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 26-Jul-2021 00:10:20 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O14921/2_msa/O14921_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O14921/3_mltree/O14921 --seed 2 --threads 3 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (3 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O14921/2_msa/O14921_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 125 sites WARNING: Sequences tr_A0A0R4IJB7_A0A0R4IJB7_DANRE_7955 and tr_A0A2R8PVQ0_A0A2R8PVQ0_DANRE_7955 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and sp_Q9PWA1_RGS20_CHICK_9031 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_G1NEJ7_G1NEJ7_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_H0ZL75_H0ZL75_TAEGU_59729 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_A0A091EDE4_A0A091EDE4_CORBR_85066 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_A0A093S9Y4_A0A093S9Y4_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_A0A091VSR7_A0A091VSR7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_A0A087QKH3_A0A087QKH3_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_A0A099YWE7_A0A099YWE7_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_A0A091FNX2_A0A091FNX2_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_A0A0A0ARX1_A0A0A0ARX1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_A0A2I0MX71_A0A2I0MX71_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_A0A093GKF2_A0A093GKF2_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_A0A1V4KG86_A0A1V4KG86_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_A0A218VBR3_A0A218VBR3_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_A0A226MML8_A0A226MML8_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5NV29_A0A1D5NV29_CHICK_9031 and tr_A0A226NZB5_A0A226NZB5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A1D5PGN5_A0A1D5PGN5_CHICK_9031 and tr_G1MWD9_G1MWD9_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NJM4_F1NJM4_CHICK_9031 and tr_G1N4B4_G1N4B4_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NJM4_F1NJM4_CHICK_9031 and tr_A0A226NJH7_A0A226NJH7_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NJM4_F1NJM4_CHICK_9031 and tr_A0A226PG13_A0A226PG13_COLVI_9014 are exactly identical! WARNING: Sequences tr_F1NLK8_F1NLK8_CHICK_9031 and tr_A0A226NGA6_A0A226NGA6_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NLK8_F1NLK8_CHICK_9031 and tr_A0A226PMJ8_A0A226PMJ8_COLVI_9014 are exactly identical! WARNING: Sequences tr_Q7ZZS5_Q7ZZS5_CHICK_9031 and tr_A0A226MMD7_A0A226MMD7_CALSU_9009 are exactly identical! WARNING: Sequences tr_R4GKX0_R4GKX0_CHICK_9031 and tr_G1N104_G1N104_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q9QZB1_RGS20_MOUSE_10090 and tr_G3V716_G3V716_RAT_10116 are exactly identical! WARNING: Sequences tr_M3XXC2_M3XXC2_MUSPF_9669 and tr_J9P4G6_J9P4G6_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3XXC2_M3XXC2_MUSPF_9669 and tr_G1L3M1_G1L3M1_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XXC2_M3XXC2_MUSPF_9669 and tr_M3X000_M3X000_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XXC2_M3XXC2_MUSPF_9669 and tr_A0A2U3W5U5_A0A2U3W5U5_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XXC2_M3XXC2_MUSPF_9669 and tr_A0A2U3XSY9_A0A2U3XSY9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XXC2_M3XXC2_MUSPF_9669 and tr_A0A2Y9K4F0_A0A2Y9K4F0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XXC2_M3XXC2_MUSPF_9669 and tr_A0A384BNT9_A0A384BNT9_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_G1S8T4_G1S8T4_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_G3QJV6_G3QJV6_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_F1PUM1_F1PUM1_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_H2Q0T4_H2Q0T4_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and sp_P41220_RGS2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_F7HBZ1_F7HBZ1_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_D2HM07_D2HM07_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_G7NXE1_G7NXE1_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_M3X7Y3_M3X7Y3_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_A0A096N0C5_A0A096N0C5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_A0A0D9RLP3_A0A0D9RLP3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_A0A1S3AS57_A0A1S3AS57_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_A0A1U7SRF3_A0A1U7SRF3_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_A0A2K5MUH8_A0A2K5MUH8_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_A0A2K6C5Z9_A0A2K6C5Z9_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_A0A2K5YJ23_A0A2K5YJ23_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_A0A2R9BEH1_A0A2R9BEH1_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_A0A2Y9JUI5_A0A2Y9JUI5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XZI6_M3XZI6_MUSPF_9669 and tr_A0A384BMT3_A0A384BMT3_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3Y991_M3Y991_MUSPF_9669 and tr_A0A2Y9J676_A0A2Y9J676_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YGV8_M3YGV8_MUSPF_9669 and tr_A0A2U3YPW3_A0A2U3YPW3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YGV8_M3YGV8_MUSPF_9669 and tr_A0A2Y9KDW7_A0A2Y9KDW7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YJE0_M3YJE0_MUSPF_9669 and tr_A0A2Y9JTJ6_A0A2Y9JTJ6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_J9PBM8_J9PBM8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_F6VQD2_F6VQD2_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_W5QCH6_W5QCH6_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A287DDG4_A0A287DDG4_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_H0XUD4_H0XUD4_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A286XN90_A0A286XN90_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A1D5Q1N3_A0A1D5Q1N3_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_G3SLJ3_G3SLJ3_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_F7HSZ2_F7HSZ2_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A287BNH7_A0A287BNH7_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_G1LMI3_G1LMI3_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_G7NXH0_G7NXH0_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_G3MX08_G3MX08_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A337RZC9_A0A337RZC9_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A2I3LN50_A0A2I3LN50_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A091CTS2_A0A091CTS2_FUKDA_885580 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A0D9RJB9_A0A0D9RJB9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A1S3WEZ8_A0A1S3WEZ8_ERIEU_9365 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A1S3F4R6_A0A1S3F4R6_DIPOR_10020 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A1U7UV01_A0A1U7UV01_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A1U8C2N5_A0A1U8C2N5_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A2K5KNB7_A0A2K5KNB7_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A2K6APU2_A0A2K6APU2_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A2K5YHA6_A0A2K5YHA6_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A2U3V4Q2_A0A2U3V4Q2_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A2U3VP56_A0A2U3VP56_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A2Y9DF27_A0A2Y9DF27_TRIMA_127582 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A2Y9JTT2_A0A2Y9JTT2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A2Y9PQ57_A0A2Y9PQ57_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A2Y9EZN4_A0A2Y9EZN4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A384CXY6_A0A384CXY6_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YJE1_M3YJE1_MUSPF_9669 and tr_A0A383ZK56_A0A383ZK56_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2I3GPA0_A0A2I3GPA0_NOMLE_61853 and tr_H2N4C6_H2N4C6_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3HXU4_A0A2I3HXU4_NOMLE_61853 and tr_H2N4Y3_H2N4Y3_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3HXU4_A0A2I3HXU4_NOMLE_61853 and sp_O15539_RGS5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3HXU4_A0A2I3HXU4_NOMLE_61853 and tr_F7AV38_F7AV38_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3HXU4_A0A2I3HXU4_NOMLE_61853 and tr_A0A096MQH7_A0A096MQH7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HXU4_A0A2I3HXU4_NOMLE_61853 and tr_A0A2K5N1B9_A0A2K5N1B9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3HXU4_A0A2I3HXU4_NOMLE_61853 and tr_A0A2K6AV82_A0A2K6AV82_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3HXU4_A0A2I3HXU4_NOMLE_61853 and tr_A0A2K5Z722_A0A2K5Z722_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3HXU4_A0A2I3HXU4_NOMLE_61853 and tr_A0A2R9ANE1_A0A2R9ANE1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RX06_G1RX06_NOMLE_61853 and tr_G3R6X0_G3R6X0_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RX06_G1RX06_NOMLE_61853 and tr_H2Q0H9_H2Q0H9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RX06_G1RX06_NOMLE_61853 and sp_P49798_RGS4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RX06_G1RX06_NOMLE_61853 and tr_F7CYN6_F7CYN6_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RX06_G1RX06_NOMLE_61853 and tr_G7NU20_G7NU20_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RX06_G1RX06_NOMLE_61853 and tr_A0A0D9RE39_A0A0D9RE39_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RX06_G1RX06_NOMLE_61853 and tr_A0A2K5LBR7_A0A2K5LBR7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RX06_G1RX06_NOMLE_61853 and tr_A0A2K6BXM7_A0A2K6BXM7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RX06_G1RX06_NOMLE_61853 and tr_A0A2R9ANC1_A0A2R9ANC1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3H4N6_G3H4N6_CRIGR_10029 and sp_Q9JHX0_RGS2_RAT_10116 are exactly identical! WARNING: Sequences tr_G3H4N6_G3H4N6_CRIGR_10029 and tr_A0A1U7QUU0_A0A1U7QUU0_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3HHZ5_G3HHZ5_CRIGR_10029 and tr_A0A3Q0CYD6_A0A3Q0CYD6_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3IBS8_G3IBS8_CRIGR_10029 and tr_A0A3Q0CXU3_A0A3Q0CXU3_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2I2Y2A0_A0A2I2Y2A0_GORGO_9595 and tr_H2N4F7_H2N4F7_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2Y2A0_A0A2I2Y2A0_GORGO_9595 and tr_A0A2I3TN73_A0A2I3TN73_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Y2A0_A0A2I2Y2A0_GORGO_9595 and sp_P57771_RGS8_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Y2A0_A0A2I2Y2A0_GORGO_9595 and tr_A0A2R9AQ01_A0A2R9AQ01_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2YDL9_A0A2I2YDL9_GORGO_9595 and tr_A0A2I3TAE7_A0A2I3TAE7_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YDL9_A0A2I2YDL9_GORGO_9595 and tr_A0A2R9BTC1_A0A2R9BTC1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QFH9_G3QFH9_GORGO_9595 and tr_A0A2I3SRD3_A0A2I3SRD3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QFH9_G3QFH9_GORGO_9595 and sp_Q08116_RGS1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QFH9_G3QFH9_GORGO_9595 and tr_A0A2R8ZTY0_A0A2R8ZTY0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QGB7_G3QGB7_GORGO_9595 and tr_H2PQB0_H2PQB0_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QGB7_G3QGB7_GORGO_9595 and tr_A0A2I3RBJ2_A0A2I3RBJ2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QGB7_G3QGB7_GORGO_9595 and sp_O76081_RGS20_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QGB7_G3QGB7_GORGO_9595 and tr_F6Q4N5_F6Q4N5_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QGB7_G3QGB7_GORGO_9595 and tr_G7PBU5_G7PBU5_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QGB7_G3QGB7_GORGO_9595 and tr_A0A2I3LYC1_A0A2I3LYC1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QGB7_G3QGB7_GORGO_9595 and tr_A0A0D9RQB2_A0A0D9RQB2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QGB7_G3QGB7_GORGO_9595 and tr_A0A2K5MFM7_A0A2K5MFM7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QGB7_G3QGB7_GORGO_9595 and tr_A0A2K6DPY8_A0A2K6DPY8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QGB7_G3QGB7_GORGO_9595 and tr_A0A2K5ZMA7_A0A2K5ZMA7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QGB7_G3QGB7_GORGO_9595 and tr_A0A2R9B0K3_A0A2R9B0K3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QH15_G3QH15_GORGO_9595 and tr_A0A2J8N697_A0A2J8N697_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QH15_G3QH15_GORGO_9595 and sp_O14921_RGS13_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QH15_G3QH15_GORGO_9595 and tr_A0A2R9CGM8_A0A2R9CGM8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QJL0_G3QJL0_GORGO_9595 and tr_H2Q0Q7_H2Q0Q7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QJL0_G3QJL0_GORGO_9595 and tr_A0A2R8ZDD3_A0A2R8ZDD3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QYV3_G3QYV3_GORGO_9595 and tr_H2PT50_H2PT50_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QYV3_G3QYV3_GORGO_9595 and tr_H2R051_H2R051_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QYV3_G3QYV3_GORGO_9595 and sp_P49796_RGS3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QYV3_G3QYV3_GORGO_9595 and tr_F7GWH7_F7GWH7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QYV3_G3QYV3_GORGO_9595 and tr_A0A096P0T4_A0A096P0T4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QYV3_G3QYV3_GORGO_9595 and tr_A0A0D9RJC7_A0A0D9RJC7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QYV3_G3QYV3_GORGO_9595 and tr_A0A2K5P268_A0A2K5P268_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QYV3_G3QYV3_GORGO_9595 and tr_A0A2K6DWZ2_A0A2K6DWZ2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QYV3_G3QYV3_GORGO_9595 and tr_A0A2K6A254_A0A2K6A254_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QYV3_G3QYV3_GORGO_9595 and tr_A0A2R9B0Z8_A0A2R9B0Z8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0A0MXL6_A0A0A0MXL6_PONAB_9601 and sp_Q5R747_RGS4_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1SUS3_G1SUS3_RABIT_9986 and tr_H0X3K9_H0X3K9_OTOGA_30611 are exactly identical! WARNING: Sequences tr_F1PYR0_F1PYR0_CANLF_9615 and tr_F6R2M9_F6R2M9_CALJA_9483 are exactly identical! WARNING: Sequences tr_F1PYR0_F1PYR0_CANLF_9615 and tr_G1M2S6_G1M2S6_AILME_9646 are exactly identical! WARNING: Sequences tr_F1PYR0_F1PYR0_CANLF_9615 and tr_L5KA41_L5KA41_PTEAL_9402 are exactly identical! WARNING: Sequences tr_F1PYR0_F1PYR0_CANLF_9615 and tr_A0A1U7TP16_A0A1U7TP16_TARSY_1868482 are exactly identical! WARNING: Sequences tr_F1PYR0_F1PYR0_CANLF_9615 and tr_A0A2U3VPG4_A0A2U3VPG4_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1PYR0_F1PYR0_CANLF_9615 and tr_A0A2U3Z2L0_A0A2U3Z2L0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_F1PYR0_F1PYR0_CANLF_9615 and tr_A0A384DGS0_A0A384DGS0_URSMA_29073 are exactly identical! WARNING: Sequences tr_F7AWM3_F7AWM3_HORSE_9796 and tr_H0X7G7_H0X7G7_OTOGA_30611 are exactly identical! WARNING: Sequences tr_F7AWM3_F7AWM3_HORSE_9796 and tr_A0A3Q0EKV2_A0A3Q0EKV2_TARSY_1868482 are exactly identical! WARNING: Sequences tr_F7AWM3_F7AWM3_HORSE_9796 and tr_A0A2U4B2T4_A0A2U4B2T4_TURTR_9739 are exactly identical! WARNING: Sequences tr_F7AWM3_F7AWM3_HORSE_9796 and tr_A0A2Y9MIX2_A0A2Y9MIX2_DELLE_9749 are exactly identical! WARNING: Sequences tr_W5P890_W5P890_SHEEP_9940 and tr_F1SN85_F1SN85_PIG_9823 are exactly identical! WARNING: Sequences tr_W5P890_W5P890_SHEEP_9940 and tr_F1MM15_F1MM15_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5P890_W5P890_SHEEP_9940 and tr_A0A2U4C8Y3_A0A2U4C8Y3_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5P890_W5P890_SHEEP_9940 and tr_A0A2Y9NKW2_A0A2Y9NKW2_DELLE_9749 are exactly identical! WARNING: Sequences tr_W5P890_W5P890_SHEEP_9940 and tr_A0A383ZSX8_A0A383ZSX8_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A3B5QWU3_A0A3B5QWU3_XIPMA_8083 and tr_A0A2I4DB45_A0A2I4DB45_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A3B5R863_A0A3B5R863_XIPMA_8083 and tr_A0A087XCJ5_A0A087XCJ5_POEFO_48698 are exactly identical! WARNING: Sequences tr_I3KCP9_I3KCP9_ORENI_8128 and tr_A0A087YPM6_A0A087YPM6_POEFO_48698 are exactly identical! WARNING: Sequences tr_I3M112_I3M112_ICTTR_43179 and tr_A0A286X7Q8_A0A286X7Q8_CAVPO_10141 are exactly identical! WARNING: Sequences tr_I3M112_I3M112_ICTTR_43179 and tr_G5ASG7_G5ASG7_HETGA_10181 are exactly identical! WARNING: Sequences tr_I3M112_I3M112_ICTTR_43179 and tr_A0A091CV20_A0A091CV20_FUKDA_885580 are exactly identical! WARNING: Sequences tr_F6W5V5_F6W5V5_MACMU_9544 and tr_G7NXH1_G7NXH1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6W5V5_F6W5V5_MACMU_9544 and tr_A0A2K5NU34_A0A2K5NU34_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6W5V5_F6W5V5_MACMU_9544 and tr_A0A2K6CVY5_A0A2K6CVY5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6W5V5_F6W5V5_MACMU_9544 and tr_A0A2K6A6Q6_A0A2K6A6Q6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5B200_G5B200_HETGA_10181 and tr_A0A091D3V1_A0A091D3V1_FUKDA_885580 are exactly identical! WARNING: Sequences tr_G3UCJ3_G3UCJ3_LOXAF_9785 and tr_A0A2Y9DWS1_A0A2Y9DWS1_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0YWJ5_H0YWJ5_TAEGU_59729 and tr_A0A091FMZ3_A0A091FMZ3_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0YWJ5_H0YWJ5_TAEGU_59729 and tr_A0A093Q8L9_A0A093Q8L9_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0YWJ5_H0YWJ5_TAEGU_59729 and tr_A0A091ULL3_A0A091ULL3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0YWJ5_H0YWJ5_TAEGU_59729 and tr_A0A091G0P3_A0A091G0P3_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0YWJ5_H0YWJ5_TAEGU_59729 and tr_A0A0A0AU70_A0A0A0AU70_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0YWJ5_H0YWJ5_TAEGU_59729 and tr_A0A091IC83_A0A091IC83_CALAN_9244 are exactly identical! WARNING: Sequences tr_H1A403_H1A403_TAEGU_59729 and tr_A0A091F3J6_A0A091F3J6_CORBR_85066 are exactly identical! WARNING: Sequences tr_H1A403_H1A403_TAEGU_59729 and tr_A0A218V4P5_A0A218V4P5_9PASE_299123 are exactly identical! WARNING: Sequences tr_H1A405_H1A405_TAEGU_59729 and tr_A0A093PW96_A0A093PW96_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A1B8Y5H4_A0A1B8Y5H4_XENTR_8364 and tr_Q66IM3_Q66IM3_XENTR_8364 are exactly identical! WARNING: Sequences tr_G7NXE2_G7NXE2_MACFA_9541 and tr_A0A2K6DH83_A0A2K6DH83_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NXE3_G7NXE3_MACFA_9541 and tr_A0A096NQB3_A0A096NQB3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NXE3_G7NXE3_MACFA_9541 and tr_A0A0D9RLN6_A0A0D9RLN6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7NXE3_G7NXE3_MACFA_9541 and tr_A0A2K6CZI9_A0A2K6CZI9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NXE3_G7NXE3_MACFA_9541 and tr_A0A2K5YYZ2_A0A2K5YYZ2_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7NXE4_G7NXE4_MACFA_9541 and tr_A0A2I3N5Q6_A0A2I3N5Q6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NXE4_G7NXE4_MACFA_9541 and tr_A0A2K5LHE4_A0A2K5LHE4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7NXE4_G7NXE4_MACFA_9541 and tr_A0A2K5YRC2_A0A2K5YRC2_MANLE_9568 are exactly identical! WARNING: Sequences tr_F1N3V3_F1N3V3_BOVIN_9913 and tr_L5KB73_L5KB73_PTEAL_9402 are exactly identical! WARNING: Sequences tr_F1N3V3_F1N3V3_BOVIN_9913 and tr_A0A2U4A4Z7_A0A2U4A4Z7_TURTR_9739 are exactly identical! WARNING: Sequences tr_F1N3V3_F1N3V3_BOVIN_9913 and tr_A0A2Y9NIW5_A0A2Y9NIW5_DELLE_9749 are exactly identical! WARNING: Sequences tr_F1N3V3_F1N3V3_BOVIN_9913 and tr_A0A2Y9T6G2_A0A2Y9T6G2_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G3N180_G3N180_BOVIN_9913 and sp_Q29RM9_RGS4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_U3JLE8_U3JLE8_FICAL_59894 and tr_A0A091EIP7_A0A091EIP7_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3JLF6_U3JLF6_FICAL_59894 and tr_A0A218V498_A0A218V498_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3K6Y9_U3K6Y9_FICAL_59894 and tr_A0A091EUB2_A0A091EUB2_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3K6Y9_U3K6Y9_FICAL_59894 and tr_A0A093PKK0_A0A093PKK0_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3IEQ0_U3IEQ0_ANAPL_8839 and tr_A0A2I0M5U6_A0A2I0M5U6_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3IEQ0_U3IEQ0_ANAPL_8839 and tr_A0A1V4KKJ9_A0A1V4KKJ9_PATFA_372326 are exactly identical! WARNING: Sequences tr_U3IQ03_U3IQ03_ANAPL_8839 and tr_A0A091JN05_A0A091JN05_EGRGA_188379 are exactly identical! WARNING: Sequences tr_U3IQ03_U3IQ03_ANAPL_8839 and tr_A0A091UY85_A0A091UY85_NIPNI_128390 are exactly identical! WARNING: Sequences tr_U3IQ03_U3IQ03_ANAPL_8839 and tr_A0A0A0B2H7_A0A0A0B2H7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0D9RLN8_A0A0D9RLN8_CHLSB_60711 and tr_A0A2K5NAR0_A0A2K5NAR0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9RLN8_A0A0D9RLN8_CHLSB_60711 and tr_A0A2K6ABX2_A0A2K6ABX2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151MI38_A0A151MI38_ALLMI_8496 and tr_A0A1U7RNJ1_A0A1U7RNJ1_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151MI40_A0A151MI40_ALLMI_8496 and tr_A0A1U7RVB7_A0A1U7RVB7_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NTF3_A0A151NTF3_ALLMI_8496 and tr_A0A1U7R7R4_A0A1U7R7R4_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0Q3PCF0_A0A0Q3PCF0_AMAAE_12930 and tr_A0A093Q242_A0A093Q242_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A0Q3PCF0_A0A0Q3PCF0_AMAAE_12930 and tr_A0A091VZM5_A0A091VZM5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A0Q3PCF0_A0A0Q3PCF0_AMAAE_12930 and tr_A0A2I0ME07_A0A2I0ME07_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A0Q3PCF0_A0A0Q3PCF0_AMAAE_12930 and tr_A0A1V4JYA2_A0A1V4JYA2_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A091UW98_A0A091UW98_NIPNI_128390 and tr_A0A087QVK4_A0A087QVK4_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UW98_A0A091UW98_NIPNI_128390 and tr_A0A099YYK4_A0A099YYK4_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091UW98_A0A091UW98_NIPNI_128390 and tr_A0A091GM67_A0A091GM67_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091UW98_A0A091UW98_NIPNI_128390 and tr_A0A2I0MBS7_A0A2I0MBS7_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091UW98_A0A091UW98_NIPNI_128390 and tr_A0A1V4JXG1_A0A1V4JXG1_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A087RDT5_A0A087RDT5_APTFO_9233 and tr_A0A091XNA2_A0A091XNA2_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A2I0LT11_A0A2I0LT11_COLLI_8932 and tr_A0A1V4J6T6_A0A1V4J6T6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MBS4_A0A2I0MBS4_COLLI_8932 and tr_A0A1V4JXG4_A0A1V4JXG4_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3KZS6_A0A1S3KZS6_SALSA_8030 and tr_A0A1S3LDZ1_A0A1S3LDZ1_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3KZS6_A0A1S3KZS6_SALSA_8030 and tr_A0A060XQ95_A0A060XQ95_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3PA83_A0A1S3PA83_SALSA_8030 and tr_A0A060YNN9_A0A060YNN9_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226MR81_A0A226MR81_CALSU_9009 and tr_A0A226PXR6_A0A226PXR6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NGA1_A0A226NGA1_CALSU_9009 and tr_A0A226PW78_A0A226PW78_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PN17_A0A2D0PN17_ICTPU_7998 and tr_A0A2D0PPQ6_A0A2D0PPQ6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SIZ7_A0A2D0SIZ7_ICTPU_7998 and tr_A0A2D0SIZ9_A0A2D0SIZ9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SIZ7_A0A2D0SIZ7_ICTPU_7998 and tr_A0A2D0SJ02_A0A2D0SJ02_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SIZ7_A0A2D0SIZ7_ICTPU_7998 and tr_A0A2D0SJ04_A0A2D0SJ04_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SIZ7_A0A2D0SIZ7_ICTPU_7998 and tr_A0A2D0SJK7_A0A2D0SJK7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SIZ7_A0A2D0SIZ7_ICTPU_7998 and tr_A0A2D0SJL3_A0A2D0SJL3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3V1X1_A0A2U3V1X1_TURTR_9739 and tr_A0A2Y9NYV5_A0A2Y9NYV5_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V6V0_A0A2U3V6V0_TURTR_9739 and tr_A0A2Y9NPV0_A0A2Y9NPV0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V735_A0A2U3V735_TURTR_9739 and tr_A0A2Y9NPU5_A0A2Y9NPU5_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V9G9_A0A2U3V9G9_TURTR_9739 and tr_A0A2Y9PUX7_A0A2Y9PUX7_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3X368_A0A2U3X368_ODORO_9708 and tr_A0A2U3XAH0_A0A2U3XAH0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3X3G8_A0A2U3X3G8_ODORO_9708 and tr_A0A384BMT0_A0A384BMT0_URSMA_29073 are exactly identical! WARNING: Duplicate sequences found: 241 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O14921/3_mltree/O14921.raxml.reduced.phy Alignment comprises 1 partitions and 125 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 125 / 125 Gaps: 0.28 % Invariant sites: 1.60 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O14921/3_mltree/O14921.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 125 / 10000 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -180206.449990] Initial branch length optimization [00:00:06 -156227.379026] Model parameter optimization (eps = 10.000000) [00:01:02 -155491.378434] AUTODETECT spr round 1 (radius: 5) [00:04:58 -95079.709682] AUTODETECT spr round 2 (radius: 10) [00:09:06 -61902.594042] AUTODETECT spr round 3 (radius: 15) [00:13:27 -49039.341873] AUTODETECT spr round 4 (radius: 20) [00:18:24 -43604.559115] AUTODETECT spr round 5 (radius: 25) [00:24:54 -41971.161507] SPR radius for FAST iterations: 25 (autodetect) [00:24:54 -41971.161507] Model parameter optimization (eps = 3.000000) [00:25:31 -41946.432462] FAST spr round 1 (radius: 25) [00:29:04 -34716.923204] FAST spr round 2 (radius: 25) [00:31:59 -34161.992177] FAST spr round 3 (radius: 25) [00:34:48 -34110.726122] FAST spr round 4 (radius: 25) [00:37:22 -34110.723267] Model parameter optimization (eps = 1.000000) [00:37:37 -34110.334249] SLOW spr round 1 (radius: 5) [00:40:52 -34094.015394] SLOW spr round 2 (radius: 5) [00:44:03 -34093.377338] SLOW spr round 3 (radius: 5) [00:47:13 -34093.376855] SLOW spr round 4 (radius: 10) [00:50:23 -34093.376786] SLOW spr round 5 (radius: 15) [00:54:41 -34093.376754] SLOW spr round 6 (radius: 20) [01:01:19 -34093.376721] SLOW spr round 7 (radius: 25) [01:09:41 -34093.376720] Model parameter optimization (eps = 0.100000) [01:10:01] [worker #0] ML tree search #1, logLikelihood: -34093.222000 [01:10:01 -179739.109172] Initial branch length optimization [01:10:07 -156335.268412] Model parameter optimization (eps = 10.000000) [01:10:51 -155522.731439] AUTODETECT spr round 1 (radius: 5) [01:14:47 -94462.189487] AUTODETECT spr round 2 (radius: 10) [01:18:44 -64309.914571] AUTODETECT spr round 3 (radius: 15) [01:19:22] [worker #2] ML tree search #3, logLikelihood: -34103.406327 [01:23:07 -48242.563555] AUTODETECT spr round 4 (radius: 20) [01:24:29] [worker #1] ML tree search #2, logLikelihood: -34099.545822 [01:28:22 -41515.747405] AUTODETECT spr round 5 (radius: 25) [01:34:44 -40396.768044] SPR radius for FAST iterations: 25 (autodetect) [01:34:44 -40396.768044] Model parameter optimization (eps = 3.000000) [01:35:19 -40369.251072] FAST spr round 1 (radius: 25) [01:38:53 -34712.008038] FAST spr round 2 (radius: 25) [01:41:53 -34262.874147] FAST spr round 3 (radius: 25) [01:44:41 -34232.699999] FAST spr round 4 (radius: 25) [01:47:16 -34231.404265] FAST spr round 5 (radius: 25) [01:49:47 -34228.672206] FAST spr round 6 (radius: 25) [01:52:17 -34228.284192] FAST spr round 7 (radius: 25) [01:54:47 -34228.284191] Model parameter optimization (eps = 1.000000) [01:55:10 -34223.631591] SLOW spr round 1 (radius: 5) [01:58:17 -34208.162938] SLOW spr round 2 (radius: 5) [02:01:23 -34207.136106] SLOW spr round 3 (radius: 5) [02:04:22 -34207.135956] SLOW spr round 4 (radius: 10) [02:07:31 -34205.635699] SLOW spr round 5 (radius: 5) [02:11:19 -34204.219982] SLOW spr round 6 (radius: 5) [02:14:44 -34204.219982] SLOW spr round 7 (radius: 10) [02:17:59 -34204.219982] SLOW spr round 8 (radius: 15) [02:22:27 -34204.219982] SLOW spr round 9 (radius: 20) [02:29:47 -34204.219982] SLOW spr round 10 (radius: 25) [02:39:13 -34204.219982] Model parameter optimization (eps = 0.100000) [02:39:22] [worker #0] ML tree search #4, logLikelihood: -34204.208661 [02:39:22 -178779.193887] Initial branch length optimization [02:39:29 -155671.178375] Model parameter optimization (eps = 10.000000) [02:40:28 -154963.650679] AUTODETECT spr round 1 (radius: 5) [02:42:42] [worker #2] ML tree search #6, logLikelihood: -34118.625393 [02:44:21 -93986.158153] AUTODETECT spr round 2 (radius: 10) [02:48:24 -61928.006126] AUTODETECT spr round 3 (radius: 15) [02:52:33 -50164.794541] AUTODETECT spr round 4 (radius: 20) [02:57:30 -43126.836322] AUTODETECT spr round 5 (radius: 25) [02:59:29] [worker #1] ML tree search #5, logLikelihood: -34099.316201 [03:03:12 -41211.851841] SPR radius for FAST iterations: 25 (autodetect) [03:03:12 -41211.851841] Model parameter optimization (eps = 3.000000) [03:03:46 -41191.948301] FAST spr round 1 (radius: 25) [03:07:21 -34568.818493] FAST spr round 2 (radius: 25) [03:10:24 -34132.491362] FAST spr round 3 (radius: 25) [03:13:07 -34108.792519] FAST spr round 4 (radius: 25) [03:15:40 -34105.766912] FAST spr round 5 (radius: 25) [03:18:10 -34105.279174] FAST spr round 6 (radius: 25) [03:20:37 -34105.278365] Model parameter optimization (eps = 1.000000) [03:20:48 -34105.099307] SLOW spr round 1 (radius: 5) [03:23:56 -34095.091342] SLOW spr round 2 (radius: 5) [03:26:54 -34095.082489] SLOW spr round 3 (radius: 10) [03:30:00 -34094.600254] SLOW spr round 4 (radius: 5) [03:33:44 -34094.600246] SLOW spr round 5 (radius: 10) [03:37:09 -34094.600246] SLOW spr round 6 (radius: 15) [03:41:25 -34094.142465] SLOW spr round 7 (radius: 5) [03:45:24 -34094.142465] SLOW spr round 8 (radius: 10) [03:48:59 -34094.142465] SLOW spr round 9 (radius: 15) [03:53:14 -34094.142465] SLOW spr round 10 (radius: 20) [04:00:17 -34094.142465] SLOW spr round 11 (radius: 25) [04:09:06 -34094.142465] Model parameter optimization (eps = 0.100000) [04:09:15] [worker #0] ML tree search #7, logLikelihood: -34094.055473 [04:09:15 -179569.904859] Initial branch length optimization [04:09:20 -156132.824251] Model parameter optimization (eps = 10.000000) [04:10:09 -155382.692307] AUTODETECT spr round 1 (radius: 5) [04:13:59 -94207.713346] AUTODETECT spr round 2 (radius: 10) [04:17:56 -62634.838389] AUTODETECT spr round 3 (radius: 15) [04:21:20] [worker #2] ML tree search #9, logLikelihood: -34092.086469 [04:22:10 -47839.079931] AUTODETECT spr round 4 (radius: 20) [04:27:38 -42226.279822] AUTODETECT spr round 5 (radius: 25) [04:33:33] [worker #1] ML tree search #8, logLikelihood: -34120.821425 [04:34:41 -41623.210938] SPR radius for FAST iterations: 25 (autodetect) [04:34:41 -41623.210938] Model parameter optimization (eps = 3.000000) [04:35:12 -41585.115361] FAST spr round 1 (radius: 25) [04:38:52 -34465.040945] FAST spr round 2 (radius: 25) [04:42:02 -34170.920960] FAST spr round 3 (radius: 25) [04:44:52 -34126.995477] FAST spr round 4 (radius: 25) [04:47:30 -34116.003187] FAST spr round 5 (radius: 25) [04:50:04 -34115.834473] FAST spr round 6 (radius: 25) [04:52:36 -34115.442681] FAST spr round 7 (radius: 25) [04:55:07 -34115.442373] Model parameter optimization (eps = 1.000000) [04:55:28 -34108.685264] SLOW spr round 1 (radius: 5) [04:58:35 -34097.243754] SLOW spr round 2 (radius: 5) [05:01:44 -34096.455709] SLOW spr round 3 (radius: 5) [05:04:53 -34096.455393] SLOW spr round 4 (radius: 10) [05:08:06 -34096.455282] SLOW spr round 5 (radius: 15) [05:12:29 -34093.323147] SLOW spr round 6 (radius: 5) [05:16:37 -34093.323038] SLOW spr round 7 (radius: 10) [05:20:20 -34093.323033] SLOW spr round 8 (radius: 15) [05:24:35 -34093.323030] SLOW spr round 9 (radius: 20) [05:31:30 -34093.323030] SLOW spr round 10 (radius: 25) [05:37:45] [worker #2] ML tree search #12, logLikelihood: -34090.240952 [05:39:43 -34093.323030] Model parameter optimization (eps = 0.100000) [05:39:55] [worker #0] ML tree search #10, logLikelihood: -34093.250027 [05:39:55 -177982.465196] Initial branch length optimization [05:39:59 -155511.520772] Model parameter optimization (eps = 10.000000) [05:40:44 -154789.176886] AUTODETECT spr round 1 (radius: 5) [05:44:42 -94708.563502] AUTODETECT spr round 2 (radius: 10) [05:48:39 -62201.142789] AUTODETECT spr round 3 (radius: 15) [05:52:46 -50445.154700] AUTODETECT spr round 4 (radius: 20) [05:57:48 -42478.586583] AUTODETECT spr round 5 (radius: 25) [06:03:29 -41245.192427] SPR radius for FAST iterations: 25 (autodetect) [06:03:29 -41245.192427] Model parameter optimization (eps = 3.000000) [06:04:01 -41219.433899] FAST spr round 1 (radius: 25) [06:07:47 -34588.840842] FAST spr round 2 (radius: 25) [06:10:54 -34150.852862] FAST spr round 3 (radius: 25) [06:12:47] [worker #1] ML tree search #11, logLikelihood: -34096.576049 [06:13:42 -34122.277530] FAST spr round 4 (radius: 25) [06:16:22 -34109.372850] FAST spr round 5 (radius: 25) [06:18:54 -34109.372846] Model parameter optimization (eps = 1.000000) [06:19:12 -34107.842256] SLOW spr round 1 (radius: 5) [06:22:18 -34100.474364] SLOW spr round 2 (radius: 5) [06:25:28 -34098.202152] SLOW spr round 3 (radius: 5) [06:28:30 -34098.080132] SLOW spr round 4 (radius: 5) [06:31:29 -34098.080074] SLOW spr round 5 (radius: 10) [06:34:36 -34098.080061] SLOW spr round 6 (radius: 15) [06:39:08 -34097.948014] SLOW spr round 7 (radius: 5) [06:43:08 -34097.947995] SLOW spr round 8 (radius: 10) [06:46:43 -34097.947995] SLOW spr round 9 (radius: 15) [06:51:04 -34097.947995] SLOW spr round 10 (radius: 20) [06:58:29 -34097.947995] SLOW spr round 11 (radius: 25) [07:07:41 -34097.947995] Model parameter optimization (eps = 0.100000) [07:07:55] [worker #0] ML tree search #13, logLikelihood: -34097.375408 [07:07:55 -179095.179513] Initial branch length optimization [07:08:00 -155686.626134] Model parameter optimization (eps = 10.000000) [07:09:08 -154910.513625] AUTODETECT spr round 1 (radius: 5) [07:09:28] [worker #2] ML tree search #15, logLikelihood: -34093.290969 [07:13:03 -94879.114133] AUTODETECT spr round 2 (radius: 10) [07:17:04 -61479.215081] AUTODETECT spr round 3 (radius: 15) [07:21:16 -50934.760344] AUTODETECT spr round 4 (radius: 20) [07:26:10 -43249.787616] AUTODETECT spr round 5 (radius: 25) [07:31:29 -41079.317052] SPR radius for FAST iterations: 25 (autodetect) [07:31:29 -41079.317052] Model parameter optimization (eps = 3.000000) [07:32:13 -41049.780904] FAST spr round 1 (radius: 25) [07:35:56 -34514.301654] FAST spr round 2 (radius: 25) [07:39:00 -34259.195637] FAST spr round 3 (radius: 25) [07:41:49 -34227.026650] FAST spr round 4 (radius: 25) [07:44:32 -34218.513911] FAST spr round 5 (radius: 25) [07:47:06 -34216.579456] FAST spr round 6 (radius: 25) [07:49:39 -34215.268439] FAST spr round 7 (radius: 25) [07:52:10 -34215.268393] Model parameter optimization (eps = 1.000000) [07:52:24 -34214.467270] SLOW spr round 1 (radius: 5) [07:55:34 -34200.689028] SLOW spr round 2 (radius: 5) [07:58:38 -34199.542455] SLOW spr round 3 (radius: 5) [08:01:39 -34199.540514] SLOW spr round 4 (radius: 10) [08:04:49 -34198.667644] SLOW spr round 5 (radius: 5) [08:08:37 -34198.667575] SLOW spr round 6 (radius: 10) [08:12:06 -34198.667555] SLOW spr round 7 (radius: 15) [08:16:08] [worker #1] ML tree search #14, logLikelihood: -34105.458646 [08:16:24 -34198.667549] SLOW spr round 8 (radius: 20) [08:23:50 -34198.667547] SLOW spr round 9 (radius: 25) [08:33:15 -34198.667546] Model parameter optimization (eps = 0.100000) [08:33:28] [worker #0] ML tree search #16, logLikelihood: -34198.655000 [08:33:28 -180279.877849] Initial branch length optimization [08:33:33 -157081.939653] Model parameter optimization (eps = 10.000000) [08:34:32 -156350.168308] AUTODETECT spr round 1 (radius: 5) [08:38:29 -96516.783325] AUTODETECT spr round 2 (radius: 10) [08:42:34 -59424.954197] AUTODETECT spr round 3 (radius: 15) [08:42:40] [worker #2] ML tree search #18, logLikelihood: -34094.888243 [08:46:51 -47705.516801] AUTODETECT spr round 4 (radius: 20) [08:51:38 -43177.947907] AUTODETECT spr round 5 (radius: 25) [08:58:23 -41720.126926] SPR radius for FAST iterations: 25 (autodetect) [08:58:23 -41720.126926] Model parameter optimization (eps = 3.000000) [08:58:49 -41699.361637] FAST spr round 1 (radius: 25) [09:02:26 -34517.777060] FAST spr round 2 (radius: 25) [09:05:21 -34167.693255] FAST spr round 3 (radius: 25) [09:08:06 -34128.035629] FAST spr round 4 (radius: 25) [09:10:37 -34123.771418] FAST spr round 5 (radius: 25) [09:13:06 -34122.241801] FAST spr round 6 (radius: 25) [09:15:32 -34122.241402] Model parameter optimization (eps = 1.000000) [09:15:54 -34116.853329] SLOW spr round 1 (radius: 5) [09:19:00 -34104.529884] SLOW spr round 2 (radius: 5) [09:22:03 -34101.911573] SLOW spr round 3 (radius: 5) [09:25:00 -34101.823111] SLOW spr round 4 (radius: 10) [09:28:05 -34101.221293] SLOW spr round 5 (radius: 5) [09:31:52 -34101.221213] SLOW spr round 6 (radius: 10) [09:35:18 -34101.221192] SLOW spr round 7 (radius: 15) [09:39:42 -34101.221186] SLOW spr round 8 (radius: 20) [09:47:25 -34101.221184] SLOW spr round 9 (radius: 25) [09:50:24] [worker #1] ML tree search #17, logLikelihood: -34093.271198 [09:57:06 -34101.221184] Model parameter optimization (eps = 0.100000) [09:57:18] [worker #0] ML tree search #19, logLikelihood: -34101.216293 [11:17:27] [worker #1] ML tree search #20, logLikelihood: -34099.904603 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.265747,0.264115) (0.241303,0.413499) (0.300730,1.368463) (0.192220,2.177170) 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: -34090.240952 AIC score: 72190.481905 / AICc score: 8116250.481905 / BIC score: 77861.250948 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=125). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O14921/3_mltree/O14921.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O14921/3_mltree/O14921.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O14921/3_mltree/O14921.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O14921/3_mltree/O14921.raxml.log Analysis started: 26-Jul-2021 00:10:20 / finished: 26-Jul-2021 11:27:47 Elapsed time: 40647.729 seconds Consumed energy: 1629.901 Wh (= 8 km in an electric car, or 41 km with an e-scooter!)