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 03-Jul-2021 04:37:23 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BX66/2_msa/Q9BX66_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BX66/3_mltree/Q9BX66 --seed 2 --threads 5 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BX66/2_msa/Q9BX66_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 308 sites WARNING: Sequences tr_A0A2R8QQ83_A0A2R8QQ83_DANRE_7955 and tr_F1QI09_F1QI09_DANRE_7955 are exactly identical! WARNING: Sequences tr_G1QW71_G1QW71_NOMLE_61853 and tr_G3R1Q3_G3R1Q3_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QW71_G1QW71_NOMLE_61853 and tr_A0A2I3T6F5_A0A2I3T6F5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QW71_G1QW71_NOMLE_61853 and tr_A0A2R9C3H9_A0A2R9C3H9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1R4A9_G1R4A9_NOMLE_61853 and tr_G3QD49_G3QD49_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R4A9_G1R4A9_NOMLE_61853 and tr_H2PEQ5_H2PEQ5_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R4A9_G1R4A9_NOMLE_61853 and tr_H2QQE8_H2QQE8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R4A9_G1R4A9_NOMLE_61853 and sp_Q7Z6J0_SH3R1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QX93_G3QX93_GORGO_9595 and tr_H2QHJ1_H2QHJ1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QX93_G3QX93_GORGO_9595 and sp_Q9NZM3_ITSN2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QYX0_G3QYX0_GORGO_9595 and tr_K7BC55_K7BC55_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3RAC2_A0A2I3RAC2_PANTR_9598 and tr_A0A2R9A053_A0A2R9A053_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3RPI3_A0A2I3RPI3_PANTR_9598 and tr_A0A2R9AN70_A0A2R9AN70_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QQJ1_H2QQJ1_PANTR_9598 and tr_A0A2R8ZYI3_A0A2R8ZYI3_PANPA_9597 are exactly identical! WARNING: Sequences tr_M4APC0_M4APC0_XIPMA_8083 and tr_A0A087XG44_A0A087XG44_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A1D5RIB7_A0A1D5RIB7_MACMU_9544 and tr_A0A2I3LQZ0_A0A2I3LQZ0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5RIB7_A0A1D5RIB7_MACMU_9544 and tr_A0A2K5LI27_A0A2K5LI27_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5RIB7_A0A1D5RIB7_MACMU_9544 and tr_A0A2K6D9T6_A0A2K6D9T6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5RIB7_A0A1D5RIB7_MACMU_9544 and tr_A0A2K6AHZ1_A0A2K6AHZ1_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6WJW0_F6WJW0_MACMU_9544 and tr_A0A2K5NB24_A0A2K5NB24_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6WJW0_F6WJW0_MACMU_9544 and tr_A0A2K6ACU6_A0A2K6ACU6_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7BB11_F7BB11_MACMU_9544 and tr_A0A096MVV9_A0A096MVV9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7BB11_F7BB11_MACMU_9544 and tr_A0A0D9RV27_A0A0D9RV27_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7BB11_F7BB11_MACMU_9544 and tr_A0A2K5MT44_A0A2K5MT44_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7BB11_F7BB11_MACMU_9544 and tr_A0A2K6D3U0_A0A2K6D3U0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DX24_F7DX24_MACMU_9544 and tr_A0A096NFL6_A0A096NFL6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DX24_F7DX24_MACMU_9544 and tr_A0A2K5P311_A0A2K5P311_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DX24_F7DX24_MACMU_9544 and tr_A0A2K6D7U1_A0A2K6D7U1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DX24_F7DX24_MACMU_9544 and tr_A0A2K5ZTT1_A0A2K5ZTT1_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7ELX5_F7ELX5_MACMU_9544 and tr_A0A096NIX5_A0A096NIX5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7ELX5_F7ELX5_MACMU_9544 and tr_A0A2K5L6R5_A0A2K5L6R5_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7ELX5_F7ELX5_MACMU_9544 and tr_A0A2K6CEK7_A0A2K6CEK7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7ELX5_F7ELX5_MACMU_9544 and tr_A0A2K6AHT0_A0A2K6AHT0_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GZK9_F7GZK9_MACMU_9544 and tr_G7P8K4_G7P8K4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GZK9_F7GZK9_MACMU_9544 and tr_A0A2K5LQ18_A0A2K5LQ18_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GZK9_F7GZK9_MACMU_9544 and tr_A0A2K5ZTQ9_A0A2K5ZTQ9_MANLE_9568 are exactly identical! WARNING: Sequences tr_E3LXK8_E3LXK8_CAERE_31234 and tr_A0A261BM98_A0A261BM98_9PELO_1503980 are exactly identical! WARNING: Sequences tr_E3MI10_E3MI10_CAERE_31234 and tr_A0A261BKJ0_A0A261BKJ0_9PELO_1503980 are exactly identical! WARNING: Sequences tr_A0A2I3M4U0_A0A2I3M4U0_PAPAN_9555 and tr_A0A2K5ZC19_A0A2K5ZC19_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9R7X0_A0A0D9R7X0_CHLSB_60711 and tr_A0A2K5KXL4_A0A2K5KXL4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9R7X0_A0A0D9R7X0_CHLSB_60711 and tr_A0A2K6CTH7_A0A2K6CTH7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D9R7X0_A0A0D9R7X0_CHLSB_60711 and tr_A0A2K5YU32_A0A2K5YU32_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151M6R1_A0A151M6R1_ALLMI_8496 and tr_A0A1U7RS00_A0A1U7RS00_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151PBC2_A0A151PBC2_ALLMI_8496 and tr_A0A1U7S8N0_A0A1U7S8N0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A093PQ89_A0A093PQ89_9PASS_328815 and tr_A0A093JKK8_A0A093JKK8_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A093PQ89_A0A093PQ89_9PASS_328815 and tr_A0A091XB54_A0A091XB54_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A093PQ89_A0A093PQ89_9PASS_328815 and tr_A0A091FUI6_A0A091FUI6_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A093PQ89_A0A093PQ89_9PASS_328815 and tr_A0A0A0AYB5_A0A0A0AYB5_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091UK09_A0A091UK09_NIPNI_128390 and tr_A0A0A0AQT1_A0A0A0AQT1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087QNU3_A0A087QNU3_APTFO_9233 and tr_A0A1V4IWA2_A0A1V4IWA2_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A226NHI6_A0A226NHI6_CALSU_9009 and tr_A0A226PCD1_A0A226PCD1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2A2JUL3_A0A2A2JUL3_9BILA_2018661 and tr_A0A2A2KQ67_A0A2A2KQ67_9BILA_2018661 are exactly identical! WARNING: Sequences tr_A0A2K6CTT4_A0A2K6CTT4_MACNE_9545 and tr_A0A2K5YL78_A0A2K5YL78_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4A839_A0A2U4A839_TURTR_9739 and tr_A0A2Y9N5I3_A0A2Y9N5I3_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 54 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/Q9BX66/3_mltree/Q9BX66.raxml.reduced.phy Alignment comprises 1 partitions and 308 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 308 / 308 Gaps: 22.02 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BX66/3_mltree/Q9BX66.raxml.rba Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 308 / 24640 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -482164.616635] Initial branch length optimization [00:00:09 -403807.912524] Model parameter optimization (eps = 10.000000) [00:01:22 -402568.179969] AUTODETECT spr round 1 (radius: 5) [00:05:49 -265889.362664] AUTODETECT spr round 2 (radius: 10) [00:10:29 -195146.971545] AUTODETECT spr round 3 (radius: 15) [00:15:35 -156205.373486] AUTODETECT spr round 4 (radius: 20) [00:21:16 -140652.477859] AUTODETECT spr round 5 (radius: 25) [00:28:03 -134144.594432] SPR radius for FAST iterations: 25 (autodetect) [00:28:03 -134144.594432] Model parameter optimization (eps = 3.000000) [00:28:49 -133846.721596] FAST spr round 1 (radius: 25) [00:34:39 -113479.997782] FAST spr round 2 (radius: 25) [00:38:53 -112232.279457] FAST spr round 3 (radius: 25) [00:42:28 -112127.263830] FAST spr round 4 (radius: 25) [00:45:40 -112119.834588] FAST spr round 5 (radius: 25) [00:48:34 -112119.828907] Model parameter optimization (eps = 1.000000) [00:49:02 -112107.090616] SLOW spr round 1 (radius: 5) [00:53:13 -112081.377939] SLOW spr round 2 (radius: 5) [00:57:11 -112073.636881] SLOW spr round 3 (radius: 5) [01:00:56 -112073.635935] SLOW spr round 4 (radius: 10) [01:04:51 -112072.525434] SLOW spr round 5 (radius: 5) [01:09:43 -112064.351491] SLOW spr round 6 (radius: 5) [01:13:55 -112064.351428] SLOW spr round 7 (radius: 10) [01:18:03 -112063.613104] SLOW spr round 8 (radius: 5) [01:22:44 -112063.613051] SLOW spr round 9 (radius: 10) [01:27:11 -112063.055594] SLOW spr round 10 (radius: 5) [01:31:48 -112063.055373] SLOW spr round 11 (radius: 10) [01:36:13 -112061.830104] SLOW spr round 12 (radius: 5) [01:40:51 -112061.818376] SLOW spr round 13 (radius: 10) [01:45:13 -112061.607495] SLOW spr round 14 (radius: 5) [01:49:51 -112061.607352] SLOW spr round 15 (radius: 10) [01:52:51] [worker #4] ML tree search #5, logLikelihood: -112038.545844 [01:54:12 -112061.607306] SLOW spr round 16 (radius: 15) [02:00:28 -112058.613157] SLOW spr round 17 (radius: 5) [02:05:36 -112055.550041] SLOW spr round 18 (radius: 5) [02:09:58 -112054.870842] SLOW spr round 19 (radius: 5) [02:10:50] [worker #1] ML tree search #2, logLikelihood: -112017.219705 [02:13:56 -112054.870788] SLOW spr round 20 (radius: 10) [02:17:53 -112054.870767] SLOW spr round 21 (radius: 15) [02:24:34 -112054.870753] SLOW spr round 22 (radius: 20) [02:35:15 -112054.870741] SLOW spr round 23 (radius: 25) [02:39:36] [worker #3] ML tree search #4, logLikelihood: -112020.641195 [02:49:10 -112054.870731] Model parameter optimization (eps = 0.100000) [02:49:24] [worker #0] ML tree search #1, logLikelihood: -112054.807071 [02:49:24 -478553.757359] Initial branch length optimization [02:49:34 -397916.781888] Model parameter optimization (eps = 10.000000) [02:50:14] [worker #2] ML tree search #3, logLikelihood: -112028.297855 [02:50:39 -396884.191524] AUTODETECT spr round 1 (radius: 5) [02:55:08 -259521.689367] AUTODETECT spr round 2 (radius: 10) [02:59:44 -186495.097725] AUTODETECT spr round 3 (radius: 15) [03:04:40 -163192.509346] AUTODETECT spr round 4 (radius: 20) [03:10:32 -148895.912135] AUTODETECT spr round 5 (radius: 25) [03:18:53 -133832.062799] SPR radius for FAST iterations: 25 (autodetect) [03:18:53 -133832.062799] Model parameter optimization (eps = 3.000000) [03:19:41 -133647.649135] FAST spr round 1 (radius: 25) [03:25:41 -113473.331597] FAST spr round 2 (radius: 25) [03:29:49 -112143.574989] FAST spr round 3 (radius: 25) [03:33:20 -112076.477569] FAST spr round 4 (radius: 25) [03:36:38 -112059.994592] FAST spr round 5 (radius: 25) [03:39:35 -112058.378530] FAST spr round 6 (radius: 25) [03:42:25 -112058.376589] Model parameter optimization (eps = 1.000000) [03:42:52 -112049.213392] SLOW spr round 1 (radius: 5) [03:46:53 -112021.535474] SLOW spr round 2 (radius: 5) [03:50:37 -112021.269901] SLOW spr round 3 (radius: 5) [03:54:17 -112021.269690] SLOW spr round 4 (radius: 10) [03:58:07 -112020.831388] SLOW spr round 5 (radius: 5) [03:59:43] [worker #1] ML tree search #7, logLikelihood: -112025.619642 [04:02:51 -112020.824762] SLOW spr round 6 (radius: 10) [04:07:14 -112020.824349] SLOW spr round 7 (radius: 15) [04:13:29 -112020.824256] SLOW spr round 8 (radius: 20) [04:25:01 -112020.824205] SLOW spr round 9 (radius: 25) [04:40:13 -112020.824163] Model parameter optimization (eps = 0.100000) [04:40:22] [worker #0] ML tree search #6, logLikelihood: -112020.761781 [04:40:22 -482218.087772] Initial branch length optimization [04:40:31 -399959.060447] Model parameter optimization (eps = 10.000000) [04:41:48 -398739.550218] AUTODETECT spr round 1 (radius: 5) [04:43:07] [worker #4] ML tree search #10, logLikelihood: -112037.775705 [04:46:17 -272573.285073] AUTODETECT spr round 2 (radius: 10) [04:50:55 -193667.063945] AUTODETECT spr round 3 (radius: 15) [04:51:49] [worker #2] ML tree search #8, logLikelihood: -112017.322929 [04:56:02 -155031.376767] AUTODETECT spr round 4 (radius: 20) [05:02:24 -139258.608238] AUTODETECT spr round 5 (radius: 25) [05:04:49] [worker #3] ML tree search #9, logLikelihood: -112041.131808 [05:08:51 -131898.722776] SPR radius for FAST iterations: 25 (autodetect) [05:08:51 -131898.722776] Model parameter optimization (eps = 3.000000) [05:09:40 -131699.987475] FAST spr round 1 (radius: 25) [05:15:14 -113428.065497] FAST spr round 2 (radius: 25) [05:19:09 -112215.552972] FAST spr round 3 (radius: 25) [05:22:37 -112096.096343] FAST spr round 4 (radius: 25) [05:25:44 -112087.860068] FAST spr round 5 (radius: 25) [05:28:39 -112087.859717] Model parameter optimization (eps = 1.000000) [05:29:10 -112081.996691] SLOW spr round 1 (radius: 5) [05:33:13 -112049.133789] SLOW spr round 2 (radius: 5) [05:37:12 -112043.185894] SLOW spr round 3 (radius: 5) [05:40:58 -112042.972784] SLOW spr round 4 (radius: 5) [05:44:43 -112042.972388] SLOW spr round 5 (radius: 10) [05:48:35 -112037.634513] SLOW spr round 6 (radius: 5) [05:53:23 -112033.872733] SLOW spr round 7 (radius: 5) [05:57:35 -112033.872716] SLOW spr round 8 (radius: 10) [06:01:39 -112033.816598] SLOW spr round 9 (radius: 15) [06:07:49 -112033.816130] SLOW spr round 10 (radius: 20) [06:18:00 -112033.816085] SLOW spr round 11 (radius: 25) [06:31:20 -112033.816067] Model parameter optimization (eps = 0.100000) [06:31:30] [worker #0] ML tree search #11, logLikelihood: -112033.740315 [06:31:30 -480725.288177] Initial branch length optimization [06:31:38 -399270.048703] Model parameter optimization (eps = 10.000000) [06:32:44 -398035.942437] AUTODETECT spr round 1 (radius: 5) [06:37:11 -268133.737700] AUTODETECT spr round 2 (radius: 10) [06:41:52 -187022.341777] AUTODETECT spr round 3 (radius: 15) [06:46:44] [worker #2] ML tree search #13, logLikelihood: -112018.945145 [06:46:58 -153427.802562] AUTODETECT spr round 4 (radius: 20) [06:53:20 -132922.224915] AUTODETECT spr round 5 (radius: 25) [06:59:25] [worker #1] ML tree search #12, logLikelihood: -112013.675195 [07:00:53 -130082.205236] SPR radius for FAST iterations: 25 (autodetect) [07:00:53 -130082.205236] Model parameter optimization (eps = 3.000000) [07:01:30 -129805.666321] FAST spr round 1 (radius: 25) [07:07:17 -113215.010584] FAST spr round 2 (radius: 25) [07:11:29 -112297.711918] FAST spr round 3 (radius: 25) [07:15:03 -112141.147633] FAST spr round 4 (radius: 25) [07:18:15 -112112.141252] FAST spr round 5 (radius: 25) [07:21:12 -112112.140465] Model parameter optimization (eps = 1.000000) [07:21:38 -112101.343355] SLOW spr round 1 (radius: 5) [07:21:42] [worker #4] ML tree search #15, logLikelihood: -112039.946242 [07:25:49 -112041.562888] SLOW spr round 2 (radius: 5) [07:29:49 -112035.753342] SLOW spr round 3 (radius: 5) [07:33:38 -112035.172050] SLOW spr round 4 (radius: 5) [07:37:22 -112035.171415] SLOW spr round 5 (radius: 10) [07:41:14 -112033.243635] SLOW spr round 6 (radius: 5) [07:45:36] [worker #3] ML tree search #14, logLikelihood: -112020.488201 [07:46:02 -112033.240150] SLOW spr round 7 (radius: 10) [07:50:28 -112033.027245] SLOW spr round 8 (radius: 5) [07:55:09 -112033.026804] SLOW spr round 9 (radius: 10) [07:59:28 -112033.026486] SLOW spr round 10 (radius: 15) [08:05:30 -112018.583407] SLOW spr round 11 (radius: 5) [08:10:38 -112015.756811] SLOW spr round 12 (radius: 5) [08:14:58 -112015.756500] SLOW spr round 13 (radius: 10) [08:19:05 -112015.234202] SLOW spr round 14 (radius: 5) [08:23:44 -112015.234185] SLOW spr round 15 (radius: 10) [08:28:03 -112015.178551] SLOW spr round 16 (radius: 15) [08:33:59 -112013.995856] SLOW spr round 17 (radius: 5) [08:38:59 -112012.248054] SLOW spr round 18 (radius: 5) [08:43:18 -112012.247851] SLOW spr round 19 (radius: 10) [08:43:54] [worker #2] ML tree search #18, logLikelihood: -112043.951245 [08:45:52] [worker #1] ML tree search #17, logLikelihood: -112024.222789 [08:47:27 -112011.530717] SLOW spr round 20 (radius: 5) [08:52:06 -112011.529967] SLOW spr round 21 (radius: 10) [08:56:24 -112011.529937] SLOW spr round 22 (radius: 15) [09:02:19 -112011.529931] SLOW spr round 23 (radius: 20) [09:12:32 -112011.529927] SLOW spr round 24 (radius: 25) [09:21:29] [worker #4] ML tree search #20, logLikelihood: -112028.969336 [09:25:41 -112011.529924] Model parameter optimization (eps = 0.100000) [09:25:54] [worker #0] ML tree search #16, logLikelihood: -112011.358870 [10:14:45] [worker #3] ML tree search #19, logLikelihood: -112038.112003 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.104930,0.528691) (0.084356,0.822427) (0.429735,0.744445) (0.380979,1.457387) 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: -112011.358870 AIC score: 228032.717740 / AICc score: 8272092.717740 / BIC score: 235511.567805 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=308). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 131 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BX66/3_mltree/Q9BX66.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BX66/3_mltree/Q9BX66.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BX66/3_mltree/Q9BX66.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BX66/3_mltree/Q9BX66.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9BX66/3_mltree/Q9BX66.raxml.log Analysis started: 03-Jul-2021 04:37:23 / finished: 03-Jul-2021 14:52:08 Elapsed time: 36885.421 seconds Consumed energy: 3367.170 Wh (= 17 km in an electric car, or 84 km with an e-scooter!)