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 06-Jul-2021 19:54:17 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3Z0/2_msa/Q7Z3Z0_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3Z0/3_mltree/Q7Z3Z0 --seed 2 --threads 6 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3Z0/2_msa/Q7Z3Z0_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 394 sites WARNING: Sequences tr_A0A1D5PZ89_A0A1D5PZ89_CHICK_9031 and sp_Q6PVZ1_K1C14_CHICK_9031 are exactly identical! WARNING: Sequences tr_M3YT82_M3YT82_MUSPF_9669 and tr_A0A2Y9JVH8_A0A2Y9JVH8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_F1PYU9_F1PYU9_CANLF_9615 and sp_Q6EIZ0_K1C10_CANLF_9615 are exactly identical! WARNING: Sequences tr_H2QCC4_H2QCC4_PANTR_9598 and tr_A0A2R9BI07_A0A2R9BI07_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCX1_H2QCX1_PANTR_9598 and tr_A0A2R9BZA1_A0A2R9BZA1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCX3_H2QCX3_PANTR_9598 and sp_P13645_K1C10_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QCX4_H2QCX4_PANTR_9598 and sp_Q99456_K1C12_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QCZ2_H2QCZ2_PANTR_9598 and tr_A0A2R9ATZ6_A0A2R9ATZ6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCZ4_H2QCZ4_PANTR_9598 and tr_A0A2R8ZHV6_A0A2R8ZHV6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCZ6_H2QCZ6_PANTR_9598 and sp_P35527_K1C9_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QCZ8_H2QCZ8_PANTR_9598 and tr_A0A2R9BML2_A0A2R9BML2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R114_H2R114_PANTR_9598 and tr_A0A2R9ALU5_A0A2R9ALU5_PANPA_9597 are exactly identical! WARNING: Sequences sp_B0LKP1_KRT35_SHEEP_9940 and tr_W5Q5N5_W5Q5N5_SHEEP_9940 are exactly identical! WARNING: Sequences tr_A0A1D5Q3N1_A0A1D5Q3N1_MACMU_9544 and tr_G7PUS3_G7PUS3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7A635_F7A635_MACMU_9544 and tr_A0A2I3MA29_A0A2I3MA29_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7A635_F7A635_MACMU_9544 and tr_A0A0D9S2G2_A0A0D9S2G2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7A670_F7A670_MACMU_9544 and tr_G7PUS4_G7PUS4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_G7PUQ0_G7PUQ0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_A0A096P5J0_A0A096P5J0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_A0A0D9S2W8_A0A0D9S2W8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_A0A2K6AP56_A0A2K6AP56_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B5M7_F7B5M7_MACMU_9544 and tr_A0A2K6BB16_A0A2K6BB16_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A140T867_A0A140T867_BOVIN_9913 and sp_A1L595_K1C17_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A2I3MX15_A0A2I3MX15_PAPAN_9555 and tr_A0A2K5KRV7_A0A2K5KRV7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MX15_A0A2I3MX15_PAPAN_9555 and tr_A0A2K6A821_A0A2K6A821_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091ESI5_A0A091ESI5_CORBR_85066 and tr_A0A093PX43_A0A093PX43_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091UUY7_A0A091UUY7_NIPNI_128390 and tr_A0A091GDA1_A0A091GDA1_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091UUY7_A0A091UUY7_NIPNI_128390 and tr_A0A0A0ART4_A0A0A0ART4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A226N7Z7_A0A226N7Z7_CALSU_9009 and tr_A0A226NRM3_A0A226NRM3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5KWM8_A0A2K5KWM8_CERAT_9531 and tr_A0A2K6AF67_A0A2K6AF67_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5LTL8_A0A2K5LTL8_CERAT_9531 and tr_A0A2K6E9C0_A0A2K6E9C0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5P1B1_A0A2K5P1B1_CERAT_9531 and tr_A0A2K5ZJV4_A0A2K5ZJV4_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 32 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/Q7Z3Z0/3_mltree/Q7Z3Z0.raxml.reduced.phy Alignment comprises 1 partitions and 394 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 394 / 394 Gaps: 5.74 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3Z0/3_mltree/Q7Z3Z0.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 2 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 / 197 / 15760 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -469485.446130] Initial branch length optimization [00:00:05 -414832.810988] Model parameter optimization (eps = 10.000000) [00:00:53 -412323.015079] AUTODETECT spr round 1 (radius: 5) [00:03:55 -271760.260132] AUTODETECT spr round 2 (radius: 10) [00:06:57 -185367.188860] AUTODETECT spr round 3 (radius: 15) [00:10:14 -158682.219387] AUTODETECT spr round 4 (radius: 20) [00:14:48 -146888.032814] AUTODETECT spr round 5 (radius: 25) [00:20:52 -142920.833637] SPR radius for FAST iterations: 25 (autodetect) [00:20:52 -142920.833637] Model parameter optimization (eps = 3.000000) [00:21:18 -142803.879639] FAST spr round 1 (radius: 25) [00:24:40 -124509.272946] FAST spr round 2 (radius: 25) [00:27:19 -122758.389004] FAST spr round 3 (radius: 25) [00:29:47 -122671.695507] FAST spr round 4 (radius: 25) [00:32:07 -122649.503581] FAST spr round 5 (radius: 25) [00:34:11 -122649.503075] Model parameter optimization (eps = 1.000000) [00:34:42 -122578.332667] SLOW spr round 1 (radius: 5) [00:37:38 -122529.667948] SLOW spr round 2 (radius: 5) [00:40:32 -122522.120689] SLOW spr round 3 (radius: 5) [00:43:15 -122522.118949] SLOW spr round 4 (radius: 10) [00:45:55 -122521.774565] SLOW spr round 5 (radius: 5) [00:49:20 -122521.774526] SLOW spr round 6 (radius: 10) [00:52:17 -122521.774526] SLOW spr round 7 (radius: 15) [00:56:21 -122521.774526] SLOW spr round 8 (radius: 20) [01:04:20 -122521.774526] SLOW spr round 9 (radius: 25) [01:15:33 -122521.774526] Model parameter optimization (eps = 0.100000) [01:15:44] [worker #0] ML tree search #1, logLikelihood: -122521.688518 [01:15:44 -471721.681758] Initial branch length optimization [01:15:49 -414796.985920] Model parameter optimization (eps = 10.000000) [01:16:38 -412110.361744] AUTODETECT spr round 1 (radius: 5) [01:19:37 -276057.620630] AUTODETECT spr round 2 (radius: 10) [01:22:28] [worker #1] ML tree search #2, logLikelihood: -122518.122123 [01:22:36 -186116.947292] AUTODETECT spr round 3 (radius: 15) [01:25:49 -148141.635695] AUTODETECT spr round 4 (radius: 20) [01:29:39] [worker #2] ML tree search #3, logLikelihood: -122527.967658 [01:29:47 -139757.076861] AUTODETECT spr round 5 (radius: 25) [01:34:46 -138067.181412] SPR radius for FAST iterations: 25 (autodetect) [01:34:46 -138067.181412] Model parameter optimization (eps = 3.000000) [01:35:09 -137972.766480] FAST spr round 1 (radius: 25) [01:38:12 -123431.680935] FAST spr round 2 (radius: 25) [01:40:51 -122729.348696] FAST spr round 3 (radius: 25) [01:43:09 -122665.436619] FAST spr round 4 (radius: 25) [01:45:20 -122649.487706] FAST spr round 5 (radius: 25) [01:47:24 -122647.937667] FAST spr round 6 (radius: 25) [01:49:28 -122645.740178] FAST spr round 7 (radius: 25) [01:51:30 -122645.740172] Model parameter optimization (eps = 1.000000) [01:51:50 -122574.753166] SLOW spr round 1 (radius: 5) [01:54:49 -122513.294764] SLOW spr round 2 (radius: 5) [01:57:39 -122509.128714] SLOW spr round 3 (radius: 5) [02:00:24 -122509.128130] SLOW spr round 4 (radius: 10) [02:03:03 -122508.911941] SLOW spr round 5 (radius: 5) [02:06:29 -122508.911939] SLOW spr round 6 (radius: 10) [02:09:26 -122508.911939] SLOW spr round 7 (radius: 15) [02:13:29 -122508.911939] SLOW spr round 8 (radius: 20) [02:21:10 -122508.911939] SLOW spr round 9 (radius: 25) [02:31:43 -122508.911939] Model parameter optimization (eps = 0.100000) [02:31:56] [worker #0] ML tree search #4, logLikelihood: -122508.796308 [02:31:56 -470018.379072] Initial branch length optimization [02:32:02 -413034.355752] Model parameter optimization (eps = 10.000000) [02:32:50 -410364.877160] AUTODETECT spr round 1 (radius: 5) [02:35:49 -274200.566657] AUTODETECT spr round 2 (radius: 10) [02:38:50 -176948.832153] AUTODETECT spr round 3 (radius: 15) [02:39:29] [worker #2] ML tree search #6, logLikelihood: -122531.851677 [02:42:16 -147149.952325] AUTODETECT spr round 4 (radius: 20) [02:46:03 -142500.495564] AUTODETECT spr round 5 (radius: 25) [02:50:01] [worker #1] ML tree search #5, logLikelihood: -122514.064795 [02:51:22 -141548.340565] SPR radius for FAST iterations: 25 (autodetect) [02:51:22 -141548.340565] Model parameter optimization (eps = 3.000000) [02:51:48 -141425.571962] FAST spr round 1 (radius: 25) [02:54:57 -123817.055302] FAST spr round 2 (radius: 25) [02:57:26 -122736.176123] FAST spr round 3 (radius: 25) [02:59:39 -122659.193680] FAST spr round 4 (radius: 25) [03:01:45 -122641.663892] FAST spr round 5 (radius: 25) [03:03:45 -122641.663712] Model parameter optimization (eps = 1.000000) [03:04:03 -122629.138276] SLOW spr round 1 (radius: 5) [03:06:59 -122582.892890] SLOW spr round 2 (radius: 5) [03:09:47 -122578.923992] SLOW spr round 3 (radius: 5) [03:12:28 -122578.058636] SLOW spr round 4 (radius: 5) [03:15:08 -122576.025192] SLOW spr round 5 (radius: 5) [03:17:46 -122576.025189] SLOW spr round 6 (radius: 10) [03:20:23 -122574.707231] SLOW spr round 7 (radius: 5) [03:23:47 -122574.673702] SLOW spr round 8 (radius: 10) [03:26:40 -122574.673702] SLOW spr round 9 (radius: 15) [03:30:41 -122574.673702] SLOW spr round 10 (radius: 20) [03:38:47 -122574.673702] SLOW spr round 11 (radius: 25) [03:49:18 -122574.673702] Model parameter optimization (eps = 0.100000) [03:49:28] [worker #0] ML tree search #7, logLikelihood: -122574.454275 [03:49:28 -472616.040554] Initial branch length optimization [03:49:32 -416466.277268] Model parameter optimization (eps = 10.000000) [03:49:41] [worker #2] ML tree search #9, logLikelihood: -122529.813245 [03:50:12 -413959.578742] AUTODETECT spr round 1 (radius: 5) [03:53:04 -273467.205492] AUTODETECT spr round 2 (radius: 10) [03:55:56 -193489.344806] AUTODETECT spr round 3 (radius: 15) [03:59:12 -151882.374927] AUTODETECT spr round 4 (radius: 20) [04:03:15 -143373.358482] AUTODETECT spr round 5 (radius: 25) [04:08:33 -143059.799742] SPR radius for FAST iterations: 25 (autodetect) [04:08:33 -143059.799742] Model parameter optimization (eps = 3.000000) [04:09:01 -142938.866443] FAST spr round 1 (radius: 25) [04:12:10 -123527.302609] FAST spr round 2 (radius: 25) [04:14:40 -122748.816250] FAST spr round 3 (radius: 25) [04:15:12] [worker #1] ML tree search #8, logLikelihood: -122515.329787 [04:17:01 -122659.410260] FAST spr round 4 (radius: 25) [04:19:07 -122655.161547] FAST spr round 5 (radius: 25) [04:21:09 -122655.161406] Model parameter optimization (eps = 1.000000) [04:21:32 -122602.258551] SLOW spr round 1 (radius: 5) [04:24:34 -122552.449919] SLOW spr round 2 (radius: 5) [04:27:23 -122550.016100] SLOW spr round 3 (radius: 5) [04:30:05 -122550.016023] SLOW spr round 4 (radius: 10) [04:32:47 -122540.256791] SLOW spr round 5 (radius: 5) [04:36:13 -122538.216655] SLOW spr round 6 (radius: 5) [04:39:14 -122538.216221] SLOW spr round 7 (radius: 10) [04:41:57 -122538.216220] SLOW spr round 8 (radius: 15) [04:45:59 -122538.216220] SLOW spr round 9 (radius: 20) [04:53:46 -122536.604407] SLOW spr round 10 (radius: 5) [04:57:21 -122536.604357] SLOW spr round 11 (radius: 10) [04:58:30] [worker #2] ML tree search #12, logLikelihood: -122538.338889 [05:00:35 -122536.604356] SLOW spr round 12 (radius: 15) [05:04:29 -122536.604356] SLOW spr round 13 (radius: 20) [05:12:36 -122536.604356] SLOW spr round 14 (radius: 25) [05:23:02 -122536.604356] Model parameter optimization (eps = 0.100000) [05:23:12] [worker #0] ML tree search #10, logLikelihood: -122536.524079 [05:23:12 -471873.669489] Initial branch length optimization [05:23:17 -415435.097354] Model parameter optimization (eps = 10.000000) [05:24:08 -412986.364911] AUTODETECT spr round 1 (radius: 5) [05:27:08 -278104.107958] AUTODETECT spr round 2 (radius: 10) [05:30:13 -180918.837835] AUTODETECT spr round 3 (radius: 15) [05:31:27] [worker #1] ML tree search #11, logLikelihood: -122502.907070 [05:33:39 -147707.880900] AUTODETECT spr round 4 (radius: 20) [05:37:41 -141003.022230] AUTODETECT spr round 5 (radius: 25) [05:43:05 -139582.047959] SPR radius for FAST iterations: 25 (autodetect) [05:43:05 -139582.047959] Model parameter optimization (eps = 3.000000) [05:43:30 -139479.987183] FAST spr round 1 (radius: 25) [05:46:51 -123589.422025] FAST spr round 2 (radius: 25) [05:49:29 -122714.463446] FAST spr round 3 (radius: 25) [05:51:57 -122665.743402] FAST spr round 4 (radius: 25) [05:54:09 -122650.422472] FAST spr round 5 (radius: 25) [05:56:10 -122650.422436] Model parameter optimization (eps = 1.000000) [05:56:27 -122641.309067] SLOW spr round 1 (radius: 5) [05:59:33 -122599.965946] SLOW spr round 2 (radius: 5) [06:02:23 -122592.342400] SLOW spr round 3 (radius: 5) [06:05:04 -122592.342394] SLOW spr round 4 (radius: 10) [06:07:44 -122590.774673] SLOW spr round 5 (radius: 5) [06:11:09 -122587.458320] SLOW spr round 6 (radius: 5) [06:14:09 -122587.458240] SLOW spr round 7 (radius: 10) [06:16:50 -122587.458240] SLOW spr round 8 (radius: 15) [06:20:52 -122587.458240] SLOW spr round 9 (radius: 20) [06:22:42] [worker #2] ML tree search #15, logLikelihood: -122531.741991 [06:28:27 -122587.458240] SLOW spr round 10 (radius: 25) [06:39:32 -122587.458240] Model parameter optimization (eps = 0.100000) [06:39:42] [worker #0] ML tree search #13, logLikelihood: -122587.407722 [06:39:42 -471778.850717] Initial branch length optimization [06:39:48 -416351.358555] Model parameter optimization (eps = 10.000000) [06:40:31 -413624.324920] AUTODETECT spr round 1 (radius: 5) [06:43:29 -267668.446365] AUTODETECT spr round 2 (radius: 10) [06:46:32 -178219.448966] AUTODETECT spr round 3 (radius: 15) [06:50:04 -150149.919298] AUTODETECT spr round 4 (radius: 20) [06:53:05] [worker #1] ML tree search #14, logLikelihood: -122507.601156 [06:54:45 -140510.676935] AUTODETECT spr round 5 (radius: 25) [07:01:38 -138995.953527] SPR radius for FAST iterations: 25 (autodetect) [07:01:38 -138995.953527] Model parameter optimization (eps = 3.000000) [07:02:06 -138845.793291] FAST spr round 1 (radius: 25) [07:05:22 -123776.633044] FAST spr round 2 (radius: 25) [07:08:04 -122766.803673] FAST spr round 3 (radius: 25) [07:10:25 -122671.027716] FAST spr round 4 (radius: 25) [07:12:36 -122650.347036] FAST spr round 5 (radius: 25) [07:14:39 -122649.473051] FAST spr round 6 (radius: 25) [07:16:39 -122649.473048] Model parameter optimization (eps = 1.000000) [07:16:59 -122611.549818] SLOW spr round 1 (radius: 5) [07:20:02 -122558.764554] SLOW spr round 2 (radius: 5) [07:22:53 -122547.620959] SLOW spr round 3 (radius: 5) [07:25:35 -122547.528113] SLOW spr round 4 (radius: 10) [07:28:16 -122541.359759] SLOW spr round 5 (radius: 5) [07:31:42 -122521.606927] SLOW spr round 6 (radius: 5) [07:34:44 -122520.982188] SLOW spr round 7 (radius: 5) [07:37:33 -122520.982179] SLOW spr round 8 (radius: 10) [07:40:14 -122520.981974] SLOW spr round 9 (radius: 15) [07:44:36 -122520.981972] SLOW spr round 10 (radius: 20) [07:52:39 -122520.981970] SLOW spr round 11 (radius: 25) [07:54:43] [worker #2] ML tree search #18, logLikelihood: -122529.592863 [08:03:50 -122520.981967] Model parameter optimization (eps = 0.100000) [08:03:58] [worker #0] ML tree search #16, logLikelihood: -122520.938946 [08:03:58 -470262.567452] Initial branch length optimization [08:04:04 -414655.787347] Model parameter optimization (eps = 10.000000) [08:04:49 -412119.201429] AUTODETECT spr round 1 (radius: 5) [08:07:40] [worker #1] ML tree search #17, logLikelihood: -122518.128949 [08:07:46 -272300.357602] AUTODETECT spr round 2 (radius: 10) [08:10:48 -184739.772610] AUTODETECT spr round 3 (radius: 15) [08:14:14 -152284.970710] AUTODETECT spr round 4 (radius: 20) [08:19:14 -144871.054991] AUTODETECT spr round 5 (radius: 25) [08:24:17 -142432.460584] SPR radius for FAST iterations: 25 (autodetect) [08:24:17 -142432.460584] Model parameter optimization (eps = 3.000000) [08:24:47 -142287.728634] FAST spr round 1 (radius: 25) [08:28:01 -123735.293330] FAST spr round 2 (radius: 25) [08:30:33 -122681.421407] FAST spr round 3 (radius: 25) [08:32:49 -122577.889755] FAST spr round 4 (radius: 25) [08:34:56 -122575.057420] FAST spr round 5 (radius: 25) [08:36:57 -122575.057387] Model parameter optimization (eps = 1.000000) [08:37:11 -122569.278366] SLOW spr round 1 (radius: 5) [08:40:05 -122543.432952] SLOW spr round 2 (radius: 5) [08:42:44 -122537.889264] SLOW spr round 3 (radius: 5) [08:45:16 -122535.821801] SLOW spr round 4 (radius: 5) [08:47:44 -122535.821797] SLOW spr round 5 (radius: 10) [08:50:19 -122532.144403] SLOW spr round 6 (radius: 5) [08:53:25 -122532.144316] SLOW spr round 7 (radius: 10) [08:56:07 -122531.885289] SLOW spr round 8 (radius: 5) [08:59:11 -122531.885276] SLOW spr round 9 (radius: 10) [09:02:03 -122531.885276] SLOW spr round 10 (radius: 15) [09:06:07 -122531.885276] SLOW spr round 11 (radius: 20) [09:14:21 -122531.885276] SLOW spr round 12 (radius: 25) [09:25:41 -122531.885276] Model parameter optimization (eps = 0.100000) [09:25:49] [worker #0] ML tree search #19, logLikelihood: -122531.786359 [09:42:53] [worker #1] ML tree search #20, logLikelihood: -122515.681275 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.240296,0.370954) (0.159568,1.123406) (0.360889,0.862381) (0.239247,1.757085) 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: -122502.907070 AIC score: 249015.814140 / AICc score: 8293075.814140 / BIC score: 256988.397713 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=394). 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/Q7Z3Z0/3_mltree/Q7Z3Z0.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3Z0/3_mltree/Q7Z3Z0.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3Z0/3_mltree/Q7Z3Z0.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7Z3Z0/3_mltree/Q7Z3Z0.raxml.log Analysis started: 06-Jul-2021 19:54:17 / finished: 07-Jul-2021 05:37:11 Elapsed time: 34974.185 seconds Consumed energy: 3195.960 Wh (= 16 km in an electric car, or 80 km with an e-scooter!)