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 19-Jul-2021 20:54:25 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UJJ9/2_msa/Q9UJJ9_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UJJ9/3_mltree/Q9UJJ9 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UJJ9/2_msa/Q9UJJ9_trimmed_msa.fasta [00:00:00] Loaded alignment with 391 taxa and 140 sites WARNING: Sequences tr_A0A0H5SMP7_A0A0H5SMP7_BRUMA_6279 and tr_A0A0N4SZC9_A0A0N4SZC9_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A0H5SMP7_A0A0H5SMP7_BRUMA_6279 and tr_A0A0R3R282_A0A0R3R282_9BILA_42155 are exactly identical! WARNING: Sequences tr_F7FKT8_F7FKT8_MACMU_9544 and tr_A0A2K5NAV0_A0A2K5NAV0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FKT8_F7FKT8_MACMU_9544 and tr_A0A2K6D1U4_A0A2K6D1U4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FKT8_F7FKT8_MACMU_9544 and tr_A0A2K5Z629_A0A2K5Z629_MANLE_9568 are exactly identical! WARNING: Sequences sp_A2WNF5_GLU2B_ORYSI_39946 and tr_I1NM75_I1NM75_ORYGL_4538 are exactly identical! WARNING: Sequences sp_A2WNF5_GLU2B_ORYSI_39946 and tr_A0A0D3EMC3_A0A0D3EMC3_9ORYZ_65489 are exactly identical! WARNING: Sequences sp_A2WNF5_GLU2B_ORYSI_39946 and tr_A0A0D9Y6Q8_A0A0D9Y6Q8_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_H0ZH50_H0ZH50_TAEGU_59729 and tr_U3KI38_U3KI38_FICAL_59894 are exactly identical! WARNING: Sequences tr_A0A0E0MUL8_A0A0E0MUL8_ORYRU_4529 and sp_Q5NBP9_GLU2B_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B3S3S3_B3S3S3_TRIAD_10228 and tr_A0A369RZM9_A0A369RZM9_9METZ_287889 are exactly identical! WARNING: Sequences tr_M4CF39_M4CF39_BRARP_51351 and tr_A0A0D3EBQ6_A0A0D3EBQ6_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078FF73_A0A078FF73_BRANA_3708 and tr_A0A0D3B371_A0A0D3B371_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0V0WM97_A0A0V0WM97_9BILA_92179 and tr_A0A0V0VRI6_A0A0V0VRI6_9BILA_181606 are exactly identical! WARNING: Sequences tr_B5XGW5_B5XGW5_SALSA_8030 and tr_A0A060VV26_A0A060VV26_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A060XRX5_A0A060XRX5_ONCMY_8022 and tr_A0A060YD97_A0A060YD97_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A2D0PW48_A0A2D0PW48_ICTPU_7998 and tr_A0A2D0PXG1_A0A2D0PXG1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2Y9LG57_A0A2Y9LG57_ENHLU_391180 and tr_A0A2Y9LLF7_A0A2Y9LLF7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2Y9EES3_A0A2Y9EES3_PHYCD_9755 and tr_A0A384A396_A0A384A396_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 19 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UJJ9/3_mltree/Q9UJJ9.raxml.reduced.phy Alignment comprises 1 partitions and 140 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 140 / 140 Gaps: 5.41 % Invariant sites: 0.71 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UJJ9/3_mltree/Q9UJJ9.raxml.rba Parallelization scheme autoconfig: 3 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 391 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 140 / 11200 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -99151.462092] Initial branch length optimization [00:00:02 -81581.934751] Model parameter optimization (eps = 10.000000) [00:00:18 -81503.082926] AUTODETECT spr round 1 (radius: 5) [00:00:43 -59718.065775] AUTODETECT spr round 2 (radius: 10) [00:01:14 -48951.581354] AUTODETECT spr round 3 (radius: 15) [00:01:53 -40790.878551] AUTODETECT spr round 4 (radius: 20) [00:02:34 -39717.416670] AUTODETECT spr round 5 (radius: 25) [00:03:14 -39334.369617] SPR radius for FAST iterations: 25 (autodetect) [00:03:14 -39334.369617] Model parameter optimization (eps = 3.000000) [00:03:24 -39247.637702] FAST spr round 1 (radius: 25) [00:03:59 -36708.098606] FAST spr round 2 (radius: 25) [00:04:27 -36608.501512] FAST spr round 3 (radius: 25) [00:04:51 -36593.252425] FAST spr round 4 (radius: 25) [00:05:13 -36590.741402] FAST spr round 5 (radius: 25) [00:05:34 -36590.738130] Model parameter optimization (eps = 1.000000) [00:05:41 -36586.094523] SLOW spr round 1 (radius: 5) [00:06:19 -36573.856701] SLOW spr round 2 (radius: 5) [00:06:55 -36565.860250] SLOW spr round 3 (radius: 5) [00:07:28 -36564.978276] SLOW spr round 4 (radius: 5) [00:08:00 -36564.978134] SLOW spr round 5 (radius: 10) [00:08:33 -36563.813942] SLOW spr round 6 (radius: 5) [00:09:16 -36563.813012] SLOW spr round 7 (radius: 10) [00:09:54 -36563.813001] SLOW spr round 8 (radius: 15) [00:10:48 -36563.620261] SLOW spr round 9 (radius: 5) [00:11:33 -36563.620226] SLOW spr round 10 (radius: 10) [00:12:14 -36563.620225] SLOW spr round 11 (radius: 15) [00:13:06 -36563.620225] SLOW spr round 12 (radius: 20) [00:14:14 -36563.620225] SLOW spr round 13 (radius: 25) [00:14:48] [worker #2] ML tree search #3, logLikelihood: -36566.213099 [00:15:20 -36563.620225] Model parameter optimization (eps = 0.100000) [00:15:25] [worker #0] ML tree search #1, logLikelihood: -36563.376974 [00:15:25 -99425.642077] Initial branch length optimization [00:15:27 -81028.223011] Model parameter optimization (eps = 10.000000) [00:15:42 -80955.214637] AUTODETECT spr round 1 (radius: 5) [00:16:07 -60062.523816] AUTODETECT spr round 2 (radius: 10) [00:16:41 -44968.164107] AUTODETECT spr round 3 (radius: 15) [00:16:50] [worker #1] ML tree search #2, logLikelihood: -36561.112247 [00:17:19 -40439.050635] AUTODETECT spr round 4 (radius: 20) [00:18:02 -39908.798006] AUTODETECT spr round 5 (radius: 25) [00:18:55 -39438.290718] SPR radius for FAST iterations: 25 (autodetect) [00:18:55 -39438.290718] Model parameter optimization (eps = 3.000000) [00:19:03 -39340.272070] FAST spr round 1 (radius: 25) [00:19:38 -36699.724229] FAST spr round 2 (radius: 25) [00:20:07 -36593.385501] FAST spr round 3 (radius: 25) [00:20:31 -36585.790915] FAST spr round 4 (radius: 25) [00:20:52 -36585.790626] Model parameter optimization (eps = 1.000000) [00:20:58 -36582.199894] SLOW spr round 1 (radius: 5) [00:21:35 -36575.367657] SLOW spr round 2 (radius: 5) [00:22:09 -36574.935154] SLOW spr round 3 (radius: 5) [00:22:41 -36574.934861] SLOW spr round 4 (radius: 10) [00:23:15 -36571.881064] SLOW spr round 5 (radius: 5) [00:23:59 -36571.393477] SLOW spr round 6 (radius: 5) [00:24:37 -36571.392469] SLOW spr round 7 (radius: 10) [00:25:12 -36570.925801] SLOW spr round 8 (radius: 5) [00:25:56 -36570.925476] SLOW spr round 9 (radius: 10) [00:26:34 -36570.925414] SLOW spr round 10 (radius: 15) [00:27:30 -36570.704859] SLOW spr round 11 (radius: 5) [00:28:17 -36570.704811] SLOW spr round 12 (radius: 10) [00:28:59 -36569.282823] SLOW spr round 13 (radius: 5) [00:29:41 -36569.276789] SLOW spr round 14 (radius: 10) [00:30:18 -36569.276014] SLOW spr round 15 (radius: 15) [00:31:14 -36569.275902] SLOW spr round 16 (radius: 20) [00:32:27 -36569.275857] SLOW spr round 17 (radius: 25) [00:33:18] [worker #1] ML tree search #5, logLikelihood: -36582.450332 [00:33:42 -36569.275818] Model parameter optimization (eps = 0.100000) [00:33:45] [worker #0] ML tree search #4, logLikelihood: -36569.142152 [00:33:45 -99095.525525] Initial branch length optimization [00:33:46 -81555.626258] Model parameter optimization (eps = 10.000000) [00:33:51] [worker #2] ML tree search #6, logLikelihood: -36555.692251 [00:34:00 -81485.940675] AUTODETECT spr round 1 (radius: 5) [00:34:25 -59117.164027] AUTODETECT spr round 2 (radius: 10) [00:34:55 -46730.340673] AUTODETECT spr round 3 (radius: 15) [00:35:33 -41174.144570] AUTODETECT spr round 4 (radius: 20) [00:36:22 -39872.875799] AUTODETECT spr round 5 (radius: 25) [00:37:11 -39645.384279] SPR radius for FAST iterations: 25 (autodetect) [00:37:11 -39645.384279] Model parameter optimization (eps = 3.000000) [00:37:23 -39583.063650] FAST spr round 1 (radius: 25) [00:37:58 -37075.974783] FAST spr round 2 (radius: 25) [00:38:28 -36615.964360] FAST spr round 3 (radius: 25) [00:38:54 -36589.537343] FAST spr round 4 (radius: 25) [00:39:16 -36585.368594] FAST spr round 5 (radius: 25) [00:39:38 -36583.536574] FAST spr round 6 (radius: 25) [00:39:58 -36583.536521] Model parameter optimization (eps = 1.000000) [00:40:05 -36576.457723] SLOW spr round 1 (radius: 5) [00:40:42 -36569.594035] SLOW spr round 2 (radius: 5) [00:41:15 -36569.490744] SLOW spr round 3 (radius: 5) [00:41:47 -36569.489825] SLOW spr round 4 (radius: 10) [00:42:20 -36569.106147] SLOW spr round 5 (radius: 5) [00:43:03 -36569.102132] SLOW spr round 6 (radius: 10) [00:43:41 -36569.101483] SLOW spr round 7 (radius: 15) [00:44:33 -36569.101381] SLOW spr round 8 (radius: 20) [00:45:42 -36569.101365] SLOW spr round 9 (radius: 25) [00:45:59] [worker #1] ML tree search #8, logLikelihood: -36561.513985 [00:46:45 -36569.101362] Model parameter optimization (eps = 0.100000) [00:46:47] [worker #0] ML tree search #7, logLikelihood: -36569.084774 [00:46:47 -99381.335098] Initial branch length optimization [00:46:48 -80784.238770] Model parameter optimization (eps = 10.000000) [00:47:01 -80648.570217] AUTODETECT spr round 1 (radius: 5) [00:47:27 -59150.468685] AUTODETECT spr round 2 (radius: 10) [00:47:58 -47603.738696] AUTODETECT spr round 3 (radius: 15) [00:48:11] [worker #2] ML tree search #9, logLikelihood: -36571.221045 [00:48:34 -40506.059220] AUTODETECT spr round 4 (radius: 20) [00:49:18 -39742.610426] AUTODETECT spr round 5 (radius: 25) [00:50:11 -39639.071038] SPR radius for FAST iterations: 25 (autodetect) [00:50:11 -39639.071038] Model parameter optimization (eps = 3.000000) [00:50:21 -39559.262222] FAST spr round 1 (radius: 25) [00:50:58 -36695.409040] FAST spr round 2 (radius: 25) [00:51:29 -36593.072361] FAST spr round 3 (radius: 25) [00:51:53 -36585.465510] FAST spr round 4 (radius: 25) [00:52:16 -36581.588537] FAST spr round 5 (radius: 25) [00:52:36 -36581.587977] Model parameter optimization (eps = 1.000000) [00:52:43 -36575.939548] SLOW spr round 1 (radius: 5) [00:53:20 -36568.766148] SLOW spr round 2 (radius: 5) [00:53:54 -36567.723262] SLOW spr round 3 (radius: 5) [00:54:27 -36567.723073] SLOW spr round 4 (radius: 10) [00:55:01 -36567.532425] SLOW spr round 5 (radius: 5) [00:55:44 -36567.532377] SLOW spr round 6 (radius: 10) [00:56:22 -36567.532376] SLOW spr round 7 (radius: 15) [00:57:16 -36567.311280] SLOW spr round 8 (radius: 5) [00:58:02 -36567.311271] SLOW spr round 9 (radius: 10) [00:58:43 -36567.311270] SLOW spr round 10 (radius: 15) [00:59:37 -36567.311270] SLOW spr round 11 (radius: 20) [01:00:53 -36567.311270] SLOW spr round 12 (radius: 25) [01:02:00 -36567.311269] Model parameter optimization (eps = 0.100000) [01:02:05] [worker #0] ML tree search #10, logLikelihood: -36567.075502 [01:02:05 -97260.407054] Initial branch length optimization [01:02:06 -80854.301418] Model parameter optimization (eps = 10.000000) [01:02:21 -80823.882130] AUTODETECT spr round 1 (radius: 5) [01:02:47 -57227.393991] AUTODETECT spr round 2 (radius: 10) [01:02:59] [worker #2] ML tree search #12, logLikelihood: -36566.478986 [01:03:16 -47581.738808] AUTODETECT spr round 3 (radius: 15) [01:03:52 -41603.670054] AUTODETECT spr round 4 (radius: 20) [01:04:35 -40315.420746] AUTODETECT spr round 5 (radius: 25) [01:05:14 -40279.734352] SPR radius for FAST iterations: 25 (autodetect) [01:05:14 -40279.734352] Model parameter optimization (eps = 3.000000) [01:05:25 -40237.617421] FAST spr round 1 (radius: 25) [01:06:02 -36743.627984] FAST spr round 2 (radius: 25) [01:06:30 -36596.723699] FAST spr round 3 (radius: 25) [01:06:56 -36577.405630] FAST spr round 4 (radius: 25) [01:07:18 -36575.838839] FAST spr round 5 (radius: 25) [01:07:38 -36575.838609] Model parameter optimization (eps = 1.000000) [01:07:44 -36570.996707] SLOW spr round 1 (radius: 5) [01:08:21 -36562.174138] SLOW spr round 2 (radius: 5) [01:08:54 -36561.985112] SLOW spr round 3 (radius: 5) [01:09:28 -36561.689717] SLOW spr round 4 (radius: 5) [01:09:45] [worker #1] ML tree search #11, logLikelihood: -36551.966613 [01:10:01 -36561.688796] SLOW spr round 5 (radius: 10) [01:10:34 -36561.688709] SLOW spr round 6 (radius: 15) [01:11:35 -36561.688669] SLOW spr round 7 (radius: 20) [01:12:45 -36561.688632] SLOW spr round 8 (radius: 25) [01:13:53 -36561.688596] Model parameter optimization (eps = 0.100000) [01:13:56] [worker #0] ML tree search #13, logLikelihood: -36561.666012 [01:13:56 -98764.624985] Initial branch length optimization [01:13:57 -80966.752026] Model parameter optimization (eps = 10.000000) [01:14:12 -80923.255872] AUTODETECT spr round 1 (radius: 5) [01:14:38 -58935.042936] AUTODETECT spr round 2 (radius: 10) [01:15:09 -48685.795669] AUTODETECT spr round 3 (radius: 15) [01:15:45 -43650.164951] AUTODETECT spr round 4 (radius: 20) [01:16:29 -41257.596821] AUTODETECT spr round 5 (radius: 25) [01:17:19 -40877.785681] SPR radius for FAST iterations: 25 (autodetect) [01:17:19 -40877.785681] Model parameter optimization (eps = 3.000000) [01:17:28 -40844.446850] FAST spr round 1 (radius: 25) [01:18:05 -36837.912457] FAST spr round 2 (radius: 25) [01:18:35 -36614.321985] FAST spr round 3 (radius: 25) [01:18:45] [worker #2] ML tree search #15, logLikelihood: -36559.187117 [01:19:01 -36596.013837] FAST spr round 4 (radius: 25) [01:19:23 -36593.351129] FAST spr round 5 (radius: 25) [01:19:44 -36589.008138] FAST spr round 6 (radius: 25) [01:20:05 -36589.007906] Model parameter optimization (eps = 1.000000) [01:20:12 -36576.532771] SLOW spr round 1 (radius: 5) [01:20:49 -36568.532876] SLOW spr round 2 (radius: 5) [01:21:23 -36565.945633] SLOW spr round 3 (radius: 5) [01:21:56 -36564.939909] SLOW spr round 4 (radius: 5) [01:22:28 -36564.939863] SLOW spr round 5 (radius: 10) [01:22:54] [worker #1] ML tree search #14, logLikelihood: -36562.345193 [01:23:02 -36562.781336] SLOW spr round 6 (radius: 5) [01:23:46 -36562.780996] SLOW spr round 7 (radius: 10) [01:24:25 -36562.780969] SLOW spr round 8 (radius: 15) [01:25:21 -36562.576813] SLOW spr round 9 (radius: 5) [01:26:07 -36562.576768] SLOW spr round 10 (radius: 10) [01:26:49 -36562.576768] SLOW spr round 11 (radius: 15) [01:27:44 -36562.576768] SLOW spr round 12 (radius: 20) [01:28:58 -36562.576768] SLOW spr round 13 (radius: 25) [01:30:09 -36562.576768] Model parameter optimization (eps = 0.100000) [01:30:11] [worker #0] ML tree search #16, logLikelihood: -36562.511540 [01:30:11 -98845.096351] Initial branch length optimization [01:30:13 -80344.219544] Model parameter optimization (eps = 10.000000) [01:30:29 -80270.461941] AUTODETECT spr round 1 (radius: 5) [01:30:54 -58088.302808] AUTODETECT spr round 2 (radius: 10) [01:31:24 -49936.124666] AUTODETECT spr round 3 (radius: 15) [01:32:02 -43024.901255] AUTODETECT spr round 4 (radius: 20) [01:32:03] [worker #2] ML tree search #18, logLikelihood: -36563.871678 [01:32:47 -40582.141201] AUTODETECT spr round 5 (radius: 25) [01:33:36 -40269.659101] SPR radius for FAST iterations: 25 (autodetect) [01:33:36 -40269.659101] Model parameter optimization (eps = 3.000000) [01:33:47 -40208.929183] FAST spr round 1 (radius: 25) [01:34:24 -36925.380031] FAST spr round 2 (radius: 25) [01:34:53 -36599.188822] FAST spr round 3 (radius: 25) [01:35:15 -36588.960460] FAST spr round 4 (radius: 25) [01:35:36 -36586.846662] FAST spr round 5 (radius: 25) [01:35:56 -36586.846456] Model parameter optimization (eps = 1.000000) [01:36:03 -36578.700683] SLOW spr round 1 (radius: 5) [01:36:38 -36568.985547] SLOW spr round 2 (radius: 5) [01:37:12 -36568.450032] SLOW spr round 3 (radius: 5) [01:37:43 -36568.447472] SLOW spr round 4 (radius: 10) [01:38:17 -36566.015363] SLOW spr round 5 (radius: 5) [01:39:02 -36563.923924] SLOW spr round 6 (radius: 5) [01:39:39 -36563.923812] SLOW spr round 7 (radius: 10) [01:40:14 -36563.923807] SLOW spr round 8 (radius: 15) [01:41:14 -36563.923806] SLOW spr round 9 (radius: 20) [01:42:07] [worker #1] ML tree search #17, logLikelihood: -36560.512698 [01:42:25 -36563.141842] SLOW spr round 10 (radius: 5) [01:43:12 -36563.132912] SLOW spr round 11 (radius: 10) [01:43:56 -36563.131111] SLOW spr round 12 (radius: 15) [01:44:52 -36563.130675] SLOW spr round 13 (radius: 20) [01:46:04 -36563.130551] SLOW spr round 14 (radius: 25) [01:47:08 -36563.130510] Model parameter optimization (eps = 0.100000) [01:47:14] [worker #0] ML tree search #19, logLikelihood: -36562.291714 [01:54:03] [worker #1] ML tree search #20, logLikelihood: -36563.061484 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.143148,0.306435) (0.205496,0.531778) (0.384440,0.915337) (0.266916,1.854379) 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: -36551.966613 AIC score: 74673.933225 / AICc score: 1308693.933225 / BIC score: 76983.122527 Free parameters (model + branch lengths): 785 WARNING: Number of free parameters (K=785) is larger than alignment size (n=140). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UJJ9/3_mltree/Q9UJJ9.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UJJ9/3_mltree/Q9UJJ9.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UJJ9/3_mltree/Q9UJJ9.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9UJJ9/3_mltree/Q9UJJ9.raxml.log Analysis started: 19-Jul-2021 20:54:25 / finished: 19-Jul-2021 22:48:28 Elapsed time: 6843.360 seconds