 25) [02:05:46 -92468.744691] FAST spr round 2 (radius: 25) [02:08:33 -91294.667073] FAST spr round 3 (radius: 25) [02:11:04 -91128.668047] FAST spr round 4 (radius: 25) [02:13:27 -91121.319348] FAST spr round 5 (radius: 25) [02:15:38 -91121.319325] Model parameter optimization (eps = 1.000000) [02:16:01 -91113.856641] SLOW spr round 1 (radius: 5) [02:19:04 -91095.400905] SLOW spr round 2 (radius: 5) [02:22:02 -91094.172431] SLOW spr round 3 (radius: 5) [02:24:51 -91094.171868] SLOW spr round 4 (radius: 10) [02:27:47 -91090.033571] SLOW spr round 5 (radius: 5) [02:31:33 -91082.552870] SLOW spr round 6 (radius: 5) [02:34:50 -91078.993328] SLOW spr round 7 (radius: 5) [02:38:06 -91078.991825] SLOW spr round 8 (radius: 10) [02:41:12 -91078.991502] SLOW spr round 9 (radius: 15) [02:46:12 -91077.696061] SLOW spr round 10 (radius: 5) [02:50:20 -91077.695985] SLOW spr round 11 (radius: 10) [02:54:01 -91077.695943] SLOW spr round 12 (radius: 15) [02:55:31] [worker #2] ML tree search #8, logLikelihood: -91077.593276 [02:58:30 -91077.695919] SLOW spr round 13 (radius: 20) [02:58:44] [worker #3] ML tree search #9, logLikelihood: -91091.159559 [03:04:50 -91077.695904] SLOW spr round 14 (radius: 25) [03:13:11 -91077.695894] Model parameter optimization (eps = 0.100000) [03:13:26] [worker #0] ML tree search #6, logLikelihood: -91077.432885 [03:13:26 -589288.716140] Initial branch length optimization [03:13:35 -477526.844129] Model parameter optimization (eps = 10.000000) [03:14:36 -473675.491876] AUTODETECT spr round 1 (radius: 5) [03:18:11 -263303.700194] AUTODETECT spr round 2 (radius: 10) [03:21:15] [worker #1] ML tree search #7, logLikelihood: -91070.158248 [03:21:42 -181701.410851] AUTODETECT spr round 3 (radius: 15) [03:25:31 -140491.410600] AUTODETECT spr round 4 (radius: 20) [03:29:50 -119811.558218] AUTODETECT spr round 5 (radius: 25) [03:31:55] [worker #4] ML tree search #10, logLikelihood: -91067.813327 [03:35:09 -113432.865153] SPR radius for FAST iterations: 25 (autodetect) [03:35:09 -113432.865153] Model parameter optimization (eps = 3.000000) [03:35:44 -112954.704653] FAST spr round 1 (radius: 25) [03:39:53 -94979.849574] FAST spr round 2 (radius: 25) [03:43:16 -91516.427499] FAST spr round 3 (radius: 25) [03:46:16 -91184.718068] FAST spr round 4 (radius: 25) [03:48:47 -91168.114285] FAST spr round 5 (radius: 25) [03:51:13 -91166.517650] FAST spr round 6 (radius: 25) [03:53:37 -91166.514486] Model parameter optimization (eps = 1.000000) [03:54:00 -91162.548736] SLOW spr round 1 (radius: 5) [03:57:25 -91140.775814] SLOW spr round 2 (radius: 5) [04:00:45 -91137.622960] SLOW spr round 3 (radius: 5) [04:03:46 -91137.420790] SLOW spr round 4 (radius: 5) [04:06:41 -91137.420160] SLOW spr round 5 (radius: 10) [04:09:39 -91137.290620] SLOW spr round 6 (radius: 5) [04:13:34 -91137.290413] SLOW spr round 7 (radius: 10) [04:17:14 -91137.290292] SLOW spr round 8 (radius: 15) [04:21:48] [worker #2] ML tree search #13, logLikelihood: -91071.443592 [04:22:17 -91136.128426] SLOW spr round 9 (radius: 5) [04:26:01] [worker #3] ML tree search #14, logLikelihood: -91073.743769 [04:26:19 -91136.125077] SLOW spr round 10 (radius: 10) [04:30:02 -91136.124413] SLOW spr round 11 (radius: 15) [04:34:44 -91136.124261] SLOW spr round 12 (radius: 20) [04:41:41 -91136.124213] SLOW spr round 13 (radius: 25) [04:50:06 -91135.343780] SLOW spr round 14 (radius: 5) [04:54:44 -91099.291646] SLOW spr round 15 (radius: 5) [04:54:57] [worker #4] ML tree search #15, logLikelihood: -91085.360868 [04:58:29 -91080.037407] SLOW spr round 16 (radius: 5) [05:00:37] [worker #1] ML tree search #12, logLikelihood: -91070.144364 [05:01:50 -91077.755163] SLOW spr round 17 (radius: 5) [05:05:12 -91076.749612] SLOW spr round 18 (radius: 5) [05:08:05 -91076.747016] SLOW spr round 19 (radius: 10) [05:11:00 -91076.746359] SLOW spr round 20 (radius: 15) [05:15:57 -91076.746166] SLOW spr round 21 (radius: 20) [05:22:40 -91076.746100] SLOW spr round 22 (radius: 25) [05:31:15 -91076.746070] Model parameter optimization (eps = 0.100000) [05:31:25] [worker #0] ML tree search #11, logLikelihood: -91076.652079 [05:31:25 -590670.211943] Initial branch length optimization [05:31:31 -476753.189516] Model parameter optimization (eps = 10.000000) [05:32:40 -473143.522964] AUTODETECT spr round 1 (radius: 5) [05:36:28 -258792.292604] AUTODETECT spr round 2 (radius: 10) [05:40:22 -173874.878136] AUTODETECT spr round 3 (radius: 15) [05:44:49 -136300.228091] AUTODETECT spr round 4 (radius: 20) [05:49:04] [worker #3] ML tree search #19, logLikelihood: -91074.188398 [05:49:28 -111305.577402] AUTODETECT spr round 5 (radius: 25) [05:53:53 -108180.245962] SPR radius for FAST iterations: 25 (autodetect) [05:53:53 -108180.245962] Model parameter optimization (eps = 3.000000) [05:54:37 -107610.039086] FAST spr round 1 (radius: 25) [05:58:25 -91955.362147] FAST spr round 2 (radius: 25) [06:01:19 -91199.273711] FAST spr round 3 (radius: 25) [06:03:48 -91136.319886] FAST spr round 4 (radius: 25) [06:06:08 -91113.451689] FAST spr round 5 (radius: 25) [06:06:21] [worker #2] ML tree search #18, logLikelihood: -91100.601433 [06:08:17 -91112.449532] FAST spr round 6 (radius: 25) [06:10:32 -91112.449484] Model parameter optimization (eps = 1.000000) [06:10:56 -91106.616928] SLOW spr round 1 (radius: 5) [06:14:29 -91085.750638] SLOW spr round 2 (radius: 5) [06:17:56 -91083.875597] SLOW spr round 3 (radius: 5) [06:20:04] [worker #1] ML tree search #17, logLikelihood: -91093.556256 [06:21:13 -91083.874844] SLOW spr round 4 (radius: 10) [06:24:03 -91077.717115] SLOW spr round 5 (radius: 5) [06:27:40 -91077.706264] SLOW spr round 6 (radius: 10) [06:31:13] [worker #4] ML tree search #20, logLikelihood: -91087.883486 [06:31:31 -91077.704430] SLOW spr round 7 (radius: 15) [06:37:09 -91077.703568] SLOW spr round 8 (radius: 20) [06:45:13 -91077.703038] SLOW spr round 9 (radius: 25) [06:55:26 -91077.702589] Model parameter optimization (eps = 0.100000) [06:55:39] [worker #0] ML tree search #16, logLikelihood: -91077.622409 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.161431,0.924396) (0.091446,0.979162) (0.439826,0.704253) (0.307296,1.469215) 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: -91061.163264 AIC score: 186124.326529 / AICc score: 8198128.326529 / BIC score: 193791.923366 Free parameters (model + branch lengths): 2001 WARNING: Number of free parameters (K=2001) is larger than alignment size (n=341). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 241 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/3_mltree/Q6AWC2.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/3_mltree/Q6AWC2.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/3_mltree/Q6AWC2.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/3_mltree/Q6AWC2.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/3_mltree/Q6AWC2.raxml.log Analysis started: 01-Jul-2021 06:50:28 / finished: 01-Jul-2021 13:46:08 Elapsed time: 24939.826 seconds Consumed energy: 2130.342 Wh (= 11 km in an electric car, or 53 km with an e-scooter!)