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 02-Jul-2021 08:24:19 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/2_msa/Q7Z5H3_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/3_mltree/Q7Z5H3 --seed 2 --threads 4 --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 (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/2_msa/Q7Z5H3_trimmed_msa.fasta [00:00:00] Loaded alignment with 995 taxa and 198 sites WARNING: Sequences tr_A0A2R8Q349_A0A2R8Q349_DANRE_7955 and tr_A0A2R8QQA3_A0A2R8QQA3_DANRE_7955 are exactly identical! WARNING: Sequences tr_E1BZR0_E1BZR0_CHICK_9031 and tr_A0A0Q3WUF1_A0A0Q3WUF1_AMAAE_12930 are exactly identical! WARNING: Sequences tr_E1BZR0_E1BZR0_CHICK_9031 and tr_A0A226PWF8_A0A226PWF8_COLVI_9014 are exactly identical! WARNING: Sequences tr_F1NYA5_F1NYA5_CHICK_9031 and tr_G1MVU2_G1MVU2_MELGA_9103 are exactly identical! WARNING: Sequences sp_Q3UIA2_RHG17_MOUSE_10090 and sp_Q99N37_RHG17_RAT_10116 are exactly identical! WARNING: Sequences sp_Q3UIA2_RHG17_MOUSE_10090 and tr_A0A3Q0CQI7_A0A3Q0CQI7_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3XT71_M3XT71_MUSPF_9669 and tr_A0A2Y9K6G6_A0A2Y9K6G6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XX06_M3XX06_MUSPF_9669 and tr_A0A2Y9L1V3_A0A2Y9L1V3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YCL1_M3YCL1_MUSPF_9669 and tr_A0A2Y9JCE3_A0A2Y9JCE3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YCL1_M3YCL1_MUSPF_9669 and tr_A0A384CIZ2_A0A384CIZ2_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YM19_M3YM19_MUSPF_9669 and tr_E2REM4_E2REM4_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YM19_M3YM19_MUSPF_9669 and tr_A0A2U3Z5A6_A0A2U3Z5A6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YM19_M3YM19_MUSPF_9669 and tr_A0A384CKS4_A0A384CKS4_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YZ62_M3YZ62_MUSPF_9669 and tr_A0A2Y9L975_A0A2Y9L975_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3GCX9_A0A2I3GCX9_NOMLE_61853 and tr_H2NQG0_H2NQG0_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3GCX9_A0A2I3GCX9_NOMLE_61853 and tr_A0A1D5QY69_A0A1D5QY69_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GCX9_A0A2I3GCX9_NOMLE_61853 and tr_U3FQD0_U3FQD0_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3GCX9_A0A2I3GCX9_NOMLE_61853 and tr_A0A096NHH5_A0A096NHH5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3GCX9_A0A2I3GCX9_NOMLE_61853 and tr_A0A2K5MM86_A0A2K5MM86_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GCX9_A0A2I3GCX9_NOMLE_61853 and tr_A0A2K6DVB8_A0A2K6DVB8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GHK1_A0A2I3GHK1_NOMLE_61853 and tr_A0A2I2ZFN0_A0A2I2ZFN0_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GHK1_A0A2I3GHK1_NOMLE_61853 and tr_A0A2I3SMH6_A0A2I3SMH6_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GHK1_A0A2I3GHK1_NOMLE_61853 and tr_A0A1D5Q1Q8_A0A1D5Q1Q8_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GHK1_A0A2I3GHK1_NOMLE_61853 and tr_G7PTQ0_G7PTQ0_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3GHK1_A0A2I3GHK1_NOMLE_61853 and tr_A0A2I3MMU9_A0A2I3MMU9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3GHK1_A0A2I3GHK1_NOMLE_61853 and tr_A0A0D9R9P7_A0A0D9R9P7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3GHK1_A0A2I3GHK1_NOMLE_61853 and tr_A0A1U7UJY8_A0A1U7UJY8_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A2I3GHK1_A0A2I3GHK1_NOMLE_61853 and tr_A0A2K5M1L1_A0A2K5M1L1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3GHK1_A0A2I3GHK1_NOMLE_61853 and tr_A0A2K6DFC1_A0A2K6DFC1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GHK1_A0A2I3GHK1_NOMLE_61853 and tr_A0A2K6AB97_A0A2K6AB97_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RDK5_G1RDK5_NOMLE_61853 and tr_G3QTU7_G3QTU7_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RDK5_G1RDK5_NOMLE_61853 and tr_H2PDT8_H2PDT8_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RDK5_G1RDK5_NOMLE_61853 and tr_H2QPU1_H2QPU1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RDK5_G1RDK5_NOMLE_61853 and sp_Q8N264_RHG24_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RDK5_G1RDK5_NOMLE_61853 and tr_G5C949_G5C949_HETGA_10181 are exactly identical! WARNING: Sequences tr_G1RDK5_G1RDK5_NOMLE_61853 and tr_A0A2R9BLQ3_A0A2R9BLQ3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_G3QT93_G3QT93_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_H2N3Y4_H2N3Y4_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_K7AGG6_K7AGG6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_A0A287D3W4_A0A287D3W4_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_H0WXU5_H0WXU5_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and sp_O75044_SRGP2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_G7MER6_G7MER6_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_G7NVB6_G7NVB6_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_A0A096NE71_A0A096NE71_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_A0A0D9RQX3_A0A0D9RQX3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_A0A3Q0DRH3_A0A3Q0DRH3_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_A0A2K6C966_A0A2K6C966_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_A0A2K6A7C7_A0A2K6A7C7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_A0A2R9C1H1_A0A2R9C1H1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_A0A2U4CRP6_A0A2U4CRP6_TURTR_9739 are exactly identical! WARNING: Sequences tr_G1NYK8_G1NYK8_MYOLU_59463 and tr_A0A2Y9PVT9_A0A2Y9PVT9_DELLE_9749 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_H2NHX0_H2NHX0_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_H2R1I1_H2R1I1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_A0A287DD63_A0A287DD63_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and sp_Q7Z6B7_SRGP1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_G7N7I9_G7N7I9_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_G7P0F8_G7P0F8_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_A0A2I3MQK2_A0A2I3MQK2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_A0A0D9QWU6_A0A0D9QWU6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_A0A2K5MYI2_A0A2K5MYI2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_A0A2K5ZMG0_A0A2K5ZMG0_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QCX6_G3QCX6_GORGO_9595 and tr_A0A2R9CEY3_A0A2R9CEY3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QG80_G3QG80_GORGO_9595 and sp_Q7Z5H3_RHG22_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QM70_G3QM70_GORGO_9595 and tr_H2QAT1_H2QAT1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QM70_G3QM70_GORGO_9595 and sp_Q68EM7_RHG17_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R2I3_G3R2I3_GORGO_9595 and sp_P42331_RHG25_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R2I3_G3R2I3_GORGO_9595 and tr_F6TL08_F6TL08_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3R2I3_G3R2I3_GORGO_9595 and tr_G7PMD2_G7PMD2_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3R2I3_G3R2I3_GORGO_9595 and tr_A0A2I3MIN6_A0A2I3MIN6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3R2I3_G3R2I3_GORGO_9595 and tr_A0A2K5NU04_A0A2K5NU04_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3R2I3_G3R2I3_GORGO_9595 and tr_A0A2K6CV84_A0A2K6CV84_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3R2I3_G3R2I3_GORGO_9595 and tr_A0A2R9B6E5_A0A2R9B6E5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PA60_H2PA60_PONAB_9601 and tr_A0A0D9REF0_A0A0D9REF0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1MWQ2_G1MWQ2_MELGA_9103 and tr_A0A151MAS3_A0A151MAS3_ALLMI_8496 are exactly identical! WARNING: Sequences tr_G1MWQ2_G1MWQ2_MELGA_9103 and tr_A0A1U7RVT5_A0A1U7RVT5_ALLSI_38654 are exactly identical! WARNING: Sequences tr_G1N7N8_G1N7N8_MELGA_9103 and tr_A0A099ZHM8_A0A099ZHM8_TINGU_94827 are exactly identical! WARNING: Sequences tr_G1N7N8_G1N7N8_MELGA_9103 and tr_A0A226N1A6_A0A226N1A6_CALSU_9009 are exactly identical! WARNING: Sequences tr_G1N7N8_G1N7N8_MELGA_9103 and tr_A0A226P2B5_A0A226P2B5_COLVI_9014 are exactly identical! WARNING: Sequences tr_F1P8C2_F1P8C2_CANLF_9615 and tr_G1MID0_G1MID0_AILME_9646 are exactly identical! WARNING: Sequences tr_F1P8C2_F1P8C2_CANLF_9615 and tr_L5JT29_L5JT29_PTEAL_9402 are exactly identical! WARNING: Sequences tr_F1P8C2_F1P8C2_CANLF_9615 and tr_M3WPB8_M3WPB8_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1P8C2_F1P8C2_CANLF_9615 and tr_A0A2U3WWQ7_A0A2U3WWQ7_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1P8C2_F1P8C2_CANLF_9615 and tr_A0A2U3XKI6_A0A2U3XKI6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_F1P8C2_F1P8C2_CANLF_9615 and tr_A0A384BIU0_A0A384BIU0_URSMA_29073 are exactly identical! WARNING: Sequences tr_F1PJZ0_F1PJZ0_CANLF_9615 and tr_A0A287B8H5_A0A287B8H5_PIG_9823 are exactly identical! WARNING: Sequences tr_F1PJZ0_F1PJZ0_CANLF_9615 and tr_M3W9I0_M3W9I0_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1PJZ0_F1PJZ0_CANLF_9615 and tr_A0A2U4C462_A0A2U4C462_TURTR_9739 are exactly identical! WARNING: Sequences tr_H2QD90_H2QD90_PANTR_9598 and sp_Q6ZUM4_RHG27_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QD90_H2QD90_PANTR_9598 and tr_A0A2R9CDP8_A0A2R9CDP8_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6QGZ1_F6QGZ1_MONDO_13616 and tr_G3WIB7_G3WIB7_SARHA_9305 are exactly identical! WARNING: Sequences tr_F6SM93_F6SM93_HORSE_9796 and tr_L5KWX7_L5KWX7_PTEAL_9402 are exactly identical! WARNING: Sequences tr_W5P0Y4_W5P0Y4_SHEEP_9940 and tr_F1MHI2_F1MHI2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5P187_W5P187_SHEEP_9940 and tr_F1MFS4_F1MFS4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5P187_W5P187_SHEEP_9940 and tr_A0A2U4CQS9_A0A2U4CQS9_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5P187_W5P187_SHEEP_9940 and tr_A0A2Y9N7F0_A0A2Y9N7F0_DELLE_9749 are exactly identical! WARNING: Sequences tr_W5PBJ2_W5PBJ2_SHEEP_9940 and tr_F1MJI3_F1MJI3_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F1M5M9_F1M5M9_RAT_10116 and tr_A0A1U7Q8L6_A0A1U7Q8L6_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3ZH10_M3ZH10_XIPMA_8083 and tr_A0A087X9W0_A0A087X9W0_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4A4X0_M4A4X0_XIPMA_8083 and tr_A0A096M228_A0A096M228_POEFO_48698 are exactly identical! WARNING: Sequences tr_I3M8B3_I3M8B3_ICTTR_43179 and tr_A0A2Y9QXF2_A0A2Y9QXF2_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0WIJ3_H0WIJ3_OTOGA_30611 and tr_A0A091E4Q4_A0A091E4Q4_FUKDA_885580 are exactly identical! WARNING: Sequences tr_F6T0E0_F6T0E0_MACMU_9544 and tr_G7PQA9_G7PQA9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6T0E0_F6T0E0_MACMU_9544 and tr_A0A2K6E3J3_A0A2K6E3J3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6UV94_F6UV94_MACMU_9544 and tr_A0A2K6AR12_A0A2K6AR12_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6ZKA6_F6ZKA6_MACMU_9544 and tr_A0A2I3N343_A0A2I3N343_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6ZKA6_F6ZKA6_MACMU_9544 and tr_A0A0D9RCQ1_A0A0D9RCQ1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6ZKA6_F6ZKA6_MACMU_9544 and tr_A0A2K6DFB9_A0A2K6DFB9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6ZKA6_F6ZKA6_MACMU_9544 and tr_A0A2K5YTJ0_A0A2K5YTJ0_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7B042_F7B042_MACMU_9544 and tr_A0A2I3MCP4_A0A2I3MCP4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7B042_F7B042_MACMU_9544 and tr_A0A0D9QUL6_A0A0D9QUL6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7B042_F7B042_MACMU_9544 and tr_A0A2K5LLX3_A0A2K5LLX3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7B042_F7B042_MACMU_9544 and tr_A0A2K6CR26_A0A2K6CR26_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B042_F7B042_MACMU_9544 and tr_A0A2K5ZCS3_A0A2K5ZCS3_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GJA5_F7GJA5_MACMU_9544 and tr_U3EWI2_U3EWI2_CALJA_9483 are exactly identical! WARNING: Sequences tr_F7GJA5_F7GJA5_MACMU_9544 and tr_G7NYV5_G7NYV5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GJA5_F7GJA5_MACMU_9544 and tr_A0A096NA88_A0A096NA88_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GJA5_F7GJA5_MACMU_9544 and tr_A0A2K5N7D9_A0A2K5N7D9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GJA5_F7GJA5_MACMU_9544 and tr_A0A2K6BDV8_A0A2K6BDV8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GJA5_F7GJA5_MACMU_9544 and tr_A0A2K5XJ85_A0A2K5XJ85_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5ALG1_G5ALG1_HETGA_10181 and tr_A0A091D1W5_A0A091D1W5_FUKDA_885580 are exactly identical! WARNING: Sequences tr_G5BRA6_G5BRA6_HETGA_10181 and tr_A0A1S3W6J0_A0A1S3W6J0_ERIEU_9365 are exactly identical! WARNING: Sequences tr_W4YIG3_W4YIG3_STRPU_7668 and tr_W4Z2T6_W4Z2T6_STRPU_7668 are exactly identical! WARNING: Sequences tr_F4NS70_F4NS70_BATDJ_684364 and tr_A0A177W788_A0A177W788_BATDE_403673 are exactly identical! WARNING: Sequences tr_G3SW94_G3SW94_LOXAF_9785 and tr_A0A2Y9D5T9_A0A2Y9D5T9_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0Z7Q6_H0Z7Q6_TAEGU_59729 and tr_U3K5N8_U3K5N8_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0Z7Q6_H0Z7Q6_TAEGU_59729 and tr_A0A091F9A4_A0A091F9A4_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0Z7Q6_H0Z7Q6_TAEGU_59729 and tr_A0A091JKJ3_A0A091JKJ3_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0Z7Q6_H0Z7Q6_TAEGU_59729 and tr_A0A093Q9T7_A0A093Q9T7_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0Z7Q6_H0Z7Q6_TAEGU_59729 and tr_A0A091UX50_A0A091UX50_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0Z7Q6_H0Z7Q6_TAEGU_59729 and tr_A0A087R5K3_A0A087R5K3_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0Z7Q6_H0Z7Q6_TAEGU_59729 and tr_A0A091VT98_A0A091VT98_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0Z7Q6_H0Z7Q6_TAEGU_59729 and tr_A0A091GF41_A0A091GF41_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0Z7Q6_H0Z7Q6_TAEGU_59729 and tr_A0A0A0AR95_A0A0A0AR95_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0Z7Q6_H0Z7Q6_TAEGU_59729 and tr_A0A2I0MJ62_A0A2I0MJ62_COLLI_8932 are exactly identical! WARNING: Sequences tr_H0Z7Q6_H0Z7Q6_TAEGU_59729 and tr_A0A093GMK4_A0A093GMK4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0Z7Q6_H0Z7Q6_TAEGU_59729 and tr_A0A091IK55_A0A091IK55_CALAN_9244 are exactly identical! WARNING: Sequences tr_H0ZCU6_H0ZCU6_TAEGU_59729 and tr_U3J9Y9_U3J9Y9_ANAPL_8839 are exactly identical! WARNING: Sequences tr_H0ZCU6_H0ZCU6_TAEGU_59729 and tr_A0A091EC64_A0A091EC64_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZCU6_H0ZCU6_TAEGU_59729 and tr_A0A091JDG5_A0A091JDG5_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0ZCU6_H0ZCU6_TAEGU_59729 and tr_A0A093QAC2_A0A093QAC2_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZCU6_H0ZCU6_TAEGU_59729 and tr_A0A087QZ02_A0A087QZ02_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0ZCU6_H0ZCU6_TAEGU_59729 and tr_A0A0A0AT71_A0A0A0AT71_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0ZCU6_H0ZCU6_TAEGU_59729 and tr_A0A218UWJ5_A0A218UWJ5_9PASE_299123 are exactly identical! WARNING: Sequences tr_G1LA36_G1LA36_AILME_9646 and tr_A0A2U3VBD0_A0A2U3VBD0_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1LA36_G1LA36_AILME_9646 and tr_A0A2U3XE97_A0A2U3XE97_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1LA36_G1LA36_AILME_9646 and tr_A0A384DBH2_A0A384DBH2_URSMA_29073 are exactly identical! WARNING: Sequences tr_F1MFA5_F1MFA5_BOVIN_9913 and tr_A0A1S3EX24_A0A1S3EX24_DIPOR_10020 are exactly identical! WARNING: Sequences tr_U3JCT7_U3JCT7_FICAL_59894 and tr_A0A218UKD4_A0A218UKD4_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3JM02_U3JM02_FICAL_59894 and tr_A0A091EPE5_A0A091EPE5_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3IKJ3_U3IKJ3_ANAPL_8839 and tr_A0A218V4D5_A0A218V4D5_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A096MUE0_A0A096MUE0_PAPAN_9555 and tr_A0A2K5MWD6_A0A2K5MWD6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MUE0_A0A096MUE0_PAPAN_9555 and tr_A0A2K5ZTC5_A0A2K5ZTC5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096MXU4_A0A096MXU4_PAPAN_9555 and tr_A0A0D9R051_A0A0D9R051_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MXU4_A0A096MXU4_PAPAN_9555 and tr_A0A2K5NY60_A0A2K5NY60_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MXU4_A0A096MXU4_PAPAN_9555 and tr_A0A2K5YJ75_A0A2K5YJ75_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151MKW9_A0A151MKW9_ALLMI_8496 and tr_A0A3Q0GYH3_A0A3Q0GYH3_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NHT6_A0A151NHT6_ALLMI_8496 and tr_A0A1U7RME2_A0A1U7RME2_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NVM3_A0A151NVM3_ALLMI_8496 and tr_A0A3Q0H5X0_A0A3Q0H5X0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NW08_A0A151NW08_ALLMI_8496 and tr_A0A1U7S806_A0A1U7S806_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0Q3XAR5_A0A0Q3XAR5_AMAAE_12930 and tr_A0A087RG85_A0A087RG85_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A0Q3XAR5_A0A0Q3XAR5_AMAAE_12930 and tr_A0A099ZW35_A0A099ZW35_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JFK9_A0A091JFK9_EGRGA_188379 and tr_A0A091GH04_A0A091GH04_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JFK9_A0A091JFK9_EGRGA_188379 and tr_A0A1V4KSV9_A0A1V4KSV9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A087QGT7_A0A087QGT7_APTFO_9233 and tr_A0A2I0LIJ1_A0A2I0LIJ1_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A087QGT7_A0A087QGT7_APTFO_9233 and tr_A0A1V4JW91_A0A1V4JW91_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0M090_A0A2I0M090_COLLI_8932 and tr_A0A1V4KD87_A0A1V4KD87_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0RTC8_A0A0V0RTC8_9BILA_6336 and tr_A0A0V1CWM6_A0A0V1CWM6_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0RTC8_A0A0V0RTC8_9BILA_6336 and tr_A0A0V0WU68_A0A0V0WU68_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0RTC8_A0A0V0RTC8_9BILA_6336 and tr_A0A0V0VKY7_A0A0V0VKY7_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0RTC8_A0A0V0RTC8_9BILA_6336 and tr_A0A0V1LR48_A0A0V1LR48_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0RTC8_A0A0V0RTC8_9BILA_6336 and tr_A0A0V0ZHT8_A0A0V0ZHT8_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0RTC8_A0A0V0RTC8_9BILA_6336 and tr_A0A0V1PI01_A0A0V1PI01_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0RTC8_A0A0V0RTC8_9BILA_6336 and tr_A0A0V0TL38_A0A0V0TL38_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1CP74_A0A0V1CP74_TRIBR_45882 and tr_A0A0V0WP24_A0A0V0WP24_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CP74_A0A0V1CP74_TRIBR_45882 and tr_A0A0V0V3J8_A0A0V0V3J8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CP74_A0A0V1CP74_TRIBR_45882 and tr_A0A0V0ZA08_A0A0V0ZA08_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CP74_A0A0V1CP74_TRIBR_45882 and tr_A0A0V1NU21_A0A0V1NU21_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CP74_A0A0V1CP74_TRIBR_45882 and tr_A0A0V0TEZ4_A0A0V0TEZ4_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1DGK2_A0A0V1DGK2_TRIBR_45882 and tr_A0A0V0X967_A0A0V0X967_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1DGK2_A0A0V1DGK2_TRIBR_45882 and tr_A0A0V0VXZ2_A0A0V0VXZ2_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DGK2_A0A0V1DGK2_TRIBR_45882 and tr_A0A0V1LNY4_A0A0V1LNY4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DGK2_A0A0V1DGK2_TRIBR_45882 and tr_A0A0V1AB15_A0A0V1AB15_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1DGK2_A0A0V1DGK2_TRIBR_45882 and tr_A0A0V1PNK1_A0A0V1PNK1_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DGK2_A0A0V1DGK2_TRIBR_45882 and tr_A0A0V0UDW5_A0A0V0UDW5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0Y8U1_A0A0V0Y8U1_TRIPS_6337 and tr_A0A0V1M7W7_A0A0V1M7W7_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V0Y8U1_A0A0V0Y8U1_TRIPS_6337 and tr_A0A0V1H040_A0A0V1H040_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3Q5G1_A0A1S3Q5G1_SALSA_8030 and tr_A0A060XDI2_A0A060XDI2_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226NEI8_A0A226NEI8_CALSU_9009 and tr_A0A226PVG5_A0A226PVG5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PLC3_A0A2D0PLC3_ICTPU_7998 and tr_A0A2D0PN14_A0A2D0PN14_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QP00_A0A2D0QP00_ICTPU_7998 and tr_A0A2D0QPG1_A0A2D0QPG1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SA22_A0A2D0SA22_ICTPU_7998 and tr_A0A2D0SAM5_A0A2D0SAM5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SJN0_A0A2D0SJN0_ICTPU_7998 and tr_W5UAT7_W5UAT7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SK64_A0A2D0SK64_ICTPU_7998 and tr_A0A2D0SKT1_A0A2D0SKT1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SY06_A0A2D0SY06_ICTPU_7998 and tr_A0A2D0SYE9_A0A2D0SYE9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T046_A0A2D0T046_ICTPU_7998 and tr_A0A2D0T0I2_A0A2D0T0I2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T046_A0A2D0T046_ICTPU_7998 and tr_W5UR97_W5UR97_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T2F5_A0A2D0T2F5_ICTPU_7998 and tr_A0A2D0T2I7_A0A2D0T2I7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T2F5_A0A2D0T2F5_ICTPU_7998 and tr_A0A2D0T2R8_A0A2D0T2R8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T2F5_A0A2D0T2F5_ICTPU_7998 and tr_A0A2D0T2U2_A0A2D0T2U2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T2F5_A0A2D0T2F5_ICTPU_7998 and tr_A0A2D0T3E0_A0A2D0T3E0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2G8JZ69_A0A2G8JZ69_STIJA_307972 and tr_A0A2G8L339_A0A2G8L339_STIJA_307972 are exactly identical! WARNING: Sequences tr_A0A2N5SJ60_A0A2N5SJ60_9BASI_200324 and tr_A0A2N5TFF1_A0A2N5TFF1_9BASI_200324 are exactly identical! WARNING: Sequences tr_A0A2G4T5J2_A0A2G4T5J2_9FUNG_1340429 and tr_A0A367JIU1_A0A367JIU1_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A2G4T5J2_A0A2G4T5J2_9FUNG_1340429 and tr_A0A367K0X0_A0A367K0X0_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A2U4A9L5_A0A2U4A9L5_TURTR_9739 and tr_A0A2Y9PN65_A0A2Y9PN65_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A9L5_A0A2U4A9L5_TURTR_9739 and tr_A0A2Y9SKZ6_A0A2Y9SKZ6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3ZK20_A0A2U3ZK20_ODORO_9708 and tr_A0A2Y9IZA7_A0A2Y9IZA7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2U3ZK20_A0A2U3ZK20_ODORO_9708 and tr_A0A2Y9MT74_A0A2Y9MT74_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3ZK20_A0A2U3ZK20_ODORO_9708 and tr_A0A2Y9SM07_A0A2Y9SM07_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9MJB5_A0A2Y9MJB5_DELLE_9749 and tr_A0A2Y9MYT1_A0A2Y9MYT1_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2Y9MME4_A0A2Y9MME4_DELLE_9749 and tr_A0A383ZV53_A0A383ZV53_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 212 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/Q7Z5H3/3_mltree/Q7Z5H3.raxml.reduced.phy Alignment comprises 1 partitions and 198 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 198 / 198 Gaps: 2.66 % Invariant sites: 1.01 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/3_mltree/Q7Z5H3.raxml.rba Parallelization scheme autoconfig: 4 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 995 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 198 / 15840 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -371301.160442] Initial branch length optimization [00:00:05 -301696.594468] Model parameter optimization (eps = 10.000000) [00:00:45 -301626.368776] AUTODETECT spr round 1 (radius: 5) [00:03:26 -184476.597730] AUTODETECT spr round 2 (radius: 10) [00:06:16 -133251.648800] AUTODETECT spr round 3 (radius: 15) [00:09:15 -98354.899346] AUTODETECT spr round 4 (radius: 20) [00:12:39 -82932.697292] AUTODETECT spr round 5 (radius: 25) [00:16:28 -77915.041884] SPR radius for FAST iterations: 25 (autodetect) [00:16:28 -77915.041884] Model parameter optimization (eps = 3.000000) [00:17:01 -77687.882393] FAST spr round 1 (radius: 25) [00:19:37 -66502.692482] FAST spr round 2 (radius: 25) [00:21:34 -65965.505079] FAST spr round 3 (radius: 25) [00:23:23 -65893.542266] FAST spr round 4 (radius: 25) [00:25:07 -65889.793847] FAST spr round 5 (radius: 25) [00:26:45 -65887.332879] FAST spr round 6 (radius: 25) [00:28:19 -65887.332549] Model parameter optimization (eps = 1.000000) [00:28:32 -65885.258331] SLOW spr round 1 (radius: 5) [00:30:40 -65864.948847] SLOW spr round 2 (radius: 5) [00:32:45 -65862.260926] SLOW spr round 3 (radius: 5) [00:34:44 -65861.952866] SLOW spr round 4 (radius: 5) [00:36:47 -65859.804000] SLOW spr round 5 (radius: 5) [00:38:48 -65858.221037] SLOW spr round 6 (radius: 5) [00:40:45 -65858.220650] SLOW spr round 7 (radius: 10) [00:42:45 -65857.848345] SLOW spr round 8 (radius: 5) [00:45:13 -65857.848344] SLOW spr round 9 (radius: 10) [00:47:29 -65857.848343] SLOW spr round 10 (radius: 15) [00:49:37] [worker #1] ML tree search #2, logLikelihood: -65828.168171 [00:50:28 -65853.887961] SLOW spr round 11 (radius: 5) [00:52:59] [worker #3] ML tree search #4, logLikelihood: -65871.914197 [00:53:04 -65853.639150] SLOW spr round 12 (radius: 5) [00:55:20 -65853.639150] SLOW spr round 13 (radius: 10) [00:57:30 -65853.299518] SLOW spr round 14 (radius: 5) [00:57:35] [worker #2] ML tree search #3, logLikelihood: -65879.240235 [00:59:56 -65853.299214] SLOW spr round 15 (radius: 10) [01:02:11 -65853.299213] SLOW spr round 16 (radius: 15) [01:05:11 -65853.299213] SLOW spr round 17 (radius: 20) [01:09:42 -65853.299213] SLOW spr round 18 (radius: 25) [01:15:35 -65853.299213] Model parameter optimization (eps = 0.100000) [01:15:41] [worker #0] ML tree search #1, logLikelihood: -65853.253557 [01:15:41 -372443.334200] Initial branch length optimization [01:15:44 -300004.113925] Model parameter optimization (eps = 10.000000) [01:16:18 -299927.255656] AUTODETECT spr round 1 (radius: 5) [01:19:00 -183968.365294] AUTODETECT spr round 2 (radius: 10) [01:21:47 -136845.945735] AUTODETECT spr round 3 (radius: 15) [01:24:44 -104113.448527] AUTODETECT spr round 4 (radius: 20) [01:28:11 -86438.598633] AUTODETECT spr round 5 (radius: 25) [01:31:48 -81762.198076] SPR radius for FAST iterations: 25 (autodetect) [01:31:48 -81762.198076] Model parameter optimization (eps = 3.000000) [01:32:11 -81527.599299] FAST spr round 1 (radius: 25) [01:34:53 -67871.179509] FAST spr round 2 (radius: 25) [01:36:58 -66022.761696] FAST spr round 3 (radius: 25) [01:38:47 -65865.642510] FAST spr round 4 (radius: 25) [01:40:27 -65856.702802] FAST spr round 5 (radius: 25) [01:42:02 -65856.702782] Model parameter optimization (eps = 1.000000) [01:42:17 -65853.276268] SLOW spr round 1 (radius: 5) [01:44:24 -65839.376143] SLOW spr round 2 (radius: 5) [01:46:33 -65834.771669] SLOW spr round 3 (radius: 5) [01:48:34 -65834.771470] SLOW spr round 4 (radius: 10) [01:50:36 -65834.771432] SLOW spr round 5 (radius: 15) [01:51:30] [worker #3] ML tree search #8, logLikelihood: -65822.910471 [01:53:43 -65834.771417] SLOW spr round 6 (radius: 20) [01:58:05 -65834.155298] SLOW spr round 7 (radius: 5) [01:59:55] [worker #1] ML tree search #6, logLikelihood: -65833.905635 [02:00:46 -65834.155252] SLOW spr round 8 (radius: 10) [02:03:16 -65834.155246] SLOW spr round 9 (radius: 15) [02:06:08 -65834.155241] SLOW spr round 10 (radius: 20) [02:10:37 -65834.155237] SLOW spr round 11 (radius: 25) [02:14:57] [worker #2] ML tree search #7, logLikelihood: -65835.511789 [02:16:24 -65834.155234] Model parameter optimization (eps = 0.100000) [02:16:31] [worker #0] ML tree search #5, logLikelihood: -65834.103430 [02:16:31 -375675.274885] Initial branch length optimization [02:16:34 -303515.853091] Model parameter optimization (eps = 10.000000) [02:17:13 -303296.334887] AUTODETECT spr round 1 (radius: 5) [02:19:52 -185232.897687] AUTODETECT spr round 2 (radius: 10) [02:22:37 -133696.239225] AUTODETECT spr round 3 (radius: 15) [02:25:27 -107045.166460] AUTODETECT spr round 4 (radius: 20) [02:28:40 -86975.908658] AUTODETECT spr round 5 (radius: 25) [02:32:08 -81145.409421] SPR radius for FAST iterations: 25 (autodetect) [02:32:08 -81145.409421] Model parameter optimization (eps = 3.000000) [02:32:31 -80949.777802] FAST spr round 1 (radius: 25) [02:35:06 -67159.383585] FAST spr round 2 (radius: 25) [02:37:15 -65956.214655] FAST spr round 3 (radius: 25) [02:39:06 -65867.810855] FAST spr round 4 (radius: 25) [02:40:45 -65860.556473] FAST spr round 5 (radius: 25) [02:42:20 -65856.608278] FAST spr round 6 (radius: 25) [02:43:51 -65856.608259] Model parameter optimization (eps = 1.000000) [02:44:09 -65851.401883] SLOW spr round 1 (radius: 5) [02:46:14 -65834.851468] SLOW spr round 2 (radius: 5) [02:48:18 -65832.593387] SLOW spr round 3 (radius: 5) [02:50:18 -65828.194862] SLOW spr round 4 (radius: 5) [02:52:16 -65828.194853] SLOW spr round 5 (radius: 10) [02:54:17 -65828.194852] SLOW spr round 6 (radius: 15) [02:56:20] [worker #3] ML tree search #12, logLikelihood: -65833.439474 [02:57:25 -65828.194852] SLOW spr round 7 (radius: 20) [03:01:45 -65828.194852] SLOW spr round 8 (radius: 25) [03:07:30 -65828.194852] Model parameter optimization (eps = 0.100000) [03:07:41] [worker #0] ML tree search #9, logLikelihood: -65828.038367 [03:07:42 -371759.124725] Initial branch length optimization [03:07:46 -299184.923658] Model parameter optimization (eps = 10.000000) [03:08:30 -299115.264983] AUTODETECT spr round 1 (radius: 5) [03:11:10 -179938.533039] AUTODETECT spr round 2 (radius: 10) [03:13:55 -131135.520338] AUTODETECT spr round 3 (radius: 15) [03:16:47 -102269.379965] AUTODETECT spr round 4 (radius: 20) [03:20:07 -85448.606734] AUTODETECT spr round 5 (radius: 25) [03:24:04 -78884.698990] SPR radius for FAST iterations: 25 (autodetect) [03:24:04 -78884.698990] Model parameter optimization (eps = 3.000000) [03:24:25 -78646.770033] FAST spr round 1 (radius: 25) [03:27:02 -66738.409626] FAST spr round 2 (radius: 25) [03:29:02 -65989.328661] FAST spr round 3 (radius: 25) [03:30:48 -65913.937015] FAST spr round 4 (radius: 25) [03:32:28 -65901.281041] FAST spr round 5 (radius: 25) [03:34:01 -65887.438085] FAST spr round 6 (radius: 25) [03:35:32 -65885.055670] FAST spr round 7 (radius: 25) [03:37:00 -65885.055537] Model parameter optimization (eps = 1.000000) [03:37:19 -65882.722453] SLOW spr round 1 (radius: 5) [03:39:21 -65870.347595] SLOW spr round 2 (radius: 5) [03:41:19 -65870.133830] SLOW spr round 3 (radius: 5) [03:43:15 -65870.133810] SLOW spr round 4 (radius: 10) [03:44:16] [worker #2] ML tree search #11, logLikelihood: -65858.639275 [03:45:14 -65870.133793] SLOW spr round 5 (radius: 15) [03:46:20] [worker #1] ML tree search #10, logLikelihood: -65818.939016 [03:48:24 -65870.133792] SLOW spr round 6 (radius: 20) [03:52:59 -65870.133792] SLOW spr round 7 (radius: 25) [03:59:08 -65870.133792] Model parameter optimization (eps = 0.100000) [03:59:15] [worker #0] ML tree search #13, logLikelihood: -65870.076084 [03:59:15 -374868.125309] Initial branch length optimization [03:59:20 -301988.317561] Model parameter optimization (eps = 10.000000) [03:59:57 -301912.159240] AUTODETECT spr round 1 (radius: 5) [04:02:38 -178761.379060] AUTODETECT spr round 2 (radius: 10) [04:04:27] [worker #3] ML tree search #16, logLikelihood: -65872.152614 [04:05:28 -132378.833239] AUTODETECT spr round 3 (radius: 15) [04:08:22 -113708.947979] AUTODETECT spr round 4 (radius: 20) [04:11:45 -94416.989133] AUTODETECT spr round 5 (radius: 25) [04:15:22 -80371.848438] SPR radius for FAST iterations: 25 (autodetect) [04:15:22 -80371.848438] Model parameter optimization (eps = 3.000000) [04:15:43 -80128.535299] FAST spr round 1 (radius: 25) [04:18:25 -66879.240089] FAST spr round 2 (radius: 25) [04:20:23 -65937.243171] FAST spr round 3 (radius: 25) [04:22:12 -65869.259768] FAST spr round 4 (radius: 25) [04:23:52 -65862.798522] FAST spr round 5 (radius: 25) [04:25:27 -65862.215514] FAST spr round 6 (radius: 25) [04:27:00 -65861.348291] FAST spr round 7 (radius: 25) [04:28:31 -65861.348215] Model parameter optimization (eps = 1.000000) [04:28:56 -65858.008373] SLOW spr round 1 (radius: 5) [04:31:03 -65842.840624] SLOW spr round 2 (radius: 5) [04:33:08 -65840.190788] SLOW spr round 3 (radius: 5) [04:35:10 -65840.096058] SLOW spr round 4 (radius: 10) [04:37:12 -65838.980743] SLOW spr round 5 (radius: 5) [04:39:40 -65838.980718] SLOW spr round 6 (radius: 10) [04:41:57 -65838.980717] SLOW spr round 7 (radius: 15) [04:44:27] [worker #2] ML tree search #15, logLikelihood: -65830.993357 [04:44:51 -65838.980717] SLOW spr round 8 (radius: 20) [04:49:20 -65838.980716] SLOW spr round 9 (radius: 25) [04:54:07] [worker #1] ML tree search #14, logLikelihood: -65865.394758 [04:55:07 -65838.980716] Model parameter optimization (eps = 0.100000) [04:55:12] [worker #0] ML tree search #17, logLikelihood: -65838.971579 [05:05:29] [worker #3] ML tree search #20, logLikelihood: -65824.651074 [05:49:50] [worker #1] ML tree search #18, logLikelihood: -65825.189047 [05:56:28] [worker #2] ML tree search #19, logLikelihood: -65865.832256 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.157746,0.308344) (0.261569,0.406862) (0.402232,1.078514) (0.178452,2.303830) 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: -65818.939016 AIC score: 135623.878033 / AICc score: 8083707.878033 / BIC score: 142177.394225 Free parameters (model + branch lengths): 1993 WARNING: Number of free parameters (K=1993) is larger than alignment size (n=198). 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/Q7Z5H3/3_mltree/Q7Z5H3.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/3_mltree/Q7Z5H3.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/3_mltree/Q7Z5H3.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z5H3/3_mltree/Q7Z5H3.raxml.log Analysis started: 02-Jul-2021 08:24:19 / finished: 02-Jul-2021 14:20:47 Elapsed time: 21388.418 seconds Consumed energy: 1651.919 Wh (= 8 km in an electric car, or 41 km with an e-scooter!)