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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 30-Jun-2021 17:57:00 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N9H8/2_msa/Q8N9H8_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N9H8/3_mltree/Q8N9H8 --seed 2 --threads 2 --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 (2 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N9H8/2_msa/Q8N9H8_trimmed_msa.fasta [00:00:00] Loaded alignment with 334 taxa and 122 sites WARNING: Sequences tr_A0A2R8QSS0_A0A2R8QSS0_DANRE_7955 and tr_E7EY45_E7EY45_DANRE_7955 are exactly identical! WARNING: Sequences tr_D8SQC3_D8SQC3_SELML_88036 and tr_D8SUK9_D8SUK9_SELML_88036 are exactly identical! WARNING: Sequences tr_F9FTD2_F9FTD2_FUSOF_660025 and tr_A0A0D2XDM5_A0A0D2XDM5_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FTD2_F9FTD2_FUSOF_660025 and tr_N4U3H9_N4U3H9_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FTD2_F9FTD2_FUSOF_660025 and tr_X0DBA8_X0DBA8_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FTD2_F9FTD2_FUSOF_660025 and tr_A0A2H3T4F9_A0A2H3T4F9_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A0A0E0IQK6_A0A0E0IQK6_ORYNI_4536 and tr_I1PJI8_I1PJI8_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0IQK6_A0A0E0IQK6_ORYNI_4536 and tr_A0A0D3FT86_A0A0D3FT86_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0H5S3P9_A0A0H5S3P9_BRUMA_6279 and tr_A0A0N4TXV7_A0A0N4TXV7_BRUPA_6280 are exactly identical! WARNING: Sequences tr_F7FM29_F7FM29_MACMU_9544 and tr_A0A096NYG9_A0A096NYG9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FM29_F7FM29_MACMU_9544 and tr_A0A2K5ND05_A0A2K5ND05_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FM29_F7FM29_MACMU_9544 and tr_A0A2K5ZK77_A0A2K5ZK77_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0YW93_H0YW93_TAEGU_59729 and tr_A0A218ULJ3_A0A218ULJ3_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A0E0P656_A0A0E0P656_ORYRU_4529 and tr_Q7XWZ1_Q7XWZ1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_S0DUD4_S0DUD4_GIBF5_1279085 and tr_A0A365MLJ2_A0A365MLJ2_GIBIN_948311 are exactly identical! WARNING: Sequences tr_W2PQF7_W2PQF7_PHYPN_761204 and tr_A0A0W8DYM7_A0A0W8DYM7_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PQF7_W2PQF7_PHYPN_761204 and tr_W2KJJ0_W2KJJ0_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2PSW8_W2PSW8_PHYPN_761204 and tr_W2KHS7_W2KHS7_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2R8I8_W2R8I8_PHYPN_761204 and tr_W2IXZ5_W2IXZ5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A2K6VIF1_A0A2K6VIF1_ONCVO_6282 and tr_A0A182E3P2_A0A182E3P2_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0D9RTF0_A0A0D9RTF0_CHLSB_60711 and tr_A0A2K6C0M9_A0A2K6C0M9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I0LMC3_A0A2I0LMC3_COLLI_8932 and tr_A0A1V4KPL3_A0A1V4KPL3_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3WV11_A0A1S3WV11_ERIEU_9365 and tr_A0A1S3WWC6_A0A1S3WWC6_ERIEU_9365 are exactly identical! WARNING: Sequences tr_A0A1S3YVX0_A0A1S3YVX0_TOBAC_4097 and tr_A0A1U7WKC5_A0A1U7WKC5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A226NGF9_A0A226NGF9_CALSU_9009 and tr_A0A226PKZ4_A0A226PKZ4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3C702_A0A2H3C702_9AGAR_1076256 and tr_A0A284RAY1_A0A284RAY1_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2G2ZUF9_A0A2G2ZUF9_CAPAN_4072 and tr_A0A2G3CRZ8_A0A2G3CRZ8_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2Y9N622_A0A2Y9N622_DELLE_9749 and tr_A0A383ZGB9_A0A383ZGB9_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 28 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/Q8N9H8/3_mltree/Q8N9H8.raxml.reduced.phy Alignment comprises 1 partitions and 122 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 122 / 122 Gaps: 6.95 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N9H8/3_mltree/Q8N9H8.raxml.rba Parallelization scheme autoconfig: 2 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 334 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 122 / 9760 [00:00:00] Data distribution: max. searches per worker: 10 Starting ML tree search with 20 distinct starting trees [00:00:00 -75159.029381] Initial branch length optimization [00:00:00 -62228.166247] Model parameter optimization (eps = 10.000000) [00:00:10 -62207.006706] AUTODETECT spr round 1 (radius: 5) [00:00:29 -49675.677338] AUTODETECT spr round 2 (radius: 10) [00:00:54 -37561.896311] AUTODETECT spr round 3 (radius: 15) [00:01:28 -33668.607994] AUTODETECT spr round 4 (radius: 20) [00:02:10 -33082.202763] AUTODETECT spr round 5 (radius: 25) [00:02:54 -33067.571822] SPR radius for FAST iterations: 25 (autodetect) [00:02:54 -33067.571822] Model parameter optimization (eps = 3.000000) [00:03:02 -33055.228323] FAST spr round 1 (radius: 25) [00:03:32 -30187.818454] FAST spr round 2 (radius: 25) [00:03:54 -30019.516931] FAST spr round 3 (radius: 25) [00:04:14 -29998.267253] FAST spr round 4 (radius: 25) [00:04:31 -29998.254535] Model parameter optimization (eps = 1.000000) [00:04:36 -29996.881800] SLOW spr round 1 (radius: 5) [00:05:03 -29989.112224] SLOW spr round 2 (radius: 5) [00:05:30 -29987.399795] SLOW spr round 3 (radius: 5) [00:05:55 -29987.367881] SLOW spr round 4 (radius: 10) [00:06:23 -29986.319210] SLOW spr round 5 (radius: 5) [00:06:58 -29985.674130] SLOW spr round 6 (radius: 5) [00:07:27 -29985.673999] SLOW spr round 7 (radius: 10) [00:07:57 -29985.673985] SLOW spr round 8 (radius: 15) [00:08:45 -29985.673983] SLOW spr round 9 (radius: 20) [00:09:50 -29985.462319] SLOW spr round 10 (radius: 5) [00:10:26 -29985.460235] SLOW spr round 11 (radius: 10) [00:11:01 -29985.459712] SLOW spr round 12 (radius: 15) [00:11:46 -29985.459472] SLOW spr round 13 (radius: 20) [00:12:51 -29985.459363] SLOW spr round 14 (radius: 25) [00:13:14] [worker #1] ML tree search #2, logLikelihood: -29980.701011 [00:13:51 -29983.753805] SLOW spr round 15 (radius: 5) [00:14:29 -29983.749976] SLOW spr round 16 (radius: 10) [00:15:05 -29983.749770] SLOW spr round 17 (radius: 15) [00:15:51 -29983.749757] SLOW spr round 18 (radius: 20) [00:16:57 -29983.749754] SLOW spr round 19 (radius: 25) [00:17:57 -29983.749752] Model parameter optimization (eps = 0.100000) [00:17:59] [worker #0] ML tree search #1, logLikelihood: -29983.677411 [00:17:59 -75223.957898] Initial branch length optimization [00:18:00 -62734.770834] Model parameter optimization (eps = 10.000000) [00:18:10 -62706.952729] AUTODETECT spr round 1 (radius: 5) [00:18:28 -48591.329530] AUTODETECT spr round 2 (radius: 10) [00:18:52 -38655.713864] AUTODETECT spr round 3 (radius: 15) [00:19:24 -33497.953978] AUTODETECT spr round 4 (radius: 20) [00:20:01 -32906.657308] AUTODETECT spr round 5 (radius: 25) [00:20:44 -32408.346869] SPR radius for FAST iterations: 25 (autodetect) [00:20:44 -32408.346869] Model parameter optimization (eps = 3.000000) [00:20:51 -32400.137864] FAST spr round 1 (radius: 25) [00:21:19 -30130.317526] FAST spr round 2 (radius: 25) [00:21:43 -30027.416911] FAST spr round 3 (radius: 25) [00:22:02 -30012.294672] FAST spr round 4 (radius: 25) [00:22:19 -30010.639807] FAST spr round 5 (radius: 25) [00:22:35 -30010.638926] Model parameter optimization (eps = 1.000000) [00:22:42 -30008.311934] SLOW spr round 1 (radius: 5) [00:23:09 -30001.555926] SLOW spr round 2 (radius: 5) [00:23:38 -29994.838741] SLOW spr round 3 (radius: 5) [00:24:06 -29989.111386] SLOW spr round 4 (radius: 5) [00:24:32 -29989.092901] SLOW spr round 5 (radius: 10) [00:25:02 -29985.996351] SLOW spr round 6 (radius: 5) [00:25:39 -29984.250673] SLOW spr round 7 (radius: 5) [00:26:10 -29983.303948] SLOW spr round 8 (radius: 5) [00:26:39 -29979.727667] SLOW spr round 9 (radius: 5) [00:27:07 -29979.727529] SLOW spr round 10 (radius: 10) [00:27:35 -29979.727523] SLOW spr round 11 (radius: 15) [00:28:28 -29977.412958] SLOW spr round 12 (radius: 5) [00:29:05 -29977.412838] SLOW spr round 13 (radius: 10) [00:29:38 -29977.412829] SLOW spr round 14 (radius: 15) [00:30:26 -29977.412826] SLOW spr round 15 (radius: 20) [00:31:30 -29977.412826] SLOW spr round 16 (radius: 25) [00:32:26 -29977.412825] Model parameter optimization (eps = 0.100000) [00:32:32] [worker #0] ML tree search #3, logLikelihood: -29976.375997 [00:32:32 -75859.231159] Initial branch length optimization [00:32:32 -63168.207372] Model parameter optimization (eps = 10.000000) [00:32:42 -63144.030992] AUTODETECT spr round 1 (radius: 5) [00:33:01 -48287.075634] AUTODETECT spr round 2 (radius: 10) [00:33:26 -36061.816301] AUTODETECT spr round 3 (radius: 15) [00:33:55 -33269.939084] AUTODETECT spr round 4 (radius: 20) [00:34:27 -32523.484770] AUTODETECT spr round 5 (radius: 25) [00:34:50] [worker #1] ML tree search #4, logLikelihood: -29991.066666 [00:35:02 -32441.142593] SPR radius for FAST iterations: 25 (autodetect) [00:35:02 -32441.142593] Model parameter optimization (eps = 3.000000) [00:35:10 -32416.897444] FAST spr round 1 (radius: 25) [00:35:38 -30090.895922] FAST spr round 2 (radius: 25) [00:36:00 -30033.388454] FAST spr round 3 (radius: 25) [00:36:20 -30017.645885] FAST spr round 4 (radius: 25) [00:36:39 -30009.218168] FAST spr round 5 (radius: 25) [00:36:56 -30009.215207] Model parameter optimization (eps = 1.000000) [00:37:03 -30006.102350] SLOW spr round 1 (radius: 5) [00:37:30 -29992.333015] SLOW spr round 2 (radius: 5) [00:37:58 -29990.484090] SLOW spr round 3 (radius: 5) [00:38:26 -29987.709917] SLOW spr round 4 (radius: 5) [00:38:55 -29986.252659] SLOW spr round 5 (radius: 5) [00:39:21 -29986.252597] SLOW spr round 6 (radius: 10) [00:39:50 -29985.504424] SLOW spr round 7 (radius: 5) [00:40:26 -29984.816005] SLOW spr round 8 (radius: 5) [00:40:56 -29984.815685] SLOW spr round 9 (radius: 10) [00:41:26 -29984.815641] SLOW spr round 10 (radius: 15) [00:42:13 -29983.290272] SLOW spr round 11 (radius: 5) [00:42:50 -29983.287660] SLOW spr round 12 (radius: 10) [00:43:24 -29983.287549] SLOW spr round 13 (radius: 15) [00:44:08 -29983.287537] SLOW spr round 14 (radius: 20) [00:45:14 -29983.287535] SLOW spr round 15 (radius: 25) [00:46:12 -29983.287534] Model parameter optimization (eps = 0.100000) [00:46:16] [worker #0] ML tree search #5, logLikelihood: -29983.229767 [00:46:16 -75463.434788] Initial branch length optimization [00:46:16 -62330.472554] Model parameter optimization (eps = 10.000000) [00:46:29 -62311.904636] AUTODETECT spr round 1 (radius: 5) [00:46:48 -48862.956545] AUTODETECT spr round 2 (radius: 10) [00:47:13 -39602.834139] AUTODETECT spr round 3 (radius: 15) [00:47:43 -36002.438900] AUTODETECT spr round 4 (radius: 20) [00:48:15 -34475.073654] AUTODETECT spr round 5 (radius: 25) [00:48:49 -34373.887571] SPR radius for FAST iterations: 25 (autodetect) [00:48:49 -34373.887571] Model parameter optimization (eps = 3.000000) [00:48:57 -34360.645487] FAST spr round 1 (radius: 25) [00:49:27 -30159.978995] FAST spr round 2 (radius: 25) [00:49:51 -30015.194235] FAST spr round 3 (radius: 25) [00:50:10 -30010.744814] FAST spr round 4 (radius: 25) [00:50:27 -30010.720277] Model parameter optimization (eps = 1.000000) [00:50:34 -30008.513715] SLOW spr round 1 (radius: 5) [00:51:04 -29991.696975] SLOW spr round 2 (radius: 5) [00:51:30 -29990.797858] SLOW spr round 3 (radius: 5) [00:51:58 -29990.408582] SLOW spr round 4 (radius: 5) [00:52:24 -29990.270433] SLOW spr round 5 (radius: 5) [00:52:35] [worker #1] ML tree search #6, logLikelihood: -29970.652894 [00:52:50 -29990.269492] SLOW spr round 6 (radius: 10) [00:53:18 -29989.383489] SLOW spr round 7 (radius: 5) [00:53:54 -29988.044524] SLOW spr round 8 (radius: 5) [00:54:24 -29988.041845] SLOW spr round 9 (radius: 10) [00:54:54 -29988.041522] SLOW spr round 10 (radius: 15) [00:55:46 -29986.494816] SLOW spr round 11 (radius: 5) [00:56:23 -29986.492888] SLOW spr round 12 (radius: 10) [00:56:58 -29986.492140] SLOW spr round 13 (radius: 15) [00:57:48 -29986.491849] SLOW spr round 14 (radius: 20) [00:58:54 -29985.678441] SLOW spr round 15 (radius: 5) [00:59:32 -29985.677752] SLOW spr round 16 (radius: 10) [01:00:09 -29985.677704] SLOW spr round 17 (radius: 15) [01:00:58 -29985.677696] SLOW spr round 18 (radius: 20) [01:02:05 -29985.677692] SLOW spr round 19 (radius: 25) [01:03:05 -29985.677691] Model parameter optimization (eps = 0.100000) [01:03:11] [worker #0] ML tree search #7, logLikelihood: -29985.572908 [01:03:11 -74777.423207] Initial branch length optimization [01:03:11 -62043.106983] Model parameter optimization (eps = 10.000000) [01:03:20 -62024.512824] AUTODETECT spr round 1 (radius: 5) [01:03:39 -47853.685801] AUTODETECT spr round 2 (radius: 10) [01:04:02 -37376.498964] AUTODETECT spr round 3 (radius: 15) [01:04:34 -32762.641022] AUTODETECT spr round 4 (radius: 20) [01:05:17 -32620.443707] AUTODETECT spr round 5 (radius: 25) [01:05:57 -32615.666023] SPR radius for FAST iterations: 25 (autodetect) [01:05:57 -32615.666023] Model parameter optimization (eps = 3.000000) [01:06:07 -32592.256861] FAST spr round 1 (radius: 25) [01:06:27] [worker #1] ML tree search #8, logLikelihood: -29982.936143 [01:06:37 -30161.956860] FAST spr round 2 (radius: 25) [01:07:00 -30042.001392] FAST spr round 3 (radius: 25) [01:07:20 -30023.750487] FAST spr round 4 (radius: 25) [01:07:38 -30014.617757] FAST spr round 5 (radius: 25) [01:07:55 -30014.468157] FAST spr round 6 (radius: 25) [01:08:11 -30014.467918] Model parameter optimization (eps = 1.000000) [01:08:17 -30012.707585] SLOW spr round 1 (radius: 5) [01:08:45 -30008.236325] SLOW spr round 2 (radius: 5) [01:09:12 -30006.787722] SLOW spr round 3 (radius: 5) [01:09:38 -30006.785499] SLOW spr round 4 (radius: 10) [01:10:06 -30005.556795] SLOW spr round 5 (radius: 5) [01:10:45 -29998.385556] SLOW spr round 6 (radius: 5) [01:11:17 -29992.477051] SLOW spr round 7 (radius: 5) [01:11:45 -29992.468063] SLOW spr round 8 (radius: 10) [01:12:14 -29991.262384] SLOW spr round 9 (radius: 5) [01:12:50 -29989.974328] SLOW spr round 10 (radius: 5) [01:13:21 -29989.913967] SLOW spr round 11 (radius: 10) [01:13:51 -29988.683999] SLOW spr round 12 (radius: 5) [01:14:27 -29984.160052] SLOW spr round 13 (radius: 5) [01:14:57 -29984.080359] SLOW spr round 14 (radius: 10) [01:15:26 -29982.731540] SLOW spr round 15 (radius: 5) [01:16:01 -29982.502105] SLOW spr round 16 (radius: 5) [01:16:31 -29982.500636] SLOW spr round 17 (radius: 10) [01:17:00 -29982.322922] SLOW spr round 18 (radius: 5) [01:17:34 -29982.322813] SLOW spr round 19 (radius: 10) [01:18:06 -29982.322807] SLOW spr round 20 (radius: 15) [01:18:47] [worker #1] ML tree search #10, logLikelihood: -29977.991326 [01:18:52 -29981.977422] SLOW spr round 21 (radius: 5) [01:19:28 -29981.977399] SLOW spr round 22 (radius: 10) [01:20:03 -29981.977385] SLOW spr round 23 (radius: 15) [01:20:49 -29981.917644] SLOW spr round 24 (radius: 20) [01:21:55 -29981.915916] SLOW spr round 25 (radius: 25) [01:22:56 -29981.147027] SLOW spr round 26 (radius: 5) [01:23:34 -29980.834893] SLOW spr round 27 (radius: 5) [01:24:06 -29980.833121] SLOW spr round 28 (radius: 10) [01:24:36 -29980.832678] SLOW spr round 29 (radius: 15) [01:25:24 -29980.832540] SLOW spr round 30 (radius: 20) [01:26:29 -29980.832491] SLOW spr round 31 (radius: 25) [01:27:30 -29980.832467] Model parameter optimization (eps = 0.100000) [01:27:36] [worker #0] ML tree search #9, logLikelihood: -29978.568897 [01:27:36 -74585.426263] Initial branch length optimization [01:27:37 -62060.668380] Model parameter optimization (eps = 10.000000) [01:27:47 -62028.521282] AUTODETECT spr round 1 (radius: 5) [01:28:06 -47846.007384] AUTODETECT spr round 2 (radius: 10) [01:28:31 -36068.047570] AUTODETECT spr round 3 (radius: 15) [01:29:02 -33044.750505] AUTODETECT spr round 4 (radius: 20) [01:29:40 -32198.177816] AUTODETECT spr round 5 (radius: 25) [01:30:18 -32190.310917] SPR radius for FAST iterations: 25 (autodetect) [01:30:18 -32190.310917] Model parameter optimization (eps = 3.000000) [01:30:25 -32183.835117] FAST spr round 1 (radius: 25) [01:30:53 -30142.274967] FAST spr round 2 (radius: 25) [01:31:17 -30061.640573] FAST spr round 3 (radius: 25) [01:31:38 -30006.727552] FAST spr round 4 (radius: 25) [01:31:55 -30002.504201] FAST spr round 5 (radius: 25) [01:32:13 -29999.146896] FAST spr round 6 (radius: 25) [01:32:29 -29999.123847] Model parameter optimization (eps = 1.000000) [01:32:37 -29995.014795] SLOW spr round 1 (radius: 5) [01:33:04 -29988.798196] SLOW spr round 2 (radius: 5) [01:33:32 -29986.858925] SLOW spr round 3 (radius: 5) [01:33:59 -29986.858717] SLOW spr round 4 (radius: 10) [01:34:27 -29986.008639] SLOW spr round 5 (radius: 5) [01:35:05 -29983.136156] SLOW spr round 6 (radius: 5) [01:35:35 -29983.135783] SLOW spr round 7 (radius: 10) [01:36:05 -29981.923089] SLOW spr round 8 (radius: 5) [01:36:41 -29976.845843] SLOW spr round 9 (radius: 5) [01:37:11 -29976.845794] SLOW spr round 10 (radius: 10) [01:37:25] [worker #1] ML tree search #12, logLikelihood: -29974.401151 [01:37:40 -29976.845793] SLOW spr round 11 (radius: 15) [01:38:29 -29976.845793] SLOW spr round 12 (radius: 20) [01:39:29 -29975.769800] SLOW spr round 13 (radius: 5) [01:40:06 -29975.769075] SLOW spr round 14 (radius: 10) [01:40:42 -29975.769019] SLOW spr round 15 (radius: 15) [01:41:27 -29975.769016] SLOW spr round 16 (radius: 20) [01:42:26 -29975.769015] SLOW spr round 17 (radius: 25) [01:43:24 -29974.968553] SLOW spr round 18 (radius: 5) [01:44:02 -29974.963044] SLOW spr round 19 (radius: 10) [01:44:38 -29974.961885] SLOW spr round 20 (radius: 15) [01:45:24 -29974.961646] SLOW spr round 21 (radius: 20) [01:46:23 -29974.961597] SLOW spr round 22 (radius: 25) [01:47:22 -29974.961587] Model parameter optimization (eps = 0.100000) [01:47:25] [worker #0] ML tree search #11, logLikelihood: -29974.886654 [01:47:25 -75457.149948] Initial branch length optimization [01:47:26 -63104.367281] Model parameter optimization (eps = 10.000000) [01:47:36 -63088.369272] AUTODETECT spr round 1 (radius: 5) [01:47:55 -47136.863252] AUTODETECT spr round 2 (radius: 10) [01:48:20 -37281.015884] AUTODETECT spr round 3 (radius: 15) [01:48:52 -33167.790709] AUTODETECT spr round 4 (radius: 20) [01:49:33 -32922.094949] AUTODETECT spr round 5 (radius: 25) [01:50:17 -32767.183711] SPR radius for FAST iterations: 25 (autodetect) [01:50:17 -32767.183711] Model parameter optimization (eps = 3.000000) [01:50:25 -32757.848346] FAST spr round 1 (radius: 25) [01:50:53 -30097.627237] FAST spr round 2 (radius: 25) [01:51:15 -30026.903876] FAST spr round 3 (radius: 25) [01:51:34 -30015.493551] FAST spr round 4 (radius: 25) [01:51:53 -30011.228722] FAST spr round 5 (radius: 25) [01:52:10 -30007.552611] FAST spr round 6 (radius: 25) [01:52:27 -30005.871963] FAST spr round 7 (radius: 25) [01:52:43 -30005.871204] Model parameter optimization (eps = 1.000000) [01:52:51 -30004.315883] SLOW spr round 1 (radius: 5) [01:53:19 -29988.099200] SLOW spr round 2 (radius: 5) [01:53:46 -29985.133456] SLOW spr round 3 (radius: 5) [01:54:11 -29985.130155] SLOW spr round 4 (radius: 10) [01:54:21] [worker #1] ML tree search #14, logLikelihood: -29987.969315 [01:54:40 -29978.024458] SLOW spr round 5 (radius: 5) [01:55:16 -29976.652352] SLOW spr round 6 (radius: 5) [01:55:45 -29976.651644] SLOW spr round 7 (radius: 10) [01:56:15 -29976.651071] SLOW spr round 8 (radius: 15) [01:57:08 -29974.242527] SLOW spr round 9 (radius: 5) [01:57:45 -29974.073478] SLOW spr round 10 (radius: 5) [01:58:16 -29974.072889] SLOW spr round 11 (radius: 10) [01:58:47 -29974.072878] SLOW spr round 12 (radius: 15) [01:59:40 -29974.072877] SLOW spr round 13 (radius: 20) [02:00:45 -29973.265507] SLOW spr round 14 (radius: 5) [02:01:23 -29973.264393] SLOW spr round 15 (radius: 10) [02:01:59 -29973.264312] SLOW spr round 16 (radius: 15) [02:02:49 -29973.264307] SLOW spr round 17 (radius: 20) [02:03:55 -29973.264307] SLOW spr round 18 (radius: 25) [02:04:52 -29973.264307] Model parameter optimization (eps = 0.100000) [02:04:59] [worker #0] ML tree search #13, logLikelihood: -29972.318730 [02:04:59 -75063.574434] Initial branch length optimization [02:04:59 -62164.610657] Model parameter optimization (eps = 10.000000) [02:05:08 -62153.154021] AUTODETECT spr round 1 (radius: 5) [02:05:26 -47661.612593] AUTODETECT spr round 2 (radius: 10) [02:05:49 -38610.111478] AUTODETECT spr round 3 (radius: 15) [02:06:20 -34389.212862] AUTODETECT spr round 4 (radius: 20) [02:06:55 -33223.626629] AUTODETECT spr round 5 (radius: 25) [02:07:33 -33223.577497] SPR radius for FAST iterations: 20 (autodetect) [02:07:33 -33223.577497] Model parameter optimization (eps = 3.000000) [02:07:45 -33189.134921] FAST spr round 1 (radius: 20) [02:08:14 -30125.173334] FAST spr round 2 (radius: 20) [02:08:37 -30016.272048] FAST spr round 3 (radius: 20) [02:08:56 -30007.550380] FAST spr round 4 (radius: 20) [02:09:13 -30006.269968] FAST spr round 5 (radius: 20) [02:09:30 -30006.268857] Model parameter optimization (eps = 1.000000) [02:09:36 -30005.025982] SLOW spr round 1 (radius: 5) [02:10:06 -29993.143652] SLOW spr round 2 (radius: 5) [02:10:34 -29990.969532] SLOW spr round 3 (radius: 5) [02:11:02 -29989.267563] SLOW spr round 4 (radius: 5) [02:11:28 -29989.252582] SLOW spr round 5 (radius: 10) [02:11:56 -29986.693125] SLOW spr round 6 (radius: 5) [02:12:00] [worker #1] ML tree search #16, logLikelihood: -29974.489549 [02:12:33 -29985.696476] SLOW spr round 7 (radius: 5) [02:13:03 -29985.579429] SLOW spr round 8 (radius: 5) [02:13:30 -29985.579121] SLOW spr round 9 (radius: 10) [02:13:58 -29975.120569] SLOW spr round 10 (radius: 5) [02:14:34 -29973.760951] SLOW spr round 11 (radius: 5) [02:15:03 -29973.760686] SLOW spr round 12 (radius: 10) [02:15:32 -29972.722069] SLOW spr round 13 (radius: 5) [02:16:07 -29970.963974] SLOW spr round 14 (radius: 5) [02:16:37 -29970.963347] SLOW spr round 15 (radius: 10) [02:17:06 -29970.963317] SLOW spr round 16 (radius: 15) [02:17:56 -29970.963311] SLOW spr round 17 (radius: 20) [02:18:58 -29970.963310] SLOW spr round 18 (radius: 25) [02:19:55 -29970.963309] Model parameter optimization (eps = 0.100000) [02:20:00] [worker #0] ML tree search #15, logLikelihood: -29970.362297 [02:20:00 -75258.257969] Initial branch length optimization [02:20:01 -62321.424772] Model parameter optimization (eps = 10.000000) [02:20:12 -62299.443808] AUTODETECT spr round 1 (radius: 5) [02:20:30 -47449.798815] AUTODETECT spr round 2 (radius: 10) [02:20:56 -38405.082794] AUTODETECT spr round 3 (radius: 15) [02:21:26 -33769.863046] AUTODETECT spr round 4 (radius: 20) [02:22:02 -33324.026191] AUTODETECT spr round 5 (radius: 25) [02:22:39 -33323.936597] SPR radius for FAST iterations: 20 (autodetect) [02:22:39 -33323.936597] Model parameter optimization (eps = 3.000000) [02:22:46 -33303.864551] FAST spr round 1 (radius: 20) [02:23:15 -30258.662537] FAST spr round 2 (radius: 20) [02:23:38 -30008.351214] FAST spr round 3 (radius: 20) [02:23:58 -29996.711179] FAST spr round 4 (radius: 20) [02:24:15 -29995.560276] FAST spr round 5 (radius: 20) [02:24:31 -29995.559121] Model parameter optimization (eps = 1.000000) [02:24:36 -29994.292507] SLOW spr round 1 (radius: 5) [02:25:06 -29980.128245] SLOW spr round 2 (radius: 5) [02:25:32 -29979.592504] SLOW spr round 3 (radius: 5) [02:25:59 -29975.951759] SLOW spr round 4 (radius: 5) [02:26:26 -29974.670233] SLOW spr round 5 (radius: 5) [02:26:43] [worker #1] ML tree search #18, logLikelihood: -29996.483326 [02:26:51 -29974.669138] SLOW spr round 6 (radius: 10) [02:27:19 -29974.549865] SLOW spr round 7 (radius: 5) [02:27:54 -29974.549222] SLOW spr round 8 (radius: 10) [02:28:26 -29974.549179] SLOW spr round 9 (radius: 15) [02:29:13 -29972.012769] SLOW spr round 10 (radius: 5) [02:29:50 -29972.009769] SLOW spr round 11 (radius: 10) [02:30:25 -29972.009503] SLOW spr round 12 (radius: 15) [02:31:12 -29972.009458] SLOW spr round 13 (radius: 20) [02:32:17 -29971.174716] SLOW spr round 14 (radius: 5) [02:32:55 -29971.168279] SLOW spr round 15 (radius: 10) [02:33:30 -29971.166957] SLOW spr round 16 (radius: 15) [02:34:17 -29971.166691] SLOW spr round 17 (radius: 20) [02:35:22 -29971.166638] SLOW spr round 18 (radius: 25) [02:36:23 -29971.166627] Model parameter optimization (eps = 0.100000) [02:36:25] [worker #0] ML tree search #17, logLikelihood: -29971.150472 [02:36:25 -75436.962170] Initial branch length optimization [02:36:26 -62345.599800] Model parameter optimization (eps = 10.000000) [02:36:37 -62322.749124] AUTODETECT spr round 1 (radius: 5) [02:36:56 -47294.987474] AUTODETECT spr round 2 (radius: 10) [02:37:21 -36437.264059] AUTODETECT spr round 3 (radius: 15) [02:37:50 -32752.391361] AUTODETECT spr round 4 (radius: 20) [02:38:27 -32482.867381] AUTODETECT spr round 5 (radius: 25) [02:39:03 -32467.369644] SPR radius for FAST iterations: 25 (autodetect) [02:39:03 -32467.369644] Model parameter optimization (eps = 3.000000) [02:39:10 -32449.004651] FAST spr round 1 (radius: 25) [02:39:37 -30184.087575] FAST spr round 2 (radius: 25) [02:40:01 -30038.933062] FAST spr round 3 (radius: 25) [02:40:21 -30017.836435] FAST spr round 4 (radius: 25) [02:40:38 -30016.996089] FAST spr round 5 (radius: 25) [02:40:54 -30016.995305] Model parameter optimization (eps = 1.000000) [02:41:00 -30013.364758] SLOW spr round 1 (radius: 5) [02:41:29 -29998.629221] SLOW spr round 2 (radius: 5) [02:41:58 -29989.627242] SLOW spr round 3 (radius: 5) [02:42:24 -29989.625017] SLOW spr round 4 (radius: 10) [02:42:53 -29989.023803] SLOW spr round 5 (radius: 5) [02:42:57] [worker #1] ML tree search #20, logLikelihood: -29976.688664 [02:43:29 -29988.261400] SLOW spr round 6 (radius: 5) [02:43:58 -29988.261104] SLOW spr round 7 (radius: 10) [02:44:28 -29987.997286] SLOW spr round 8 (radius: 5) [02:45:03 -29987.996675] SLOW spr round 9 (radius: 10) [02:45:36 -29987.996369] SLOW spr round 10 (radius: 15) [02:46:22 -29986.299194] SLOW spr round 11 (radius: 5) [02:46:59 -29986.298361] SLOW spr round 12 (radius: 10) [02:47:33 -29986.298173] SLOW spr round 13 (radius: 15) [02:48:18 -29986.298086] SLOW spr round 14 (radius: 20) [02:49:20 -29986.298043] SLOW spr round 15 (radius: 25) [02:50:15 -29986.298021] Model parameter optimization (eps = 0.100000) [02:50:18] [worker #0] ML tree search #19, logLikelihood: -29986.128069 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.140039,0.233974) (0.284081,0.477524) (0.346701,0.956495) (0.229179,2.181531) 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: -29970.362297 AIC score: 61282.724594 / AICc score: 963106.724594 / BIC score: 63164.222715 Free parameters (model + branch lengths): 671 WARNING: Number of free parameters (K=671) is larger than alignment size (n=122). 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/Q8N9H8/3_mltree/Q8N9H8.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N9H8/3_mltree/Q8N9H8.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N9H8/3_mltree/Q8N9H8.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N9H8/3_mltree/Q8N9H8.raxml.log Analysis started: 30-Jun-2021 17:57:00 / finished: 30-Jun-2021 20:47:19 Elapsed time: 10218.802 seconds Consumed energy: 691.938 Wh (= 3 km in an electric car, or 17 km with an e-scooter!)