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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 14-Jul-2021 23:14:07 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RXF5/2_msa/B2RXF5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RXF5/3_mltree/B2RXF5 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RXF5/2_msa/B2RXF5_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 223 sites WARNING: Sequences tr_B4Q340_B4Q340_DROSI_7240 and sp_P20385_CF2_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QUF3_B4QUF3_DROSI_7240 and sp_P13360_GLAS_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QUF3_B4QUF3_DROSI_7240 and tr_B4I295_B4I295_DROSE_7238 are exactly identical! WARNING: Sequences tr_H0WEV6_H0WEV6_DANRE_7955 and tr_K7DYF2_K7DYF2_DANRE_7955 are exactly identical! WARNING: Sequences tr_E1C4C1_E1C4C1_CHICK_9031 and tr_G1NG24_G1NG24_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1C4C1_E1C4C1_CHICK_9031 and tr_A0A093ILQ2_A0A093ILQ2_DRYPU_118200 are exactly identical! WARNING: Sequences tr_E1C4C1_E1C4C1_CHICK_9031 and tr_A0A226PLU0_A0A226PLU0_COLVI_9014 are exactly identical! WARNING: Sequences tr_F1NVH0_F1NVH0_CHICK_9031 and tr_U3J4Y9_U3J4Y9_ANAPL_8839 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_M3Z4A3_M3Z4A3_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_A0A2I3GAA6_A0A2I3GAA6_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_A0A2I2YTK4_A0A2I2YTK4_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_H2PRQ1_H2PRQ1_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_J9PBG1_J9PBG1_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_H2QXA0_H2QXA0_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_I3NBV8_I3NBV8_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and sp_O15062_ZBTB5_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_F7F1G9_F7F1G9_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_G7PRX1_G7PRX1_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_A0A2I3MLG0_A0A2I3MLG0_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_A0A0D9S9K8_A0A0D9S9K8_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_A0A1U7UQ51_A0A1U7UQ51_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_A0A2K5KZI2_A0A2K5KZI2_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_A0A2K6B297_A0A2K6B297_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_A0A2K5XS01_A0A2K5XS01_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_A0A2R8ZEG4_A0A2R8ZEG4_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q7TQG0_ZBTB5_MOUSE_10090 and tr_A0A2Y9J9T6_A0A2Y9J9T6_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_G3SB87_G3SB87_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_H2N389_H2N389_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_G1SU62_G1SU62_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_H2Q1F5_H2Q1F5_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_I3M3Y2_I3M3Y2_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_H0XY56_H0XY56_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_A0A286Y481_A0A286Y481_CAVPO_10141 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and sp_Q99592_ZBT18_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_F7IJR1_F7IJR1_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_G7NWL2_G7NWL2_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_L5KH13_L5KH13_PTEAL_9402 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_A0A096MXN0_A0A096MXN0_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_A0A1U7TI82_A0A1U7TI82_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_A0A1U7R2L8_A0A1U7R2L8_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_A0A2K5NC99_A0A2K5NC99_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_A0A2K5XQ34_A0A2K5XQ34_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q9WUK6_ZBT18_MOUSE_10090 and tr_A0A2R9B6N2_A0A2R9B6N2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3G9G1_A0A2I3G9G1_NOMLE_61853 and tr_H2ND43_H2ND43_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_G3RQB6_G3RQB6_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_H2NWL7_H2NWL7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_H2QEQ6_H2QEQ6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and sp_Q9UL36_ZN236_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_A0A1D5QSW3_A0A1D5QSW3_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_G5C0K8_G5C0K8_HETGA_10181 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_G7PW99_G7PW99_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_A0A2I3MNE4_A0A2I3MNE4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_A0A0D9S067_A0A0D9S067_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_A0A2K5M0C3_A0A2K5M0C3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_A0A2K6D1J3_A0A2K6D1J3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_A0A2K5Z066_A0A2K5Z066_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_A0A2R9BWH1_A0A2R9BWH1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3IMW9_G3IMW9_CRIGR_10029 and tr_D3ZGK0_D3ZGK0_RAT_10116 are exactly identical! WARNING: Sequences tr_G3IMW9_G3IMW9_CRIGR_10029 and tr_I3LUL2_I3LUL2_PIG_9823 are exactly identical! WARNING: Sequences tr_G3IMW9_G3IMW9_CRIGR_10029 and tr_E1BLD0_E1BLD0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G3IMW9_G3IMW9_CRIGR_10029 and tr_A0A1S3ERQ3_A0A1S3ERQ3_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G3IMW9_G3IMW9_CRIGR_10029 and tr_A0A2Y9PFD2_A0A2Y9PFD2_DELLE_9749 are exactly identical! WARNING: Sequences tr_G3IMW9_G3IMW9_CRIGR_10029 and tr_A0A2Y9ESU6_A0A2Y9ESU6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G3R7U7_G3R7U7_GORGO_9595 and tr_H2Q3W8_H2Q3W8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R7U7_G3R7U7_GORGO_9595 and sp_Q9H5J0_ZBTB3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R7U7_G3R7U7_GORGO_9595 and tr_A0A2R9AND7_A0A2R9AND7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R8Q3_G3R8Q3_GORGO_9595 and tr_H2N8Y5_H2N8Y5_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3R8Q3_G3R8Q3_GORGO_9595 and tr_H2PY43_H2PY43_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R8Q3_G3R8Q3_GORGO_9595 and tr_A0A2R9B2P9_A0A2R9B2P9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SGB9_G3SGB9_GORGO_9595 and tr_A0A096NMG9_A0A096NMG9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3SGB9_G3SGB9_GORGO_9595 and tr_A0A0D9R0P6_A0A0D9R0P6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3SGB9_G3SGB9_GORGO_9595 and tr_A0A2K5LXX5_A0A2K5LXX5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3SGB9_G3SGB9_GORGO_9595 and tr_A0A2K6BD17_A0A2K6BD17_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3SGB9_G3SGB9_GORGO_9595 and tr_A0A2K5ZE25_A0A2K5ZE25_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2J8TIN0_A0A2J8TIN0_PONAB_9601 and tr_H2QNP9_H2QNP9_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2J8TIN0_A0A2J8TIN0_PONAB_9601 and sp_Q9NPC7_MYNN_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8TIN0_A0A2J8TIN0_PONAB_9601 and tr_F6UBH1_F6UBH1_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2J8TIN0_A0A2J8TIN0_PONAB_9601 and tr_G7NZG3_G7NZG3_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2J8TIN0_A0A2J8TIN0_PONAB_9601 and tr_A0A096N2E1_A0A096N2E1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2J8TIN0_A0A2J8TIN0_PONAB_9601 and tr_A0A0D9RJE6_A0A0D9RJE6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2J8TIN0_A0A2J8TIN0_PONAB_9601 and tr_A0A2K5NH27_A0A2K5NH27_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2J8TIN0_A0A2J8TIN0_PONAB_9601 and tr_A0A2K6E4J3_A0A2K6E4J3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2J8TIN0_A0A2J8TIN0_PONAB_9601 and tr_A0A2K5YM74_A0A2K5YM74_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2J8TIN0_A0A2J8TIN0_PONAB_9601 and tr_A0A2R8Z7Q2_A0A2R8Z7Q2_PANPA_9597 are exactly identical! WARNING: Sequences tr_F1PSY3_F1PSY3_CANLF_9615 and tr_A0A337SHN3_A0A337SHN3_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1PSY3_F1PSY3_CANLF_9615 and tr_A0A2U3W9W8_A0A2U3W9W8_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1PSY3_F1PSY3_CANLF_9615 and tr_A0A2Y9IGY7_A0A2Y9IGY7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2J8IY56_A0A2J8IY56_PANTR_9598 and tr_A0A2R8ZHZ1_A0A2R8ZHZ1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PYK7_H2PYK7_PANTR_9598 and tr_G7NWY2_G7NWY2_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2PYK7_H2PYK7_PANTR_9598 and tr_A0A096MW42_A0A096MW42_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PYK7_H2PYK7_PANTR_9598 and tr_A0A0D9S7W7_A0A0D9S7W7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2PYK7_H2PYK7_PANTR_9598 and tr_A0A2K6CQ35_A0A2K6CQ35_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PYK7_H2PYK7_PANTR_9598 and tr_A0A2K5XDV1_A0A2K5XDV1_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2R2T4_H2R2T4_PANTR_9598 and sp_Q3KNS6_ZN829_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R2T4_H2R2T4_PANTR_9598 and tr_A0A2R9B3L5_A0A2R9B3L5_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7B3F6_F7B3F6_MONDO_13616 and tr_G3W3K4_G3W3K4_SARHA_9305 are exactly identical! WARNING: Sequences tr_A0A158NHM0_A0A158NHM0_ATTCE_12957 and tr_A0A151I603_A0A151I603_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NHM0_A0A158NHM0_ATTCE_12957 and tr_A0A195AZB7_A0A195AZB7_9HYME_520822 are exactly identical! WARNING: Sequences tr_I3N528_I3N528_ICTTR_43179 and tr_A0A3Q0DGS0_A0A3Q0DGS0_MESAU_10036 are exactly identical! WARNING: Sequences tr_H0XT84_H0XT84_OTOGA_30611 and tr_A0A384DGA7_A0A384DGA7_URSMA_29073 are exactly identical! WARNING: Sequences sp_Q6DD87_ZN787_HUMAN_9606 and tr_A0A0A0MX46_A0A0A0MX46_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q6DD87_ZN787_HUMAN_9606 and tr_A0A0D9S655_A0A0D9S655_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q6DD87_ZN787_HUMAN_9606 and tr_A0A2K5M686_A0A2K5M686_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q6DD87_ZN787_HUMAN_9606 and tr_A0A2K6DGP5_A0A2K6DGP5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5Q6Y1_A0A1D5Q6Y1_MACMU_9544 and tr_G7PPT1_G7PPT1_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5Q6Y1_A0A1D5Q6Y1_MACMU_9544 and tr_A0A096MPD9_A0A096MPD9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5Q6Y1_A0A1D5Q6Y1_MACMU_9544 and tr_A0A0D9R311_A0A0D9R311_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5Q6Y1_A0A1D5Q6Y1_MACMU_9544 and tr_A0A2K5M889_A0A2K5M889_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5Q6Y1_A0A1D5Q6Y1_MACMU_9544 and tr_A0A2K6BY89_A0A2K6BY89_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5Q6Y1_A0A1D5Q6Y1_MACMU_9544 and tr_A0A2K6AA03_A0A2K6AA03_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1D5QWU3_A0A1D5QWU3_MACMU_9544 and tr_G7PXD9_G7PXD9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6QNH1_F6QNH1_MACMU_9544 and tr_G7PBR0_G7PBR0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_G7PXE3_G7PXE3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A0A0MUP5_A0A0A0MUP5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A2K5MYE8_A0A2K5MYE8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A2K6CUG7_A0A2K6CUG7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A2K5ZQH5_A0A2K5ZQH5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5C1E0_G5C1E0_HETGA_10181 and tr_F6QDR1_F6QDR1_CALJA_9483 are exactly identical! WARNING: Sequences tr_K7F5U9_K7F5U9_PELSI_13735 and tr_A0A0Q3Q0R8_A0A0Q3Q0R8_AMAAE_12930 are exactly identical! WARNING: Sequences tr_K7F5U9_K7F5U9_PELSI_13735 and tr_A0A087QIT8_A0A087QIT8_APTFO_9233 are exactly identical! WARNING: Sequences tr_K7F5U9_K7F5U9_PELSI_13735 and tr_A0A093HP89_A0A093HP89_STRCA_441894 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_U3KAB9_U3KAB9_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A0Q3PWD5_A0A0Q3PWD5_AMAAE_12930 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A091EVF8_A0A091EVF8_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A091JIH7_A0A091JIH7_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A093SF50_A0A093SF50_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A091VN07_A0A091VN07_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A087QHZ4_A0A087QHZ4_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A093HTL8_A0A093HTL8_STRCA_441894 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A091WM29_A0A091WM29_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A099ZCC3_A0A099ZCC3_TINGU_94827 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A091G210_A0A091G210_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A0A0B1R9_A0A0A0B1R9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A2I0MV20_A0A2I0MV20_COLLI_8932 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A091IMV5_A0A091IMV5_CALAN_9244 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A1U7RRV9_A0A1U7RRV9_ALLSI_38654 are exactly identical! WARNING: Sequences tr_H0ZD33_H0ZD33_TAEGU_59729 and tr_A0A218V376_A0A218V376_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZFL5_H0ZFL5_TAEGU_59729 and tr_U3JQ35_U3JQ35_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZFL5_H0ZFL5_TAEGU_59729 and tr_A0A218VE19_A0A218VE19_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A1B8YA55_A0A1B8YA55_XENTR_8364 and tr_F6QDF7_F6QDF7_XENTR_8364 are exactly identical! WARNING: Sequences tr_G7NU92_G7NU92_MACFA_9541 and tr_A0A096N2Z6_A0A096N2Z6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7NU92_G7NU92_MACFA_9541 and tr_A0A2K5M274_A0A2K5M274_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7NU92_G7NU92_MACFA_9541 and tr_A0A2K6CXM9_A0A2K6CXM9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NU92_G7NU92_MACFA_9541 and tr_A0A2K5XBB8_A0A2K5XBB8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A140T829_A0A140T829_BOVIN_9913 and sp_A0JN76_ZBT18_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A140T829_A0A140T829_BOVIN_9913 and tr_A0A1S3AGU1_A0A1S3AGU1_ERIEU_9365 are exactly identical! WARNING: Sequences tr_A0A140T829_A0A140T829_BOVIN_9913 and tr_A0A2U4A4Z6_A0A2U4A4Z6_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A140T829_A0A140T829_BOVIN_9913 and tr_A0A2Y9NZB5_A0A2Y9NZB5_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A140T829_A0A140T829_BOVIN_9913 and tr_A0A2Y9EUF7_A0A2Y9EUF7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A140T829_A0A140T829_BOVIN_9913 and tr_A0A384A566_A0A384A566_BALAS_310752 are exactly identical! WARNING: Sequences tr_U3KKF9_U3KKF9_FICAL_59894 and tr_A0A091F2V0_A0A091F2V0_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3KKF9_U3KKF9_FICAL_59894 and tr_A0A093Q5I6_A0A093Q5I6_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3KKF9_U3KKF9_FICAL_59894 and tr_A0A091GXC3_A0A091GXC3_9AVES_55661 are exactly identical! WARNING: Sequences tr_U3KKF9_U3KKF9_FICAL_59894 and tr_A0A0A0A8Q5_A0A0A0A8Q5_CHAVO_50402 are exactly identical! WARNING: Sequences tr_U3KKF9_U3KKF9_FICAL_59894 and tr_A0A093FVM7_A0A093FVM7_DRYPU_118200 are exactly identical! WARNING: Sequences tr_U3KKF9_U3KKF9_FICAL_59894 and tr_A0A218UQU5_A0A218UQU5_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A0P7XTQ1_A0A0P7XTQ1_9TELE_113540 and tr_A0A0P7XUC2_A0A0P7XUC2_9TELE_113540 are exactly identical! WARNING: Sequences tr_A0A151NDU7_A0A151NDU7_ALLMI_8496 and tr_A0A1U7RWH2_A0A1U7RWH2_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A2I0MVS7_A0A2I0MVS7_COLLI_8932 and tr_A0A1V4J8V1_A0A1V4J8V1_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3L4L6_A0A1S3L4L6_SALSA_8030 and tr_A0A1S3QMF7_A0A1S3QMF7_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3L4L6_A0A1S3L4L6_SALSA_8030 and tr_A0A1S3QPZ6_A0A1S3QPZ6_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A226MBR8_A0A226MBR8_CALSU_9009 and tr_A0A226MBN3_A0A226MBN3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PWX8_A0A2D0PWX8_ICTPU_7998 and tr_W5UIU2_W5UIU2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QNP1_A0A2D0QNP1_ICTPU_7998 and tr_A0A2D0QR25_A0A2D0QR25_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KJ38_A0A2K5KJ38_CERAT_9531 and tr_A0A2K5YUD4_A0A2K5YUD4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3V302_A0A2U3V302_TURTR_9739 and tr_A0A2U4CGK6_A0A2U4CGK6_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U3V302_A0A2U3V302_TURTR_9739 and tr_A0A2Y9QDT8_A0A2Y9QDT8_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V302_A0A2U3V302_TURTR_9739 and tr_A0A384BBJ3_A0A384BBJ3_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4B4Z9_A0A2U4B4Z9_TURTR_9739 and tr_A0A2Y9PWI0_A0A2Y9PWI0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3WYK2_A0A2U3WYK2_ODORO_9708 and tr_A0A2U3YPS2_A0A2U3YPS2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3YZA2_A0A2U3YZA2_LEPWE_9713 and tr_A0A2Y9JTI6_A0A2Y9JTI6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2Y9K7X4_A0A2Y9K7X4_ENHLU_391180 and tr_A0A2Y9K8U2_A0A2Y9K8U2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2Y9PDP0_A0A2Y9PDP0_DELLE_9749 and tr_A0A2Y9S651_A0A2Y9S651_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9QFT2_A0A2Y9QFT2_DELLE_9749 and tr_A0A2Y9FQ43_A0A2Y9FQ43_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 174 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RXF5/3_mltree/B2RXF5.raxml.reduced.phy Alignment comprises 1 partitions and 223 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 223 / 223 Gaps: 13.80 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RXF5/3_mltree/B2RXF5.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 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 223 / 17840 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -397375.972902] Initial branch length optimization [00:00:07 -337707.434254] Model parameter optimization (eps = 10.000000) [00:01:03 -336769.887743] AUTODETECT spr round 1 (radius: 5) [00:04:29 -201758.243611] AUTODETECT spr round 2 (radius: 10) [00:07:54 -146173.888056] AUTODETECT spr round 3 (radius: 15) [00:11:37 -123870.097769] AUTODETECT spr round 4 (radius: 20) [00:16:02 -106309.847412] AUTODETECT spr round 5 (radius: 25) [00:21:33 -99770.965276] SPR radius for FAST iterations: 25 (autodetect) [00:21:33 -99770.965276] Model parameter optimization (eps = 3.000000) [00:22:03 -99543.010922] FAST spr round 1 (radius: 25) [00:26:12 -89179.038471] FAST spr round 2 (radius: 25) [00:29:28 -88647.294257] FAST spr round 3 (radius: 25) [00:32:15 -88592.006482] FAST spr round 4 (radius: 25) [00:34:49 -88575.186057] FAST spr round 5 (radius: 25) [00:37:15 -88556.815727] FAST spr round 6 (radius: 25) [00:39:37 -88556.813520] Model parameter optimization (eps = 1.000000) [00:39:55 -88552.155313] SLOW spr round 1 (radius: 5) [00:42:56 -88514.820094] SLOW spr round 2 (radius: 5) [00:45:56 -88500.754171] SLOW spr round 3 (radius: 5) [00:48:48 -88499.581756] SLOW spr round 4 (radius: 5) [00:51:37 -88499.580192] SLOW spr round 5 (radius: 10) [00:54:39 -88490.564339] SLOW spr round 6 (radius: 5) [00:58:10 -88489.821845] SLOW spr round 7 (radius: 5) [01:01:16 -88489.821715] SLOW spr round 8 (radius: 10) [01:04:23 -88484.277361] SLOW spr round 9 (radius: 5) [01:07:51 -88483.766262] SLOW spr round 10 (radius: 5) [01:10:58 -88483.766084] SLOW spr round 11 (radius: 10) [01:14:03 -88483.766084] SLOW spr round 12 (radius: 15) [01:19:10 -88477.975207] SLOW spr round 13 (radius: 5) [01:22:49 -88470.761205] SLOW spr round 14 (radius: 5) [01:26:06 -88463.447223] SLOW spr round 15 (radius: 5) [01:29:09 -88461.312585] SLOW spr round 16 (radius: 5) [01:32:00 -88461.312472] SLOW spr round 17 (radius: 10) [01:34:57 -88461.312453] SLOW spr round 18 (radius: 15) [01:40:03 -88458.909679] SLOW spr round 19 (radius: 5) [01:43:41 -88458.419059] SLOW spr round 20 (radius: 5) [01:46:52 -88458.418997] SLOW spr round 21 (radius: 10) [01:49:58 -88458.418992] SLOW spr round 22 (radius: 15) [01:54:55 -88458.418991] SLOW spr round 23 (radius: 20) [02:00:08] [worker #3] ML tree search #4, logLikelihood: -88476.193509 [02:01:44 -88457.861604] SLOW spr round 24 (radius: 5) [02:05:26 -88457.534214] SLOW spr round 25 (radius: 5) [02:08:42 -88457.173889] SLOW spr round 26 (radius: 5) [02:11:42 -88457.173798] SLOW spr round 27 (radius: 10) [02:14:43 -88457.113718] SLOW spr round 28 (radius: 15) [02:19:43 -88457.113300] SLOW spr round 29 (radius: 20) [02:26:27 -88457.113292] SLOW spr round 30 (radius: 25) [02:29:45] [worker #2] ML tree search #3, logLikelihood: -88444.306904 [02:34:29 -88456.626383] SLOW spr round 31 (radius: 5) [02:38:11 -88456.626102] SLOW spr round 32 (radius: 10) [02:41:53 -88456.626091] SLOW spr round 33 (radius: 15) [02:46:37] [worker #1] ML tree search #2, logLikelihood: -88478.807316 [02:46:40 -88456.626090] SLOW spr round 34 (radius: 20) [02:53:35 -88456.626089] SLOW spr round 35 (radius: 25) [03:01:37 -88456.626089] Model parameter optimization (eps = 0.100000) [03:01:50] [worker #0] ML tree search #1, logLikelihood: -88456.396120 [03:01:50 -395627.907464] Initial branch length optimization [03:01:56 -336968.850304] Model parameter optimization (eps = 10.000000) [03:02:57 -336030.838696] AUTODETECT spr round 1 (radius: 5) [03:06:23 -205076.367483] AUTODETECT spr round 2 (radius: 10) [03:09:54 -143738.876606] AUTODETECT spr round 3 (radius: 15) [03:13:49 -116964.442150] AUTODETECT spr round 4 (radius: 20) [03:18:20 -104556.362975] AUTODETECT spr round 5 (radius: 25) [03:24:32 -99670.887932] SPR radius for FAST iterations: 25 (autodetect) [03:24:32 -99670.887932] Model parameter optimization (eps = 3.000000) [03:25:09 -99485.513949] FAST spr round 1 (radius: 25) [03:29:11 -89062.771830] FAST spr round 2 (radius: 25) [03:32:20 -88590.627451] FAST spr round 3 (radius: 25) [03:35:05 -88534.168573] FAST spr round 4 (radius: 25) [03:37:32 -88528.884349] FAST spr round 5 (radius: 25) [03:39:48 -88527.347790] FAST spr round 6 (radius: 25) [03:42:00 -88527.347512] Model parameter optimization (eps = 1.000000) [03:42:12 -88526.584003] SLOW spr round 1 (radius: 5) [03:45:07 -88497.873646] SLOW spr round 2 (radius: 5) [03:48:04 -88491.717208] SLOW spr round 3 (radius: 5) [03:50:54 -88491.716469] SLOW spr round 4 (radius: 10) [03:54:02 -88486.270226] SLOW spr round 5 (radius: 5) [03:57:37 -88480.342393] SLOW spr round 6 (radius: 5) [04:00:47 -88480.234174] SLOW spr round 7 (radius: 5) [04:03:44 -88480.231811] SLOW spr round 8 (radius: 10) [04:06:48 -88480.231601] SLOW spr round 9 (radius: 15) [04:12:03 -88473.639422] SLOW spr round 10 (radius: 5) [04:15:47 -88466.275611] SLOW spr round 11 (radius: 5) [04:19:00 -88466.275276] SLOW spr round 12 (radius: 10) [04:22:11 -88466.275233] SLOW spr round 13 (radius: 15) [04:27:12 -88466.275221] SLOW spr round 14 (radius: 20) [04:34:34 -88466.275217] SLOW spr round 15 (radius: 25) [04:41:39] [worker #1] ML tree search #6, logLikelihood: -88458.641424 [04:42:59 -88465.073620] SLOW spr round 16 (radius: 5) [04:46:44 -88465.073609] SLOW spr round 17 (radius: 10) [04:50:39 -88465.073605] SLOW spr round 18 (radius: 15) [04:55:30 -88465.073604] SLOW spr round 19 (radius: 20) [04:58:40] [worker #2] ML tree search #7, logLikelihood: -88454.514232 [05:02:57 -88465.073603] SLOW spr round 20 (radius: 25) [05:11:23 -88465.073602] Model parameter optimization (eps = 0.100000) [05:11:33] [worker #0] ML tree search #5, logLikelihood: -88465.014422 [05:11:33 -396779.502267] Initial branch length optimization [05:11:39 -338091.708714] Model parameter optimization (eps = 10.000000) [05:12:31 -337410.159705] AUTODETECT spr round 1 (radius: 5) [05:15:56 -207647.885653] AUTODETECT spr round 2 (radius: 10) [05:19:32 -151473.240775] AUTODETECT spr round 3 (radius: 15) [05:23:25 -128659.381512] AUTODETECT spr round 4 (radius: 20) [05:26:49] [worker #3] ML tree search #8, logLikelihood: -88479.679140 [05:27:42 -114806.539570] AUTODETECT spr round 5 (radius: 25) [05:33:06 -103164.758284] SPR radius for FAST iterations: 25 (autodetect) [05:33:06 -103164.758284] Model parameter optimization (eps = 3.000000) [05:33:44 -102859.435741] FAST spr round 1 (radius: 25) [05:38:08 -89208.592779] FAST spr round 2 (radius: 25) [05:41:39 -88678.284746] FAST spr round 3 (radius: 25) [05:44:34 -88570.507313] FAST spr round 4 (radius: 25) [05:47:15 -88533.646265] FAST spr round 5 (radius: 25) [05:49:35 -88529.619886] FAST spr round 6 (radius: 25) [05:51:52 -88522.724793] FAST spr round 7 (radius: 25) [05:54:02 -88522.724691] Model parameter optimization (eps = 1.000000) [05:54:19 -88517.707129] SLOW spr round 1 (radius: 5) [05:57:16 -88488.358230] SLOW spr round 2 (radius: 5) [06:00:12 -88486.078757] SLOW spr round 3 (radius: 5) [06:02:59 -88486.078102] SLOW spr round 4 (radius: 10) [06:05:55 -88486.010382] SLOW spr round 5 (radius: 15) [06:11:03 -88486.010379] SLOW spr round 6 (radius: 20) [06:17:43 -88484.277379] SLOW spr round 7 (radius: 5) [06:19:09] [worker #1] ML tree search #10, logLikelihood: -88464.408906 [06:21:27 -88483.758453] SLOW spr round 8 (radius: 5) [06:24:43 -88483.757563] SLOW spr round 9 (radius: 10) [06:27:55 -88483.411260] SLOW spr round 10 (radius: 5) [06:31:18 -88483.410909] SLOW spr round 11 (radius: 10) [06:34:36 -88483.410866] SLOW spr round 12 (radius: 15) [06:39:35 -88481.232593] SLOW spr round 13 (radius: 5) [06:43:15 -88473.923560] SLOW spr round 14 (radius: 5) [06:46:30 -88473.680823] SLOW spr round 15 (radius: 5) [06:49:29 -88473.680736] SLOW spr round 16 (radius: 10) [06:52:30 -88473.680691] SLOW spr round 17 (radius: 15) [06:52:37] [worker #2] ML tree search #11, logLikelihood: -88460.077020 [06:57:41 -88473.232206] SLOW spr round 18 (radius: 5) [07:01:18 -88473.129301] SLOW spr round 19 (radius: 5) [07:04:29 -88473.129178] SLOW spr round 20 (radius: 10) [07:07:37 -88473.129138] SLOW spr round 21 (radius: 15) [07:12:40 -88473.129104] SLOW spr round 22 (radius: 20) [07:18:57] [worker #3] ML tree search #12, logLikelihood: -88457.034650 [07:19:31 -88473.129069] SLOW spr round 23 (radius: 25) [07:28:03 -88473.129043] Model parameter optimization (eps = 0.100000) [07:28:14] [worker #0] ML tree search #9, logLikelihood: -88473.029928 [07:28:15 -395274.279568] Initial branch length optimization [07:28:25 -335628.029085] Model parameter optimization (eps = 10.000000) [07:29:11 -334746.100713] AUTODETECT spr round 1 (radius: 5) [07:32:40 -209988.632611] AUTODETECT spr round 2 (radius: 10) [07:36:16 -148598.070255] AUTODETECT spr round 3 (radius: 15) [07:40:05 -118365.028245] AUTODETECT spr round 4 (radius: 20) [07:44:17 -107497.868873] AUTODETECT spr round 5 (radius: 25) [07:48:48 -104267.391468] SPR radius for FAST iterations: 25 (autodetect) [07:48:48 -104267.391468] Model parameter optimization (eps = 3.000000) [07:49:26 -104070.322683] FAST spr round 1 (radius: 25) [07:53:42 -89741.029066] FAST spr round 2 (radius: 25) [07:56:56 -88683.983057] FAST spr round 3 (radius: 25) [07:58:06] [worker #1] ML tree search #14, logLikelihood: -88473.804224 [07:59:47 -88559.848382] FAST spr round 4 (radius: 25) [08:02:22 -88539.879240] FAST spr round 5 (radius: 25) [08:04:45 -88538.941886] FAST spr round 6 (radius: 25) [08:07:03 -88538.941864] Model parameter optimization (eps = 1.000000) [08:07:23 -88534.105939] SLOW spr round 1 (radius: 5) [08:10:25 -88498.303935] SLOW spr round 2 (radius: 5) [08:13:23 -88497.518226] SLOW spr round 3 (radius: 5) [08:16:21 -88497.517732] SLOW spr round 4 (radius: 10) [08:19:27 -88485.545629] SLOW spr round 5 (radius: 5) [08:23:05 -88479.774920] SLOW spr round 6 (radius: 5) [08:26:22 -88473.426155] SLOW spr round 7 (radius: 5) [08:29:23 -88473.425817] SLOW spr round 8 (radius: 10) [08:32:26 -88472.746705] SLOW spr round 9 (radius: 5) [08:35:59 -88472.148737] SLOW spr round 10 (radius: 5) [08:39:11 -88468.298393] SLOW spr round 11 (radius: 5) [08:42:10 -88468.298340] SLOW spr round 12 (radius: 10) [08:45:11 -88468.298333] SLOW spr round 13 (radius: 15) [08:50:15 -88468.298326] SLOW spr round 14 (radius: 20) [08:57:13 -88468.045461] SLOW spr round 15 (radius: 5) [09:00:54 -88468.045438] SLOW spr round 16 (radius: 10) [09:04:31 -88468.045437] SLOW spr round 17 (radius: 15) [09:09:20 -88468.045437] SLOW spr round 18 (radius: 20) [09:13:17] [worker #2] ML tree search #15, logLikelihood: -88501.497002 [09:16:24 -88468.045437] SLOW spr round 19 (radius: 25) [09:16:31] [worker #3] ML tree search #16, logLikelihood: -88499.721236 [09:24:36 -88468.045437] Model parameter optimization (eps = 0.100000) [09:24:47] [worker #0] ML tree search #13, logLikelihood: -88467.810366 [09:24:48 -399212.906943] Initial branch length optimization [09:24:55 -340749.621352] Model parameter optimization (eps = 10.000000) [09:25:44 -339924.905299] AUTODETECT spr round 1 (radius: 5) [09:29:13 -210957.385582] AUTODETECT spr round 2 (radius: 10) [09:32:49 -143885.744384] AUTODETECT spr round 3 (radius: 15) [09:36:39 -118474.080769] AUTODETECT spr round 4 (radius: 20) [09:41:05 -104960.042449] AUTODETECT spr round 5 (radius: 25) [09:46:14 -100390.103732] SPR radius for FAST iterations: 25 (autodetect) [09:46:14 -100390.103732] Model parameter optimization (eps = 3.000000) [09:46:53 -100219.317545] FAST spr round 1 (radius: 25) [09:51:20 -89281.423729] FAST spr round 2 (radius: 25) [09:54:45 -88665.435680] FAST spr round 3 (radius: 25) [09:54:52] [worker #1] ML tree search #18, logLikelihood: -88500.746326 [09:57:42 -88547.756891] FAST spr round 4 (radius: 25) [10:00:13 -88539.582341] FAST spr round 5 (radius: 25) [10:02:34 -88538.000418] FAST spr round 6 (radius: 25) [10:04:50 -88537.843216] FAST spr round 7 (radius: 25) [10:07:04 -88537.843211] Model parameter optimization (eps = 1.000000) [10:07:25 -88528.461568] SLOW spr round 1 (radius: 5) [10:10:26 -88490.179219] SLOW spr round 2 (radius: 5) [10:13:24 -88479.519925] SLOW spr round 3 (radius: 5) [10:16:22 -88475.401102] SLOW spr round 4 (radius: 5) [10:19:13 -88474.982229] SLOW spr round 5 (radius: 5) [10:22:02 -88474.981578] SLOW spr round 6 (radius: 10) [10:25:02 -88471.865199] SLOW spr round 7 (radius: 5) [10:28:39 -88469.037615] SLOW spr round 8 (radius: 5) [10:31:47 -88469.037154] SLOW spr round 9 (radius: 10) [10:34:55 -88469.037107] SLOW spr round 10 (radius: 15) [10:40:03 -88464.670852] SLOW spr round 11 (radius: 5) [10:43:46 -88464.359602] SLOW spr round 12 (radius: 5) [10:47:02 -88464.274385] SLOW spr round 13 (radius: 10) [10:50:12 -88464.273908] SLOW spr round 14 (radius: 15) [10:55:15 -88464.273845] SLOW spr round 15 (radius: 20) [11:02:11 -88464.273826] SLOW spr round 16 (radius: 25) [11:10:20 -88464.273820] Model parameter optimization (eps = 0.100000) [11:10:34] [worker #0] ML tree search #17, logLikelihood: -88463.748778 [11:23:16] [worker #2] ML tree search #19, logLikelihood: -88453.793019 [11:48:32] [worker #3] ML tree search #20, logLikelihood: -88458.936935 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.145891,0.412903) (0.121298,1.092501) (0.420716,0.907612) (0.312095,1.363033) 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: -88444.306904 AIC score: 180898.613807 / AICc score: 8224958.613807 / BIC score: 187729.993209 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=223). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 1 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RXF5/3_mltree/B2RXF5.raxml.bestTreeCollapsed Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RXF5/3_mltree/B2RXF5.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RXF5/3_mltree/B2RXF5.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RXF5/3_mltree/B2RXF5.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/B2RXF5/3_mltree/B2RXF5.raxml.log Analysis started: 14-Jul-2021 23:14:07 / finished: 15-Jul-2021 11:02:39 Elapsed time: 42512.529 seconds