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 05-Jul-2021 20:06:15 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/2_msa/Q92824_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/3_mltree/Q92824 --seed 2 --threads 7 --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 (7 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/2_msa/Q92824_trimmed_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 484 sites WARNING: Sequences tr_B4QWQ8_B4QWQ8_DROSI_7240 and tr_B4ICP4_B4ICP4_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A1D5NXR1_A0A1D5NXR1_CHICK_9031 and tr_A0A091J1J1_A0A091J1J1_EGRGA_188379 are exactly identical! WARNING: Sequences tr_Q91000_Q91000_CHICK_9031 and tr_A0A226N5B8_A0A226N5B8_CALSU_9009 are exactly identical! WARNING: Sequences tr_Q91000_Q91000_CHICK_9031 and tr_A0A226PCB9_A0A226PCB9_COLVI_9014 are exactly identical! WARNING: Sequences tr_M3XZ36_M3XZ36_MUSPF_9669 and tr_A0A2Y9JLS2_A0A2Y9JLS2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3GED9_A0A2I3GED9_NOMLE_61853 and tr_G3QVR2_G3QVR2_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GED9_A0A2I3GED9_NOMLE_61853 and tr_H2QR92_H2QR92_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GED9_A0A2I3GED9_NOMLE_61853 and sp_P29120_NEC1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GED9_A0A2I3GED9_NOMLE_61853 and tr_A0A2R9BI06_A0A2R9BI06_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1QNB0_G1QNB0_NOMLE_61853 and tr_H2PSF2_H2PSF2_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QNB0_G1QNB0_NOMLE_61853 and tr_H2QXD2_H2QXD2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QNB0_G1QNB0_NOMLE_61853 and sp_Q92824_PCSK5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QNB0_G1QNB0_NOMLE_61853 and tr_A0A1D5R646_A0A1D5R646_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QNB0_G1QNB0_NOMLE_61853 and tr_A0A2R8P431_A0A2R8P431_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1QNB0_G1QNB0_NOMLE_61853 and tr_A0A2K5LYE9_A0A2K5LYE9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QNB0_G1QNB0_NOMLE_61853 and tr_A0A2K6B2R9_A0A2K6B2R9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QNB0_G1QNB0_NOMLE_61853 and tr_A0A2K5ZRT2_A0A2K5ZRT2_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QNB0_G1QNB0_NOMLE_61853 and tr_A0A2R8ZWZ0_A0A2R8ZWZ0_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and sp_Q5REC2_NEC2_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_H2QJZ8_H2QJZ8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_I3MEG8_I3MEG8_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and sp_P16519_NEC2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_F7GNE5_F7GNE5_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_G7PH08_G7PH08_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_A0A2I3LHF8_A0A2I3LHF8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_A0A0D9RGX4_A0A0D9RGX4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_A0A2K6DWA7_A0A2K6DWA7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_A0A2K5ZBF3_A0A2K5ZBF3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QWE4_G3QWE4_GORGO_9595 and tr_A0A2R9C4T7_A0A2R9C4T7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QYP4_G3QYP4_GORGO_9595 and tr_H2QA34_H2QA34_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QYP4_G3QYP4_GORGO_9595 and sp_P09958_FURIN_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QYP4_G3QYP4_GORGO_9595 and tr_A0A2R9B4W5_A0A2R9B4W5_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6VT99_F6VT99_HORSE_9796 and tr_L5K6S8_L5K6S8_PTEAL_9402 are exactly identical! WARNING: Sequences tr_F6VT99_F6VT99_HORSE_9796 and tr_A0A2Y9DY82_A0A2Y9DY82_TRIMA_127582 are exactly identical! WARNING: Sequences tr_W5PSJ0_W5PSJ0_SHEEP_9940 and tr_F1N7K2_F1N7K2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A088AB96_A0A088AB96_APIME_7460 and tr_A0A2A3ES43_A0A2A3ES43_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NHZ8_A0A158NHZ8_ATTCE_12957 and tr_A0A195AWU5_A0A195AWU5_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0K0J9M6_A0A0K0J9M6_BRUMA_6279 and tr_A0A158PSX1_A0A158PSX1_9BILA_42155 are exactly identical! WARNING: Sequences tr_F6VEN2_F6VEN2_MACMU_9544 and tr_A0A2K5P7W4_A0A2K5P7W4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7H767_F7H767_MACMU_9544 and tr_A0A2I3MZS7_A0A2I3MZS7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7H767_F7H767_MACMU_9544 and tr_A0A2K5KPH6_A0A2K5KPH6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7H767_F7H767_MACMU_9544 and tr_A0A2K6ANP9_A0A2K6ANP9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MVY8_G7MVY8_MACMU_9544 and tr_G7P9G7_G7P9G7_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7MVY8_G7MVY8_MACMU_9544 and tr_A0A0D9RWU9_A0A0D9RWU9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7MVY8_G7MVY8_MACMU_9544 and tr_A0A2K5P1F0_A0A2K5P1F0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MVY8_G7MVY8_MACMU_9544 and tr_A0A2K6CBX3_A0A2K6CBX3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MVY8_G7MVY8_MACMU_9544 and tr_A0A2K6AKU9_A0A2K6AKU9_MANLE_9568 are exactly identical! WARNING: Sequences tr_H9FVB9_H9FVB9_MACMU_9544 and tr_G7P7Z4_G7P7Z4_MACFA_9541 are exactly identical! WARNING: Sequences tr_H9FVB9_H9FVB9_MACMU_9544 and tr_A0A2K6B7M1_A0A2K6B7M1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3UKG4_G3UKG4_LOXAF_9785 and tr_A0A2Y9DKR5_A0A2Y9DKR5_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0YR65_H0YR65_TAEGU_59729 and tr_U3K3C2_U3K3C2_FICAL_59894 are exactly identical! WARNING: Sequences tr_F4WPU9_F4WPU9_ACREC_103372 and tr_A0A195FEG1_A0A195FEG1_9HYME_34720 are exactly identical! WARNING: Sequences tr_E3LTU2_E3LTU2_CAERE_31234 and tr_A0A261C718_A0A261C718_9PELO_1503980 are exactly identical! WARNING: Sequences tr_A8X8V5_A8X8V5_CAEBR_6238 and tr_A0A2G5TIU1_A0A2G5TIU1_9PELO_1611254 are exactly identical! WARNING: Sequences tr_A8XMZ6_A8XMZ6_CAEBR_6238 and tr_A0A2G5VR07_A0A2G5VR07_9PELO_1611254 are exactly identical! WARNING: Sequences tr_B3RSJ2_B3RSJ2_TRIAD_10228 and tr_A0A369SHI3_A0A369SHI3_9METZ_287889 are exactly identical! WARNING: Sequences sp_A0A044RE18_BLI_ONCVO_6282 and tr_A0A182EDT9_A0A182EDT9_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A044SCF0_A0A044SCF0_ONCVO_6282 and tr_A0A182EBF9_A0A182EBF9_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A044UUX2_A0A044UUX2_ONCVO_6282 and tr_A0A182DX18_A0A182DX18_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A2I0MG42_A0A2I0MG42_COLLI_8932 and tr_A0A1V4J985_A0A1V4J985_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0S5W7_A0A0V0S5W7_9BILA_6336 and tr_A0A0V1D7D4_A0A0V1D7D4_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0S5W7_A0A0V0S5W7_9BILA_6336 and tr_A0A0V0W964_A0A0V0W964_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0S5W7_A0A0V0S5W7_9BILA_6336 and tr_A0A0V0UUJ0_A0A0V0UUJ0_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0S5W7_A0A0V0S5W7_9BILA_6336 and tr_A0A0V1L1V1_A0A0V1L1V1_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0S5W7_A0A0V0S5W7_9BILA_6336 and tr_A0A0V1NVA9_A0A0V1NVA9_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0S5W7_A0A0V0S5W7_9BILA_6336 and tr_A0A0V0TPY5_A0A0V0TPY5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1CXQ2_A0A0V1CXQ2_TRIBR_45882 and tr_A0A0V0WZ98_A0A0V0WZ98_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CXQ2_A0A0V1CXQ2_TRIBR_45882 and tr_A0A0V0VID3_A0A0V0VID3_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CXQ2_A0A0V1CXQ2_TRIBR_45882 and tr_A0A0V1A1P5_A0A0V1A1P5_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1CXQ2_A0A0V1CXQ2_TRIBR_45882 and tr_A0A0V0U5L3_A0A0V0U5L3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0V983_A0A0V0V983_9BILA_181606 and tr_A0A0V0UFG1_A0A0V0UFG1_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1KV00_A0A0V1KV00_9BILA_6335 and tr_A0A0V1A6H1_A0A0V1A6H1_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1M754_A0A0V1M754_9BILA_268474 and tr_A0A0V1H5S5_A0A0V1H5S5_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A0V1MZF4_A0A0V1MZF4_9BILA_268474 and tr_A0A0V1H1A4_A0A0V1H1A4_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3HEX5_A0A1S3HEX5_LINUN_7574 and tr_A0A1S3HHW3_A0A1S3HHW3_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A2D0QZ24_A0A2D0QZ24_ICTPU_7998 and tr_A0A2D0QZ99_A0A2D0QZ99_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QZ24_A0A2D0QZ24_ICTPU_7998 and tr_A0A2D0R0U1_A0A2D0R0U1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RWE6_A0A2D0RWE6_ICTPU_7998 and tr_A0A2D0RX26_A0A2D0RX26_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5NPA9_A0A2K5NPA9_CERAT_9531 and tr_A0A2K5YTT9_A0A2K5YTT9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4BAG5_A0A2U4BAG5_TURTR_9739 and tr_A0A2Y9NIS5_A0A2Y9NIS5_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3WSM1_A0A2U3WSM1_ODORO_9708 and tr_A0A2U3YKQ6_A0A2U3YKQ6_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 81 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/Q92824/3_mltree/Q92824.raxml.reduced.phy Alignment comprises 1 partitions and 484 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 484 / 484 Gaps: 3.63 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/3_mltree/Q92824.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 7 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 999 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 70 / 5600 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -673303.277397] Initial branch length optimization [00:00:04 -576023.497554] Model parameter optimization (eps = 10.000000) [00:00:25 -574135.201167] AUTODETECT spr round 1 (radius: 5) [00:02:12 -353907.722632] AUTODETECT spr round 2 (radius: 10) [00:04:34 -248819.978793] AUTODETECT spr round 3 (radius: 15) [00:06:42 -211988.587887] AUTODETECT spr round 4 (radius: 20) [00:09:16 -184357.986372] AUTODETECT spr round 5 (radius: 25) [00:12:07 -179093.048634] SPR radius for FAST iterations: 25 (autodetect) [00:12:07 -179093.048634] Model parameter optimization (eps = 3.000000) [00:12:25 -178855.603835] FAST spr round 1 (radius: 25) [00:14:31 -152994.685357] FAST spr round 2 (radius: 25) [00:16:16 -151801.766306] FAST spr round 3 (radius: 25) [00:17:53 -151629.607335] FAST spr round 4 (radius: 25) [00:19:27 -151581.996918] FAST spr round 5 (radius: 25) [00:20:54 -151580.425396] FAST spr round 6 (radius: 25) [00:22:19 -151580.425184] Model parameter optimization (eps = 1.000000) [00:22:31 -151575.549543] SLOW spr round 1 (radius: 5) [00:24:19 -151538.018522] SLOW spr round 2 (radius: 5) [00:26:05 -151532.833127] SLOW spr round 3 (radius: 5) [00:27:50 -151532.832800] SLOW spr round 4 (radius: 10) [00:29:37 -151531.720611] SLOW spr round 5 (radius: 5) [00:31:41 -151531.718649] SLOW spr round 6 (radius: 10) [00:33:34 -151531.718252] SLOW spr round 7 (radius: 15) [00:35:49 -151531.718217] SLOW spr round 8 (radius: 20) [00:39:28 -151531.718193] SLOW spr round 9 (radius: 25) [00:44:16 -151531.718172] Model parameter optimization (eps = 0.100000) [00:44:25] ML tree search #1, logLikelihood: -151531.451389 [00:44:25 -674942.267947] Initial branch length optimization [00:44:29 -579461.207042] Model parameter optimization (eps = 10.000000) [00:44:51 -577490.454292] AUTODETECT spr round 1 (radius: 5) [00:46:37 -365034.332246] AUTODETECT spr round 2 (radius: 10) [00:48:47 -257512.227346] AUTODETECT spr round 3 (radius: 15) [00:50:54 -222443.545869] AUTODETECT spr round 4 (radius: 20) [00:53:25 -188495.709183] AUTODETECT spr round 5 (radius: 25) [00:56:27 -182118.141168] SPR radius for FAST iterations: 25 (autodetect) [00:56:27 -182118.141168] Model parameter optimization (eps = 3.000000) [00:56:47 -181932.946886] FAST spr round 1 (radius: 25) [00:58:52 -153278.138896] FAST spr round 2 (radius: 25) [01:00:38 -151721.471278] FAST spr round 3 (radius: 25) [01:02:13 -151599.513502] FAST spr round 4 (radius: 25) [01:03:43 -151577.973080] FAST spr round 5 (radius: 25) [01:05:15 -151572.334746] FAST spr round 6 (radius: 25) [01:06:59 -151566.065102] FAST spr round 7 (radius: 25) [01:08:24 -151566.064074] Model parameter optimization (eps = 1.000000) [01:08:39 -151561.448199] SLOW spr round 1 (radius: 5) [01:10:28 -151530.418763] SLOW spr round 2 (radius: 5) [01:12:12 -151527.513310] SLOW spr round 3 (radius: 5) [01:13:56 -151526.569079] SLOW spr round 4 (radius: 5) [01:15:38 -151526.508171] SLOW spr round 5 (radius: 10) [01:17:22 -151525.755464] SLOW spr round 6 (radius: 5) [01:19:26 -151525.755354] SLOW spr round 7 (radius: 10) [01:21:19 -151525.755334] SLOW spr round 8 (radius: 15) [01:23:33 -151525.755333] SLOW spr round 9 (radius: 20) [01:27:05 -151525.755332] SLOW spr round 10 (radius: 25) [01:31:54 -151525.755332] Model parameter optimization (eps = 0.100000) [01:31:59] ML tree search #2, logLikelihood: -151525.727161 [01:31:59 -671105.294059] Initial branch length optimization [01:32:02 -573958.349220] Model parameter optimization (eps = 10.000000) [01:32:31 -572084.770393] AUTODETECT spr round 1 (radius: 5) [01:34:16 -351991.007639] AUTODETECT spr round 2 (radius: 10) [01:36:36 -261878.208176] AUTODETECT spr round 3 (radius: 15) [01:38:53 -219115.435461] AUTODETECT spr round 4 (radius: 20) [01:41:59 -187699.326926] AUTODETECT spr round 5 (radius: 25) [01:45:02 -182726.920353] SPR radius for FAST iterations: 25 (autodetect) [01:45:02 -182726.920353] Model parameter optimization (eps = 3.000000) [01:45:25 -182578.419032] FAST spr round 1 (radius: 25) [01:47:29 -152797.521743] FAST spr round 2 (radius: 25) [01:49:13 -151714.418378] FAST spr round 3 (radius: 25) [01:50:48 -151587.615392] FAST spr round 4 (radius: 25) [01:52:16 -151585.399005] FAST spr round 5 (radius: 25) [01:53:41 -151585.398578] Model parameter optimization (eps = 1.000000) [01:53:53 -151583.980176] SLOW spr round 1 (radius: 5) [01:55:39 -151535.384943] SLOW spr round 2 (radius: 5) [01:57:22 -151531.661322] SLOW spr round 3 (radius: 5) [01:59:04 -151531.660051] SLOW spr round 4 (radius: 10) [02:00:47 -151530.199170] SLOW spr round 5 (radius: 5) [02:02:48 -151530.197256] SLOW spr round 6 (radius: 10) [02:04:40 -151530.196952] SLOW spr round 7 (radius: 15) [02:06:51 -151530.196814] SLOW spr round 8 (radius: 20) [02:10:23 -151530.196727] SLOW spr round 9 (radius: 25) [02:15:07 -151530.196666] Model parameter optimization (eps = 0.100000) [02:15:13] ML tree search #3, logLikelihood: -151530.132875 [02:15:13 -667112.752142] Initial branch length optimization [02:15:17 -572369.820087] Model parameter optimization (eps = 10.000000) [02:15:53 -570402.788350] AUTODETECT spr round 1 (radius: 5) [02:17:37 -355525.044312] AUTODETECT spr round 2 (radius: 10) [02:20:03 -245879.928868] AUTODETECT spr round 3 (radius: 15) [02:22:15 -195982.734172] AUTODETECT spr round 4 (radius: 20) [02:24:44 -183439.082728] AUTODETECT spr round 5 (radius: 25) [02:27:23 -179956.878568] SPR radius for FAST iterations: 25 (autodetect) [02:27:23 -179956.878568] Model parameter optimization (eps = 3.000000) [02:27:46 -179769.885751] FAST spr round 1 (radius: 25) [02:29:50 -153537.941965] FAST spr round 2 (radius: 25) [02:31:35 -151658.074011] FAST spr round 3 (radius: 25) [02:33:11 -151570.685048] FAST spr round 4 (radius: 25) [02:34:38 -151567.156370] FAST spr round 5 (radius: 25) [02:36:02 -151567.156301] Model parameter optimization (eps = 1.000000) [02:36:14 -151562.847929] SLOW spr round 1 (radius: 5) [02:38:00 -151527.821755] SLOW spr round 2 (radius: 5) [02:39:44 -151518.441037] SLOW spr round 3 (radius: 5) [02:41:27 -151518.020555] SLOW spr round 4 (radius: 5) [02:43:09 -151517.685900] SLOW spr round 5 (radius: 5) [02:44:51 -151517.685822] SLOW spr round 6 (radius: 10) [02:46:36 -151517.685745] SLOW spr round 7 (radius: 15) [02:48:56 -151517.685688] SLOW spr round 8 (radius: 20) [02:52:30 -151517.685631] SLOW spr round 9 (radius: 25) [02:57:25 -151517.685574] Model parameter optimization (eps = 0.100000) [02:57:36] ML tree search #4, logLikelihood: -151516.896745 [02:57:36 -669110.754423] Initial branch length optimization [02:57:40 -574982.646908] Model parameter optimization (eps = 10.000000) [02:58:03 -573089.566807] AUTODETECT spr round 1 (radius: 5) [02:59:49 -356786.135992] AUTODETECT spr round 2 (radius: 10) [03:02:12 -254454.438292] AUTODETECT spr round 3 (radius: 15) [03:04:20 -213641.614566] AUTODETECT spr round 4 (radius: 20) [03:06:56 -183613.034939] AUTODETECT spr round 5 (radius: 25) [03:10:00 -179851.071703] SPR radius for FAST iterations: 25 (autodetect) [03:10:00 -179851.071703] Model parameter optimization (eps = 3.000000) [03:10:29 -179659.681357] FAST spr round 1 (radius: 25) [03:12:34 -152830.162261] FAST spr round 2 (radius: 25) [03:14:17 -151700.645718] FAST spr round 3 (radius: 25) [03:15:49 -151558.049815] FAST spr round 4 (radius: 25) [03:17:31 -151554.798429] FAST spr round 5 (radius: 25) [03:19:24 -151554.798258] Model parameter optimization (eps = 1.000000) [03:19:36 -151553.316348] SLOW spr round 1 (radius: 5) [03:21:21 -151516.824367] SLOW spr round 2 (radius: 5) [03:23:06 -151510.913958] SLOW spr round 3 (radius: 5) [03:24:50 -151509.204817] SLOW spr round 4 (radius: 5) [03:26:33 -151509.202942] SLOW spr round 5 (radius: 10) [03:28:18 -151508.864298] SLOW spr round 6 (radius: 5) [03:30:21 -151508.864242] SLOW spr round 7 (radius: 10) [03:32:11 -151508.864209] SLOW spr round 8 (radius: 15) [03:34:24 -151508.864176] SLOW spr round 9 (radius: 20) [03:37:56 -151508.864145] SLOW spr round 10 (radius: 25) [03:42:44 -151508.864113] Model parameter optimization (eps = 0.100000) [03:42:51] ML tree search #5, logLikelihood: -151508.648958 [03:42:51 -676357.617665] Initial branch length optimization [03:42:55 -578313.488516] Model parameter optimization (eps = 10.000000) [03:43:26 -576350.933185] AUTODETECT spr round 1 (radius: 5) [03:45:13 -350648.981504] AUTODETECT spr round 2 (radius: 10) [03:47:37 -256963.266657] AUTODETECT spr round 3 (radius: 15) [03:49:47 -224687.855555] AUTODETECT spr round 4 (radius: 20) [03:52:23 -194763.872125] AUTODETECT spr round 5 (radius: 25) [03:55:43 -181901.352949] SPR radius for FAST iterations: 25 (autodetect) [03:55:43 -181901.352949] Model parameter optimization (eps = 3.000000) [03:56:04 -181699.467085] FAST spr round 1 (radius: 25) [03:58:03 -153565.677216] FAST spr round 2 (radius: 25) [03:59:46 -151789.863156] FAST spr round 3 (radius: 25) [04:01:22 -151590.363244] FAST spr round 4 (radius: 25) [04:02:54 -151568.036317] FAST spr round 5 (radius: 25) [04:04:20 -151568.035300] Model parameter optimization (eps = 1.000000) [04:04:28 -151566.522747] SLOW spr round 1 (radius: 5) [04:06:16 -151519.008312] SLOW spr round 2 (radius: 5) [04:08:01 -151511.959863] SLOW spr round 3 (radius: 5) [04:09:43 -151511.959658] SLOW spr round 4 (radius: 10) [04:11:27 -151511.959253] SLOW spr round 5 (radius: 15) [04:13:44 -151511.959210] SLOW spr round 6 (radius: 20) [04:17:07 -151511.959173] SLOW spr round 7 (radius: 25) [04:21:52 -151511.959140] Model parameter optimization (eps = 0.100000) [04:22:01] ML tree search #6, logLikelihood: -151511.855267 [04:22:01 -672731.187552] Initial branch length optimization [04:22:05 -576086.708337] Model parameter optimization (eps = 10.000000) [04:22:29 -574157.130850] AUTODETECT spr round 1 (radius: 5) [04:24:13 -360757.548744] AUTODETECT spr round 2 (radius: 10) [04:26:22 -249883.537805] AUTODETECT spr round 3 (radius: 15) [04:28:24 -203271.018414] AUTODETECT spr round 4 (radius: 20) [04:30:48 -176495.937248] AUTODETECT spr round 5 (radius: 25) [04:33:30 -173638.531593] SPR radius for FAST iterations: 25 (autodetect) [04:33:30 -173638.531593] Model parameter optimization (eps = 3.000000) [04:33:55 -173431.479871] FAST spr round 1 (radius: 25) [04:35:58 -152366.750814] FAST spr round 2 (radius: 25) [04:37:40 -151637.220065] FAST spr round 3 (radius: 25) [04:39:13 -151576.561313] FAST spr round 4 (radius: 25) [04:40:41 -151574.097361] FAST spr round 5 (radius: 25) [04:42:06 -151574.097230] Model parameter optimization (eps = 1.000000) [04:42:24 -151555.814129] SLOW spr round 1 (radius: 5) [04:44:10 -151524.844851] SLOW spr round 2 (radius: 5) [04:45:54 -151517.827596] SLOW spr round 3 (radius: 5) [04:47:37 -151517.789094] SLOW spr round 4 (radius: 10) [04:49:21 -151513.618247] SLOW spr round 5 (radius: 5) [04:51:24 -151513.557271] SLOW spr round 6 (radius: 10) [04:53:15 -151513.557242] SLOW spr round 7 (radius: 15) [04:55:28 -151512.449963] SLOW spr round 8 (radius: 5) [04:57:36 -151512.448410] SLOW spr round 9 (radius: 10) [04:59:31 -151512.448269] SLOW spr round 10 (radius: 15) [05:01:41 -151512.448227] SLOW spr round 11 (radius: 20) [05:05:11 -151512.448197] SLOW spr round 12 (radius: 25) [05:09:52 -151512.448168] Model parameter optimization (eps = 0.100000) [05:10:00] ML tree search #7, logLikelihood: -151512.301776 [05:10:00 -671332.922063] Initial branch length optimization [05:10:04 -575054.654486] Model parameter optimization (eps = 10.000000) [05:10:30 -573091.391057] AUTODETECT spr round 1 (radius: 5) [05:12:15 -356736.154861] AUTODETECT spr round 2 (radius: 10) [05:14:27 -247442.704241] AUTODETECT spr round 3 (radius: 15) [05:16:33 -198734.584766] AUTODETECT spr round 4 (radius: 20) [05:19:20 -179192.191018] AUTODETECT spr round 5 (radius: 25) [05:22:15 -176517.219020] SPR radius for FAST iterations: 25 (autodetect) [05:22:15 -176517.219020] Model parameter optimization (eps = 3.000000) [05:22:38 -176270.564242] FAST spr round 1 (radius: 25) [05:24:42 -152918.685281] FAST spr round 2 (radius: 25) [05:26:26 -151660.253758] FAST spr round 3 (radius: 25) [05:28:00 -151559.647284] FAST spr round 4 (radius: 25) [05:29:27 -151554.648621] FAST spr round 5 (radius: 25) [05:30:52 -151554.558496] Model parameter optimization (eps = 1.000000) [05:31:06 -151552.157360] SLOW spr round 1 (radius: 5) [05:32:56 -151531.824235] SLOW spr round 2 (radius: 5) [05:34:41 -151530.310727] SLOW spr round 3 (radius: 5) [05:36:24 -151530.310473] SLOW spr round 4 (radius: 10) [05:38:11 -151529.161943] SLOW spr round 5 (radius: 5) [05:40:14 -151529.159342] SLOW spr round 6 (radius: 10) [05:42:05 -151529.159204] SLOW spr round 7 (radius: 15) [05:44:19 -151529.159191] SLOW spr round 8 (radius: 20) [05:47:59 -151529.159189] SLOW spr round 9 (radius: 25) [05:52:53 -151529.159187] Model parameter optimization (eps = 0.100000) [05:52:57] ML tree search #8, logLikelihood: -151529.074542 [05:52:57 -675200.657568] Initial branch length optimization [05:53:02 -581602.827269] Model parameter optimization (eps = 10.000000) [05:53:38 -579759.898368] AUTODETECT spr round 1 (radius: 5) [05:55:25 -349604.143455] AUTODETECT spr round 2 (radius: 10) [05:57:51 -250536.348220] AUTODETECT spr round 3 (radius: 15) [06:00:01 -206893.459424] AUTODETECT spr round 4 (radius: 20) [06:02:37 -187020.757001] AUTODETECT spr round 5 (radius: 25) [06:05:35 -179094.278943] SPR radius for FAST iterations: 25 (autodetect) [06:05:35 -179094.278943] Model parameter optimization (eps = 3.000000) [06:05:58 -178862.142890] FAST spr round 1 (radius: 25) [06:08:00 -152744.823331] FAST spr round 2 (radius: 25) [06:09:42 -151684.398702] FAST spr round 3 (radius: 25) [06:11:15 -151605.457636] FAST spr round 4 (radius: 25) [06:12:43 -151600.804106] FAST spr round 5 (radius: 25) [06:14:08 -151600.804012] Model parameter optimization (eps = 1.000000) [06:14:21 -151597.152343] SLOW spr round 1 (radius: 5) [06:16:09 -151546.365660] SLOW spr round 2 (radius: 5) [06:17:54 -151538.950434] SLOW spr round 3 (radius: 5) [06:19:37 -151538.905307] SLOW spr round 4 (radius: 10) [06:21:21 -151538.904715] SLOW spr round 5 (radius: 15) [06:23:38 -151538.559291] SLOW spr round 6 (radius: 5) [06:25:45 -151538.558973] SLOW spr round 7 (radius: 10) [06:27:42 -151530.069793] SLOW spr round 8 (radius: 5) [06:29:43 -151526.142689] SLOW spr round 9 (radius: 5) [06:31:33 -151526.142415] SLOW spr round 10 (radius: 10) [06:33:19 -151526.142398] SLOW spr round 11 (radius: 15) [06:35:35 -151526.142396] SLOW spr round 12 (radius: 20) [06:39:07 -151526.142395] SLOW spr round 13 (radius: 25) [06:43:59 -151526.142395] Model parameter optimization (eps = 0.100000) [06:44:07] ML tree search #9, logLikelihood: -151526.009604 [06:44:07 -669558.749912] Initial branch length optimization [06:44:10 -574631.655033] Model parameter optimization (eps = 10.000000) [06:44:38 -572743.551630] AUTODETECT spr round 1 (radius: 5) [06:46:23 -354988.338874] AUTODETECT spr round 2 (radius: 10) [06:48:40 -251821.199072] AUTODETECT spr round 3 (radius: 15) [06:50:52 -206858.725080] AUTODETECT spr round 4 (radius: 20) [06:53:32 -182962.512945] AUTODETECT spr round 5 (radius: 25) [06:56:00 -175495.574811] SPR radius for FAST iterations: 25 (autodetect) [06:56:00 -175495.574811] Model parameter optimization (eps = 3.000000) [06:56:25 -175323.959944] FAST spr round 1 (radius: 25) [06:58:30 -153144.734742] FAST spr round 2 (radius: 25) [07:00:15 -151660.352966] FAST spr round 3 (radius: 25) [07:01:48 -151587.733397] FAST spr round 4 (radius: 25) [07:03:17 -151575.095590] FAST spr round 5 (radius: 25) [07:04:41 -151575.095350] Model parameter optimization (eps = 1.000000) [07:04:54 -151571.685865] SLOW spr round 1 (radius: 5) [07:06:42 -151529.282707] SLOW spr round 2 (radius: 5) [07:08:27 -151528.040325] SLOW spr round 3 (radius: 5) [07:10:11 -151528.040024] SLOW spr round 4 (radius: 10) [07:11:55 -151526.946398] SLOW spr round 5 (radius: 5) [07:13:57 -151526.944440] SLOW spr round 6 (radius: 10) [07:15:48 -151526.944259] SLOW spr round 7 (radius: 15) [07:18:02 -151526.944212] SLOW spr round 8 (radius: 20) [07:21:31 -151526.944178] SLOW spr round 9 (radius: 25) [07:26:09 -151526.944146] Model parameter optimization (eps = 0.100000) [07:26:18] ML tree search #10, logLikelihood: -151526.520615 [07:26:18 -670034.286002] Initial branch length optimization [07:26:20 -571283.170857] Model parameter optimization (eps = 10.000000) [07:26:48 -569408.458540] AUTODETECT spr round 1 (radius: 5) [07:28:34 -357686.119999] AUTODETECT spr round 2 (radius: 10) [07:30:48 -240634.842322] AUTODETECT spr round 3 (radius: 15) [07:32:53 -193211.521740] AUTODETECT spr round 4 (radius: 20) [07:35:08 -177944.474469] AUTODETECT spr round 5 (radius: 25) [07:37:46 -171538.552582] SPR radius for FAST iterations: 25 (autodetect) [07:37:46 -171538.552582] Model parameter optimization (eps = 3.000000) [07:38:09 -171393.740578] FAST spr round 1 (radius: 25) [07:40:06 -152431.130867] FAST spr round 2 (radius: 25) [07:41:47 -151640.009820] FAST spr round 3 (radius: 25) [07:43:19 -151585.694809] FAST spr round 4 (radius: 25) [07:44:44 -151583.931661] FAST spr round 5 (radius: 25) [07:46:08 -151583.931487] Model parameter optimization (eps = 1.000000) [07:46:24 -151575.162496] SLOW spr round 1 (radius: 5) [07:48:14 -151527.927007] SLOW spr round 2 (radius: 5) [07:49:58 -151522.843638] SLOW spr round 3 (radius: 5) [07:51:38 -151522.787318] SLOW spr round 4 (radius: 10) [07:53:21 -151519.560645] SLOW spr round 5 (radius: 5) [07:55:23 -151518.616680] SLOW spr round 6 (radius: 5) [07:57:14 -151518.555895] SLOW spr round 7 (radius: 10) [07:59:01 -151518.555869] SLOW spr round 8 (radius: 15) [08:01:12 -151517.448422] SLOW spr round 9 (radius: 5) [08:03:19 -151517.446447] SLOW spr round 10 (radius: 10) [08:05:16 -151517.446312] SLOW spr round 11 (radius: 15) [08:07:25 -151517.446277] SLOW spr round 12 (radius: 20) [08:10:52 -151517.446254] SLOW spr round 13 (radius: 25) [08:15:27 -151517.446233] Model parameter optimization (eps = 0.100000) [08:15:37] ML tree search #11, logLikelihood: -151516.908368 [08:15:37 -670031.275128] Initial branch length optimization [08:15:41 -574979.968844] Model parameter optimization (eps = 10.000000) [08:16:03 -573005.418059] AUTODETECT spr round 1 (radius: 5) [08:17:50 -356495.275610] AUTODETECT spr round 2 (radius: 10) [08:20:13 -248783.339037] AUTODETECT spr round 3 (radius: 15) [08:22:25 -198712.785912] AUTODETECT spr round 4 (radius: 20) [08:24:49 -179380.275591] AUTODETECT spr round 5 (radius: 25) [08:27:45 -177285.814687] SPR radius for FAST iterations: 25 (autodetect) [08:27:45 -177285.814687] Model parameter optimization (eps = 3.000000) [08:28:03 -177118.885347] FAST spr round 1 (radius: 25) [08:30:08 -152662.458048] FAST spr round 2 (radius: 25) [08:31:49 -151669.743389] FAST spr round 3 (radius: 25) [08:33:26 -151574.727206] FAST spr round 4 (radius: 25) [08:34:54 -151568.914592] FAST spr round 5 (radius: 25) [08:36:19 -151564.663507] FAST spr round 6 (radius: 25) [08:37:45 -151564.662891] Model parameter optimization (eps = 1.000000) [08:38:01 -151552.807221] SLOW spr round 1 (radius: 5) [08:39:48 -151521.299946] SLOW spr round 2 (radius: 5) [08:41:33 -151518.086496] SLOW spr round 3 (radius: 5) [08:43:14 -151518.086359] SLOW spr round 4 (radius: 10) [08:44:59 -151516.980684] SLOW spr round 5 (radius: 5) [08:47:02 -151516.979029] SLOW spr round 6 (radius: 10) [08:48:54 -151516.978905] SLOW spr round 7 (radius: 15) [08:51:07 -151516.634969] SLOW spr round 8 (radius: 5) [08:53:16 -151516.634674] SLOW spr round 9 (radius: 10) [08:55:12 -151516.634423] SLOW spr round 10 (radius: 15) [08:57:24 -151516.634420] SLOW spr round 11 (radius: 20) [09:00:58 -151516.634418] SLOW spr round 12 (radius: 25) [09:05:42 -151516.634417] Model parameter optimization (eps = 0.100000) [09:05:51] ML tree search #12, logLikelihood: -151516.417961 [09:05:51 -675111.245656] Initial branch length optimization [09:05:54 -576606.954041] Model parameter optimization (eps = 10.000000) [09:06:16 -574677.161940] AUTODETECT spr round 1 (radius: 5) [09:08:03 -342881.911131] AUTODETECT spr round 2 (radius: 10) [09:10:10 -239744.003233] AUTODETECT spr round 3 (radius: 15) [09:12:12 -200471.035106] AUTODETECT spr round 4 (radius: 20) [09:14:52 -181469.008795] AUTODETECT spr round 5 (radius: 25) [09:17:47 -175697.043168] SPR radius for FAST iterations: 25 (autodetect) [09:17:47 -175697.043168] Model parameter optimization (eps = 3.000000) [09:18:11 -175507.096367] FAST spr round 1 (radius: 25) [09:20:13 -152684.590650] FAST spr round 2 (radius: 25) [09:21:55 -151664.485124] FAST spr round 3 (radius: 25) [09:23:28 -151556.930431] FAST spr round 4 (radius: 25) [09:24:54 -151553.141939] FAST spr round 5 (radius: 25) [09:26:18 -151553.141831] Model parameter optimization (eps = 1.000000) [09:26:23 -151552.330341] SLOW spr round 1 (radius: 5) [09:28:09 -151518.709622] SLOW spr round 2 (radius: 5) [09:29:54 -151517.469155] SLOW spr round 3 (radius: 5) [09:31:37 -151517.469070] SLOW spr round 4 (radius: 10) [09:33:21 -151516.013688] SLOW spr round 5 (radius: 5) [09:35:24 -151516.012526] SLOW spr round 6 (radius: 10) [09:37:14 -151516.012191] SLOW spr round 7 (radius: 15) [09:39:29 -151516.012156] SLOW spr round 8 (radius: 20) [09:43:05 -151516.012133] SLOW spr round 9 (radius: 25) [09:47:54 -151516.012111] Model parameter optimization (eps = 0.100000) [09:48:02] ML tree search #13, logLikelihood: -151515.885431 [09:48:02 -673960.225190] Initial branch length optimization [09:48:05 -580299.537461] Model parameter optimization (eps = 10.000000) [09:48:30 -578449.511688] AUTODETECT spr round 1 (radius: 5) [09:50:18 -352686.997828] AUTODETECT spr round 2 (radius: 10) [09:52:32 -248810.369549] AUTODETECT spr round 3 (radius: 15) [09:54:39 -196181.494296] AUTODETECT spr round 4 (radius: 20) [09:57:21 -174921.472875] AUTODETECT spr round 5 (radius: 25) [09:59:47 -172184.220759] SPR radius for FAST iterations: 25 (autodetect) [09:59:47 -172184.220759] Model parameter optimization (eps = 3.000000) [10:00:07 -172021.592314] FAST spr round 1 (radius: 25) [10:02:11 -152356.832267] FAST spr round 2 (radius: 25) [10:03:56 -151615.884143] FAST spr round 3 (radius: 25) [10:05:30 -151581.973837] FAST spr round 4 (radius: 25) [10:06:59 -151579.622408] FAST spr round 5 (radius: 25) [10:08:25 -151577.914055] FAST spr round 6 (radius: 25) [10:09:50 -151577.913398] Model parameter optimization (eps = 1.000000) [10:10:06 -151561.345767] SLOW spr round 1 (radius: 5) [10:11:54 -151524.507253] SLOW spr round 2 (radius: 5) [10:13:39 -151523.060116] SLOW spr round 3 (radius: 5) [10:15:23 -151523.059102] SLOW spr round 4 (radius: 10) [10:17:09 -151522.318828] SLOW spr round 5 (radius: 5) [10:19:11 -151522.318729] SLOW spr round 6 (radius: 10) [10:21:03 -151522.318702] SLOW spr round 7 (radius: 15) [10:23:15 -151522.318700] SLOW spr round 8 (radius: 20) [10:26:48 -151522.318700] SLOW spr round 9 (radius: 25) [10:31:36 -151522.318699] Model parameter optimization (eps = 0.100000) [10:31:47] ML tree search #14, logLikelihood: -151521.725639 [10:31:47 -673541.371083] Initial branch length optimization [10:31:50 -575807.827472] Model parameter optimization (eps = 10.000000) [10:32:13 -573863.232706] AUTODETECT spr round 1 (radius: 5) [10:33:58 -346387.633787] AUTODETECT spr round 2 (radius: 10) [10:36:12 -258763.323113] AUTODETECT spr round 3 (radius: 15) [10:38:26 -206150.616655] AUTODETECT spr round 4 (radius: 20) [10:41:14 -182820.938209] AUTODETECT spr round 5 (radius: 25) [10:44:06 -179678.268307] SPR radius for FAST iterations: 25 (autodetect) [10:44:06 -179678.268307] Model parameter optimization (eps = 3.000000) [10:44:27 -179506.406951] FAST spr round 1 (radius: 25) [10:46:25 -152805.519058] FAST spr round 2 (radius: 25) [10:48:04 -151642.430541] FAST spr round 3 (radius: 25) [10:49:37 -151571.545661] FAST spr round 4 (radius: 25) [10:51:03 -151571.544532] Model parameter optimization (eps = 1.000000) [10:51:17 -151565.396772] SLOW spr round 1 (radius: 5) [10:53:04 -151520.008743] SLOW spr round 2 (radius: 5) [10:54:48 -151515.741722] SLOW spr round 3 (radius: 5) [10:56:30 -151515.741479] SLOW spr round 4 (radius: 10) [10:58:13 -151514.303076] SLOW spr round 5 (radius: 5) [11:00:14 -151514.299210] SLOW spr round 6 (radius: 10) [11:02:02 -151514.299058] SLOW spr round 7 (radius: 15) [11:04:16 -151514.299023] SLOW spr round 8 (radius: 20) [11:07:49 -151513.950035] SLOW spr round 9 (radius: 5) [11:09:59 -151513.936883] SLOW spr round 10 (radius: 10) [11:11:56 -151513.936699] SLOW spr round 11 (radius: 15) [11:14:09 -151513.936583] SLOW spr round 12 (radius: 20) [11:17:40 -151513.936506] SLOW spr round 13 (radius: 25) [11:22:24 -151513.936451] Model parameter optimization (eps = 0.100000) [11:22:35] ML tree search #15, logLikelihood: -151513.222301 [11:22:35 -672953.235957] Initial branch length optimization [11:22:41 -577488.755601] Model parameter optimization (eps = 10.000000) [11:23:05 -575550.895204] AUTODETECT spr round 1 (radius: 5) [11:24:50 -359605.481513] AUTODETECT spr round 2 (radius: 10) [11:27:02 -251182.953406] AUTODETECT spr round 3 (radius: 15) [11:29:10 -213614.856774] AUTODETECT spr round 4 (radius: 20) [11:31:48 -194491.608644] AUTODETECT spr round 5 (radius: 25) [11:34:40 -181717.327051] SPR radius for FAST iterations: 25 (autodetect) [11:34:40 -181717.327051] Model parameter optimization (eps = 3.000000) [11:35:05 -181506.123671] FAST spr round 1 (radius: 25) [11:37:11 -152747.494044] FAST spr round 2 (radius: 25) [11:38:55 -151726.424080] FAST spr round 3 (radius: 25) [11:40:28 -151599.628661] FAST spr round 4 (radius: 25) [11:41:56 -151589.338830] FAST spr round 5 (radius: 25) [11:43:21 -151589.338276] Model parameter optimization (eps = 1.000000) [11:43:34 -151584.926636] SLOW spr round 1 (radius: 5) [11:45:22 -151543.228313] SLOW spr round 2 (radius: 5) [11:47:07 -151535.032845] SLOW spr round 3 (radius: 5) [11:48:52 -151531.847618] SLOW spr round 4 (radius: 5) [11:50:34 -151531.101897] SLOW spr round 5 (radius: 5) [11:52:18 -151528.781992] SLOW spr round 6 (radius: 5) [11:53:59 -151528.141704] SLOW spr round 7 (radius: 5) [11:55:40 -151528.141620] SLOW spr round 8 (radius: 10) [11:57:24 -151527.032663] SLOW spr round 9 (radius: 5) [11:59:25 -151527.031592] SLOW spr round 10 (radius: 10) [12:01:15 -151527.031469] SLOW spr round 11 (radius: 15) [12:03:26 -151526.680944] SLOW spr round 12 (radius: 5) [12:05:34 -151526.680911] SLOW spr round 13 (radius: 10) [12:07:30 -151526.680888] SLOW spr round 14 (radius: 15) [12:09:40 -151526.680867] SLOW spr round 15 (radius: 20) [12:13:13 -151526.680846] SLOW spr round 16 (radius: 25) [12:17:59 -151526.680825] Model parameter optimization (eps = 0.100000) [12:18:06] ML tree search #16, logLikelihood: -151526.579152 [12:18:06 -672917.883094] Initial branch length optimization [12:18:09 -576134.605128] Model parameter optimization (eps = 10.000000) [12:18:34 -574187.179869] AUTODETECT spr round 1 (radius: 5) [12:20:21 -361124.097859] AUTODETECT spr round 2 (radius: 10) [12:22:40 -253879.468323] AUTODETECT spr round 3 (radius: 15) [12:24:45 -208939.619086] AUTODETECT spr round 4 (radius: 20) [12:27:20 -196106.167518] AUTODETECT spr round 5 (radius: 25) [12:30:01 -190127.041855] SPR radius for FAST iterations: 25 (autodetect) [12:30:01 -190127.041855] Model parameter optimization (eps = 3.000000) [12:30:21 -189952.447386] FAST spr round 1 (radius: 25) [12:32:25 -158425.061973] FAST spr round 2 (radius: 25) [12:34:05 -151806.894206] FAST spr round 3 (radius: 25) [12:35:41 -151620.246148] FAST spr round 4 (radius: 25) [12:37:13 -151594.148897] FAST spr round 5 (radius: 25) [12:38:39 -151594.148565] Model parameter optimization (eps = 1.000000) [12:38:53 -151584.206753] SLOW spr round 1 (radius: 5) [12:40:41 -151534.884275] SLOW spr round 2 (radius: 5) [12:42:24 -151529.788588] SLOW spr round 3 (radius: 5) [12:44:04 -151528.244455] SLOW spr round 4 (radius: 5) [12:45:46 -151526.639946] SLOW spr round 5 (radius: 5) [12:47:27 -151526.639302] SLOW spr round 6 (radius: 10) [12:49:11 -151525.168140] SLOW spr round 7 (radius: 5) [12:51:13 -151525.167068] SLOW spr round 8 (radius: 10) [12:53:05 -151525.166957] SLOW spr round 9 (radius: 15) [12:55:17 -151525.166937] SLOW spr round 10 (radius: 20) [12:58:50 -151525.166930] SLOW spr round 11 (radius: 25) [13:03:28 -151525.166926] Model parameter optimization (eps = 0.100000) [13:03:36] ML tree search #17, logLikelihood: -151525.050975 [13:03:36 -664055.358656] Initial branch length optimization [13:03:39 -569663.402023] Model parameter optimization (eps = 10.000000) [13:04:11 -567757.842013] AUTODETECT spr round 1 (radius: 5) [13:05:55 -342788.875282] AUTODETECT spr round 2 (radius: 10) [13:08:13 -253666.181092] AUTODETECT spr round 3 (radius: 15) [13:10:21 -211292.846602] AUTODETECT spr round 4 (radius: 20) [13:12:52 -192832.398420] AUTODETECT spr round 5 (radius: 25) [13:15:45 -184497.092738] SPR radius for FAST iterations: 25 (autodetect) [13:15:45 -184497.092738] Model parameter optimization (eps = 3.000000) [13:16:12 -184342.036340] FAST spr round 1 (radius: 25) [13:18:14 -154652.254278] FAST spr round 2 (radius: 25) [13:20:00 -151886.186795] FAST spr round 3 (radius: 25) [13:21:37 -151593.475742] FAST spr round 4 (radius: 25) [13:23:06 -151582.723261] FAST spr round 5 (radius: 25) [13:24:29 -151574.751281] FAST spr round 6 (radius: 25) [13:25:52 -151572.268286] FAST spr round 7 (radius: 25) [13:27:15 -151572.267812] Model parameter optimization (eps = 1.000000) [13:27:35 -151557.728588] SLOW spr round 1 (radius: 5) [13:29:21 -151525.677766] SLOW spr round 2 (radius: 5) [13:31:04 -151521.765658] SLOW spr round 3 (radius: 5) [13:32:43 -151520.901371] SLOW spr round 4 (radius: 5) [13:34:23 -151520.900992] SLOW spr round 5 (radius: 10) [13:36:07 -151519.394554] SLOW spr round 6 (radius: 5) [13:38:08 -151519.393185] SLOW spr round 7 (radius: 10) [13:39:58 -151519.393043] SLOW spr round 8 (radius: 15) [13:42:11 -151519.045522] SLOW spr round 9 (radius: 5) [13:44:19 -151519.045247] SLOW spr round 10 (radius: 10) [13:46:16 -151519.045002] SLOW spr round 11 (radius: 15) [13:48:28 -151519.044999] SLOW spr round 12 (radius: 20) [13:51:58 -151519.044996] SLOW spr round 13 (radius: 25) [13:56:38 -151519.044994] Model parameter optimization (eps = 0.100000) [13:56:48] ML tree search #18, logLikelihood: -151518.531778 [13:56:48 -672876.185516] Initial branch length optimization [13:56:52 -576946.835576] Model parameter optimization (eps = 10.000000) [13:57:30 -574600.482010] AUTODETECT spr round 1 (radius: 5) [13:59:17 -357439.423601] AUTODETECT spr round 2 (radius: 10) [14:01:41 -248331.916583] AUTODETECT spr round 3 (radius: 15) [14:03:53 -195522.100941] AUTODETECT spr round 4 (radius: 20) [14:06:46 -178412.884417] AUTODETECT spr round 5 (radius: 25) [14:09:44 -172778.067460] SPR radius for FAST iterations: 25 (autodetect) [14:09:44 -172778.067460] Model parameter optimization (eps = 3.000000) [14:10:04 -172609.794636] FAST spr round 1 (radius: 25) [14:12:06 -152882.531882] FAST spr round 2 (radius: 25) [14:13:51 -151747.411877] FAST spr round 3 (radius: 25) [14:15:28 -151603.979785] FAST spr round 4 (radius: 25) [14:16:56 -151598.764475] FAST spr round 5 (radius: 25) [14:18:22 -151596.621108] FAST spr round 6 (radius: 25) [14:19:45 -151596.621062] Model parameter optimization (eps = 1.000000) [14:20:05 -151573.209931] SLOW spr round 1 (radius: 5) [14:21:51 -151529.770937] SLOW spr round 2 (radius: 5) [14:23:36 -151526.062897] SLOW spr round 3 (radius: 5) [14:25:19 -151525.218428] SLOW spr round 4 (radius: 5) [14:27:03 -151525.218182] SLOW spr round 5 (radius: 10) [14:28:51 -151523.697551] SLOW spr round 6 (radius: 5) [14:30:53 -151523.696410] SLOW spr round 7 (radius: 10) [14:32:45 -151523.696274] SLOW spr round 8 (radius: 15) [14:35:03 -151523.350006] SLOW spr round 9 (radius: 5) [14:37:12 -151523.349938] SLOW spr round 10 (radius: 10) [14:39:09 -151523.349893] SLOW spr round 11 (radius: 15) [14:41:25 -151523.349892] SLOW spr round 12 (radius: 20) [14:45:13 -151523.349892] SLOW spr round 13 (radius: 25) [14:50:15 -151523.349891] Model parameter optimization (eps = 0.100000) [14:50:26] ML tree search #19, logLikelihood: -151522.912527 [14:50:26 -674465.833724] Initial branch length optimization [14:50:29 -577683.239646] Model parameter optimization (eps = 10.000000) [14:51:17 -575643.154945] AUTODETECT spr round 1 (radius: 5) [14:53:02 -357444.140643] AUTODETECT spr round 2 (radius: 10) [14:55:14 -249344.229913] AUTODETECT spr round 3 (radius: 15) [14:57:24 -213803.517492] AUTODETECT spr round 4 (radius: 20) [14:59:54 -201752.472318] AUTODETECT spr round 5 (radius: 25) [15:03:03 -187165.801384] SPR radius for FAST iterations: 25 (autodetect) [15:03:03 -187165.801384] Model parameter optimization (eps = 3.000000) [15:03:31 -186980.759375] FAST spr round 1 (radius: 25) [15:05:35 -153875.589329] FAST spr round 2 (radius: 25) [15:07:22 -151675.004716] FAST spr round 3 (radius: 25) [15:08:55 -151567.834610] FAST spr round 4 (radius: 25) [15:10:26 -151566.058070] FAST spr round 5 (radius: 25) [15:11:52 -151566.057358] Model parameter optimization (eps = 1.000000) [15:12:03 -151564.861341] SLOW spr round 1 (radius: 5) [15:13:47 -151520.769600] SLOW spr round 2 (radius: 5) [15:15:32 -151516.125356] SLOW spr round 3 (radius: 5) [15:17:17 -151516.123713] SLOW spr round 4 (radius: 10) [15:19:05 -151514.612084] SLOW spr round 5 (radius: 5) [15:21:07 -151514.610461] SLOW spr round 6 (radius: 10) [15:23:01 -151514.609775] SLOW spr round 7 (radius: 15) [15:25:18 -151514.085052] SLOW spr round 8 (radius: 5) [15:27:28 -151513.841337] SLOW spr round 9 (radius: 5) [15:29:25 -151513.838159] SLOW spr round 10 (radius: 10) [15:31:15 -151513.836472] SLOW spr round 11 (radius: 15) [15:33:33 -151513.835500] SLOW spr round 12 (radius: 20) [15:37:07 -151513.834939] SLOW spr round 13 (radius: 25) [15:41:53 -151513.834611] Model parameter optimization (eps = 0.100000) [15:41:59] ML tree search #20, logLikelihood: -151513.743927 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.251577,0.338830) (0.270967,0.422961) (0.278885,1.066341) (0.198571,2.531909) 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: -151508.648958 AIC score: 307019.297917 / AICc score: 8319023.297917 / BIC score: 315387.649815 Free parameters (model + branch lengths): 2001 WARNING: Number of free parameters (K=2001) is larger than alignment size (n=484). 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/Q92824/3_mltree/Q92824.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/3_mltree/Q92824.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/3_mltree/Q92824.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92824/3_mltree/Q92824.raxml.log Analysis started: 05-Jul-2021 20:06:15 / finished: 06-Jul-2021 11:48:14 Elapsed time: 56519.500 seconds Consumed energy: 5187.859 Wh (= 26 km in an electric car, or 130 km with an e-scooter!)