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 04-Jul-2021 12:13:09 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VWG9/2_msa/Q5VWG9_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VWG9/3_mltree/Q5VWG9 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VWG9/2_msa/Q5VWG9_trimmed_msa.fasta [00:00:00] Loaded alignment with 347 taxa and 162 sites WARNING: Sequences tr_F1NZW0_F1NZW0_CHICK_9031 and sp_Q5F489_TAF3_CHICK_9031 are exactly identical! WARNING: Sequences tr_F1NZW0_F1NZW0_CHICK_9031 and tr_A0A218V9Y7_A0A218V9Y7_9PASE_299123 are exactly identical! WARNING: Sequences tr_M3YTB9_M3YTB9_MUSPF_9669 and tr_A0A2Y9KRR3_A0A2Y9KRR3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_H2Q1L6_H2Q1L6_PANTR_9598 and tr_F7I4L2_F7I4L2_CALJA_9483 are exactly identical! WARNING: Sequences tr_W5Q1Z8_W5Q1Z8_SHEEP_9940 and tr_F1N3U7_F1N3U7_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A087ZNL4_A0A087ZNL4_APIME_7460 and tr_A0A2A3DZY9_A0A2A3DZY9_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A088ASJ7_A0A088ASJ7_APIME_7460 and tr_A0A2A3EE76_A0A2A3EE76_APICC_94128 are exactly identical! WARNING: Sequences tr_F6X0V0_F6X0V0_MACMU_9544 and tr_A0A096P3E1_A0A096P3E1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6X0V0_F6X0V0_MACMU_9544 and tr_A0A2K5LI99_A0A2K5LI99_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6X0V0_F6X0V0_MACMU_9544 and tr_A0A2K6CF73_A0A2K6CF73_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3SPH0_G3SPH0_LOXAF_9785 and tr_A0A2Y9DRP6_A0A2Y9DRP6_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G3TJ49_G3TJ49_LOXAF_9785 and tr_G1MJB5_G1MJB5_AILME_9646 are exactly identical! WARNING: Sequences tr_B4MF08_B4MF08_DROVI_7244 and tr_D0Z7A9_D0Z7A9_DROVI_7244 are exactly identical! WARNING: Sequences tr_W2REB5_W2REB5_PHYPN_761204 and tr_A0A0W8CMX5_A0A0W8CMX5_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A084WP70_A0A084WP70_ANOSI_74873 and tr_A0A084WV10_A0A084WV10_ANOSI_74873 are exactly identical! WARNING: Sequences tr_A0A091ITK5_A0A091ITK5_EGRGA_188379 and tr_A0A093Q456_A0A093Q456_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091ITK5_A0A091ITK5_EGRGA_188379 and tr_A0A087QMI3_A0A087QMI3_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091UWJ5_A0A091UWJ5_NIPNI_128390 and tr_A0A093GDF5_A0A093GDF5_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091UWJ5_A0A091UWJ5_NIPNI_128390 and tr_A0A091HYT9_A0A091HYT9_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0L7QJW2_A0A0L7QJW2_9HYME_597456 and tr_A0A154NWX9_A0A154NWX9_9HYME_178035 are exactly identical! WARNING: Sequences tr_A0A1I7TZH7_A0A1I7TZH7_9PELO_1561998 and tr_A0A1I7TZH8_A0A1I7TZH8_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A226N9X5_A0A226N9X5_CALSU_9009 and tr_A0A226PDW4_A0A226PDW4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4B6E3_A0A2U4B6E3_TURTR_9739 and tr_A0A2Y9NPS0_A0A2Y9NPS0_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B6E3_A0A2U4B6E3_TURTR_9739 and tr_A0A2Y9T9F7_A0A2Y9T9F7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4B6E3_A0A2U4B6E3_TURTR_9739 and tr_A0A383YX83_A0A383YX83_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4C3I0_A0A2U4C3I0_TURTR_9739 and tr_A0A2Y9PNN3_A0A2Y9PNN3_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 26 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/Q5VWG9/3_mltree/Q5VWG9.raxml.reduced.phy Alignment comprises 1 partitions and 162 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 162 / 162 Gaps: 19.65 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VWG9/3_mltree/Q5VWG9.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 347 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 162 / 12960 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -96920.378834] Initial branch length optimization [00:00:00 -74679.901872] Model parameter optimization (eps = 10.000000) [00:00:14 -73994.552160] AUTODETECT spr round 1 (radius: 5) [00:00:32 -62906.073095] AUTODETECT spr round 2 (radius: 10) [00:00:55 -54116.080659] AUTODETECT spr round 3 (radius: 15) [00:01:26 -44925.892377] AUTODETECT spr round 4 (radius: 20) [00:02:05 -42766.206470] AUTODETECT spr round 5 (radius: 25) [00:02:39 -42523.114882] SPR radius for FAST iterations: 25 (autodetect) [00:02:40 -42523.114882] Model parameter optimization (eps = 3.000000) [00:02:51 -42323.928934] FAST spr round 1 (radius: 25) [00:03:28 -38624.802335] FAST spr round 2 (radius: 25) [00:03:55 -38393.169240] FAST spr round 3 (radius: 25) [00:04:18 -38362.319431] FAST spr round 4 (radius: 25) [00:04:36 -38357.085090] FAST spr round 5 (radius: 25) [00:04:53 -38355.671986] FAST spr round 6 (radius: 25) [00:05:09 -38355.670289] Model parameter optimization (eps = 1.000000) [00:05:19 -38349.848874] SLOW spr round 1 (radius: 5) [00:05:48 -38331.777105] SLOW spr round 2 (radius: 5) [00:06:15 -38330.369032] SLOW spr round 3 (radius: 5) [00:06:42 -38330.367636] SLOW spr round 4 (radius: 10) [00:07:10 -38328.727522] SLOW spr round 5 (radius: 5) [00:07:44 -38328.726767] SLOW spr round 6 (radius: 10) [00:08:17 -38326.752034] SLOW spr round 7 (radius: 5) [00:08:50 -38326.126083] SLOW spr round 8 (radius: 5) [00:09:18 -38326.124758] SLOW spr round 9 (radius: 10) [00:09:48 -38326.124695] SLOW spr round 10 (radius: 15) [00:10:42 -38325.719630] SLOW spr round 11 (radius: 5) [00:11:18 -38325.716322] SLOW spr round 12 (radius: 10) [00:11:52 -38325.715802] SLOW spr round 13 (radius: 15) [00:12:41 -38325.587313] SLOW spr round 14 (radius: 5) [00:13:16 -38325.587016] SLOW spr round 15 (radius: 10) [00:13:50 -38325.586985] SLOW spr round 16 (radius: 15) [00:14:36] [worker #1] ML tree search #2, logLikelihood: -38331.595529 [00:14:38 -38325.586981] SLOW spr round 17 (radius: 20) [00:15:43 -38325.586980] SLOW spr round 18 (radius: 25) [00:15:52] [worker #2] ML tree search #3, logLikelihood: -38332.165057 [00:16:53 -38325.586980] Model parameter optimization (eps = 0.100000) [00:16:57] [worker #0] ML tree search #1, logLikelihood: -38325.477890 [00:16:57 -97715.893338] Initial branch length optimization [00:16:58 -75407.585857] Model parameter optimization (eps = 10.000000) [00:17:12 -74700.323920] AUTODETECT spr round 1 (radius: 5) [00:17:31 -63262.456550] AUTODETECT spr round 2 (radius: 10) [00:17:55 -51100.773788] AUTODETECT spr round 3 (radius: 15) [00:18:28 -45784.612141] AUTODETECT spr round 4 (radius: 20) [00:19:08 -43169.575466] AUTODETECT spr round 5 (radius: 25) [00:19:51 -42643.075353] SPR radius for FAST iterations: 25 (autodetect) [00:19:51 -42643.075353] Model parameter optimization (eps = 3.000000) [00:20:01 -42374.876232] FAST spr round 1 (radius: 25) [00:20:33 -38551.506439] FAST spr round 2 (radius: 25) [00:20:57 -38362.588162] FAST spr round 3 (radius: 25) [00:21:19 -38341.737219] FAST spr round 4 (radius: 25) [00:21:37 -38340.707944] FAST spr round 5 (radius: 25) [00:21:54 -38340.707332] Model parameter optimization (eps = 1.000000) [00:21:58 -38339.607150] SLOW spr round 1 (radius: 5) [00:22:27 -38330.897921] SLOW spr round 2 (radius: 5) [00:22:55 -38330.139588] SLOW spr round 3 (radius: 5) [00:23:22 -38330.035011] SLOW spr round 4 (radius: 5) [00:23:48 -38330.034271] SLOW spr round 5 (radius: 10) [00:24:17 -38329.421189] SLOW spr round 6 (radius: 5) [00:24:51 -38329.420133] SLOW spr round 7 (radius: 10) [00:25:25 -38329.420049] SLOW spr round 8 (radius: 15) [00:26:20 -38329.420040] SLOW spr round 9 (radius: 20) [00:27:36 -38329.420039] SLOW spr round 10 (radius: 25) [00:27:51] [worker #2] ML tree search #6, logLikelihood: -38327.640294 [00:28:48 -38329.420038] Model parameter optimization (eps = 0.100000) [00:28:52] [worker #0] ML tree search #4, logLikelihood: -38329.245765 [00:28:53 -96096.471535] Initial branch length optimization [00:28:53 -74804.163406] Model parameter optimization (eps = 10.000000) [00:29:11 -74173.831658] AUTODETECT spr round 1 (radius: 5) [00:29:30 -63893.043076] AUTODETECT spr round 2 (radius: 10) [00:29:55 -50681.648115] AUTODETECT spr round 3 (radius: 15) [00:30:25 -41914.398500] AUTODETECT spr round 4 (radius: 20) [00:30:57 -41242.176347] AUTODETECT spr round 5 (radius: 25) [00:31:12] [worker #1] ML tree search #5, logLikelihood: -38320.457266 [00:31:38 -40694.797820] SPR radius for FAST iterations: 25 (autodetect) [00:31:38 -40694.797820] Model parameter optimization (eps = 3.000000) [00:31:48 -40478.750819] FAST spr round 1 (radius: 25) [00:32:19 -38527.617118] FAST spr round 2 (radius: 25) [00:32:43 -38389.734757] FAST spr round 3 (radius: 25) [00:33:05 -38378.403527] FAST spr round 4 (radius: 25) [00:33:24 -38370.331702] FAST spr round 5 (radius: 25) [00:33:41 -38369.316694] FAST spr round 6 (radius: 25) [00:33:57 -38369.315528] Model parameter optimization (eps = 1.000000) [00:34:04 -38366.667218] SLOW spr round 1 (radius: 5) [00:34:31 -38356.577198] SLOW spr round 2 (radius: 5) [00:34:59 -38354.104243] SLOW spr round 3 (radius: 5) [00:35:27 -38352.096369] SLOW spr round 4 (radius: 5) [00:35:53 -38352.091448] SLOW spr round 5 (radius: 10) [00:36:22 -38352.091446] SLOW spr round 6 (radius: 15) [00:37:21 -38352.091445] SLOW spr round 7 (radius: 20) [00:38:34 -38352.091444] SLOW spr round 8 (radius: 25) [00:39:43 -38352.091444] Model parameter optimization (eps = 0.100000) [00:39:50] [worker #0] ML tree search #7, logLikelihood: -38349.299856 [00:39:50 -96416.683978] Initial branch length optimization [00:39:51 -74884.678792] Model parameter optimization (eps = 10.000000) [00:40:06 -74214.057188] AUTODETECT spr round 1 (radius: 5) [00:40:25 -62572.498184] AUTODETECT spr round 2 (radius: 10) [00:40:48 -51778.151098] AUTODETECT spr round 3 (radius: 15) [00:41:07] [worker #2] ML tree search #9, logLikelihood: -38325.005307 [00:41:18 -44738.363255] AUTODETECT spr round 4 (radius: 20) [00:41:51 -42340.215613] AUTODETECT spr round 5 (radius: 25) [00:42:30 -42261.444348] SPR radius for FAST iterations: 25 (autodetect) [00:42:30 -42261.444348] Model parameter optimization (eps = 3.000000) [00:42:42] [worker #1] ML tree search #8, logLikelihood: -38328.242785 [00:42:43 -42088.546031] FAST spr round 1 (radius: 25) [00:43:16 -38497.239423] FAST spr round 2 (radius: 25) [00:43:40 -38361.108276] FAST spr round 3 (radius: 25) [00:44:01 -38347.345822] FAST spr round 4 (radius: 25) [00:44:20 -38343.273289] FAST spr round 5 (radius: 25) [00:44:36 -38343.272471] Model parameter optimization (eps = 1.000000) [00:44:43 -38341.416858] SLOW spr round 1 (radius: 5) [00:45:11 -38332.383245] SLOW spr round 2 (radius: 5) [00:45:40 -38329.692207] SLOW spr round 3 (radius: 5) [00:46:06 -38329.685508] SLOW spr round 4 (radius: 10) [00:46:35 -38329.360890] SLOW spr round 5 (radius: 5) [00:47:08 -38329.360853] SLOW spr round 6 (radius: 10) [00:47:42 -38329.360851] SLOW spr round 7 (radius: 15) [00:48:38 -38328.948114] SLOW spr round 8 (radius: 5) [00:49:13 -38328.944380] SLOW spr round 9 (radius: 10) [00:49:50 -38328.942784] SLOW spr round 10 (radius: 15) [00:50:45 -38328.942177] SLOW spr round 11 (radius: 20) [00:51:58 -38328.941948] SLOW spr round 12 (radius: 25) [00:53:04 -38328.941862] Model parameter optimization (eps = 0.100000) [00:53:07] [worker #0] ML tree search #10, logLikelihood: -38328.924577 [00:53:07 -97217.311127] Initial branch length optimization [00:53:08 -75347.320040] Model parameter optimization (eps = 10.000000) [00:53:24 -74678.162908] AUTODETECT spr round 1 (radius: 5) [00:53:43 -64253.836747] AUTODETECT spr round 2 (radius: 10) [00:54:07 -53302.707802] AUTODETECT spr round 3 (radius: 15) [00:54:36 -48942.144010] AUTODETECT spr round 4 (radius: 20) [00:55:09 -45434.874393] AUTODETECT spr round 5 (radius: 25) [00:55:49 -43243.503816] SPR radius for FAST iterations: 25 (autodetect) [00:55:49 -43243.503816] Model parameter optimization (eps = 3.000000) [00:56:00 -42979.832060] FAST spr round 1 (radius: 25) [00:56:37 -38543.889262] FAST spr round 2 (radius: 25) [00:57:05 -38381.791067] FAST spr round 3 (radius: 25) [00:57:27 -38367.656972] FAST spr round 4 (radius: 25) [00:57:45 -38364.356991] FAST spr round 5 (radius: 25) [00:58:03 -38361.189550] FAST spr round 6 (radius: 25) [00:58:21 -38357.173967] FAST spr round 7 (radius: 25) [00:58:36] [worker #2] ML tree search #12, logLikelihood: -38323.105014 [00:58:38 -38355.037827] FAST spr round 8 (radius: 25) [00:58:55 -38352.567404] FAST spr round 9 (radius: 25) [00:59:12 -38352.245464] FAST spr round 10 (radius: 25) [00:59:28 -38352.245172] Model parameter optimization (eps = 1.000000) [00:59:35] [worker #1] ML tree search #11, logLikelihood: -38325.648780 [00:59:35 -38348.332647] SLOW spr round 1 (radius: 5) [01:00:03 -38335.208155] SLOW spr round 2 (radius: 5) [01:00:30 -38333.901853] SLOW spr round 3 (radius: 5) [01:00:56 -38333.899188] SLOW spr round 4 (radius: 10) [01:01:25 -38333.895684] SLOW spr round 5 (radius: 15) [01:02:24 -38333.432608] SLOW spr round 6 (radius: 5) [01:02:59 -38333.432528] SLOW spr round 7 (radius: 10) [01:03:35 -38333.432455] SLOW spr round 8 (radius: 15) [01:04:29 -38333.432453] SLOW spr round 9 (radius: 20) [01:05:40 -38333.432451] SLOW spr round 10 (radius: 25) [01:06:51 -38333.432450] Model parameter optimization (eps = 0.100000) [01:06:55] [worker #0] ML tree search #13, logLikelihood: -38333.271231 [01:06:55 -97871.854506] Initial branch length optimization [01:06:56 -75256.032303] Model parameter optimization (eps = 10.000000) [01:07:09 -74570.810547] AUTODETECT spr round 1 (radius: 5) [01:07:28 -63874.637393] AUTODETECT spr round 2 (radius: 10) [01:07:52 -52701.741304] AUTODETECT spr round 3 (radius: 15) [01:08:19 -47228.334757] AUTODETECT spr round 4 (radius: 20) [01:08:47] [worker #2] ML tree search #15, logLikelihood: -38342.090295 [01:08:56 -43313.527051] AUTODETECT spr round 5 (radius: 25) [01:09:36 -42817.654458] SPR radius for FAST iterations: 25 (autodetect) [01:09:36 -42817.654458] Model parameter optimization (eps = 3.000000) [01:09:49 -42574.526976] FAST spr round 1 (radius: 25) [01:10:26 -38603.723676] FAST spr round 2 (radius: 25) [01:10:53 -38373.283458] FAST spr round 3 (radius: 25) [01:11:16 -38349.161355] FAST spr round 4 (radius: 25) [01:11:35 -38347.167660] FAST spr round 5 (radius: 25) [01:11:52 -38346.860121] FAST spr round 6 (radius: 25) [01:12:09 -38346.858971] Model parameter optimization (eps = 1.000000) [01:12:17 -38339.768972] SLOW spr round 1 (radius: 5) [01:12:45 -38330.254540] SLOW spr round 2 (radius: 5) [01:12:48] [worker #1] ML tree search #14, logLikelihood: -38332.260955 [01:13:14 -38328.877630] SLOW spr round 3 (radius: 5) [01:13:40 -38328.876521] SLOW spr round 4 (radius: 10) [01:14:09 -38328.683220] SLOW spr round 5 (radius: 5) [01:14:43 -38328.683178] SLOW spr round 6 (radius: 10) [01:15:18 -38328.683165] SLOW spr round 7 (radius: 15) [01:16:09 -38328.683160] SLOW spr round 8 (radius: 20) [01:17:14 -38328.683156] SLOW spr round 9 (radius: 25) [01:18:19 -38328.683152] Model parameter optimization (eps = 0.100000) [01:18:21] [worker #0] ML tree search #16, logLikelihood: -38328.609396 [01:18:21 -96982.513296] Initial branch length optimization [01:18:22 -74753.340580] Model parameter optimization (eps = 10.000000) [01:18:35 -74058.145453] AUTODETECT spr round 1 (radius: 5) [01:18:53 -65420.419031] AUTODETECT spr round 2 (radius: 10) [01:19:18 -53066.613439] AUTODETECT spr round 3 (radius: 15) [01:19:51 -45992.593795] AUTODETECT spr round 4 (radius: 20) [01:20:28 -43648.822182] AUTODETECT spr round 5 (radius: 25) [01:21:06 -43550.375116] SPR radius for FAST iterations: 25 (autodetect) [01:21:06 -43550.375116] Model parameter optimization (eps = 3.000000) [01:21:17 -43262.471144] FAST spr round 1 (radius: 25) [01:21:23] [worker #2] ML tree search #18, logLikelihood: -38334.175082 [01:21:55 -38675.806078] FAST spr round 2 (radius: 25) [01:22:22 -38369.570030] FAST spr round 3 (radius: 25) [01:22:44 -38350.844232] FAST spr round 4 (radius: 25) [01:23:03 -38345.833222] FAST spr round 5 (radius: 25) [01:23:18] [worker #1] ML tree search #17, logLikelihood: -38327.649961 [01:23:21 -38342.508951] FAST spr round 6 (radius: 25) [01:23:38 -38342.508336] Model parameter optimization (eps = 1.000000) [01:23:44 -38335.311804] SLOW spr round 1 (radius: 5) [01:24:12 -38323.393249] SLOW spr round 2 (radius: 5) [01:24:39 -38322.444040] SLOW spr round 3 (radius: 5) [01:25:05 -38322.443684] SLOW spr round 4 (radius: 10) [01:25:34 -38322.264830] SLOW spr round 5 (radius: 5) [01:26:08 -38322.264816] SLOW spr round 6 (radius: 10) [01:26:41 -38322.264812] SLOW spr round 7 (radius: 15) [01:27:35 -38322.264811] SLOW spr round 8 (radius: 20) [01:28:44 -38322.264811] SLOW spr round 9 (radius: 25) [01:29:48 -38322.264811] Model parameter optimization (eps = 0.100000) [01:29:51] [worker #0] ML tree search #19, logLikelihood: -38322.220622 [01:33:23] [worker #1] ML tree search #20, logLikelihood: -38326.514266 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.111991,0.872203) (0.063864,0.772077) (0.333100,0.724820) (0.491045,1.245458) 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: -38320.457266 AIC score: 78034.914532 / AICc score: 1051046.914532 / BIC score: 80186.969178 Free parameters (model + branch lengths): 697 WARNING: Number of free parameters (K=697) is larger than alignment size (n=162). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VWG9/3_mltree/Q5VWG9.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VWG9/3_mltree/Q5VWG9.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VWG9/3_mltree/Q5VWG9.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q5VWG9/3_mltree/Q5VWG9.raxml.log Analysis started: 04-Jul-2021 12:13:09 / finished: 04-Jul-2021 13:46:33 Elapsed time: 5603.672 seconds Consumed energy: 435.066 Wh (= 2 km in an electric car, or 11 km with an e-scooter!)