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 01-Jul-2021 06:31:52 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95622/2_msa/O95622_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95622/3_mltree/O95622 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95622/2_msa/O95622_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1132 sites WARNING: Sequences tr_A0A2I2ZTJ4_A0A2I2ZTJ4_GORGO_9595 and tr_A0A1D5Q874_A0A1D5Q874_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2ZTJ4_A0A2I2ZTJ4_GORGO_9595 and tr_G7PCU6_G7PCU6_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I2ZTJ4_A0A2I2ZTJ4_GORGO_9595 and tr_A0A096N068_A0A096N068_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2ZTJ4_A0A2I2ZTJ4_GORGO_9595 and tr_A0A2K5M765_A0A2K5M765_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2ZTJ4_A0A2I2ZTJ4_GORGO_9595 and tr_A0A2K6DDC0_A0A2K6DDC0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QN93_G3QN93_GORGO_9595 and tr_H2QHJ5_H2QHJ5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QN93_G3QN93_GORGO_9595 and tr_A0A2R9BLU9_A0A2R9BLU9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SK46_A0A2I3SK46_PANTR_9598 and tr_A0A2R9BI25_A0A2R9BI25_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5RFY5_A0A1D5RFY5_MACMU_9544 and tr_A0A2K5MN50_A0A2K5MN50_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5RHE7_A0A1D5RHE7_MACMU_9544 and tr_A0A096MMZ6_A0A096MMZ6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6PIV7_F6PIV7_MACMU_9544 and tr_G7P9Z3_G7P9Z3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H582_F7H582_MACMU_9544 and tr_G7PHR3_G7PHR3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HUD3_F7HUD3_MACMU_9544 and tr_A0A096N1U3_A0A096N1U3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A091INZ5_A0A091INZ5_EGRGA_188379 and tr_A0A0A0A977_A0A0A0A977_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0M3QWE1_A0A0M3QWE1_DROBS_30019 and tr_A0A0M4EYI5_A0A0M4EYI5_DROBS_30019 are exactly identical! WARNING: Sequences tr_A0A2K5KK62_A0A2K5KK62_CERAT_9531 and tr_A0A2K5XHR8_A0A2K5XHR8_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 16 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/O95622/3_mltree/O95622.raxml.reduced.phy Alignment comprises 1 partitions and 1132 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 1132 / 1132 Gaps: 18.23 % Invariant sites: 0.09 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95622/3_mltree/O95622.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 8 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 142 / 11360 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -1686912.715518] Initial branch length optimization [00:00:06 -1423714.002951] Model parameter optimization (eps = 10.000000) [00:00:45 -1422704.126878] AUTODETECT spr round 1 (radius: 5) [00:03:01 -870005.186441] AUTODETECT spr round 2 (radius: 10) [00:05:28 -606112.480991] AUTODETECT spr round 3 (radius: 15) [00:08:03 -482682.784298] AUTODETECT spr round 4 (radius: 20) [00:10:45 -436284.146000] AUTODETECT spr round 5 (radius: 25) [00:14:10 -422658.379818] SPR radius for FAST iterations: 25 (autodetect) [00:14:10 -422658.379818] Model parameter optimization (eps = 3.000000) [00:14:38 -420654.336990] FAST spr round 1 (radius: 25) [00:17:10 -367044.129708] FAST spr round 2 (radius: 25) [00:19:07 -364379.645517] FAST spr round 3 (radius: 25) [00:20:53 -364014.833911] FAST spr round 4 (radius: 25) [00:22:29 -364013.533928] FAST spr round 5 (radius: 25) [00:24:02 -364013.532923] Model parameter optimization (eps = 1.000000) [00:24:18 -364008.352039] SLOW spr round 1 (radius: 5) [00:26:25 -363925.830067] SLOW spr round 2 (radius: 5) [00:28:28 -363918.458000] SLOW spr round 3 (radius: 5) [00:30:27 -363918.456649] SLOW spr round 4 (radius: 10) [00:32:29 -363913.443917] SLOW spr round 5 (radius: 5) [00:34:57 -363913.443913] SLOW spr round 6 (radius: 10) [00:37:11 -363912.979125] SLOW spr round 7 (radius: 5) [00:39:36 -363912.978586] SLOW spr round 8 (radius: 10) [00:41:47 -363912.978582] SLOW spr round 9 (radius: 15) [00:44:44 -363912.978577] SLOW spr round 10 (radius: 20) [00:49:45 -363912.978572] SLOW spr round 11 (radius: 25) [00:56:40 -363912.978567] Model parameter optimization (eps = 0.100000) [00:56:49] ML tree search #1, logLikelihood: -363912.862089 [00:56:49 -1677283.409753] Initial branch length optimization [00:56:55 -1409037.647760] Model parameter optimization (eps = 10.000000) [00:57:32 -1408147.604199] AUTODETECT spr round 1 (radius: 5) [00:59:47 -871857.169918] AUTODETECT spr round 2 (radius: 10) [01:02:17 -599239.552660] AUTODETECT spr round 3 (radius: 15) [01:04:46 -463109.487763] AUTODETECT spr round 4 (radius: 20) [01:07:18 -423464.444302] AUTODETECT spr round 5 (radius: 25) [01:10:12 -420356.871416] SPR radius for FAST iterations: 25 (autodetect) [01:10:12 -420356.871416] Model parameter optimization (eps = 3.000000) [01:10:46 -418592.796406] FAST spr round 1 (radius: 25) [01:13:20 -366269.865613] FAST spr round 2 (radius: 25) [01:15:24 -364195.809265] FAST spr round 3 (radius: 25) [01:17:12 -364059.038284] FAST spr round 4 (radius: 25) [01:18:49 -364043.439258] FAST spr round 5 (radius: 25) [01:20:24 -364043.439217] Model parameter optimization (eps = 1.000000) [01:20:38 -364037.266039] SLOW spr round 1 (radius: 5) [01:22:48 -363946.797561] SLOW spr round 2 (radius: 5) [01:24:52 -363942.671196] SLOW spr round 3 (radius: 5) [01:26:56 -363939.334476] SLOW spr round 4 (radius: 5) [01:28:56 -363939.333843] SLOW spr round 5 (radius: 10) [01:30:58 -363938.943299] SLOW spr round 6 (radius: 5) [01:33:27 -363938.941926] SLOW spr round 7 (radius: 10) [01:35:42 -363938.941575] SLOW spr round 8 (radius: 15) [01:38:40 -363938.941483] SLOW spr round 9 (radius: 20) [01:43:42 -363938.941459] SLOW spr round 10 (radius: 25) [01:50:38 -363938.941453] Model parameter optimization (eps = 0.100000) [01:50:50] ML tree search #2, logLikelihood: -363938.772463 [01:50:50 -1682810.687450] Initial branch length optimization [01:50:57 -1412577.121363] Model parameter optimization (eps = 10.000000) [01:51:32 -1411647.868313] AUTODETECT spr round 1 (radius: 5) [01:53:46 -842795.724148] AUTODETECT spr round 2 (radius: 10) [01:56:12 -579505.858036] AUTODETECT spr round 3 (radius: 15) [01:58:40 -494742.156414] AUTODETECT spr round 4 (radius: 20) [02:01:24 -437445.754020] AUTODETECT spr round 5 (radius: 25) [02:04:51 -429784.465165] SPR radius for FAST iterations: 25 (autodetect) [02:04:51 -429784.465165] Model parameter optimization (eps = 3.000000) [02:05:14 -427873.560704] FAST spr round 1 (radius: 25) [02:07:46 -367862.929935] FAST spr round 2 (radius: 25) [02:09:47 -364419.154769] FAST spr round 3 (radius: 25) [02:11:35 -364050.246576] FAST spr round 4 (radius: 25) [02:13:15 -364046.296013] FAST spr round 5 (radius: 25) [02:14:51 -364045.607325] FAST spr round 6 (radius: 25) [02:16:24 -364045.606580] Model parameter optimization (eps = 1.000000) [02:16:47 -364034.216375] SLOW spr round 1 (radius: 5) [02:18:56 -363949.943194] SLOW spr round 2 (radius: 5) [02:21:02 -363938.724620] SLOW spr round 3 (radius: 5) [02:23:02 -363938.722395] SLOW spr round 4 (radius: 10) [02:25:07 -363922.689920] SLOW spr round 5 (radius: 5) [02:27:38 -363922.677180] SLOW spr round 6 (radius: 10) [02:29:58 -363922.674433] SLOW spr round 7 (radius: 15) [02:33:01 -363922.673796] SLOW spr round 8 (radius: 20) [02:38:24 -363922.673642] SLOW spr round 9 (radius: 25) [02:45:40 -363922.673604] Model parameter optimization (eps = 0.100000) [02:45:48] ML tree search #3, logLikelihood: -363922.610891 [02:45:48 -1698249.251000] Initial branch length optimization [02:45:56 -1431176.313734] Model parameter optimization (eps = 10.000000) [02:46:41 -1430186.459007] AUTODETECT spr round 1 (radius: 5) [02:48:58 -856344.352026] AUTODETECT spr round 2 (radius: 10) [02:51:29 -583069.800123] AUTODETECT spr round 3 (radius: 15) [02:53:52 -458817.239274] AUTODETECT spr round 4 (radius: 20) [02:56:33 -432201.379246] AUTODETECT spr round 5 (radius: 25) [02:59:46 -419817.118924] SPR radius for FAST iterations: 25 (autodetect) [02:59:46 -419817.118924] Model parameter optimization (eps = 3.000000) [03:00:13 -417804.331133] FAST spr round 1 (radius: 25) [03:02:52 -365747.101595] FAST spr round 2 (radius: 25) [03:04:58 -364113.740414] FAST spr round 3 (radius: 25) [03:06:46 -364028.453177] FAST spr round 4 (radius: 25) [03:08:26 -364018.358893] FAST spr round 5 (radius: 25) [03:10:00 -364018.196595] FAST spr round 6 (radius: 25) [03:11:35 -364018.196346] Model parameter optimization (eps = 1.000000) [03:11:50 -364013.056852] SLOW spr round 1 (radius: 5) [03:13:56 -363932.366563] SLOW spr round 2 (radius: 5) [03:15:59 -363926.613298] SLOW spr round 3 (radius: 5) [03:17:57 -363926.612570] SLOW spr round 4 (radius: 10) [03:19:58 -363926.612355] SLOW spr round 5 (radius: 15) [03:23:05 -363926.612283] SLOW spr round 6 (radius: 20) [03:27:50 -363926.612250] SLOW spr round 7 (radius: 25) [03:34:39 -363926.612234] Model parameter optimization (eps = 0.100000) [03:34:45] ML tree search #4, logLikelihood: -363926.559933 [03:34:45 -1669781.194568] Initial branch length optimization [03:34:52 -1403400.363779] Model parameter optimization (eps = 10.000000) [03:35:26 -1402601.059584] AUTODETECT spr round 1 (radius: 5) [03:37:40 -889591.828743] AUTODETECT spr round 2 (radius: 10) [03:40:22 -628187.484463] AUTODETECT spr round 3 (radius: 15) [03:43:20 -498254.215960] AUTODETECT spr round 4 (radius: 20) [03:47:08 -446950.928058] AUTODETECT spr round 5 (radius: 25) [03:51:26 -433596.105624] SPR radius for FAST iterations: 25 (autodetect) [03:51:26 -433596.105624] Model parameter optimization (eps = 3.000000) [03:51:59 -431573.489014] FAST spr round 1 (radius: 25) [03:55:00 -366452.152741] FAST spr round 2 (radius: 25) [03:57:15 -364151.170851] FAST spr round 3 (radius: 25) [03:59:18 -364074.624508] FAST spr round 4 (radius: 25) [04:01:10 -364045.428728] FAST spr round 5 (radius: 25) [04:02:58 -364002.778286] FAST spr round 6 (radius: 25) [04:04:43 -364002.776534] Model parameter optimization (eps = 1.000000) [04:04:58 -363997.254078] SLOW spr round 1 (radius: 5) [04:07:19 -363928.573967] SLOW spr round 2 (radius: 5) [04:09:35 -363923.737905] SLOW spr round 3 (radius: 5) [04:11:47 -363923.735712] SLOW spr round 4 (radius: 10) [04:14:02 -363918.791250] SLOW spr round 5 (radius: 5) [04:16:46 -363918.791046] SLOW spr round 6 (radius: 10) [04:19:20 -363915.154194] SLOW spr round 7 (radius: 5) [04:22:04 -363915.083019] SLOW spr round 8 (radius: 10) [04:24:33 -363915.080696] SLOW spr round 9 (radius: 15) [04:27:51 -363915.080600] SLOW spr round 10 (radius: 20) [04:33:35 -363915.080597] SLOW spr round 11 (radius: 25) [04:41:31 -363915.080597] Model parameter optimization (eps = 0.100000) [04:41:37] ML tree search #5, logLikelihood: -363915.044601 [04:41:37 -1687073.520584] Initial branch length optimization [04:41:44 -1429687.651087] Model parameter optimization (eps = 10.000000) [04:42:47 -1428542.899080] AUTODETECT spr round 1 (radius: 5) [04:45:17 -829722.504596] AUTODETECT spr round 2 (radius: 10) [04:47:52 -591566.034298] AUTODETECT spr round 3 (radius: 15) [04:50:38 -454895.020601] AUTODETECT spr round 4 (radius: 20) [04:53:44 -431233.343962] AUTODETECT spr round 5 (radius: 25) [04:57:33 -417588.396512] SPR radius for FAST iterations: 25 (autodetect) [04:57:33 -417588.396512] Model parameter optimization (eps = 3.000000) [04:58:11 -415548.600766] FAST spr round 1 (radius: 25) [05:00:57 -366116.596608] FAST spr round 2 (radius: 25) [05:03:12 -364137.049611] FAST spr round 3 (radius: 25) [05:05:18 -364019.829143] FAST spr round 4 (radius: 25) [05:07:08 -364014.688150] FAST spr round 5 (radius: 25) [05:08:52 -364012.872269] FAST spr round 6 (radius: 25) [05:10:35 -364012.871940] Model parameter optimization (eps = 1.000000) [05:10:52 -364009.026034] SLOW spr round 1 (radius: 5) [05:13:15 -363943.093472] SLOW spr round 2 (radius: 5) [05:15:30 -363934.458435] SLOW spr round 3 (radius: 5) [05:17:42 -363933.797667] SLOW spr round 4 (radius: 5) [05:19:52 -363933.797191] SLOW spr round 5 (radius: 10) [05:22:06 -363932.697270] SLOW spr round 6 (radius: 5) [05:24:49 -363932.666160] SLOW spr round 7 (radius: 10) [05:27:18 -363932.665022] SLOW spr round 8 (radius: 15) [05:30:35 -363932.664749] SLOW spr round 9 (radius: 20) [05:36:17 -363932.664682] SLOW spr round 10 (radius: 25) [05:44:10 -363932.664665] Model parameter optimization (eps = 0.100000) [05:44:15] ML tree search #6, logLikelihood: -363932.630737 [05:44:15 -1680227.767290] Initial branch length optimization [05:44:21 -1416973.037783] Model parameter optimization (eps = 10.000000) [05:45:08 -1416217.719667] AUTODETECT spr round 1 (radius: 5) [05:47:37 -839227.587321] AUTODETECT spr round 2 (radius: 10) [05:50:20 -579248.241168] AUTODETECT spr round 3 (radius: 15) [05:53:01 -483570.927087] AUTODETECT spr round 4 (radius: 20) [05:56:01 -435069.999501] AUTODETECT spr round 5 (radius: 25) [05:59:28 -419715.627103] SPR radius for FAST iterations: 25 (autodetect) [05:59:28 -419715.627103] Model parameter optimization (eps = 3.000000) [06:00:01 -417803.800204] FAST spr round 1 (radius: 25) [06:02:45 -366681.125394] FAST spr round 2 (radius: 25) [06:04:56 -364188.533998] FAST spr round 3 (radius: 25) [06:06:54 -364059.285872] FAST spr round 4 (radius: 25) [06:08:42 -364048.434713] FAST spr round 5 (radius: 25) [06:10:25 -364048.272987] FAST spr round 6 (radius: 25) [06:12:05 -364048.272895] Model parameter optimization (eps = 1.000000) [06:12:18 -364045.193281] SLOW spr round 1 (radius: 5) [06:14:37 -363936.768855] SLOW spr round 2 (radius: 5) [06:16:53 -363929.944301] SLOW spr round 3 (radius: 5) [06:19:05 -363924.127716] SLOW spr round 4 (radius: 5) [06:21:15 -363924.044593] SLOW spr round 5 (radius: 10) [06:23:29 -363922.783825] SLOW spr round 6 (radius: 5) [06:26:12 -363922.754576] SLOW spr round 7 (radius: 10) [06:28:41 -363922.753570] SLOW spr round 8 (radius: 15) [06:32:00 -363922.753337] SLOW spr round 9 (radius: 20) [06:37:40 -363922.753281] SLOW spr round 10 (radius: 25) [06:45:30 -363922.753267] Model parameter optimization (eps = 0.100000) [06:45:41] ML tree search #7, logLikelihood: -363922.350724 [06:45:42 -1704559.513373] Initial branch length optimization [06:45:51 -1434500.752339] Model parameter optimization (eps = 10.000000) [06:47:08 -1433268.518684] AUTODETECT spr round 1 (radius: 5) [06:49:38 -857090.495593] AUTODETECT spr round 2 (radius: 10) [06:52:15 -615518.185899] AUTODETECT spr round 3 (radius: 15) [06:54:59 -524417.848538] AUTODETECT spr round 4 (radius: 20) [06:58:12 -453927.962851] AUTODETECT spr round 5 (radius: 25) [07:01:57 -436215.071777] SPR radius for FAST iterations: 25 (autodetect) [07:01:57 -436215.071777] Model parameter optimization (eps = 3.000000) [07:02:33 -433808.494655] FAST spr round 1 (radius: 25) [07:05:24 -370683.228758] FAST spr round 2 (radius: 25) [07:07:41 -364555.609589] FAST spr round 3 (radius: 25) [07:09:40 -364068.743043] FAST spr round 4 (radius: 25) [07:11:32 -364039.824073] FAST spr round 5 (radius: 25) [07:13:17 -364034.854501] FAST spr round 6 (radius: 25) [07:15:00 -364034.854415] Model parameter optimization (eps = 1.000000) [07:15:17 -364024.061905] SLOW spr round 1 (radius: 5) [07:17:39 -363946.938291] SLOW spr round 2 (radius: 5) [07:19:57 -363943.770222] SLOW spr round 3 (radius: 5) [07:22:09 -363943.769403] SLOW spr round 4 (radius: 10) [07:24:25 -363926.852285] SLOW spr round 5 (radius: 5) [07:27:09 -363926.849967] SLOW spr round 6 (radius: 10) [07:29:39 -363925.702006] SLOW spr round 7 (radius: 5) [07:32:19 -363925.700978] SLOW spr round 8 (radius: 10) [07:34:46 -363925.700731] SLOW spr round 9 (radius: 15) [07:38:06 -363925.700671] SLOW spr round 10 (radius: 20) [07:43:52 -363925.700655] SLOW spr round 11 (radius: 25) [07:51:53 -363925.700650] Model parameter optimization (eps = 0.100000) [07:52:02] ML tree search #8, logLikelihood: -363925.507982 [07:52:02 -1695645.974493] Initial branch length optimization [07:52:09 -1431937.564478] Model parameter optimization (eps = 10.000000) [07:53:01 -1430844.828200] AUTODETECT spr round 1 (radius: 5) [07:55:32 -859983.089170] AUTODETECT spr round 2 (radius: 10) [07:58:15 -627723.802969] AUTODETECT spr round 3 (radius: 15) [08:01:17 -469440.593503] AUTODETECT spr round 4 (radius: 20) [08:04:13 -422364.417969] AUTODETECT spr round 5 (radius: 25) [08:07:41 -419295.395538] SPR radius for FAST iterations: 25 (autodetect) [08:07:41 -419295.395538] Model parameter optimization (eps = 3.000000) [08:08:13 -417125.818334] FAST spr round 1 (radius: 25) [08:10:58 -367724.854728] FAST spr round 2 (radius: 25) [08:13:13 -364196.047423] FAST spr round 3 (radius: 25) [08:15:20 -364090.842207] FAST spr round 4 (radius: 25) [08:17:14 -364016.823086] FAST spr round 5 (radius: 25) [08:19:00 -364014.662647] FAST spr round 6 (radius: 25) [08:20:43 -364014.659560] Model parameter optimization (eps = 1.000000) [08:21:05 -364005.589559] SLOW spr round 1 (radius: 5) [08:23:31 -363924.849765] SLOW spr round 2 (radius: 5) [08:25:45 -363923.512451] SLOW spr round 3 (radius: 5) [08:27:56 -363923.512314] SLOW spr round 4 (radius: 10) [08:30:09 -363923.512283] SLOW spr round 5 (radius: 15) [08:33:41 -363923.512272] SLOW spr round 6 (radius: 20) [08:39:23 -363923.512268] SLOW spr round 7 (radius: 25) [08:47:24 -363923.512266] Model parameter optimization (eps = 0.100000) [08:47:31] ML tree search #9, logLikelihood: -363923.381363 [08:47:32 -1679659.683204] Initial branch length optimization [08:47:37 -1416463.067075] Model parameter optimization (eps = 10.000000) [08:48:26 -1415312.082509] AUTODETECT spr round 1 (radius: 5) [08:50:53 -874826.291885] AUTODETECT spr round 2 (radius: 10) [08:53:38 -627353.369667] AUTODETECT spr round 3 (radius: 15) [08:56:33 -513442.326727] AUTODETECT spr round 4 (radius: 20) [08:59:39 -455852.289532] AUTODETECT spr round 5 (radius: 25) [09:03:27 -442330.961112] SPR radius for FAST iterations: 25 (autodetect) [09:03:27 -442330.961112] Model parameter optimization (eps = 3.000000) [09:03:58 -440148.819964] FAST spr round 1 (radius: 25) [09:06:56 -367126.925216] FAST spr round 2 (radius: 25) [09:09:19 -364187.426264] FAST spr round 3 (radius: 25) [09:11:24 -364050.490108] FAST spr round 4 (radius: 25) [09:13:11 -364049.204950] FAST spr round 5 (radius: 25) [09:14:55 -364048.322701] FAST spr round 6 (radius: 25) [09:16:37 -364048.322662] Model parameter optimization (eps = 1.000000) [09:17:00 -364037.372854] SLOW spr round 1 (radius: 5) [09:19:24 -363947.619785] SLOW spr round 2 (radius: 5) [09:21:41 -363937.282645] SLOW spr round 3 (radius: 5) [09:23:53 -363937.023565] SLOW spr round 4 (radius: 5) [09:26:06 -363933.774799] SLOW spr round 5 (radius: 5) [09:28:15 -363933.774562] SLOW spr round 6 (radius: 10) [09:30:31 -363929.476197] SLOW spr round 7 (radius: 5) [09:33:14 -363929.474797] SLOW spr round 8 (radius: 10) [09:35:43 -363929.474440] SLOW spr round 9 (radius: 15) [09:38:59 -363929.474349] SLOW spr round 10 (radius: 20) [09:44:37 -363929.474326] SLOW spr round 11 (radius: 25) [09:52:24 -363929.474320] Model parameter optimization (eps = 0.100000) [09:52:38] ML tree search #10, logLikelihood: -363928.833533 [09:52:38 -1694612.117987] Initial branch length optimization [09:52:44 -1425284.521273] Model parameter optimization (eps = 10.000000) [09:53:24 -1424387.287528] AUTODETECT spr round 1 (radius: 5) [09:55:55 -840422.683607] AUTODETECT spr round 2 (radius: 10) [09:58:36 -602196.237519] AUTODETECT spr round 3 (radius: 15) [10:01:23 -490130.615700] AUTODETECT spr round 4 (radius: 20) [10:04:20 -437638.672642] AUTODETECT spr round 5 (radius: 25) [10:07:53 -427387.475423] SPR radius for FAST iterations: 25 (autodetect) [10:07:53 -427387.475423] Model parameter optimization (eps = 3.000000) [10:08:31 -425265.651470] FAST spr round 1 (radius: 25) [10:11:17 -366609.790987] FAST spr round 2 (radius: 25) [10:13:33 -364208.942037] FAST spr round 3 (radius: 25) [10:15:38 -364039.144934] FAST spr round 4 (radius: 25) [10:17:25 -364028.252451] FAST spr round 5 (radius: 25) [10:19:09 -364028.250290] Model parameter optimization (eps = 1.000000) [10:19:25 -364024.228413] SLOW spr round 1 (radius: 5) [10:21:44 -363942.607880] SLOW spr round 2 (radius: 5) [10:23:58 -363940.576069] SLOW spr round 3 (radius: 5) [10:26:08 -363940.494394] SLOW spr round 4 (radius: 10) [10:28:23 -363924.410876] SLOW spr round 5 (radius: 5) [10:31:06 -363922.013938] SLOW spr round 6 (radius: 5) [10:33:32 -363922.013928] SLOW spr round 7 (radius: 10) [10:35:51 -363922.013924] SLOW spr round 8 (radius: 15) [10:39:14 -363922.013922] SLOW spr round 9 (radius: 20) [10:44:45 -363922.013921] SLOW spr round 10 (radius: 25) [10:52:31 -363922.013921] Model parameter optimization (eps = 0.100000) [10:52:42] ML tree search #11, logLikelihood: -363921.706007 [10:52:42 -1677459.101798] Initial branch length optimization [10:52:50 -1413124.376141] Model parameter optimization (eps = 10.000000) [10:53:22 -1412155.809274] AUTODETECT spr round 1 (radius: 5) [10:55:50 -846123.540880] AUTODETECT spr round 2 (radius: 10) [10:58:34 -595330.045570] AUTODETECT spr round 3 (radius: 15) [11:01:19 -491523.114287] AUTODETECT spr round 4 (radius: 20) [11:04:28 -439340.183461] AUTODETECT spr round 5 (radius: 25) [11:07:51 -425837.297568] SPR radius for FAST iterations: 25 (autodetect) [11:07:51 -425837.297568] Model parameter optimization (eps = 3.000000) [11:08:21 -423649.182167] FAST spr round 1 (radius: 25) [11:11:01 -365562.093033] FAST spr round 2 (radius: 25) [11:13:14 -364108.185753] FAST spr round 3 (radius: 25) [11:15:17 -364039.032517] FAST spr round 4 (radius: 25) [11:17:04 -364037.829678] FAST spr round 5 (radius: 25) [11:18:47 -364037.828553] Model parameter optimization (eps = 1.000000) [11:19:03 -364028.086159] SLOW spr round 1 (radius: 5) [11:21:22 -363941.004517] SLOW spr round 2 (radius: 5) [11:23:40 -363933.688814] SLOW spr round 3 (radius: 5) [11:25:52 -363931.024557] SLOW spr round 4 (radius: 5) [11:28:03 -363931.024152] SLOW spr round 5 (radius: 10) [11:30:19 -363930.549113] SLOW spr round 6 (radius: 5) [11:33:06 -363930.113339] SLOW spr round 7 (radius: 5) [11:35:33 -363930.111580] SLOW spr round 8 (radius: 10) [11:37:54 -363930.111250] SLOW spr round 9 (radius: 15) [11:41:19 -363930.111164] SLOW spr round 10 (radius: 20) [11:46:50 -363930.111142] SLOW spr round 11 (radius: 25) [11:54:41 -363930.111135] Model parameter optimization (eps = 0.100000) [11:54:53] ML tree search #12, logLikelihood: -363929.907198 [11:54:54 -1689704.277290] Initial branch length optimization [11:55:00 -1423409.673391] Model parameter optimization (eps = 10.000000) [11:55:49 -1422445.547664] AUTODETECT spr round 1 (radius: 5) [11:58:22 -884985.132371] AUTODETECT spr round 2 (radius: 10) [12:01:07 -607642.906512] AUTODETECT spr round 3 (radius: 15) [12:03:59 -486228.509228] AUTODETECT spr round 4 (radius: 20) [12:07:09 -422412.670327] AUTODETECT spr round 5 (radius: 25) [12:10:50 -418100.274571] SPR radius for FAST iterations: 25 (autodetect) [12:10:50 -418100.274571] Model parameter optimization (eps = 3.000000) [12:11:23 -415989.510365] FAST spr round 1 (radius: 25) [12:14:07 -366132.588880] FAST spr round 2 (radius: 25) [12:16:23 -364132.748610] FAST spr round 3 (radius: 25) [12:18:25 -364043.276218] FAST spr round 4 (radius: 25) [12:20:14 -364036.809878] FAST spr round 5 (radius: 25) [12:22:00 -364032.469808] FAST spr round 6 (radius: 25) [12:23:42 -364032.469690] Model parameter optimization (eps = 1.000000) [12:23:57 -364029.325771] SLOW spr round 1 (radius: 5) [12:26:23 -363931.639813] SLOW spr round 2 (radius: 5) [12:28:38 -363924.874099] SLOW spr round 3 (radius: 5) [12:30:48 -363924.872713] SLOW spr round 4 (radius: 10) [12:33:03 -363924.872605] SLOW spr round 5 (radius: 15) [12:36:33 -363924.872599] SLOW spr round 6 (radius: 20) [12:42:05 -363924.872598] SLOW spr round 7 (radius: 25) [12:50:03 -363924.872597] Model parameter optimization (eps = 0.100000) [12:50:09] ML tree search #13, logLikelihood: -363924.780444 [12:50:09 -1685608.194341] Initial branch length optimization [12:50:15 -1423327.113197] Model parameter optimization (eps = 10.000000) [12:51:07 -1422394.885970] AUTODETECT spr round 1 (radius: 5) [12:53:38 -859639.429077] AUTODETECT spr round 2 (radius: 10) [12:56:23 -627172.072210] AUTODETECT spr round 3 (radius: 15) [12:59:19 -496052.977323] AUTODETECT spr round 4 (radius: 20) [13:02:25 -435608.106784] AUTODETECT spr round 5 (radius: 25) [13:05:50 -419337.225257] SPR radius for FAST iterations: 25 (autodetect) [13:05:50 -419337.225257] Model parameter optimization (eps = 3.000000) [13:06:18 -417267.103213] FAST spr round 1 (radius: 25) [13:09:07 -365776.988527] FAST spr round 2 (radius: 25) [13:11:24 -364150.360669] FAST spr round 3 (radius: 25) [13:13:21 -364092.022827] FAST spr round 4 (radius: 25) [13:15:10 -364063.056728] FAST spr round 5 (radius: 25) [13:16:54 -364051.238626] FAST spr round 6 (radius: 25) [13:18:37 -364010.734484] FAST spr round 7 (radius: 25) [13:20:18 -364010.733601] Model parameter optimization (eps = 1.000000) [13:20:35 -364003.502767] SLOW spr round 1 (radius: 5) [13:22:57 -363947.931686] SLOW spr round 2 (radius: 5) [13:25:11 -363937.486240] SLOW spr round 3 (radius: 5) [13:27:25 -363934.287949] SLOW spr round 4 (radius: 5) [13:29:34 -363934.287597] SLOW spr round 5 (radius: 10) [13:31:48 -363921.852979] SLOW spr round 6 (radius: 5) [13:34:30 -363919.485041] SLOW spr round 7 (radius: 5) [13:36:54 -363919.484941] SLOW spr round 8 (radius: 10) [13:39:13 -363919.484900] SLOW spr round 9 (radius: 15) [13:42:36 -363919.484877] SLOW spr round 10 (radius: 20) [13:48:14 -363919.484858] SLOW spr round 11 (radius: 25) [13:56:10 -363919.484840] Model parameter optimization (eps = 0.100000) [13:56:16] ML tree search #14, logLikelihood: -363919.432408 [13:56:16 -1683109.835512] Initial branch length optimization [13:56:23 -1412571.326757] Model parameter optimization (eps = 10.000000) [13:57:06 -1411601.485377] AUTODETECT spr round 1 (radius: 5) [13:59:37 -871241.394086] AUTODETECT spr round 2 (radius: 10) [14:02:19 -610181.320352] AUTODETECT spr round 3 (radius: 15) [14:05:06 -474695.480250] AUTODETECT spr round 4 (radius: 20) [14:08:23 -433098.100855] AUTODETECT spr round 5 (radius: 25) [14:12:13 -419788.237629] SPR radius for FAST iterations: 25 (autodetect) [14:12:13 -419788.237629] Model parameter optimization (eps = 3.000000) [14:12:48 -417930.726093] FAST spr round 1 (radius: 25) [14:15:36 -367067.398385] FAST spr round 2 (radius: 25) [14:17:47 -364480.944482] FAST spr round 3 (radius: 25) [14:19:40 -364082.830037] FAST spr round 4 (radius: 25) [14:21:28 -364052.483217] FAST spr round 5 (radius: 25) [14:23:09 -364052.482752] Model parameter optimization (eps = 1.000000) [14:23:22 -364050.568900] SLOW spr round 1 (radius: 5) [14:25:38 -363929.059419] SLOW spr round 2 (radius: 5) [14:27:53 -363925.124925] SLOW spr round 3 (radius: 5) [14:30:02 -363925.123403] SLOW spr round 4 (radius: 10) [14:32:13 -363924.674453] SLOW spr round 5 (radius: 5) [14:34:53 -363924.674373] SLOW spr round 6 (radius: 10) [14:37:20 -363924.674345] SLOW spr round 7 (radius: 15) [14:40:34 -363924.674334] SLOW spr round 8 (radius: 20) [14:46:12 -363924.674329] SLOW spr round 9 (radius: 25) [14:53:56 -363924.674327] Model parameter optimization (eps = 0.100000) [14:54:03] ML tree search #15, logLikelihood: -363924.501753 [14:54:03 -1692545.233203] Initial branch length optimization [14:54:11 -1422795.614612] Model parameter optimization (eps = 10.000000) [14:54:51 -1421801.162243] AUTODETECT spr round 1 (radius: 5) [14:57:17 -873249.764075] AUTODETECT spr round 2 (radius: 10) [15:00:05 -596761.426077] AUTODETECT spr round 3 (radius: 15) [15:02:45 -464260.559487] AUTODETECT spr round 4 (radius: 20) [15:05:37 -425399.316198] AUTODETECT spr round 5 (radius: 25) [15:09:09 -416555.195883] SPR radius for FAST iterations: 25 (autodetect) [15:09:09 -416555.195883] Model parameter optimization (eps = 3.000000) [15:09:40 -414525.576107] FAST spr round 1 (radius: 25) [15:12:19 -367782.130626] FAST spr round 2 (radius: 25) [15:14:32 -366162.564152] FAST spr round 3 (radius: 25) [15:16:25 -364116.139196] FAST spr round 4 (radius: 25) [15:18:10 -364050.124839] FAST spr round 5 (radius: 25) [15:19:50 -364048.328629] FAST spr round 6 (radius: 25) [15:21:29 -364048.328317] Model parameter optimization (eps = 1.000000) [15:21:45 -364039.020959] SLOW spr round 1 (radius: 5) [15:24:00 -363940.995493] SLOW spr round 2 (radius: 5) [15:26:15 -363934.429125] SLOW spr round 3 (radius: 5) [15:28:27 -363931.546282] SLOW spr round 4 (radius: 5) [15:30:35 -363931.545604] SLOW spr round 5 (radius: 10) [15:32:49 -363927.371359] SLOW spr round 6 (radius: 5) [15:35:29 -363927.359708] SLOW spr round 7 (radius: 10) [15:37:44 -363927.356837] SLOW spr round 8 (radius: 15) [15:40:44 -363927.356177] SLOW spr round 9 (radius: 20) [15:45:52 -363927.356009] SLOW spr round 10 (radius: 25) [15:52:39 -363927.355966] Model parameter optimization (eps = 0.100000) [15:52:44] ML tree search #16, logLikelihood: -363927.318861 [15:52:44 -1687909.553407] Initial branch length optimization [15:52:49 -1426047.727254] Model parameter optimization (eps = 10.000000) [15:53:28 -1425187.080990] AUTODETECT spr round 1 (radius: 5) [15:55:41 -848474.263887] AUTODETECT spr round 2 (radius: 10) [15:58:06 -591771.647638] AUTODETECT spr round 3 (radius: 15) [16:00:33 -470705.173102] AUTODETECT spr round 4 (radius: 20) [16:03:15 -431712.632829] AUTODETECT spr round 5 (radius: 25) [16:06:37 -424416.424773] SPR radius for FAST iterations: 25 (autodetect) [16:06:37 -424416.424773] Model parameter optimization (eps = 3.000000) [16:07:11 -422400.420945] FAST spr round 1 (radius: 25) [16:09:44 -365966.490112] FAST spr round 2 (radius: 25) [16:11:48 -364117.232204] FAST spr round 3 (radius: 25) [16:13:36 -364021.924597] FAST spr round 4 (radius: 25) [16:15:15 -363996.825042] FAST spr round 5 (radius: 25) [16:16:48 -363996.138948] FAST spr round 6 (radius: 25) [16:18:19 -363996.138270] Model parameter optimization (eps = 1.000000) [16:18:38 -363985.562135] SLOW spr round 1 (radius: 5) [16:20:44 -363927.272532] SLOW spr round 2 (radius: 5) [16:22:45 -363925.216786] SLOW spr round 3 (radius: 5) [16:24:45 -363922.380174] SLOW spr round 4 (radius: 5) [16:26:42 -363922.379751] SLOW spr round 5 (radius: 10) [16:28:42 -363922.379652] SLOW spr round 6 (radius: 15) [16:31:51 -363922.379625] SLOW spr round 7 (radius: 20) [16:37:00 -363922.379617] SLOW spr round 8 (radius: 25) [16:44:17 -363922.379614] Model parameter optimization (eps = 0.100000) [16:44:27] ML tree search #17, logLikelihood: -363922.165260 [16:44:27 -1682307.132096] Initial branch length optimization [16:44:33 -1411306.151512] Model parameter optimization (eps = 10.000000) [16:45:07 -1410482.861113] AUTODETECT spr round 1 (radius: 5) [16:47:20 -836693.099138] AUTODETECT spr round 2 (radius: 10) [16:49:46 -578962.871614] AUTODETECT spr round 3 (radius: 15) [16:52:04 -478805.466556] AUTODETECT spr round 4 (radius: 20) [16:54:56 -423080.610930] AUTODETECT spr round 5 (radius: 25) [16:58:10 -415245.752657] SPR radius for FAST iterations: 25 (autodetect) [16:58:10 -415245.752657] Model parameter optimization (eps = 3.000000) [16:58:48 -413244.074063] FAST spr round 1 (radius: 25) [17:01:13 -366752.263383] FAST spr round 2 (radius: 25) [17:03:12 -364152.857585] FAST spr round 3 (radius: 25) [17:05:02 -364048.487727] FAST spr round 4 (radius: 25) [17:06:39 -364047.827340] FAST spr round 5 (radius: 25) [17:08:12 -364047.827217] Model parameter optimization (eps = 1.000000) [17:08:26 -364042.776274] SLOW spr round 1 (radius: 5) [17:10:32 -363952.148814] SLOW spr round 2 (radius: 5) [17:12:32 -363947.753051] SLOW spr round 3 (radius: 5) [17:14:31 -363946.213705] SLOW spr round 4 (radius: 5) [17:16:29 -363946.213227] SLOW spr round 5 (radius: 10) [17:18:32 -363933.017077] SLOW spr round 6 (radius: 5) [17:21:02 -363929.920072] SLOW spr round 7 (radius: 5) [17:23:14 -363929.918551] SLOW spr round 8 (radius: 10) [17:25:21 -363929.918223] SLOW spr round 9 (radius: 15) [17:28:28 -363929.918136] SLOW spr round 10 (radius: 20) [17:33:40 -363929.918109] SLOW spr round 11 (radius: 25) [17:40:53 -363929.918096] Model parameter optimization (eps = 0.100000) [17:41:03] ML tree search #18, logLikelihood: -363929.636043 [17:41:03 -1692176.951861] Initial branch length optimization [17:41:11 -1424248.815783] Model parameter optimization (eps = 10.000000) [17:41:43 -1423244.678770] AUTODETECT spr round 1 (radius: 5) [17:43:52 -841333.404780] AUTODETECT spr round 2 (radius: 10) [17:46:08 -615396.821840] AUTODETECT spr round 3 (radius: 15) [17:48:36 -512824.891640] AUTODETECT spr round 4 (radius: 20) [17:51:20 -454963.332916] AUTODETECT spr round 5 (radius: 25) [17:54:59 -431387.893138] SPR radius for FAST iterations: 25 (autodetect) [17:55:00 -431387.893138] Model parameter optimization (eps = 3.000000) [17:55:37 -429248.883204] FAST spr round 1 (radius: 25) [17:58:34 -368546.743897] FAST spr round 2 (radius: 25) [18:00:56 -364331.791666] FAST spr round 3 (radius: 25) [18:02:59 -364009.257301] FAST spr round 4 (radius: 25) [18:04:47 -363997.947007] FAST spr round 5 (radius: 25) [18:06:29 -363997.817256] FAST spr round 6 (radius: 25) [18:08:11 -363997.804078] Model parameter optimization (eps = 1.000000) [18:08:36 -363985.983434] SLOW spr round 1 (radius: 5) [18:10:55 -363933.116981] SLOW spr round 2 (radius: 5) [18:13:08 -363932.215147] SLOW spr round 3 (radius: 5) [18:15:21 -363931.264813] SLOW spr round 4 (radius: 5) [18:17:31 -363931.264783] SLOW spr round 5 (radius: 10) [18:19:46 -363923.797479] SLOW spr round 6 (radius: 5) [18:22:07 -363923.797434] SLOW spr round 7 (radius: 10) [18:24:23 -363923.797434] SLOW spr round 8 (radius: 15) [18:27:57 -363923.797433] SLOW spr round 9 (radius: 20) [18:34:15 -363923.797433] SLOW spr round 10 (radius: 25) [18:42:56 -363923.797433] Model parameter optimization (eps = 0.100000) [18:43:07] ML tree search #19, logLikelihood: -363923.626604 [18:43:07 -1696135.923096] Initial branch length optimization [18:43:13 -1427979.182649] Model parameter optimization (eps = 10.000000) [18:44:10 -1426863.308019] AUTODETECT spr round 1 (radius: 5) [18:46:52 -870471.778328] AUTODETECT spr round 2 (radius: 10) [18:49:46 -629168.464422] AUTODETECT spr round 3 (radius: 15) [18:52:49 -486855.458882] AUTODETECT spr round 4 (radius: 20) [18:56:16 -419759.973519] AUTODETECT spr round 5 (radius: 25) [19:00:14 -415751.835993] SPR radius for FAST iterations: 25 (autodetect) [19:00:14 -415751.835993] Model parameter optimization (eps = 3.000000) [19:00:51 -413818.432971] FAST spr round 1 (radius: 25) [19:03:48 -367665.577134] FAST spr round 2 (radius: 25) [19:06:16 -364255.577597] FAST spr round 3 (radius: 25) [19:08:23 -364061.960377] FAST spr round 4 (radius: 25) [19:10:20 -364030.256007] FAST spr round 5 (radius: 25) [19:12:11 -364029.541199] FAST spr round 6 (radius: 25) [19:13:59 -364029.539944] Model parameter optimization (eps = 1.000000) [19:14:23 -364018.567248] SLOW spr round 1 (radius: 5) [19:16:56 -363942.704965] SLOW spr round 2 (radius: 5) [19:19:23 -363934.284219] SLOW spr round 3 (radius: 5) [19:21:44 -363934.281923] SLOW spr round 4 (radius: 10) [19:24:10 -363916.722712] SLOW spr round 5 (radius: 5) [19:27:05 -363916.713226] SLOW spr round 6 (radius: 10) [19:29:45 -363916.711227] SLOW spr round 7 (radius: 15) [19:33:21 -363916.710765] SLOW spr round 8 (radius: 20) [19:39:39 -363916.710655] SLOW spr round 9 (radius: 25) [19:48:19 -363916.710629] Model parameter optimization (eps = 0.100000) [19:48:28] ML tree search #20, logLikelihood: -363916.611591 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.197620,0.270534) (0.193814,1.206921) (0.384983,0.713292) (0.223583,1.959066) 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: -363912.862089 AIC score: 731835.724178 / AICc score: 8775895.724178 / BIC score: 741924.365402 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1132). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 89 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95622/3_mltree/O95622.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95622/3_mltree/O95622.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95622/3_mltree/O95622.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95622/3_mltree/O95622.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O95622/3_mltree/O95622.raxml.log Analysis started: 01-Jul-2021 06:31:52 / finished: 02-Jul-2021 02:20:21 Elapsed time: 71308.579 seconds Consumed energy: 6678.842 Wh (= 33 km in an electric car, or 167 km with an e-scooter!)