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 02-Jul-2021 01:26:17 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/2_msa/Q01518_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/3_mltree/Q01518 --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/Q01518/2_msa/Q01518_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 531 sites WARNING: Sequences tr_J3K918_J3K918_COCIM_246410 and tr_A0A0J6YAH1_A0A0J6YAH1_COCIT_404692 are exactly identical! WARNING: Sequences tr_B8N6C9_B8N6C9_ASPFN_332952 and tr_Q2UCD3_Q2UCD3_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8N6C9_B8N6C9_ASPFN_332952 and tr_A0A0F0IEV0_A0A0F0IEV0_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8N6C9_B8N6C9_ASPFN_332952 and tr_A0A1S9DR54_A0A1S9DR54_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8N6C9_B8N6C9_ASPFN_332952 and tr_A0A2G7G2G3_A0A2G7G2G3_9EURO_656916 are exactly identical! WARNING: Sequences tr_C6HFU8_C6HFU8_AJECH_544712 and tr_F0UMH6_F0UMH6_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A0E0ICN9_A0A0E0ICN9_ORYNI_4536 and tr_A2YVR2_A2YVR2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A2QRC4_A2QRC4_ASPNC_425011 and tr_A0A319AN78_A0A319AN78_9EURO_1450533 are exactly identical! WARNING: Sequences tr_I1QJ48_I1QJ48_ORYGL_4538 and tr_A0A0D3H0W0_A0A0D3H0W0_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1QJ48_I1QJ48_ORYGL_4538 and tr_A0A0E0AW30_A0A0E0AW30_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_I1QJ48_I1QJ48_ORYGL_4538 and tr_Q6ZAC2_Q6ZAC2_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G2YLB9_G2YLB9_BOTF4_999810 and tr_M7TJL0_M7TJL0_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SZ39_F2SZ39_TRIRC_559305 and tr_A0A178F498_A0A178F498_TRIRU_5551 are exactly identical! WARNING: Sequences tr_F2Q5F1_F2Q5F1_TRIEC_559882 and tr_A0A059JIS9_A0A059JIS9_9EURO_1215338 are exactly identical! WARNING: Sequences tr_A0A015LXW7_A0A015LXW7_9GLOM_1432141 and tr_A0A2I1G7D0_A0A2I1G7D0_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015LXW7_A0A015LXW7_9GLOM_1432141 and tr_A0A2H5T5J9_A0A2H5T5J9_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A096N1K2_A0A096N1K2_PAPAN_9555 and tr_A0A0D9S7N5_A0A0D9S7N5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096N1K2_A0A096N1K2_PAPAN_9555 and tr_A0A2K6CU40_A0A2K6CU40_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0V1D9Y5_A0A0V1D9Y5_TRIBR_45882 and tr_A0A0V1NH27_A0A0V1NH27_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1D9Y5_A0A0V1D9Y5_TRIBR_45882 and tr_A0A0V0U3L3_A0A0V0U3L3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S4AVZ0_A0A1S4AVZ0_TOBAC_4097 and tr_A0A1U7W9D2_A0A1U7W9D2_NICSY_4096 are exactly identical! WARNING: Duplicate sequences found: 21 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/Q01518/3_mltree/Q01518.raxml.reduced.phy Alignment comprises 1 partitions and 531 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 531 / 531 Gaps: 14.89 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/3_mltree/Q01518.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 / 266 / 21280 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -845358.821033] Initial branch length optimization [00:00:08 -737188.038627] Model parameter optimization (eps = 10.000000) [00:01:13 -734649.437098] AUTODETECT spr round 1 (radius: 5) [00:05:11 -524844.957288] AUTODETECT spr round 2 (radius: 10) [00:09:31 -394273.667608] AUTODETECT spr round 3 (radius: 15) [00:14:01 -340422.992423] AUTODETECT spr round 4 (radius: 20) [00:19:09 -320699.888562] AUTODETECT spr round 5 (radius: 25) [00:25:42 -319431.434291] SPR radius for FAST iterations: 25 (autodetect) [00:25:42 -319431.434291] Model parameter optimization (eps = 3.000000) [00:26:06 -319423.615937] FAST spr round 1 (radius: 25) [00:31:44 -288114.638657] FAST spr round 2 (radius: 25) [00:35:47 -287142.931571] FAST spr round 3 (radius: 25) [00:39:10 -287052.507447] FAST spr round 4 (radius: 25) [00:42:09 -287038.388190] FAST spr round 5 (radius: 25) [00:44:57 -287033.703252] FAST spr round 6 (radius: 25) [00:47:41 -287033.703239] Model parameter optimization (eps = 1.000000) [00:47:53 -287033.117120] SLOW spr round 1 (radius: 5) [00:52:01 -286966.307457] SLOW spr round 2 (radius: 5) [00:55:55 -286955.659335] SLOW spr round 3 (radius: 5) [00:59:37 -286953.410702] SLOW spr round 4 (radius: 5) [01:03:14 -286953.410655] SLOW spr round 5 (radius: 10) [01:07:02 -286950.874301] SLOW spr round 6 (radius: 5) [01:11:40 -286950.873835] SLOW spr round 7 (radius: 10) [01:15:58 -286950.665389] SLOW spr round 8 (radius: 5) [01:20:31 -286948.846280] SLOW spr round 9 (radius: 5) [01:24:31 -286948.846169] SLOW spr round 10 (radius: 10) [01:28:26 -286948.846168] SLOW spr round 11 (radius: 15) [01:34:54 -286948.608503] SLOW spr round 12 (radius: 5) [01:39:48 -286948.608502] SLOW spr round 13 (radius: 10) [01:44:22 -286948.608502] SLOW spr round 14 (radius: 15) [01:46:30] [worker #1] ML tree search #2, logLikelihood: -286915.157411 [01:50:35 -286948.608502] SLOW spr round 15 (radius: 20) [02:00:46 -286948.608502] SLOW spr round 16 (radius: 25) [02:11:53] [worker #2] ML tree search #3, logLikelihood: -286932.567639 [02:13:26 -286948.608502] Model parameter optimization (eps = 0.100000) [02:13:41] [worker #0] ML tree search #1, logLikelihood: -286948.443501 [02:13:41 -847686.935192] Initial branch length optimization [02:13:47 -739719.661176] Model parameter optimization (eps = 10.000000) [02:15:07 -737074.955457] AUTODETECT spr round 1 (radius: 5) [02:19:00 -536226.125250] AUTODETECT spr round 2 (radius: 10) [02:23:16 -413200.645036] AUTODETECT spr round 3 (radius: 15) [02:28:02 -339480.513756] AUTODETECT spr round 4 (radius: 20) [02:33:34 -323995.267546] AUTODETECT spr round 5 (radius: 25) [02:39:50 -323146.863046] SPR radius for FAST iterations: 25 (autodetect) [02:39:50 -323146.863046] Model parameter optimization (eps = 3.000000) [02:40:19 -323112.564325] FAST spr round 1 (radius: 25) [02:46:00 -288358.021534] FAST spr round 2 (radius: 25) [02:50:05 -287121.468207] FAST spr round 3 (radius: 25) [02:53:41 -287023.237117] FAST spr round 4 (radius: 25) [02:56:47 -287012.623647] FAST spr round 5 (radius: 25) [02:59:38 -287011.918339] FAST spr round 6 (radius: 25) [03:02:23 -287011.918180] Model parameter optimization (eps = 1.000000) [03:02:47 -286997.637611] SLOW spr round 1 (radius: 5) [03:06:57 -286921.993519] SLOW spr round 2 (radius: 5) [03:10:45 -286915.533533] SLOW spr round 3 (radius: 5) [03:14:24 -286915.530359] SLOW spr round 4 (radius: 10) [03:18:12 -286915.135845] SLOW spr round 5 (radius: 5) [03:22:52 -286914.494073] SLOW spr round 6 (radius: 5) [03:26:57 -286914.480406] SLOW spr round 7 (radius: 10) [03:30:53 -286914.480273] SLOW spr round 8 (radius: 15) [03:37:11 -286914.022444] SLOW spr round 9 (radius: 5) [03:42:07 -286914.022439] SLOW spr round 10 (radius: 10) [03:46:40 -286914.022438] SLOW spr round 11 (radius: 15) [03:49:36] [worker #1] ML tree search #5, logLikelihood: -286925.851306 [03:52:43 -286914.022438] SLOW spr round 12 (radius: 20) [04:02:36 -286914.022437] SLOW spr round 13 (radius: 25) [04:15:19 -286914.022437] Model parameter optimization (eps = 0.100000) [04:15:32] [worker #0] ML tree search #4, logLikelihood: -286913.887563 [04:15:32 -846779.605928] Initial branch length optimization [04:15:41 -740060.471025] Model parameter optimization (eps = 10.000000) [04:16:42 -737413.794228] AUTODETECT spr round 1 (radius: 5) [04:20:40 -535921.393478] AUTODETECT spr round 2 (radius: 10) [04:24:56 -402744.075728] AUTODETECT spr round 3 (radius: 15) [04:29:26 -341743.648428] AUTODETECT spr round 4 (radius: 20) [04:34:35 -323844.498778] AUTODETECT spr round 5 (radius: 25) [04:35:32] [worker #2] ML tree search #6, logLikelihood: -286919.877609 [04:41:00 -321322.465368] SPR radius for FAST iterations: 25 (autodetect) [04:41:00 -321322.465368] Model parameter optimization (eps = 3.000000) [04:41:39 -321274.482234] FAST spr round 1 (radius: 25) [04:47:11 -289244.100859] FAST spr round 2 (radius: 25) [04:51:23 -287212.262655] FAST spr round 3 (radius: 25) [04:54:55 -287064.492427] FAST spr round 4 (radius: 25) [04:58:04 -287035.706180] FAST spr round 5 (radius: 25) [05:00:53 -287035.705627] Model parameter optimization (eps = 1.000000) [05:01:19 -287022.799889] SLOW spr round 1 (radius: 5) [05:05:29 -286938.053099] SLOW spr round 2 (radius: 5) [05:09:23 -286930.557084] SLOW spr round 3 (radius: 5) [05:13:04 -286930.474956] SLOW spr round 4 (radius: 10) [05:16:55 -286922.159152] SLOW spr round 5 (radius: 5) [05:21:36 -286922.159036] SLOW spr round 6 (radius: 10) [05:25:53 -286922.159036] SLOW spr round 7 (radius: 15) [05:32:13 -286921.845831] SLOW spr round 8 (radius: 5) [05:34:35] [worker #1] ML tree search #8, logLikelihood: -286913.190753 [05:37:10 -286921.845828] SLOW spr round 9 (radius: 10) [05:41:44 -286921.845828] SLOW spr round 10 (radius: 15) [05:48:00 -286921.845828] SLOW spr round 11 (radius: 20) [05:58:24 -286921.845828] SLOW spr round 12 (radius: 25) [06:11:12 -286921.845827] Model parameter optimization (eps = 0.100000) [06:11:28] [worker #0] ML tree search #7, logLikelihood: -286921.296933 [06:11:28 -850759.411392] Initial branch length optimization [06:11:35 -743101.066624] Model parameter optimization (eps = 10.000000) [06:12:37 -740059.692262] AUTODETECT spr round 1 (radius: 5) [06:16:34 -532693.879810] AUTODETECT spr round 2 (radius: 10) [06:20:57 -398422.646836] AUTODETECT spr round 3 (radius: 15) [06:22:53] [worker #2] ML tree search #9, logLikelihood: -286931.437696 [06:25:47 -335528.962874] AUTODETECT spr round 4 (radius: 20) [06:30:58 -320351.432413] AUTODETECT spr round 5 (radius: 25) [06:36:51 -318604.653737] SPR radius for FAST iterations: 25 (autodetect) [06:36:51 -318604.653737] Model parameter optimization (eps = 3.000000) [06:37:23 -318581.969019] FAST spr round 1 (radius: 25) [06:42:51 -288321.860264] FAST spr round 2 (radius: 25) [06:46:44 -287119.000560] FAST spr round 3 (radius: 25) [06:50:11 -287063.843652] FAST spr round 4 (radius: 25) [06:53:15 -287052.929104] FAST spr round 5 (radius: 25) [06:56:08 -287045.458842] FAST spr round 6 (radius: 25) [06:58:53 -287045.458784] Model parameter optimization (eps = 1.000000) [06:59:11 -287043.838645] SLOW spr round 1 (radius: 5) [07:03:18 -286961.201267] SLOW spr round 2 (radius: 5) [07:07:16 -286948.907431] SLOW spr round 3 (radius: 5) [07:11:03 -286946.085387] SLOW spr round 4 (radius: 5) [07:14:42 -286946.085051] SLOW spr round 5 (radius: 10) [07:18:33 -286943.710979] SLOW spr round 6 (radius: 5) [07:23:15 -286942.663879] SLOW spr round 7 (radius: 5) [07:27:26 -286937.946215] SLOW spr round 8 (radius: 5) [07:31:15 -286937.943731] SLOW spr round 9 (radius: 10) [07:35:10 -286931.496433] SLOW spr round 10 (radius: 5) [07:37:37] [worker #1] ML tree search #11, logLikelihood: -286914.961942 [07:39:50 -286931.073044] SLOW spr round 11 (radius: 5) [07:43:55 -286931.071706] SLOW spr round 12 (radius: 10) [07:47:55 -286930.775763] SLOW spr round 13 (radius: 5) [07:52:32 -286930.775689] SLOW spr round 14 (radius: 10) [07:56:49 -286930.775687] SLOW spr round 15 (radius: 15) [08:03:13 -286930.524808] SLOW spr round 16 (radius: 5) [08:08:09 -286930.524808] SLOW spr round 17 (radius: 10) [08:12:46 -286930.524808] SLOW spr round 18 (radius: 15) [08:19:02 -286930.524808] SLOW spr round 19 (radius: 20) [08:24:21] [worker #2] ML tree search #12, logLikelihood: -286921.165438 [08:29:33 -286930.524808] SLOW spr round 20 (radius: 25) [08:42:27 -286930.524808] Model parameter optimization (eps = 0.100000) [08:42:39] [worker #0] ML tree search #10, logLikelihood: -286930.363917 [08:42:39 -847643.658090] Initial branch length optimization [08:42:49 -740400.984640] Model parameter optimization (eps = 10.000000) [08:44:42 -737944.522239] AUTODETECT spr round 1 (radius: 5) [08:48:41 -537616.205038] AUTODETECT spr round 2 (radius: 10) [08:53:05 -390143.193117] AUTODETECT spr round 3 (radius: 15) [08:57:46 -340196.284946] AUTODETECT spr round 4 (radius: 20) [09:03:13 -320191.779406] AUTODETECT spr round 5 (radius: 25) [09:08:50 -318296.372432] SPR radius for FAST iterations: 25 (autodetect) [09:08:50 -318296.372432] Model parameter optimization (eps = 3.000000) [09:09:19 -318250.678881] FAST spr round 1 (radius: 25) [09:14:53 -288269.403369] FAST spr round 2 (radius: 25) [09:18:55 -287182.692211] FAST spr round 3 (radius: 25) [09:22:28 -287063.261896] FAST spr round 4 (radius: 25) [09:25:36 -287039.543637] FAST spr round 5 (radius: 25) [09:28:37 -287027.365504] FAST spr round 6 (radius: 25) [09:29:29] [worker #1] ML tree search #14, logLikelihood: -286932.383959 [09:31:22 -287027.365431] Model parameter optimization (eps = 1.000000) [09:31:46 -287019.135725] SLOW spr round 1 (radius: 5) [09:35:48 -286941.550532] SLOW spr round 2 (radius: 5) [09:39:38 -286932.951541] SLOW spr round 3 (radius: 5) [09:43:20 -286927.995279] SLOW spr round 4 (radius: 5) [09:46:51 -286927.995257] SLOW spr round 5 (radius: 10) [09:50:35 -286927.779550] SLOW spr round 6 (radius: 5) [09:55:12 -286927.094848] SLOW spr round 7 (radius: 5) [09:59:14 -286927.094811] SLOW spr round 8 (radius: 10) [10:03:07 -286927.094810] SLOW spr round 9 (radius: 15) [10:09:28 -286926.790095] SLOW spr round 10 (radius: 5) [10:13:26] [worker #2] ML tree search #15, logLikelihood: -286938.439523 [10:14:21 -286926.790092] SLOW spr round 11 (radius: 10) [10:18:51 -286926.790092] SLOW spr round 12 (radius: 15) [10:24:57 -286926.790092] SLOW spr round 13 (radius: 20) [10:34:52 -286926.790092] SLOW spr round 14 (radius: 25) [10:47:30 -286926.790092] Model parameter optimization (eps = 0.100000) [10:47:49] [worker #0] ML tree search #13, logLikelihood: -286926.054653 [10:47:49 -841179.964539] Initial branch length optimization [10:47:56 -738206.497886] Model parameter optimization (eps = 10.000000) [10:48:54 -735275.659011] AUTODETECT spr round 1 (radius: 5) [10:52:48 -526610.840107] AUTODETECT spr round 2 (radius: 10) [10:56:53 -394234.967237] AUTODETECT spr round 3 (radius: 15) [11:01:42 -344009.632981] AUTODETECT spr round 4 (radius: 20) [11:06:35 -325660.030683] AUTODETECT spr round 5 (radius: 25) [11:12:38 -324920.880500] SPR radius for FAST iterations: 25 (autodetect) [11:12:38 -324920.880500] Model parameter optimization (eps = 3.000000) [11:13:09 -324833.720438] FAST spr round 1 (radius: 25) [11:18:40 -288411.957832] FAST spr round 2 (radius: 25) [11:22:39 -287128.085615] FAST spr round 3 (radius: 25) [11:26:09 -287023.514434] FAST spr round 4 (radius: 25) [11:29:13 -287008.752940] FAST spr round 5 (radius: 25) [11:30:51] [worker #1] ML tree search #17, logLikelihood: -286931.760219 [11:32:02 -287006.467844] FAST spr round 6 (radius: 25) [11:34:47 -287006.467430] Model parameter optimization (eps = 1.000000) [11:35:08 -287002.143458] SLOW spr round 1 (radius: 5) [11:39:07 -286931.871088] SLOW spr round 2 (radius: 5) [11:42:53 -286929.691249] SLOW spr round 3 (radius: 5) [11:46:32 -286929.331632] SLOW spr round 4 (radius: 5) [11:50:08 -286929.331602] SLOW spr round 5 (radius: 10) [11:53:57 -286928.344058] SLOW spr round 6 (radius: 5) [11:58:33 -286928.344054] SLOW spr round 7 (radius: 10) [12:02:49 -286928.344054] SLOW spr round 8 (radius: 15) [12:09:01 -286925.873047] SLOW spr round 9 (radius: 5) [12:13:56 -286925.872858] SLOW spr round 10 (radius: 10) [12:16:48] [worker #2] ML tree search #18, logLikelihood: -286916.743207 [12:18:29 -286925.006779] SLOW spr round 11 (radius: 5) [12:23:06 -286917.440950] SLOW spr round 12 (radius: 5) [12:27:05 -286916.592034] SLOW spr round 13 (radius: 5) [12:30:48 -286916.591052] SLOW spr round 14 (radius: 10) [12:34:38 -286916.358319] SLOW spr round 15 (radius: 5) [12:39:05 -286916.357615] SLOW spr round 16 (radius: 10) [12:43:19 -286916.357598] SLOW spr round 17 (radius: 15) [12:49:25 -286916.357598] SLOW spr round 18 (radius: 20) [12:59:09 -286916.357598] SLOW spr round 19 (radius: 25) [13:11:36 -286916.357598] Model parameter optimization (eps = 0.100000) [13:11:51] [worker #0] ML tree search #16, logLikelihood: -286916.018500 [13:11:51 -848988.641614] Initial branch length optimization [13:12:01 -741063.385860] Model parameter optimization (eps = 10.000000) [13:13:17 -738419.348390] AUTODETECT spr round 1 (radius: 5) [13:17:09 -525055.517898] AUTODETECT spr round 2 (radius: 10) [13:21:17 -386685.436876] AUTODETECT spr round 3 (radius: 15) [13:26:00 -334192.765570] AUTODETECT spr round 4 (radius: 20) [13:28:27] [worker #1] ML tree search #20, logLikelihood: -286928.219222 [13:31:56 -321172.848669] AUTODETECT spr round 5 (radius: 25) [13:39:37 -321032.568490] SPR radius for FAST iterations: 25 (autodetect) [13:39:37 -321032.568490] Model parameter optimization (eps = 3.000000) [13:40:03 -320986.937300] FAST spr round 1 (radius: 25) [13:45:35 -288500.008376] FAST spr round 2 (radius: 25) [13:49:40 -287138.082525] FAST spr round 3 (radius: 25) [13:53:04 -287018.932266] FAST spr round 4 (radius: 25) [13:55:57 -287018.932064] Model parameter optimization (eps = 1.000000) [13:56:23 -287011.561592] SLOW spr round 1 (radius: 5) [14:00:32 -286937.123978] SLOW spr round 2 (radius: 5) [14:04:24 -286932.689273] SLOW spr round 3 (radius: 5) [14:08:03 -286932.688804] SLOW spr round 4 (radius: 10) [14:11:48 -286932.688786] SLOW spr round 5 (radius: 15) [14:18:11 -286932.192144] SLOW spr round 6 (radius: 5) [14:23:03 -286932.074698] SLOW spr round 7 (radius: 5) [14:27:13 -286932.072259] SLOW spr round 8 (radius: 10) [14:31:11 -286932.071894] SLOW spr round 9 (radius: 15) [14:37:21 -286932.071840] SLOW spr round 10 (radius: 20) [14:47:07 -286932.071832] SLOW spr round 11 (radius: 25) [14:59:45 -286932.071831] Model parameter optimization (eps = 0.100000) [15:00:09] [worker #0] ML tree search #19, logLikelihood: -286931.586408 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.165228,0.431227) (0.211779,0.446727) (0.264608,0.764323) (0.358385,1.763176) 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: -286913.190753 AIC score: 577836.381505 / AICc score: 8621896.381505 / BIC score: 586407.279358 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=531). 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/Q01518/3_mltree/Q01518.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/3_mltree/Q01518.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/3_mltree/Q01518.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q01518/3_mltree/Q01518.raxml.log Analysis started: 02-Jul-2021 01:26:17 / finished: 02-Jul-2021 16:26:27 Elapsed time: 54009.480 seconds Consumed energy: 5054.159 Wh (= 25 km in an electric car, or 126 km with an e-scooter!)