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 07-Jul-2021 11:30:16 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDN2/2_msa/Q8TDN2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDN2/3_mltree/Q8TDN2 --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/Q8TDN2/2_msa/Q8TDN2_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 339 sites WARNING: Sequences tr_A0A1D5PCF8_A0A1D5PCF8_CHICK_9031 and tr_A0A226N481_A0A226N481_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5PCF8_A0A1D5PCF8_CHICK_9031 and tr_A0A226NPM6_A0A226NPM6_COLVI_9014 are exactly identical! WARNING: Sequences tr_E1BWF1_E1BWF1_CHICK_9031 and tr_G1NRE2_G1NRE2_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1BYX3_E1BYX3_CHICK_9031 and tr_G1N040_G1N040_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1BYX3_E1BYX3_CHICK_9031 and tr_U3J7Y4_U3J7Y4_ANAPL_8839 are exactly identical! WARNING: Sequences tr_E1BYX3_E1BYX3_CHICK_9031 and tr_A0A0Q3PNF8_A0A0Q3PNF8_AMAAE_12930 are exactly identical! WARNING: Sequences sp_A6H8H5_KCNB2_MOUSE_10090 and sp_Q63099_KCNB2_RAT_10116 are exactly identical! WARNING: Sequences sp_A6H8H5_KCNB2_MOUSE_10090 and tr_A0A1U7QIJ7_A0A1U7QIJ7_MESAU_10036 are exactly identical! WARNING: Sequences sp_O35174_KCNS2_MOUSE_10090 and sp_Q9ER26_KCNS2_RAT_10116 are exactly identical! WARNING: Sequences sp_O35174_KCNS2_MOUSE_10090 and tr_A0A287AFI7_A0A287AFI7_PIG_9823 are exactly identical! WARNING: Sequences sp_O35174_KCNS2_MOUSE_10090 and tr_A0A2Y9DA16_A0A2Y9DA16_TRIMA_127582 are exactly identical! WARNING: Sequences sp_Q03717_KCNB1_MOUSE_10090 and sp_P15387_KCNB1_RAT_10116 are exactly identical! WARNING: Sequences sp_Q03717_KCNB1_MOUSE_10090 and tr_A0A3Q0CYQ2_A0A3Q0CYQ2_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q7TSH7_KCNF1_MOUSE_10090 and tr_G1SCD5_G1SCD5_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q7TSH7_KCNF1_MOUSE_10090 and tr_G3R265_G3R265_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q7TSH7_KCNF1_MOUSE_10090 and tr_H2P6Y6_H2P6Y6_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q7TSH7_KCNF1_MOUSE_10090 and tr_H2R8Z5_H2R8Z5_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q7TSH7_KCNF1_MOUSE_10090 and tr_D4ADX7_D4ADX7_RAT_10116 are exactly identical! WARNING: Sequences sp_Q7TSH7_KCNF1_MOUSE_10090 and sp_Q9H3M0_KCNF1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q7TSH7_KCNF1_MOUSE_10090 and tr_F7H076_F7H076_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q7TSH7_KCNF1_MOUSE_10090 and tr_F7H006_F7H006_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q7TSH7_KCNF1_MOUSE_10090 and tr_A0A096N9H4_A0A096N9H4_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q7TSH7_KCNF1_MOUSE_10090 and tr_A0A0D9S9T6_A0A0D9S9T6_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q7TSH7_KCNF1_MOUSE_10090 and tr_A0A2K5KW49_A0A2K5KW49_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q7TSH7_KCNF1_MOUSE_10090 and tr_A0A2K6DB08_A0A2K6DB08_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q7TSH7_KCNF1_MOUSE_10090 and tr_A0A2R9CNV2_A0A2R9CNV2_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3Y2V0_M3Y2V0_MUSPF_9669 and tr_F7BL22_F7BL22_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3Y2V0_M3Y2V0_MUSPF_9669 and tr_A0A2U3W6U1_A0A2U3W6U1_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y2V0_M3Y2V0_MUSPF_9669 and tr_A0A2U3X929_A0A2U3X929_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Y2V0_M3Y2V0_MUSPF_9669 and tr_A0A2Y9JK49_A0A2Y9JK49_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z1H2_M3Z1H2_MUSPF_9669 and tr_F1PWP7_F1PWP7_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z1H2_M3Z1H2_MUSPF_9669 and tr_A0A2Y9IPH8_A0A2Y9IPH8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_G1R5M2_G1R5M2_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_G3QVG8_G3QVG8_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A2J8SF99_A0A2J8SF99_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_G1TJT3_G1TJT3_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and sp_Q9MZ19_KCNB1_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_E2QY00_E2QY00_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A2J8MJF2_A0A2J8MJF2_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_F6T2Z2_F6T2Z2_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_W5PSR3_W5PSR3_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A287D1T8_A0A287D1T8_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_H0XY87_H0XY87_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and sp_Q14721_KCNB1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A1D5Q0L6_A0A1D5Q0L6_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_G3SYH6_G3SYH6_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_U3FAP5_U3FAP5_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_F1SBE6_F1SBE6_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and sp_O18868_KCNB1_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_G1M4P3_G1M4P3_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_E1BDC5_E1BDC5_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_M3WBK9_M3WBK9_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A096NNR7_A0A096NNR7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A2K6AZE6_A0A2K6AZE6_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A2R9ADU2_A0A2R9ADU2_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A2U4C2J2_A0A2U4C2J2_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A2U3ZT33_A0A2U3ZT33_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A2Y9DA58_A0A2Y9DA58_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A2Y9IPZ4_A0A2Y9IPZ4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A2Y9Q6K4_A0A2Y9Q6K4_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A2Y9EDU2_A0A2Y9EDU2_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3Z1J4_M3Z1J4_MUSPF_9669 and tr_A0A384ADE2_A0A384ADE2_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3Z1R9_M3Z1R9_MUSPF_9669 and tr_A0A2U3WXH5_A0A2U3WXH5_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z6Z0_M3Z6Z0_MUSPF_9669 and tr_F1PCL5_F1PCL5_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z6Z0_M3Z6Z0_MUSPF_9669 and tr_D2HH95_D2HH95_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z6Z0_M3Z6Z0_MUSPF_9669 and tr_A0A2U3W1P5_A0A2U3W1P5_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z6Z0_M3Z6Z0_MUSPF_9669 and tr_A0A2Y9KCT2_A0A2Y9KCT2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z7R2_M3Z7R2_MUSPF_9669 and tr_G1MN46_G1MN46_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z7R2_M3Z7R2_MUSPF_9669 and tr_M3WQW4_M3WQW4_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z7R2_M3Z7R2_MUSPF_9669 and tr_A0A2Y9JF10_A0A2Y9JF10_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z7R2_M3Z7R2_MUSPF_9669 and tr_A0A384BXW5_A0A384BXW5_URSMA_29073 are exactly identical! WARNING: Sequences tr_B4IYI2_B4IYI2_DROGR_7222 and tr_A0A0M3QWX0_A0A0M3QWX0_DROBS_30019 are exactly identical! WARNING: Sequences tr_B4IYI2_B4IYI2_DROGR_7222 and tr_A0A0M4EGZ5_A0A0M4EGZ5_DROBS_30019 are exactly identical! WARNING: Sequences tr_G1QKQ9_G1QKQ9_NOMLE_61853 and tr_G3QL66_G3QL66_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QKQ9_G1QKQ9_NOMLE_61853 and tr_H2QWA6_H2QWA6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QKQ9_G1QKQ9_NOMLE_61853 and sp_Q92953_KCNB2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QKQ9_G1QKQ9_NOMLE_61853 and tr_F6Q7Z0_F6Q7Z0_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QKQ9_G1QKQ9_NOMLE_61853 and tr_U3CM81_U3CM81_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1QKQ9_G1QKQ9_NOMLE_61853 and tr_A0A096MKX7_A0A096MKX7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QKQ9_G1QKQ9_NOMLE_61853 and tr_A0A2K5KVE4_A0A2K5KVE4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QKQ9_G1QKQ9_NOMLE_61853 and tr_A0A2K6DI77_A0A2K6DI77_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QKQ9_G1QKQ9_NOMLE_61853 and tr_A0A2K5ZDL1_A0A2K5ZDL1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QKQ9_G1QKQ9_NOMLE_61853 and tr_A0A2R9C703_A0A2R9C703_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1R5R7_G1R5R7_NOMLE_61853 and tr_G3QEX6_G3QEX6_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R5R7_G1R5R7_NOMLE_61853 and tr_H2P2B0_H2P2B0_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R5R7_G1R5R7_NOMLE_61853 and tr_H2R2Y3_H2R2Y3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R5R7_G1R5R7_NOMLE_61853 and sp_Q9UIX4_KCNG1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R5R7_G1R5R7_NOMLE_61853 and tr_F6Z0A7_F6Z0A7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R5R7_G1R5R7_NOMLE_61853 and tr_A0A096NNN4_A0A096NNN4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R5R7_G1R5R7_NOMLE_61853 and tr_A0A0D9RRT0_A0A0D9RRT0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R5R7_G1R5R7_NOMLE_61853 and tr_A0A2K5NDH0_A0A2K5NDH0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R5R7_G1R5R7_NOMLE_61853 and tr_A0A2K6BD18_A0A2K6BD18_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R5R7_G1R5R7_NOMLE_61853 and tr_A0A2K6A0X1_A0A2K6A0X1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1R5R7_G1R5R7_NOMLE_61853 and tr_A0A2R9AKC5_A0A2R9AKC5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RBL7_G1RBL7_NOMLE_61853 and tr_G3QDB6_G3QDB6_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RBL7_G1RBL7_NOMLE_61853 and tr_H2PS93_H2PS93_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3HB05_G3HB05_CRIGR_10029 and tr_A0A1U8CVI5_A0A1U8CVI5_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2I2YND0_A0A2I2YND0_GORGO_9595 and sp_A4K2R3_KCNS1_GORGO_9595 are exactly identical! WARNING: Sequences tr_G3QJZ2_G3QJZ2_GORGO_9595 and tr_A0A2J8UF77_A0A2J8UF77_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QJZ2_G3QJZ2_GORGO_9595 and tr_A0A2J8PMB3_A0A2J8PMB3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QJZ2_G3QJZ2_GORGO_9595 and sp_Q9ULS6_KCNS2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QJZ2_G3QJZ2_GORGO_9595 and tr_F6PWB2_F6PWB2_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QJZ2_G3QJZ2_GORGO_9595 and tr_G7PCA8_G7PCA8_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QJZ2_G3QJZ2_GORGO_9595 and tr_A0A096MPK3_A0A096MPK3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QJZ2_G3QJZ2_GORGO_9595 and tr_A0A0D9SB95_A0A0D9SB95_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QJZ2_G3QJZ2_GORGO_9595 and tr_A0A2K5KXJ8_A0A2K5KXJ8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QJZ2_G3QJZ2_GORGO_9595 and tr_A0A2K6B157_A0A2K6B157_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QJZ2_G3QJZ2_GORGO_9595 and tr_A0A2K5XFX9_A0A2K5XFX9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QJZ2_G3QJZ2_GORGO_9595 and tr_A0A2R8Z807_A0A2R8Z807_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QZG7_G3QZG7_GORGO_9595 and sp_Q5RC10_KCNV1_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QZG7_G3QZG7_GORGO_9595 and sp_Q6PIU1_KCNV1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QZG7_G3QZG7_GORGO_9595 and tr_F6YIN0_F6YIN0_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QZG7_G3QZG7_GORGO_9595 and tr_G7PCI9_G7PCI9_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QZG7_G3QZG7_GORGO_9595 and tr_A0A096N5E8_A0A096N5E8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QZG7_G3QZG7_GORGO_9595 and tr_A0A2K5LU17_A0A2K5LU17_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QZG7_G3QZG7_GORGO_9595 and tr_A0A2K6BAS7_A0A2K6BAS7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QZG7_G3QZG7_GORGO_9595 and tr_A0A2K5ZTG9_A0A2K5ZTG9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2J8V4D9_A0A2J8V4D9_PONAB_9601 and tr_A0A2J8NLN6_A0A2J8NLN6_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2J8V4D9_A0A2J8V4D9_PONAB_9601 and sp_Q9BQ31_KCNS3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8V4D9_A0A2J8V4D9_PONAB_9601 and tr_A0A2R8Z5X2_A0A2R8Z5X2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1SIB5_G1SIB5_RABIT_9986 and sp_Q95L11_KCNB2_RABIT_9986 are exactly identical! WARNING: Sequences sp_A4K2N8_KCNS1_PANTR_9598 and sp_Q96KK3_KCNS1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_A4K2N8_KCNS1_PANTR_9598 and tr_A0A2R9BES1_A0A2R9BES1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QWL3_H2QWL3_PANTR_9598 and tr_A0A2R9C7X9_A0A2R9C7X9_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5PZ34_W5PZ34_SHEEP_9940 and tr_F1MPV7_F1MPV7_BOVIN_9913 are exactly identical! WARNING: Sequences sp_O88759_KCNS3_RAT_10116 and tr_A0A1U8C746_A0A1U8C746_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A3B5QVJ9_A0A3B5QVJ9_XIPMA_8083 and tr_A0A087XE31_A0A087XE31_POEFO_48698 are exactly identical! WARNING: Sequences tr_M3ZT34_M3ZT34_XIPMA_8083 and tr_A0A087Y1Y0_A0A087Y1Y0_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4AP23_M4AP23_XIPMA_8083 and tr_I3J8N6_I3J8N6_ORENI_8128 are exactly identical! WARNING: Sequences tr_M4AP23_M4AP23_XIPMA_8083 and tr_A0A087YH09_A0A087YH09_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NTV8_A0A158NTV8_ATTCE_12957 and tr_A0A151WW01_A0A151WW01_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NTV8_A0A158NTV8_ATTCE_12957 and tr_A0A195ECZ5_A0A195ECZ5_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NTV8_A0A158NTV8_ATTCE_12957 and tr_A0A195B7G4_A0A195B7G4_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NTV8_A0A158NTV8_ATTCE_12957 and tr_A0A151IKP7_A0A151IKP7_9HYME_456900 are exactly identical! WARNING: Sequences tr_I3NAR0_I3NAR0_ICTTR_43179 and tr_H0XSK5_H0XSK5_OTOGA_30611 are exactly identical! WARNING: Sequences sp_A4K2T1_KCNS1_MACMU_9544 and tr_A0A2K6DHP6_A0A2K6DHP6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WNK5_F6WNK5_MACMU_9544 and tr_G7PSG1_G7PSG1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WNK5_F6WNK5_MACMU_9544 and tr_A0A2K6AUB3_A0A2K6AUB3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HGM9_F7HGM9_MACMU_9544 and tr_G8F573_G8F573_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HGM9_F7HGM9_MACMU_9544 and tr_A0A096NP34_A0A096NP34_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HGM9_F7HGM9_MACMU_9544 and tr_A0A0D9S9T2_A0A0D9S9T2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HGM9_F7HGM9_MACMU_9544 and tr_A0A2K5KZC2_A0A2K5KZC2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HGM9_F7HGM9_MACMU_9544 and tr_A0A2K6AT51_A0A2K6AT51_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HGM9_F7HGM9_MACMU_9544 and tr_A0A2K5XQM3_A0A2K5XQM3_MANLE_9568 are exactly identical! WARNING: Sequences tr_Q7Q6C3_Q7Q6C3_ANOGA_7165 and tr_A0A084W2K5_A0A084W2K5_ANOSI_74873 are exactly identical! WARNING: Sequences tr_H0Z1M5_H0Z1M5_TAEGU_59729 and tr_A0A218V6G3_A0A218V6G3_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZS57_H0ZS57_TAEGU_59729 and tr_A0A218VBW5_A0A218VBW5_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZSC1_H0ZSC1_TAEGU_59729 and tr_U3KKJ0_U3KKJ0_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZSC1_H0ZSC1_TAEGU_59729 and tr_A0A218VC51_A0A218VC51_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A0Q9WPB4_A0A0Q9WPB4_DROWI_7260 and tr_A0A0Q9XEJ5_A0A0Q9XEJ5_DROMO_7230 are exactly identical! WARNING: Sequences tr_A0A0N8P0W4_A0A0N8P0W4_DROAN_7217 and tr_A0A1W4VNR1_A0A1W4VNR1_DROFC_30025 are exactly identical! WARNING: Sequences tr_F1MXZ4_F1MXZ4_BOVIN_9913 and sp_Q0P583_KCNV1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G3X8A0_G3X8A0_BOVIN_9913 and sp_Q4ZHA6_KCNB2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G3X8A0_G3X8A0_BOVIN_9913 and tr_U3K1I0_U3K1I0_FICAL_59894 are exactly identical! WARNING: Sequences tr_G3X8A0_G3X8A0_BOVIN_9913 and tr_A0A2I0MVQ9_A0A2I0MVQ9_COLLI_8932 are exactly identical! WARNING: Sequences tr_G3X8A0_G3X8A0_BOVIN_9913 and tr_A0A1V4KGH8_A0A1V4KGH8_PATFA_372326 are exactly identical! WARNING: Sequences tr_G3X8A0_G3X8A0_BOVIN_9913 and tr_A0A218UQ81_A0A218UQ81_9PASE_299123 are exactly identical! WARNING: Sequences tr_G3X8A0_G3X8A0_BOVIN_9913 and tr_A0A2Y9PVV5_A0A2Y9PVV5_DELLE_9749 are exactly identical! WARNING: Sequences tr_G3X8A0_G3X8A0_BOVIN_9913 and tr_A0A2Y9F4G4_A0A2Y9F4G4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G3X8A0_G3X8A0_BOVIN_9913 and tr_A0A384ACQ7_A0A384ACQ7_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3WH41_M3WH41_FELCA_9685 and tr_A0A2Y9KWW4_A0A2Y9KWW4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3WH41_M3WH41_FELCA_9685 and tr_A0A384DPM7_A0A384DPM7_URSMA_29073 are exactly identical! WARNING: Sequences tr_U3KEQ8_U3KEQ8_FICAL_59894 and tr_A0A2I0M287_A0A2I0M287_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3KEQ8_U3KEQ8_FICAL_59894 and tr_A0A1V4KL58_A0A1V4KL58_PATFA_372326 are exactly identical! WARNING: Sequences tr_U3KEQ8_U3KEQ8_FICAL_59894 and tr_A0A218UGA4_A0A218UGA4_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3KKJ2_U3KKJ2_FICAL_59894 and tr_U3HZ15_U3HZ15_ANAPL_8839 are exactly identical! WARNING: Sequences tr_U3KKJ2_U3KKJ2_FICAL_59894 and tr_A0A091EKC0_A0A091EKC0_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3KKJ2_U3KKJ2_FICAL_59894 and tr_A0A091J4K8_A0A091J4K8_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3KKJ2_U3KKJ2_FICAL_59894 and tr_A0A093PXD5_A0A093PXD5_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3KKJ2_U3KKJ2_FICAL_59894 and tr_A0A091VGY4_A0A091VGY4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_U3KKJ2_U3KKJ2_FICAL_59894 and tr_A0A087QUR8_A0A087QUR8_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3KKJ2_U3KKJ2_FICAL_59894 and tr_A0A2I0MWQ3_A0A2I0MWQ3_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3KKJ2_U3KKJ2_FICAL_59894 and tr_A0A218UR86_A0A218UR86_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A096P1N4_A0A096P1N4_PAPAN_9555 and tr_A0A0D9R8J8_A0A0D9R8J8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096P1N4_A0A096P1N4_PAPAN_9555 and tr_A0A2K5MTV6_A0A2K5MTV6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P1N4_A0A096P1N4_PAPAN_9555 and tr_A0A2K5YL77_A0A2K5YL77_MANLE_9568 are exactly identical! WARNING: Sequences sp_A4K2M4_KCNS1_PAPAN_9555 and tr_A0A2K5MH63_A0A2K5MH63_CERAT_9531 are exactly identical! WARNING: Sequences sp_A4K2M4_KCNS1_PAPAN_9555 and tr_A0A2K5ZW50_A0A2K5ZW50_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9RR73_A0A0D9RR73_CHLSB_60711 and tr_A0A1U7U4C9_A0A1U7U4C9_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A151MY06_A0A151MY06_ALLMI_8496 and tr_A0A1U7S2G1_A0A1U7S2G1_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091JNU3_A0A091JNU3_EGRGA_188379 and tr_A0A091V3G1_A0A091V3G1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JNU3_A0A091JNU3_EGRGA_188379 and tr_A0A087QS23_A0A087QS23_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JNU3_A0A091JNU3_EGRGA_188379 and tr_A0A093HTK3_A0A093HTK3_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091JNU3_A0A091JNU3_EGRGA_188379 and tr_A0A091W3S4_A0A091W3S4_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JNU3_A0A091JNU3_EGRGA_188379 and tr_A0A0A0B192_A0A0A0B192_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JNU3_A0A091JNU3_EGRGA_188379 and tr_A0A2I0M5Z1_A0A2I0M5Z1_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091VTH9_A0A091VTH9_NIPNI_128390 and tr_A0A099ZL03_A0A099ZL03_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091VTH9_A0A091VTH9_NIPNI_128390 and tr_A0A099ZUE3_A0A099ZUE3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087QH58_A0A087QH58_APTFO_9233 and tr_A0A0A0AJA7_A0A0A0AJA7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0LSW6_A0A2I0LSW6_COLLI_8932 and tr_A0A1V4KE85_A0A1V4KE85_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0LXF7_A0A2I0LXF7_COLLI_8932 and tr_A0A1V4L1N9_A0A1V4L1N9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0M0G5_A0A2I0M0G5_COLLI_8932 and tr_A0A1V4K152_A0A1V4K152_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0M252_A0A2I0M252_COLLI_8932 and tr_A0A1V4KKW2_A0A1V4KKW2_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MTJ7_A0A2I0MTJ7_COLLI_8932 and tr_A0A1V4JN05_A0A1V4JN05_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0RN07_A0A0V0RN07_9BILA_6336 and tr_A0A0V1D0E8_A0A0V1D0E8_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RN07_A0A0V0RN07_9BILA_6336 and tr_A0A0V0X4M7_A0A0V0X4M7_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RN07_A0A0V0RN07_9BILA_6336 and tr_A0A0V0VRT5_A0A0V0VRT5_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0RN07_A0A0V0RN07_9BILA_6336 and tr_A0A0V1KWU2_A0A0V1KWU2_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0RN07_A0A0V0RN07_9BILA_6336 and tr_A0A0V0ZKN1_A0A0V0ZKN1_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0RN07_A0A0V0RN07_9BILA_6336 and tr_A0A0V0XK37_A0A0V0XK37_TRIPS_6337 are exactly identical! WARNING: Sequences tr_A0A0V0RN07_A0A0V0RN07_9BILA_6336 and tr_A0A0V1N7Y8_A0A0V1N7Y8_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V0RN07_A0A0V0RN07_9BILA_6336 and tr_A0A0V1NWA0_A0A0V1NWA0_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0RN07_A0A0V0RN07_9BILA_6336 and tr_A0A0V1HJR1_A0A0V1HJR1_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A0V0RN07_A0A0V0RN07_9BILA_6336 and tr_A0A0V0TNT7_A0A0V0TNT7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3A0A1_A0A1S3A0A1_ERIEU_9365 and tr_A0A1S3G4Z5_A0A1S3G4Z5_DIPOR_10020 are exactly identical! WARNING: Sequences tr_A0A1S3M8Z9_A0A1S3M8Z9_SALSA_8030 and tr_A0A060WEG8_A0A060WEG8_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3NNP3_A0A1S3NNP3_SALSA_8030 and tr_A0A060Y170_A0A060Y170_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1U8C538_A0A1U8C538_MESAU_10036 and sp_Q60565_KCNV1_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A226MLK8_A0A226MLK8_CALSU_9009 and tr_A0A226PMU7_A0A226PMU7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MWA8_A0A226MWA8_CALSU_9009 and tr_A0A226PWC8_A0A226PWC8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226N3F0_A0A226N3F0_CALSU_9009 and tr_A0A226PHR7_A0A226PHR7_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U3UYG2_A0A2U3UYG2_TURTR_9739 and tr_A0A2Y9LMC3_A0A2Y9LMC3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V6G1_A0A2U3V6G1_TURTR_9739 and tr_A0A2Y9NZJ9_A0A2Y9NZJ9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V6G1_A0A2U3V6G1_TURTR_9739 and tr_A0A384ANB5_A0A384ANB5_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4AJ18_A0A2U4AJ18_TURTR_9739 and tr_A0A2Y9NZG4_A0A2Y9NZG4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C1P4_A0A2U4C1P4_TURTR_9739 and tr_A0A2Y9QD31_A0A2Y9QD31_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C1P4_A0A2U4C1P4_TURTR_9739 and tr_A0A384ADA9_A0A384ADA9_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3ZIS8_A0A2U3ZIS8_ODORO_9708 and tr_A0A2U3XFN7_A0A2U3XFN7_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 218 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/Q8TDN2/3_mltree/Q8TDN2.raxml.reduced.phy Alignment comprises 1 partitions and 339 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 339 / 339 Gaps: 0.46 % Invariant sites: 4.42 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDN2/3_mltree/Q8TDN2.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 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 339 / 27120 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -523365.061084] Initial branch length optimization [00:00:12 -433734.529680] Model parameter optimization (eps = 10.000000) [00:01:17 -431927.808793] AUTODETECT spr round 1 (radius: 5) [00:04:50 -222107.787648] AUTODETECT spr round 2 (radius: 10) [00:08:33 -150869.551492] AUTODETECT spr round 3 (radius: 15) [00:12:37 -112209.159301] AUTODETECT spr round 4 (radius: 20) [00:16:59 -92568.644618] AUTODETECT spr round 5 (radius: 25) [00:22:04 -80378.911691] SPR radius for FAST iterations: 25 (autodetect) [00:22:04 -80378.911691] Model parameter optimization (eps = 3.000000) [00:22:42 -80252.166480] FAST spr round 1 (radius: 25) [00:26:11 -63344.128241] FAST spr round 2 (radius: 25) [00:28:44 -61343.940892] FAST spr round 3 (radius: 25) [00:30:50 -61272.181270] FAST spr round 4 (radius: 25) [00:32:44 -61264.718212] FAST spr round 5 (radius: 25) [00:34:28 -61264.718148] Model parameter optimization (eps = 1.000000) [00:34:44 -61262.554630] SLOW spr round 1 (radius: 5) [00:37:14 -61251.994334] SLOW spr round 2 (radius: 5) [00:39:37 -61251.993161] SLOW spr round 3 (radius: 10) [00:42:05 -61251.594609] SLOW spr round 4 (radius: 5) [00:45:16 -61251.594604] SLOW spr round 5 (radius: 10) [00:48:10 -61251.594603] SLOW spr round 6 (radius: 15) [00:52:09 -61251.594602] SLOW spr round 7 (radius: 20) [00:59:23 -61251.594601] SLOW spr round 8 (radius: 25) [01:06:03] [worker #4] ML tree search #5, logLikelihood: -61271.384112 [01:07:55] [worker #2] ML tree search #3, logLikelihood: -61242.940450 [01:10:01 -61251.594600] Model parameter optimization (eps = 0.100000) [01:10:07] [worker #0] ML tree search #1, logLikelihood: -61251.580059 [01:10:07 -530339.021351] Initial branch length optimization [01:10:20 -439407.554481] Model parameter optimization (eps = 10.000000) [01:11:23 -437674.409692] AUTODETECT spr round 1 (radius: 5) [01:13:45] [worker #3] ML tree search #4, logLikelihood: -61234.571871 [01:15:13 -224490.923613] AUTODETECT spr round 2 (radius: 10) [01:17:57] [worker #1] ML tree search #2, logLikelihood: -61242.630512 [01:19:12 -140522.030064] AUTODETECT spr round 3 (radius: 15) [01:23:34 -104011.266664] AUTODETECT spr round 4 (radius: 20) [01:28:15 -88326.825733] AUTODETECT spr round 5 (radius: 25) [01:34:36 -78719.664286] SPR radius for FAST iterations: 25 (autodetect) [01:34:36 -78719.664286] Model parameter optimization (eps = 3.000000) [01:35:03 -78613.598694] FAST spr round 1 (radius: 25) [01:38:16 -62848.169097] FAST spr round 2 (radius: 25) [01:40:28 -61370.725979] FAST spr round 3 (radius: 25) [01:42:31 -61280.044461] FAST spr round 4 (radius: 25) [01:44:28 -61267.214053] FAST spr round 5 (radius: 25) [01:46:13 -61265.658649] FAST spr round 6 (radius: 25) [01:47:55 -61265.658641] Model parameter optimization (eps = 1.000000) [01:48:05 -61264.275753] SLOW spr round 1 (radius: 5) [01:50:34 -61245.092791] SLOW spr round 2 (radius: 5) [01:53:00 -61242.234774] SLOW spr round 3 (radius: 5) [01:55:21 -61242.234768] SLOW spr round 4 (radius: 10) [01:57:49 -61241.125785] SLOW spr round 5 (radius: 5) [02:00:53 -61241.125714] SLOW spr round 6 (radius: 10) [02:03:45 -61241.125712] SLOW spr round 7 (radius: 15) [02:07:46 -61241.125710] SLOW spr round 8 (radius: 20) [02:15:23 -61241.125709] SLOW spr round 9 (radius: 25) [02:15:34] [worker #4] ML tree search #10, logLikelihood: -61255.714150 [02:18:14] [worker #2] ML tree search #8, logLikelihood: -61244.786189 [02:21:19] [worker #3] ML tree search #9, logLikelihood: -61264.899144 [02:26:35 -61241.125707] Model parameter optimization (eps = 0.100000) [02:26:42] [worker #0] ML tree search #6, logLikelihood: -61241.112706 [02:26:42 -524457.709604] Initial branch length optimization [02:26:54 -436394.072430] Model parameter optimization (eps = 10.000000) [02:27:56 -434705.277253] AUTODETECT spr round 1 (radius: 5) [02:31:42 -217624.129128] AUTODETECT spr round 2 (radius: 10) [02:35:29 -146680.304822] AUTODETECT spr round 3 (radius: 15) [02:36:57] [worker #1] ML tree search #7, logLikelihood: -61249.600394 [02:39:24 -106677.001402] AUTODETECT spr round 4 (radius: 20) [02:44:19 -84781.656337] AUTODETECT spr round 5 (radius: 25) [02:50:45 -75841.253250] SPR radius for FAST iterations: 25 (autodetect) [02:50:45 -75841.253250] Model parameter optimization (eps = 3.000000) [02:51:13 -75733.659095] FAST spr round 1 (radius: 25) [02:54:18 -62744.456578] FAST spr round 2 (radius: 25) [02:56:40 -61472.350910] FAST spr round 3 (radius: 25) [02:58:50 -61283.049252] FAST spr round 4 (radius: 25) [03:00:46 -61273.877827] FAST spr round 5 (radius: 25) [03:02:31 -61272.417299] FAST spr round 6 (radius: 25) [03:04:13 -61272.417296] Model parameter optimization (eps = 1.000000) [03:04:28 -61268.832099] SLOW spr round 1 (radius: 5) [03:06:59 -61250.858191] SLOW spr round 2 (radius: 5) [03:09:24 -61250.858081] SLOW spr round 3 (radius: 10) [03:11:52 -61250.513429] SLOW spr round 4 (radius: 5) [03:15:02 -61250.513427] SLOW spr round 5 (radius: 10) [03:17:52 -61250.513426] SLOW spr round 6 (radius: 15) [03:21:48 -61250.513426] SLOW spr round 7 (radius: 20) [03:23:57] [worker #4] ML tree search #15, logLikelihood: -61246.776999 [03:28:40 -61250.513426] SLOW spr round 8 (radius: 25) [03:35:22] [worker #3] ML tree search #14, logLikelihood: -61234.121470 [03:38:33 -61250.513426] Model parameter optimization (eps = 0.100000) [03:38:45] [worker #0] ML tree search #11, logLikelihood: -61250.372139 [03:38:45 -527925.616687] Initial branch length optimization [03:38:53 -436690.190868] Model parameter optimization (eps = 10.000000) [03:39:52 -434818.391610] AUTODETECT spr round 1 (radius: 5) [03:42:25] [worker #2] ML tree search #13, logLikelihood: -61231.246361 [03:43:34 -208703.402404] AUTODETECT spr round 2 (radius: 10) [03:44:54] [worker #1] ML tree search #12, logLikelihood: -61235.009600 [03:47:14 -136337.637618] AUTODETECT spr round 3 (radius: 15) [03:51:12 -100926.596451] AUTODETECT spr round 4 (radius: 20) [03:55:08 -89110.913410] AUTODETECT spr round 5 (radius: 25) [03:59:48 -79572.687808] SPR radius for FAST iterations: 25 (autodetect) [03:59:48 -79572.687808] Model parameter optimization (eps = 3.000000) [04:00:18 -79468.813203] FAST spr round 1 (radius: 25) [04:03:41 -65031.480755] FAST spr round 2 (radius: 25) [04:06:12 -61746.169577] FAST spr round 3 (radius: 25) [04:08:21 -61438.497708] FAST spr round 4 (radius: 25) [04:10:15 -61312.256470] FAST spr round 5 (radius: 25) [04:11:56 -61267.373278] FAST spr round 6 (radius: 25) [04:13:32 -61267.373269] Model parameter optimization (eps = 1.000000) [04:13:47 -61263.745869] SLOW spr round 1 (radius: 5) [04:16:07 -61248.446408] SLOW spr round 2 (radius: 5) [04:18:22 -61248.445622] SLOW spr round 3 (radius: 10) [04:20:41 -61248.386069] SLOW spr round 4 (radius: 15) [04:24:44 -61244.968976] SLOW spr round 5 (radius: 5) [04:27:58 -61244.968924] SLOW spr round 6 (radius: 10) [04:30:52 -61244.968923] SLOW spr round 7 (radius: 15) [04:32:40] [worker #4] ML tree search #20, logLikelihood: -61249.775976 [04:34:50 -61244.968922] SLOW spr round 8 (radius: 20) [04:42:20 -61244.968922] SLOW spr round 9 (radius: 25) [04:46:30] [worker #3] ML tree search #19, logLikelihood: -61240.281574 [04:51:45] [worker #2] ML tree search #18, logLikelihood: -61258.009713 [04:52:58 -61244.968921] Model parameter optimization (eps = 0.100000) [04:53:04] [worker #0] ML tree search #16, logLikelihood: -61244.955473 [04:54:15] [worker #1] ML tree search #17, logLikelihood: -61248.666598 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.304236,0.329251) (0.349435,0.647564) (0.256039,1.622826) (0.090290,2.857918) 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: -61231.246361 AIC score: 126472.492723 / AICc score: 8170532.492723 / BIC score: 134143.622938 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=339). 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/Q8TDN2/3_mltree/Q8TDN2.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDN2/3_mltree/Q8TDN2.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDN2/3_mltree/Q8TDN2.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TDN2/3_mltree/Q8TDN2.raxml.log Analysis started: 07-Jul-2021 11:30:16 / finished: 07-Jul-2021 16:24:32 Elapsed time: 17656.010 seconds Consumed energy: 1174.628 Wh (= 6 km in an electric car, or 29 km with an e-scooter!)