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 07-Jul-2021 22:11:19 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JA4/2_msa/Q96JA4_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JA4/3_mltree/Q96JA4 --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/Q96JA4/2_msa/Q96JA4_trimmed_msa.fasta [00:00:00] Loaded alignment with 309 taxa and 113 sites WARNING: Sequences tr_G3QIL7_G3QIL7_GORGO_9595 and tr_H2Q3S2_H2Q3S2_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NDB3_H2NDB3_PONAB_9601 and tr_H2Q3S1_H2Q3S1_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NDB3_H2NDB3_PONAB_9601 and tr_A0A2R9CDU6_A0A2R9CDU6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5Q3J9_A0A1D5Q3J9_MACMU_9544 and tr_G7PQ05_G7PQ05_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5Q3J9_A0A1D5Q3J9_MACMU_9544 and tr_A0A096MPA3_A0A096MPA3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5Q3J9_A0A1D5Q3J9_MACMU_9544 and tr_A0A2K5LI61_A0A2K5LI61_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5Q3J9_A0A1D5Q3J9_MACMU_9544 and tr_A0A2K6C6N5_A0A2K6C6N5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5Q3J9_A0A1D5Q3J9_MACMU_9544 and tr_A0A2K5Z1M4_A0A2K5Z1M4_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6Q9P2_F6Q9P2_MACMU_9544 and tr_A0A2I3M852_A0A2I3M852_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6Q9P2_F6Q9P2_MACMU_9544 and tr_A0A2K5LBJ1_A0A2K5LBJ1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6Q9P2_F6Q9P2_MACMU_9544 and tr_A0A2K6CT58_A0A2K6CT58_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6Q9P2_F6Q9P2_MACMU_9544 and tr_A0A2K5YGH3_A0A2K5YGH3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1L0N4_G1L0N4_AILME_9646 and tr_A0A384DG08_A0A384DG08_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7PPZ8_G7PPZ8_MACFA_9541 and tr_A0A2K6B449_A0A2K6B449_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PQ01_G7PQ01_MACFA_9541 and tr_A0A0D9R1K7_A0A0D9R1K7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7PQ01_G7PQ01_MACFA_9541 and tr_A0A2K6E7R1_A0A2K6E7R1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PQ02_G7PQ02_MACFA_9541 and tr_A0A0D9R1K0_A0A0D9R1K0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096MPS7_A0A096MPS7_PAPAN_9555 and tr_A0A2K5N7I0_A0A2K5N7I0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MPS7_A0A096MPS7_PAPAN_9555 and tr_A0A2K5Y7J7_A0A2K5Y7J7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3LI91_A0A2I3LI91_PAPAN_9555 and tr_A0A2K5LBV1_A0A2K5LBV1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LI91_A0A2I3LI91_PAPAN_9555 and tr_A0A2K5Y0Y3_A0A2K5Y0Y3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5LCA6_A0A2K5LCA6_CERAT_9531 and tr_A0A2K5Z2M9_A0A2K5Z2M9_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 22 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/Q96JA4/3_mltree/Q96JA4.raxml.reduced.phy Alignment comprises 1 partitions and 113 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 113 / 113 Gaps: 2.36 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JA4/3_mltree/Q96JA4.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 309 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 113 / 9040 [00:00:00] Data distribution: max. searches per worker: 10 Starting ML tree search with 20 distinct starting trees [00:00:00 -68376.858531] Initial branch length optimization [00:00:00 -58455.103786] Model parameter optimization (eps = 10.000000) [00:00:16 -57290.284476] AUTODETECT spr round 1 (radius: 5) [00:00:27 -40889.625138] AUTODETECT spr round 2 (radius: 10) [00:00:42 -29993.624345] AUTODETECT spr round 3 (radius: 15) [00:00:58 -28497.800034] AUTODETECT spr round 4 (radius: 20) [00:01:23 -27311.785141] AUTODETECT spr round 5 (radius: 25) [00:01:47 -27311.782605] SPR radius for FAST iterations: 20 (autodetect) [00:01:47 -27311.782605] Model parameter optimization (eps = 3.000000) [00:01:53 -27194.489204] FAST spr round 1 (radius: 20) [00:02:08 -25325.870040] FAST spr round 2 (radius: 20) [00:02:20 -25156.868906] FAST spr round 3 (radius: 20) [00:02:31 -25130.568258] FAST spr round 4 (radius: 20) [00:02:41 -25124.728267] FAST spr round 5 (radius: 20) [00:02:50 -25124.727586] Model parameter optimization (eps = 1.000000) [00:02:54 -25121.265030] SLOW spr round 1 (radius: 5) [00:03:12 -25113.751448] SLOW spr round 2 (radius: 5) [00:03:28 -25113.748837] SLOW spr round 3 (radius: 10) [00:03:43 -25113.748311] SLOW spr round 4 (radius: 15) [00:04:12 -25113.748191] SLOW spr round 5 (radius: 20) [00:04:50 -25113.748178] SLOW spr round 6 (radius: 25) [00:05:25] [worker #1] ML tree search #2, logLikelihood: -25114.018401 [00:05:26 -25113.748173] Model parameter optimization (eps = 0.100000) [00:05:27] [worker #0] ML tree search #1, logLikelihood: -25113.729761 [00:05:27 -68423.225301] Initial branch length optimization [00:05:27 -58550.475375] Model parameter optimization (eps = 10.000000) [00:05:38 -57718.879255] AUTODETECT spr round 1 (radius: 5) [00:05:49 -39130.803518] AUTODETECT spr round 2 (radius: 10) [00:06:05 -29832.043666] AUTODETECT spr round 3 (radius: 15) [00:06:27 -28114.682217] AUTODETECT spr round 4 (radius: 20) [00:06:53 -27465.909853] AUTODETECT spr round 5 (radius: 25) [00:07:14 -27465.905519] SPR radius for FAST iterations: 20 (autodetect) [00:07:14 -27465.905519] Model parameter optimization (eps = 3.000000) [00:07:21 -27415.969444] FAST spr round 1 (radius: 20) [00:07:35 -25318.363997] FAST spr round 2 (radius: 20) [00:07:47 -25166.462985] FAST spr round 3 (radius: 20) [00:07:57 -25157.710243] FAST spr round 4 (radius: 20) [00:08:06 -25157.710212] Model parameter optimization (eps = 1.000000) [00:08:10 -25156.062545] SLOW spr round 1 (radius: 5) [00:08:27 -25146.278528] SLOW spr round 2 (radius: 5) [00:08:43 -25144.845396] SLOW spr round 3 (radius: 5) [00:08:58 -25144.843986] SLOW spr round 4 (radius: 10) [00:09:14 -25144.843824] SLOW spr round 5 (radius: 15) [00:09:43 -25144.563434] SLOW spr round 6 (radius: 5) [00:10:07 -25144.562819] SLOW spr round 7 (radius: 10) [00:10:25 -25143.832004] SLOW spr round 8 (radius: 5) [00:10:46 -25143.831821] SLOW spr round 9 (radius: 10) [00:11:04 -25143.831816] SLOW spr round 10 (radius: 15) [00:11:31 -25143.831816] SLOW spr round 11 (radius: 20) [00:12:10 -25143.831815] SLOW spr round 12 (radius: 25) [00:12:41] [worker #1] ML tree search #4, logLikelihood: -25100.052635 [00:12:44 -25143.831815] Model parameter optimization (eps = 0.100000) [00:12:47] [worker #0] ML tree search #3, logLikelihood: -25143.719266 [00:12:47 -68865.365410] Initial branch length optimization [00:12:47 -59006.242612] Model parameter optimization (eps = 10.000000) [00:12:58 -58145.503970] AUTODETECT spr round 1 (radius: 5) [00:13:10 -40447.475610] AUTODETECT spr round 2 (radius: 10) [00:13:24 -31463.069150] AUTODETECT spr round 3 (radius: 15) [00:13:44 -27586.915389] AUTODETECT spr round 4 (radius: 20) [00:14:11 -27365.380835] AUTODETECT spr round 5 (radius: 25) [00:14:37 -27365.350582] SPR radius for FAST iterations: 20 (autodetect) [00:14:37 -27365.350582] Model parameter optimization (eps = 3.000000) [00:14:43 -27318.683330] FAST spr round 1 (radius: 20) [00:14:56 -25328.447261] FAST spr round 2 (radius: 20) [00:15:09 -25194.306120] FAST spr round 3 (radius: 20) [00:15:20 -25181.303252] FAST spr round 4 (radius: 20) [00:15:29 -25180.230201] FAST spr round 5 (radius: 20) [00:15:39 -25179.784044] FAST spr round 6 (radius: 20) [00:15:48 -25179.783715] Model parameter optimization (eps = 1.000000) [00:15:53 -25159.690704] SLOW spr round 1 (radius: 5) [00:16:10 -25153.957614] SLOW spr round 2 (radius: 5) [00:16:26 -25151.928779] SLOW spr round 3 (radius: 5) [00:16:41 -25151.785862] SLOW spr round 4 (radius: 5) [00:16:55 -25151.785852] SLOW spr round 5 (radius: 10) [00:17:11 -25151.715834] SLOW spr round 6 (radius: 15) [00:17:39 -25151.712638] SLOW spr round 7 (radius: 20) [00:18:17 -25151.711663] SLOW spr round 8 (radius: 25) [00:18:52 -25151.711196] Model parameter optimization (eps = 0.100000) [00:18:53] [worker #0] ML tree search #5, logLikelihood: -25151.700942 [00:18:53 -67945.789545] Initial branch length optimization [00:18:54 -58351.410204] Model parameter optimization (eps = 10.000000) [00:18:57] [worker #1] ML tree search #6, logLikelihood: -25102.112811 [00:19:05 -57774.710742] AUTODETECT spr round 1 (radius: 5) [00:19:16 -40461.624290] AUTODETECT spr round 2 (radius: 10) [00:19:30 -30024.503847] AUTODETECT spr round 3 (radius: 15) [00:19:49 -27753.544189] AUTODETECT spr round 4 (radius: 20) [00:20:15 -27621.542431] AUTODETECT spr round 5 (radius: 25) [00:20:38 -27509.024677] SPR radius for FAST iterations: 25 (autodetect) [00:20:38 -27509.024677] Model parameter optimization (eps = 3.000000) [00:20:44 -27471.517940] FAST spr round 1 (radius: 25) [00:20:58 -25365.311034] FAST spr round 2 (radius: 25) [00:21:11 -25193.580670] FAST spr round 3 (radius: 25) [00:21:23 -25160.254996] FAST spr round 4 (radius: 25) [00:21:33 -25160.090782] FAST spr round 5 (radius: 25) [00:21:42 -25160.090174] Model parameter optimization (eps = 1.000000) [00:21:46 -25156.461011] SLOW spr round 1 (radius: 5) [00:22:03 -25153.285019] SLOW spr round 2 (radius: 5) [00:22:19 -25152.313559] SLOW spr round 3 (radius: 5) [00:22:35 -25152.310501] SLOW spr round 4 (radius: 10) [00:22:50 -25147.223414] SLOW spr round 5 (radius: 5) [00:23:13 -25145.845942] SLOW spr round 6 (radius: 5) [00:23:31 -25145.350567] SLOW spr round 7 (radius: 5) [00:23:48 -25144.942853] SLOW spr round 8 (radius: 5) [00:24:04 -25144.942813] SLOW spr round 9 (radius: 10) [00:24:19 -25143.421059] SLOW spr round 10 (radius: 5) [00:24:41 -25138.525102] SLOW spr round 11 (radius: 5) [00:25:00 -25138.462494] SLOW spr round 12 (radius: 10) [00:25:15 -25138.462092] SLOW spr round 13 (radius: 15) [00:25:41] [worker #1] ML tree search #8, logLikelihood: -25137.460036 [00:25:43 -25138.462084] SLOW spr round 14 (radius: 20) [00:26:21 -25138.462083] SLOW spr round 15 (radius: 25) [00:26:57 -25138.462083] Model parameter optimization (eps = 0.100000) [00:26:59] [worker #0] ML tree search #7, logLikelihood: -25138.338294 [00:26:59 -67918.327627] Initial branch length optimization [00:27:00 -58431.262542] Model parameter optimization (eps = 10.000000) [00:27:12 -57637.408745] AUTODETECT spr round 1 (radius: 5) [00:27:23 -39740.144611] AUTODETECT spr round 2 (radius: 10) [00:27:38 -29084.473434] AUTODETECT spr round 3 (radius: 15) [00:27:56 -27350.847995] AUTODETECT spr round 4 (radius: 20) [00:28:24 -27342.536586] AUTODETECT spr round 5 (radius: 25) [00:28:49 -27286.410208] SPR radius for FAST iterations: 25 (autodetect) [00:28:49 -27286.410208] Model parameter optimization (eps = 3.000000) [00:28:56 -27229.464557] FAST spr round 1 (radius: 25) [00:29:10 -25264.356716] FAST spr round 2 (radius: 25) [00:29:23 -25172.390003] FAST spr round 3 (radius: 25) [00:29:34 -25162.055039] FAST spr round 4 (radius: 25) [00:29:44 -25158.457816] FAST spr round 5 (radius: 25) [00:29:53 -25156.253587] FAST spr round 6 (radius: 25) [00:30:03 -25155.512640] FAST spr round 7 (radius: 25) [00:30:12 -25155.512412] Model parameter optimization (eps = 1.000000) [00:30:18 -25154.250311] SLOW spr round 1 (radius: 5) [00:30:35 -25145.730347] SLOW spr round 2 (radius: 5) [00:30:51 -25145.405613] SLOW spr round 3 (radius: 5) [00:31:07 -25141.226788] SLOW spr round 4 (radius: 5) [00:31:23 -25140.619763] SLOW spr round 5 (radius: 5) [00:31:39 -25140.617342] SLOW spr round 6 (radius: 10) [00:31:48] [worker #1] ML tree search #10, logLikelihood: -25104.883414 [00:31:54 -25140.616979] SLOW spr round 7 (radius: 15) [00:32:23 -25139.786778] SLOW spr round 8 (radius: 5) [00:32:46 -25139.780391] SLOW spr round 9 (radius: 10) [00:33:04 -25139.552980] SLOW spr round 10 (radius: 5) [00:33:25 -25139.552616] SLOW spr round 11 (radius: 10) [00:33:43 -25139.552612] SLOW spr round 12 (radius: 15) [00:34:09 -25139.552612] SLOW spr round 13 (radius: 20) [00:34:47 -25139.552612] SLOW spr round 14 (radius: 25) [00:35:22 -25139.552612] Model parameter optimization (eps = 0.100000) [00:35:26] [worker #0] ML tree search #9, logLikelihood: -25139.378673 [00:35:27 -68766.745125] Initial branch length optimization [00:35:27 -58747.670872] Model parameter optimization (eps = 10.000000) [00:35:38 -58064.127467] AUTODETECT spr round 1 (radius: 5) [00:35:49 -40437.822029] AUTODETECT spr round 2 (radius: 10) [00:36:03 -29262.078079] AUTODETECT spr round 3 (radius: 15) [00:36:21 -27687.064638] AUTODETECT spr round 4 (radius: 20) [00:36:44 -27496.141860] AUTODETECT spr round 5 (radius: 25) [00:37:07 -27496.131951] SPR radius for FAST iterations: 20 (autodetect) [00:37:07 -27496.131951] Model parameter optimization (eps = 3.000000) [00:37:14 -27440.593973] FAST spr round 1 (radius: 20) [00:37:29 -25241.511371] FAST spr round 2 (radius: 20) [00:37:41 -25168.971223] FAST spr round 3 (radius: 20) [00:37:52 -25153.851817] FAST spr round 4 (radius: 20) [00:38:02 -25151.094734] FAST spr round 5 (radius: 20) [00:38:02] [worker #1] ML tree search #12, logLikelihood: -25134.640789 [00:38:11 -25151.094572] Model parameter optimization (eps = 1.000000) [00:38:16 -25148.347375] SLOW spr round 1 (radius: 5) [00:38:34 -25138.809328] SLOW spr round 2 (radius: 5) [00:38:50 -25138.073699] SLOW spr round 3 (radius: 5) [00:39:06 -25138.073445] SLOW spr round 4 (radius: 10) [00:39:22 -25137.400569] SLOW spr round 5 (radius: 5) [00:39:43 -25137.400070] SLOW spr round 6 (radius: 10) [00:40:01 -25137.400061] SLOW spr round 7 (radius: 15) [00:40:28 -25137.400061] SLOW spr round 8 (radius: 20) [00:41:06 -25137.400061] SLOW spr round 9 (radius: 25) [00:41:41 -25137.400061] Model parameter optimization (eps = 0.100000) [00:41:43] [worker #0] ML tree search #11, logLikelihood: -25137.295308 [00:41:43 -67981.354793] Initial branch length optimization [00:41:44 -58239.134983] Model parameter optimization (eps = 10.000000) [00:42:00 -57014.669039] AUTODETECT spr round 1 (radius: 5) [00:42:12 -41882.572069] AUTODETECT spr round 2 (radius: 10) [00:42:26 -29701.772381] AUTODETECT spr round 3 (radius: 15) [00:42:44 -27466.442967] AUTODETECT spr round 4 (radius: 20) [00:43:07 -27423.763580] AUTODETECT spr round 5 (radius: 25) [00:43:31 -27423.740034] SPR radius for FAST iterations: 20 (autodetect) [00:43:31 -27423.740034] Model parameter optimization (eps = 3.000000) [00:43:38 -27293.155962] FAST spr round 1 (radius: 20) [00:43:52 -25253.041224] FAST spr round 2 (radius: 20) [00:44:05 -25134.887497] FAST spr round 3 (radius: 20) [00:44:15 -25125.270909] FAST spr round 4 (radius: 20) [00:44:25 -25120.121903] FAST spr round 5 (radius: 20) [00:44:34] [worker #1] ML tree search #14, logLikelihood: -25141.243724 [00:44:34 -25120.121883] Model parameter optimization (eps = 1.000000) [00:44:38 -25116.231762] SLOW spr round 1 (radius: 5) [00:44:55 -25106.530021] SLOW spr round 2 (radius: 5) [00:45:11 -25105.558003] SLOW spr round 3 (radius: 5) [00:45:26 -25105.557973] SLOW spr round 4 (radius: 10) [00:45:41 -25105.242335] SLOW spr round 5 (radius: 5) [00:46:03 -25101.117155] SLOW spr round 6 (radius: 5) [00:46:21 -25101.117075] SLOW spr round 7 (radius: 10) [00:46:36 -25101.117072] SLOW spr round 8 (radius: 15) [00:47:04 -25101.117072] SLOW spr round 9 (radius: 20) [00:47:41 -25101.117072] SLOW spr round 10 (radius: 25) [00:48:15 -25101.117072] Model parameter optimization (eps = 0.100000) [00:48:17] [worker #0] ML tree search #13, logLikelihood: -25101.070871 [00:48:17 -68059.586261] Initial branch length optimization [00:48:17 -58438.356927] Model parameter optimization (eps = 10.000000) [00:48:27 -57715.814213] AUTODETECT spr round 1 (radius: 5) [00:48:38 -38941.351690] AUTODETECT spr round 2 (radius: 10) [00:48:53 -29179.304998] AUTODETECT spr round 3 (radius: 15) [00:49:10 -27257.575178] AUTODETECT spr round 4 (radius: 20) [00:49:31 -27007.630439] AUTODETECT spr round 5 (radius: 25) [00:49:59 -27006.774184] SPR radius for FAST iterations: 25 (autodetect) [00:49:59 -27006.774184] Model parameter optimization (eps = 3.000000) [00:50:04 -26964.900804] FAST spr round 1 (radius: 25) [00:50:18 -25354.077022] FAST spr round 2 (radius: 25) [00:50:29 -25152.313534] FAST spr round 3 (radius: 25) [00:50:40 -25140.931934] FAST spr round 4 (radius: 25) [00:50:49 -25140.150662] FAST spr round 5 (radius: 25) [00:50:59 -25140.148880] Model parameter optimization (eps = 1.000000) [00:51:03 -25136.942038] SLOW spr round 1 (radius: 5) [00:51:06] [worker #1] ML tree search #16, logLikelihood: -25138.306823 [00:51:20 -25129.918231] SLOW spr round 2 (radius: 5) [00:51:38 -25125.249551] SLOW spr round 3 (radius: 5) [00:51:53 -25125.089141] SLOW spr round 4 (radius: 5) [00:52:08 -25125.089066] SLOW spr round 5 (radius: 10) [00:52:24 -25125.089065] SLOW spr round 6 (radius: 15) [00:52:53 -25124.731580] SLOW spr round 7 (radius: 5) [00:53:17 -25124.506212] SLOW spr round 8 (radius: 5) [00:53:36 -25124.505598] SLOW spr round 9 (radius: 10) [00:53:52 -25124.505418] SLOW spr round 10 (radius: 15) [00:54:21 -25124.505363] SLOW spr round 11 (radius: 20) [00:54:58 -25124.505346] SLOW spr round 12 (radius: 25) [00:55:33 -25124.505341] Model parameter optimization (eps = 0.100000) [00:55:37] [worker #0] ML tree search #15, logLikelihood: -25124.112636 [00:55:37 -67759.832639] Initial branch length optimization [00:55:37 -58092.541228] Model parameter optimization (eps = 10.000000) [00:55:51 -56916.012054] AUTODETECT spr round 1 (radius: 5) [00:56:03 -41628.787674] AUTODETECT spr round 2 (radius: 10) [00:56:18 -30092.616416] AUTODETECT spr round 3 (radius: 15) [00:56:38 -27271.895027] AUTODETECT spr round 4 (radius: 20) [00:57:06 -27108.946895] AUTODETECT spr round 5 (radius: 25) [00:57:31 -27108.942987] SPR radius for FAST iterations: 20 (autodetect) [00:57:31 -27108.942987] Model parameter optimization (eps = 3.000000) [00:57:37 -26997.274460] FAST spr round 1 (radius: 20) [00:57:52 -25245.306522] FAST spr round 2 (radius: 20) [00:58:01] [worker #1] ML tree search #18, logLikelihood: -25096.146877 [00:58:04 -25133.489565] FAST spr round 3 (radius: 20) [00:58:15 -25121.189062] FAST spr round 4 (radius: 20) [00:58:25 -25118.318795] FAST spr round 5 (radius: 20) [00:58:34 -25118.318686] Model parameter optimization (eps = 1.000000) [00:58:38 -25116.211595] SLOW spr round 1 (radius: 5) [00:58:56 -25112.426613] SLOW spr round 2 (radius: 5) [00:59:12 -25112.127164] SLOW spr round 3 (radius: 5) [00:59:27 -25112.126767] SLOW spr round 4 (radius: 10) [00:59:44 -25111.816832] SLOW spr round 5 (radius: 5) [01:00:06 -25111.816222] SLOW spr round 6 (radius: 10) [01:00:23 -25111.816213] SLOW spr round 7 (radius: 15) [01:00:50 -25111.816212] SLOW spr round 8 (radius: 20) [01:01:29 -25111.816212] SLOW spr round 9 (radius: 25) [01:02:03 -25111.816212] Model parameter optimization (eps = 0.100000) [01:02:07] [worker #0] ML tree search #17, logLikelihood: -25111.422875 [01:02:07 -68017.871889] Initial branch length optimization [01:02:07 -58353.170636] Model parameter optimization (eps = 10.000000) [01:02:19 -57207.024610] AUTODETECT spr round 1 (radius: 5) [01:02:30 -39160.296261] AUTODETECT spr round 2 (radius: 10) [01:02:45 -30513.044013] AUTODETECT spr round 3 (radius: 15) [01:03:03 -28225.511499] AUTODETECT spr round 4 (radius: 20) [01:03:28 -27832.336872] AUTODETECT spr round 5 (radius: 25) [01:03:53 -27818.855989] SPR radius for FAST iterations: 25 (autodetect) [01:03:53 -27818.855989] Model parameter optimization (eps = 3.000000) [01:03:59 -27773.511818] FAST spr round 1 (radius: 25) [01:04:13 -25456.288314] FAST spr round 2 (radius: 25) [01:04:26 -25196.475432] FAST spr round 3 (radius: 25) [01:04:38 -25167.327409] FAST spr round 4 (radius: 25) [01:04:48 -25153.770846] FAST spr round 5 (radius: 25) [01:04:57 -25153.770806] Model parameter optimization (eps = 1.000000) [01:05:03 -25135.299062] SLOW spr round 1 (radius: 5) [01:05:04] [worker #1] ML tree search #20, logLikelihood: -25096.905958 [01:05:20 -25124.802996] SLOW spr round 2 (radius: 5) [01:05:37 -25122.139944] SLOW spr round 3 (radius: 5) [01:05:52 -25122.139584] SLOW spr round 4 (radius: 10) [01:06:08 -25120.539461] SLOW spr round 5 (radius: 5) [01:06:30 -25120.044644] SLOW spr round 6 (radius: 5) [01:06:47 -25120.044333] SLOW spr round 7 (radius: 10) [01:07:03 -25120.044295] SLOW spr round 8 (radius: 15) [01:07:31 -25119.397214] SLOW spr round 9 (radius: 5) [01:07:54 -25119.394859] SLOW spr round 10 (radius: 10) [01:08:13 -25119.393748] SLOW spr round 11 (radius: 15) [01:08:40 -25119.393203] SLOW spr round 12 (radius: 20) [01:09:19 -25119.392935] SLOW spr round 13 (radius: 25) [01:09:53 -25119.392803] Model parameter optimization (eps = 0.100000) [01:09:54] [worker #0] ML tree search #19, logLikelihood: -25119.354236 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.292285,1.089790) (0.216909,0.806717) (0.452518,1.109404) (0.038289,0.116539) 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: -25096.146877 AIC score: 51434.293754 / AICc score: 823958.293754 / BIC score: 53128.001589 Free parameters (model + branch lengths): 621 WARNING: Number of free parameters (K=621) is larger than alignment size (n=113). 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/Q96JA4/3_mltree/Q96JA4.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JA4/3_mltree/Q96JA4.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JA4/3_mltree/Q96JA4.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JA4/3_mltree/Q96JA4.raxml.log Analysis started: 07-Jul-2021 22:11:19 / finished: 07-Jul-2021 23:21:13 Elapsed time: 4194.864 seconds Consumed energy: 307.130 Wh (= 2 km in an electric car, or 8 km with an e-scooter!)