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 18-Jun-2021 04:11:38 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75165/2_msa/O75165_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75165/3_mltree/O75165 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75165/2_msa/O75165_trimmed_msa.fasta [00:00:00] Loaded alignment with 603 taxa and 297 sites WARNING: Sequences tr_B4QGT6_B4QGT6_DROSI_7240 and tr_A1Z7S0_A1Z7S0_DROME_7227 are exactly identical! WARNING: Sequences tr_H2PBG0_H2PBG0_PONAB_9601 and tr_H2QND9_H2QND9_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PBG0_H2PBG0_PONAB_9601 and tr_A0A1D5QAF3_A0A1D5QAF3_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PBG0_H2PBG0_PONAB_9601 and tr_G7NXZ6_G7NXZ6_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2PBG0_H2PBG0_PONAB_9601 and tr_A0A2I3LIF9_A0A2I3LIF9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PBG0_H2PBG0_PONAB_9601 and tr_A0A0D9RDU4_A0A0D9RDU4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2PBG0_H2PBG0_PONAB_9601 and tr_A0A2K5LBG0_A0A2K5LBG0_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2PBG0_H2PBG0_PONAB_9601 and tr_A0A2K6E191_A0A2K6E191_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PBG0_H2PBG0_PONAB_9601 and tr_A0A2R9BTG4_A0A2R9BTG4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0R3NP70_A0A0R3NP70_DROPS_46245 and tr_B4GH45_B4GH45_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2J8KAN0_A0A2J8KAN0_PANTR_9598 and tr_A0A2R8Z9J2_A0A2R8Z9J2_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7D1L4_K7D1L4_PANTR_9598 and sp_Q8WW22_DNJA4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7D1L4_K7D1L4_PANTR_9598 and tr_A0A2R9B809_A0A2R9B809_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6YA31_F6YA31_HORSE_9796 and tr_A0A2U4B924_A0A2U4B924_TURTR_9739 are exactly identical! WARNING: Sequences tr_F6YA31_F6YA31_HORSE_9796 and tr_A0A2U3ZWK8_A0A2U3ZWK8_ODORO_9708 are exactly identical! WARNING: Sequences tr_F6YA31_F6YA31_HORSE_9796 and tr_A0A2Y9NW02_A0A2Y9NW02_DELLE_9749 are exactly identical! WARNING: Sequences tr_F6YA31_F6YA31_HORSE_9796 and tr_A0A2Y9F7F5_A0A2Y9F7F5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_W5PGX8_W5PGX8_SHEEP_9940 and tr_F1MDR7_F1MDR7_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A088AL57_A0A088AL57_APIME_7460 and tr_A0A2A3ERU6_A0A2A3ERU6_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NWG3_A0A158NWG3_ATTCE_12957 and tr_A0A151I1S1_A0A151I1S1_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0E0IWW8_A0A0E0IWW8_ORYNI_4536 and tr_A2ZAI6_A2ZAI6_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0IWW8_A0A0E0IWW8_ORYNI_4536 and tr_I1QW79_I1QW79_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0IWW8_A0A0E0IWW8_ORYNI_4536 and tr_A0A0E0R2V2_A0A0E0R2V2_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0IWW8_A0A0E0IWW8_ORYNI_4536 and tr_A0A0D3HGW7_A0A0D3HGW7_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0IWW8_A0A0E0IWW8_ORYNI_4536 and tr_A0A0P0XYL0_A0A0P0XYL0_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A1P6BYH4_A0A1P6BYH4_BRUMA_6279 and tr_A0A158PRV3_A0A158PRV3_BRUPA_6280 are exactly identical! WARNING: Sequences tr_F7DDU9_F7DDU9_MACMU_9544 and tr_A0A2I3LY88_A0A2I3LY88_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DDU9_F7DDU9_MACMU_9544 and tr_A0A0D9RQU7_A0A0D9RQU7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7DDU9_F7DDU9_MACMU_9544 and tr_A0A2K5L8B1_A0A2K5L8B1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DDU9_F7DDU9_MACMU_9544 and tr_A0A2K6BIF3_A0A2K6BIF3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FCL8_F7FCL8_MACMU_9544 and tr_Q4R6T6_Q4R6T6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FCL8_F7FCL8_MACMU_9544 and tr_A0A2K6ATS6_A0A2K6ATS6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FCL8_F7FCL8_MACMU_9544 and tr_A0A2K5XJ97_A0A2K5XJ97_MANLE_9568 are exactly identical! WARNING: Sequences tr_G0NFQ8_G0NFQ8_CAEBE_135651 and tr_G0NPH3_G0NPH3_CAEBE_135651 are exactly identical! WARNING: Sequences tr_A8XWD2_A8XWD2_CAEBR_6238 and tr_A0A2G5VSF9_A0A2G5VSF9_9PELO_1611254 are exactly identical! WARNING: Sequences tr_G1LWC5_G1LWC5_AILME_9646 and tr_A0A2U3XZZ1_A0A2U3XZZ1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1LWC5_G1LWC5_AILME_9646 and tr_A0A2Y9KGV7_A0A2Y9KGV7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1LWC5_G1LWC5_AILME_9646 and tr_A0A384DIJ0_A0A384DIJ0_URSMA_29073 are exactly identical! WARNING: Sequences tr_B3RR77_B3RR77_TRIAD_10228 and tr_A0A369SFD7_A0A369SFD7_9METZ_287889 are exactly identical! WARNING: Sequences tr_M7ZTU7_M7ZTU7_TRIUA_4572 and tr_A0A3B5XZM9_A0A3B5XZM9_WHEAT_4565 are exactly identical! WARNING: Sequences tr_M7ZTU7_M7ZTU7_TRIUA_4572 and tr_A0A3B5YY68_A0A3B5YY68_WHEAT_4565 are exactly identical! WARNING: Sequences tr_M7ZTU7_M7ZTU7_TRIUA_4572 and tr_A0A3B5ZVJ3_A0A3B5ZVJ3_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067GLB1_A0A067GLB1_CITSI_2711 and tr_V4WCW6_V4WCW6_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067GLB1_A0A067GLB1_CITSI_2711 and tr_A0A2H5PDQ5_A0A2H5PDQ5_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2U5N4_A0A0D2U5N4_GOSRA_29730 and tr_A0A1U8IWY0_A0A1U8IWY0_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2U5N4_A0A0D2U5N4_GOSRA_29730 and tr_A0A1U8PTY0_A0A1U8PTY0_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A2I0MRJ2_A0A2I0MRJ2_COLLI_8932 and tr_A0A1V4KCA6_A0A1V4KCA6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A151IV68_A0A151IV68_9HYME_471704 and tr_A0A195BBH4_A0A195BBH4_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A151IV68_A0A151IV68_9HYME_471704 and tr_A0A151K052_A0A151K052_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A1S3Z258_A0A1S3Z258_TOBAC_4097 and tr_A0A1U7YIP9_A0A1U7YIP9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3URB8_A0A1S3URB8_VIGRR_3916 and tr_A0A3Q0F5V1_A0A3Q0F5V1_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A226NEM1_A0A226NEM1_CALSU_9009 and tr_A0A226PTC9_A0A226PTC9_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2G4TAD3_A0A2G4TAD3_9FUNG_1340429 and tr_A0A367JRF5_A0A367JRF5_9FUNG_86630 are exactly identical! WARNING: Duplicate sequences found: 53 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75165/3_mltree/O75165.raxml.reduced.phy Alignment comprises 1 partitions and 297 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 297 / 297 Gaps: 20.12 % Invariant sites: 0.34 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75165/3_mltree/O75165.raxml.rba Parallelization scheme autoconfig: 6 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 603 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 297 / 23760 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -281046.613470] Initial branch length optimization [00:00:04 -224256.253083] Model parameter optimization (eps = 10.000000) [00:00:59 -223826.600914] AUTODETECT spr round 1 (radius: 5) [00:02:33 -152008.464751] AUTODETECT spr round 2 (radius: 10) [00:04:18 -111948.007126] AUTODETECT spr round 3 (radius: 15) [00:06:33 -83941.261987] AUTODETECT spr round 4 (radius: 20) [00:08:54 -78595.806074] AUTODETECT spr round 5 (radius: 25) [00:11:44 -75753.436048] SPR radius for FAST iterations: 25 (autodetect) [00:11:44 -75753.436048] Model parameter optimization (eps = 3.000000) [00:12:09 -75643.613027] FAST spr round 1 (radius: 25) [00:14:14 -67286.228163] FAST spr round 2 (radius: 25) [00:15:53 -66743.914702] FAST spr round 3 (radius: 25) [00:17:15 -66686.461806] FAST spr round 4 (radius: 25) [00:18:27 -66678.825465] FAST spr round 5 (radius: 25) [00:19:30 -66678.808000] Model parameter optimization (eps = 1.000000) [00:19:48 -66642.461786] SLOW spr round 1 (radius: 5) [00:21:22 -66629.025623] SLOW spr round 2 (radius: 5) [00:22:59 -66627.577093] SLOW spr round 3 (radius: 5) [00:24:37 -66624.314090] SLOW spr round 4 (radius: 5) [00:26:11 -66624.313981] SLOW spr round 5 (radius: 10) [00:27:45 -66622.848542] SLOW spr round 6 (radius: 5) [00:29:54 -66622.460266] SLOW spr round 7 (radius: 5) [00:31:46 -66621.268409] SLOW spr round 8 (radius: 5) [00:33:26 -66621.267741] SLOW spr round 9 (radius: 10) [00:35:00 -66621.267689] SLOW spr round 10 (radius: 15) [00:37:43 -66619.060033] SLOW spr round 11 (radius: 5) [00:39:54 -66619.058108] SLOW spr round 12 (radius: 10) [00:41:08] [worker #3] ML tree search #4, logLikelihood: -66621.726382 [00:41:50 -66619.058029] SLOW spr round 13 (radius: 15) [00:44:19 -66618.979232] SLOW spr round 14 (radius: 20) [00:47:39 -66618.909566] SLOW spr round 15 (radius: 25) [00:47:46] [worker #1] ML tree search #2, logLikelihood: -66623.522445 [00:51:38 -66618.770028] SLOW spr round 16 (radius: 5) [00:53:56 -66618.629707] SLOW spr round 17 (radius: 5) [00:55:52 -66618.625057] SLOW spr round 18 (radius: 10) [00:56:12] [worker #5] ML tree search #6, logLikelihood: -66615.415236 [00:57:02] [worker #4] ML tree search #5, logLikelihood: -66618.046669 [00:57:36 -66618.625020] SLOW spr round 19 (radius: 15) [01:00:08 -66618.625004] SLOW spr round 20 (radius: 20) [01:03:29 -66618.624997] SLOW spr round 21 (radius: 25) [01:07:28 -66618.624992] Model parameter optimization (eps = 0.100000) [01:07:36] [worker #0] ML tree search #1, logLikelihood: -66618.519632 [01:07:37 -277623.796738] Initial branch length optimization [01:07:40 -219398.847762] Model parameter optimization (eps = 10.000000) [01:08:25 -218997.595157] AUTODETECT spr round 1 (radius: 5) [01:09:59 -149337.992398] AUTODETECT spr round 2 (radius: 10) [01:11:20] [worker #2] ML tree search #3, logLikelihood: -66618.961507 [01:11:38 -108632.382009] AUTODETECT spr round 3 (radius: 15) [01:13:32 -88026.484293] AUTODETECT spr round 4 (radius: 20) [01:15:42 -80114.604592] AUTODETECT spr round 5 (radius: 25) [01:18:37 -78889.919385] SPR radius for FAST iterations: 25 (autodetect) [01:18:37 -78889.919385] Model parameter optimization (eps = 3.000000) [01:19:18 -78754.137938] FAST spr round 1 (radius: 25) [01:21:24 -67288.766982] FAST spr round 2 (radius: 25) [01:22:57 -66733.686214] FAST spr round 3 (radius: 25) [01:24:15 -66665.415809] FAST spr round 4 (radius: 25) [01:25:24 -66650.614190] FAST spr round 5 (radius: 25) [01:26:28 -66648.547053] FAST spr round 6 (radius: 25) [01:27:29 -66648.546849] Model parameter optimization (eps = 1.000000) [01:27:46 -66641.523613] SLOW spr round 1 (radius: 5) [01:29:15 -66626.777808] SLOW spr round 2 (radius: 5) [01:30:48 -66622.596605] SLOW spr round 3 (radius: 5) [01:32:21 -66622.595076] SLOW spr round 4 (radius: 10) [01:33:55 -66622.199396] SLOW spr round 5 (radius: 5) [01:36:05 -66617.004096] SLOW spr round 6 (radius: 5) [01:37:54 -66617.003378] SLOW spr round 7 (radius: 10) [01:39:35 -66617.002964] SLOW spr round 8 (radius: 15) [01:40:38] [worker #3] ML tree search #10, logLikelihood: -66620.863136 [01:42:12] [worker #1] ML tree search #8, logLikelihood: -66634.260388 [01:42:23 -66616.003606] SLOW spr round 9 (radius: 5) [01:43:37] [worker #4] ML tree search #11, logLikelihood: -66612.835826 [01:44:35 -66615.974880] SLOW spr round 10 (radius: 10) [01:46:35 -66615.974561] SLOW spr round 11 (radius: 15) [01:49:16 -66615.600836] SLOW spr round 12 (radius: 5) [01:51:29 -66615.299075] SLOW spr round 13 (radius: 5) [01:53:22 -66615.287630] SLOW spr round 14 (radius: 10) [01:55:06 -66615.287463] SLOW spr round 15 (radius: 15) [01:57:51 -66615.287408] SLOW spr round 16 (radius: 20) [01:58:35] [worker #5] ML tree search #12, logLikelihood: -66610.212148 [02:01:35 -66614.950738] SLOW spr round 17 (radius: 5) [02:03:52 -66614.896996] SLOW spr round 18 (radius: 10) [02:05:43] [worker #2] ML tree search #9, logLikelihood: -66620.591400 [02:05:58 -66614.895732] SLOW spr round 19 (radius: 15) [02:08:36 -66614.895119] SLOW spr round 20 (radius: 20) [02:12:21 -66614.894823] SLOW spr round 21 (radius: 25) [02:16:53 -66614.894678] Model parameter optimization (eps = 0.100000) [02:17:04] [worker #0] ML tree search #7, logLikelihood: -66614.051714 [02:17:04 -279523.972476] Initial branch length optimization [02:17:09 -220435.110864] Model parameter optimization (eps = 10.000000) [02:17:51 -220080.562208] AUTODETECT spr round 1 (radius: 5) [02:19:26 -150810.742786] AUTODETECT spr round 2 (radius: 10) [02:21:13 -111207.869761] AUTODETECT spr round 3 (radius: 15) [02:23:09 -87043.595586] AUTODETECT spr round 4 (radius: 20) [02:25:22 -81608.694102] AUTODETECT spr round 5 (radius: 25) [02:28:12 -76427.691525] SPR radius for FAST iterations: 25 (autodetect) [02:28:12 -76427.691525] Model parameter optimization (eps = 3.000000) [02:28:38 -76285.539280] FAST spr round 1 (radius: 25) [02:30:43 -67195.198688] FAST spr round 2 (radius: 25) [02:32:15 -66703.098075] FAST spr round 3 (radius: 25) [02:33:32 -66663.069650] FAST spr round 4 (radius: 25) [02:34:43 -66644.330520] FAST spr round 5 (radius: 25) [02:35:49 -66637.068284] FAST spr round 6 (radius: 25) [02:36:51 -66637.055790] Model parameter optimization (eps = 1.000000) [02:37:09 -66630.869575] SLOW spr round 1 (radius: 5) [02:38:40 -66620.117824] SLOW spr round 2 (radius: 5) [02:40:15 -66619.987092] SLOW spr round 3 (radius: 5) [02:41:27] [worker #3] ML tree search #16, logLikelihood: -66605.627027 [02:41:52 -66619.322699] SLOW spr round 4 (radius: 5) [02:43:25 -66619.322510] SLOW spr round 5 (radius: 10) [02:45:00 -66619.322386] SLOW spr round 6 (radius: 15) [02:47:54 -66618.440449] SLOW spr round 7 (radius: 5) [02:48:04] [worker #1] ML tree search #14, logLikelihood: -66610.054985 [02:48:54] [worker #4] ML tree search #17, logLikelihood: -66623.809788 [02:50:06 -66618.414974] SLOW spr round 8 (radius: 10) [02:50:42] [worker #5] ML tree search #18, logLikelihood: -66611.886800 [02:52:07 -66618.414311] SLOW spr round 9 (radius: 15) [02:54:43 -66618.414054] SLOW spr round 10 (radius: 20) [02:58:25 -66617.878558] SLOW spr round 11 (radius: 5) [03:00:41 -66617.860344] SLOW spr round 12 (radius: 10) [03:02:47 -66617.858009] SLOW spr round 13 (radius: 15) [03:05:23 -66617.856749] SLOW spr round 14 (radius: 20) [03:09:03 -66617.856070] SLOW spr round 15 (radius: 25) [03:11:59] [worker #2] ML tree search #15, logLikelihood: -66609.115065 [03:13:17 -66617.855702] Model parameter optimization (eps = 0.100000) [03:13:23] [worker #0] ML tree search #13, logLikelihood: -66617.756657 [03:13:23 -277174.428548] Initial branch length optimization [03:13:28 -219034.603292] Model parameter optimization (eps = 10.000000) [03:14:00 -218690.541663] AUTODETECT spr round 1 (radius: 5) [03:15:35 -152395.512012] AUTODETECT spr round 2 (radius: 10) [03:17:18 -109092.593284] AUTODETECT spr round 3 (radius: 15) [03:19:14 -86746.766429] AUTODETECT spr round 4 (radius: 20) [03:21:42 -75566.749136] AUTODETECT spr round 5 (radius: 25) [03:24:11 -74882.977445] SPR radius for FAST iterations: 25 (autodetect) [03:24:11 -74882.977445] Model parameter optimization (eps = 3.000000) [03:24:38 -74754.547538] FAST spr round 1 (radius: 25) [03:26:34 -67099.114818] FAST spr round 2 (radius: 25) [03:28:05 -66678.931263] FAST spr round 3 (radius: 25) [03:29:22 -66652.459347] FAST spr round 4 (radius: 25) [03:30:29 -66648.929766] FAST spr round 5 (radius: 25) [03:31:31 -66648.913720] Model parameter optimization (eps = 1.000000) [03:31:45 -66638.481234] SLOW spr round 1 (radius: 5) [03:33:17 -66624.088914] SLOW spr round 2 (radius: 5) [03:34:55 -66619.745811] SLOW spr round 3 (radius: 5) [03:36:29 -66619.744661] SLOW spr round 4 (radius: 10) [03:38:02 -66619.742634] SLOW spr round 5 (radius: 15) [03:40:44 -66619.740394] SLOW spr round 6 (radius: 20) [03:42:47] [worker #1] ML tree search #20, logLikelihood: -66606.271499 [03:44:16 -66619.740149] SLOW spr round 7 (radius: 25) [03:48:47 -66619.739981] Model parameter optimization (eps = 0.100000) [03:48:58] [worker #0] ML tree search #19, logLikelihood: -66619.633570 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.209326,0.716743) (0.157953,0.774359) (0.351872,0.856375) (0.280849,1.517970) 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: -66605.627027 AIC score: 135629.254054 / AICc score: 3061409.254054 / BIC score: 140094.976210 Free parameters (model + branch lengths): 1209 WARNING: Number of free parameters (K=1209) is larger than alignment size (n=297). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75165/3_mltree/O75165.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75165/3_mltree/O75165.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75165/3_mltree/O75165.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/O75165/3_mltree/O75165.raxml.log Analysis started: 18-Jun-2021 04:11:38 / finished: 18-Jun-2021 08:00:37 Elapsed time: 13738.604 seconds