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 03-Jul-2021 00:21:42 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P38117/2_msa/P38117_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P38117/3_mltree/P38117 --seed 2 --threads 5 --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 (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P38117/2_msa/P38117_trimmed_msa.fasta [00:00:00] Loaded alignment with 918 taxa and 266 sites WARNING: Sequences tr_B4R0S9_B4R0S9_DROSI_7240 and tr_Q0KHZ6_Q0KHZ6_DROME_7227 are exactly identical! WARNING: Sequences tr_B4R0S9_B4R0S9_DROSI_7240 and tr_B4HZF2_B4HZF2_DROSE_7238 are exactly identical! WARNING: Sequences tr_J3K7C1_J3K7C1_COCIM_246410 and tr_E9CUK6_E9CUK6_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3K7C1_J3K7C1_COCIM_246410 and tr_A0A0J6Y3C6_A0A0J6Y3C6_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QG87_B6QG87_TALMQ_441960 and tr_A0A093UVR9_A0A093UVR9_TALMA_1077442 are exactly identical! WARNING: Sequences tr_G3R168_G3R168_GORGO_9595 and tr_A0A2I3S0S3_A0A2I3S0S3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R168_G3R168_GORGO_9595 and tr_A0A2K5NIQ8_A0A2K5NIQ8_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q5RFK0_ETFB_PONAB_9601 and tr_A0A0D9S566_A0A0D9S566_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G2WS14_G2WS14_VERDV_498257 and tr_A0A0G4KGH2_A0A0G4KGH2_9PEZI_100787 are exactly identical! WARNING: Sequences tr_B8NDC4_B8NDC4_ASPFN_332952 and tr_A0A0F0IBY3_A0A0F0IBY3_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8NDC4_B8NDC4_ASPFN_332952 and tr_A0A1S9DA30_A0A1S9DA30_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UNV4_A0A179UNV4_BLAGS_559298 and tr_C5GUC2_C5GUC2_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9FK80_F9FK80_FUSOF_660025 and tr_A0A0D2XQK4_A0A0D2XQK4_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FK80_F9FK80_FUSOF_660025 and tr_A0A2H3TA08_A0A2H3TA08_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FK80_F9FK80_FUSOF_660025 and tr_A0A2H3HW30_A0A2H3HW30_FUSOX_327505 are exactly identical! WARNING: Sequences tr_C6HSQ0_C6HSQ0_AJECH_544712 and tr_F0UEW2_F0UEW2_AJEC8_544711 are exactly identical! WARNING: Sequences tr_J4UUS5_J4UUS5_BEAB2_655819 and tr_A0A0A2W5T7_A0A0A2W5T7_BEABA_1245745 are exactly identical! WARNING: Sequences tr_G9P2J3_G9P2J3_HYPAI_452589 and tr_A0A0W7VP17_A0A0W7VP17_9HYPO_398673 are exactly identical! WARNING: Sequences tr_A0A0E0FL67_A0A0E0FL67_ORYNI_4536 and sp_A2XQV4_ETFB_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0FL67_A0A0E0FL67_ORYNI_4536 and tr_A0A0E0P5I7_A0A0E0P5I7_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0J9XNB9_A0A0J9XNB9_BRUMA_6279 and tr_A0A0R3QK36_A0A0R3QK36_9BILA_42155 are exactly identical! WARNING: Sequences tr_A2R9B0_A2R9B0_ASPNC_425011 and tr_G3Y4G7_G3Y4G7_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2R9B0_A2R9B0_ASPNC_425011 and tr_A0A319A4U3_A0A319A4U3_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XSA8_G7XSA8_ASPKW_1033177 and tr_A0A146FZZ3_A0A146FZZ3_9EURO_1069201 are exactly identical! WARNING: Sequences tr_F4NTC5_F4NTC5_BATDJ_684364 and tr_A0A177WBY6_A0A177WBY6_BATDE_403673 are exactly identical! WARNING: Sequences tr_F2SPM0_F2SPM0_TRIRC_559305 and tr_A0A178F4U0_A0A178F4U0_TRIRU_5551 are exactly identical! WARNING: Sequences tr_B3RU85_B3RU85_TRIAD_10228 and tr_A0A369SGJ2_A0A369SGJ2_9METZ_287889 are exactly identical! WARNING: Sequences tr_F2PQ30_F2PQ30_TRIEC_559882 and tr_A0A059JCE4_A0A059JCE4_9EURO_1215338 are exactly identical! WARNING: Sequences tr_S0DP67_S0DP67_GIBF5_1279085 and tr_A0A365N7B2_A0A365N7B2_GIBIN_948311 are exactly identical! WARNING: Sequences tr_V2X8Z8_V2X8Z8_MONRO_1381753 and tr_A0A0W0FF48_A0A0W0FF48_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2RH96_W2RH96_PHYPN_761204 and tr_A0A0W8BWW9_A0A0W8BWW9_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A010RES3_A0A010RES3_9PEZI_1445577 and tr_A0A135UYY5_A0A135UYY5_9PEZI_1209931 are exactly identical! WARNING: Sequences tr_A0A010RES3_A0A010RES3_9PEZI_1445577 and tr_A0A1G4B1L8_A0A1G4B1L8_9PEZI_1209926 are exactly identical! WARNING: Sequences tr_A0A015JKT0_A0A015JKT0_9GLOM_1432141 and tr_A0A2I1EL55_A0A2I1EL55_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015JKT0_A0A015JKT0_9GLOM_1432141 and tr_A0A2H5TY25_A0A2H5TY25_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A094H878_A0A094H878_9PEZI_1420912 and tr_A0A1B8GNB1_A0A1B8GNB1_9PEZI_342668 are exactly identical! WARNING: Sequences tr_V4RZT8_V4RZT8_9ROSI_85681 and tr_A0A2H5PJP1_A0A2H5PJP1_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0F9XN48_A0A0F9XN48_TRIHA_5544 and tr_A0A2T4AVS9_A0A2T4AVS9_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A0F8XSN3_A0A0F8XSN3_9EURO_308745 and tr_A0A2T5M8D5_A0A2T5M8D5_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0A1NBS9_A0A0A1NBS9_9FUNG_58291 and tr_A0A367JYE8_A0A367JYE8_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0L9VBN7_A0A0L9VBN7_PHAAN_3914 and tr_A0A1S3UYF3_A0A1S3UYF3_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A0G4PH72_A0A0G4PH72_PENCA_1429867 and tr_A0A1V6P4C3_A0A1V6P4C3_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A0V1CML0_A0A0V1CML0_TRIBR_45882 and tr_A0A0V0WXV1_A0A0V0WXV1_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CML0_A0A0V1CML0_TRIBR_45882 and tr_A0A0V0VR88_A0A0V0VR88_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CML0_A0A0V1CML0_TRIBR_45882 and tr_A0A0V1KY06_A0A0V1KY06_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CML0_A0A0V1CML0_TRIBR_45882 and tr_A0A0V1P6R3_A0A0V1P6R3_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CML0_A0A0V1CML0_TRIBR_45882 and tr_A0A0V0TLN5_A0A0V0TLN5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A117E2D6_A0A117E2D6_ASPNG_5061 and tr_A0A1L9N5H4_A0A1L9N5H4_ASPTU_767770 are exactly identical! WARNING: Sequences tr_I1RYU6_I1RYU6_GIBZE_229533 and tr_A0A2T4GEG6_A0A2T4GEG6_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A1S3Z028_A0A1S3Z028_TOBAC_4097 and tr_A0A1U7W545_A0A1U7W545_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1B8ED17_A0A1B8ED17_9PEZI_1524831 and tr_A0A1B8FBZ3_A0A1B8FBZ3_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_A0A1V8V3G8_A0A1V8V3G8_9PEZI_1974281 and tr_A0A1V8SFK4_A0A1V8SFK4_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A2H3CA38_A0A2H3CA38_9AGAR_1076256 and tr_A0A284QLB7_A0A284QLB7_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2G5HQ82_A0A2G5HQ82_CERBT_122368 and tr_A0A2S6BU10_A0A2S6BU10_9PEZI_357750 are exactly identical! WARNING: Duplicate sequences found: 54 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/P38117/3_mltree/P38117.raxml.reduced.phy Alignment comprises 1 partitions and 266 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 266 / 266 Gaps: 7.99 % Invariant sites: 0.75 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P38117/3_mltree/P38117.raxml.rba Parallelization scheme autoconfig: 5 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 918 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 266 / 21280 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -282073.560659] Initial branch length optimization [00:00:04 -246329.616498] Model parameter optimization (eps = 10.000000) [00:00:52 -245298.803119] AUTODETECT spr round 1 (radius: 5) [00:03:49 -176750.856098] AUTODETECT spr round 2 (radius: 10) [00:07:04 -126368.083849] AUTODETECT spr round 3 (radius: 15) [00:10:36 -106081.051992] AUTODETECT spr round 4 (radius: 20) [00:15:05 -101269.989405] AUTODETECT spr round 5 (radius: 25) [00:20:19 -101232.502235] SPR radius for FAST iterations: 25 (autodetect) [00:20:19 -101232.502235] Model parameter optimization (eps = 3.000000) [00:20:44 -101177.993058] FAST spr round 1 (radius: 25) [00:24:08 -90495.218799] FAST spr round 2 (radius: 25) [00:26:40 -90076.917370] FAST spr round 3 (radius: 25) [00:28:51 -90029.967056] FAST spr round 4 (radius: 25) [00:30:48 -90026.829445] FAST spr round 5 (radius: 25) [00:32:39 -90026.829014] Model parameter optimization (eps = 1.000000) [00:32:55 -90026.168651] SLOW spr round 1 (radius: 5) [00:35:48 -90004.272187] SLOW spr round 2 (radius: 5) [00:38:28 -90000.839164] SLOW spr round 3 (radius: 5) [00:41:04 -90000.583759] SLOW spr round 4 (radius: 5) [00:43:36 -90000.583669] SLOW spr round 5 (radius: 10) [00:46:15 -90000.295531] SLOW spr round 6 (radius: 5) [00:49:38 -90000.295530] SLOW spr round 7 (radius: 10) [00:52:36 -90000.295529] SLOW spr round 8 (radius: 15) [00:56:49 -89997.554062] SLOW spr round 9 (radius: 5) [01:00:22 -89997.554062] SLOW spr round 10 (radius: 10) [01:03:31 -89997.554062] SLOW spr round 11 (radius: 15) [01:07:40 -89997.554062] SLOW spr round 12 (radius: 20) [01:14:52 -89997.534495] SLOW spr round 13 (radius: 25) [01:24:14 -89997.534363] Model parameter optimization (eps = 0.100000) [01:24:21] [worker #0] ML tree search #1, logLikelihood: -89997.525373 [01:24:21 -283397.967422] Initial branch length optimization [01:24:26 -246893.421136] Model parameter optimization (eps = 10.000000) [01:25:13 -245870.101761] AUTODETECT spr round 1 (radius: 5) [01:25:56] [worker #2] ML tree search #3, logLikelihood: -89985.720330 [01:28:12 -178818.115718] AUTODETECT spr round 2 (radius: 10) [01:29:26] [worker #1] ML tree search #2, logLikelihood: -89980.828864 [01:31:25 -132092.246515] AUTODETECT spr round 3 (radius: 15) [01:34:58 -110131.037303] AUTODETECT spr round 4 (radius: 20) [01:39:34 -103598.674673] AUTODETECT spr round 5 (radius: 25) [01:45:19 -102773.522780] SPR radius for FAST iterations: 25 (autodetect) [01:45:19 -102773.522780] Model parameter optimization (eps = 3.000000) [01:45:42 -102712.768337] FAST spr round 1 (radius: 25) [01:47:43] [worker #3] ML tree search #4, logLikelihood: -90014.496848 [01:49:11 -90782.569960] FAST spr round 2 (radius: 25) [01:51:46 -90109.762456] FAST spr round 3 (radius: 25) [01:54:04 -90053.320924] FAST spr round 4 (radius: 25) [01:56:02 -90051.707749] FAST spr round 5 (radius: 25) [01:57:55 -90051.707179] Model parameter optimization (eps = 1.000000) [01:58:07 -90050.019474] SLOW spr round 1 (radius: 5) [02:00:28] [worker #4] ML tree search #5, logLikelihood: -90026.799775 [02:01:01 -90024.484924] SLOW spr round 2 (radius: 5) [02:03:47 -90018.253382] SLOW spr round 3 (radius: 5) [02:06:22 -90018.252910] SLOW spr round 4 (radius: 10) [02:09:03 -90005.400352] SLOW spr round 5 (radius: 5) [02:12:32 -89997.442530] SLOW spr round 6 (radius: 5) [02:15:31 -89996.454481] SLOW spr round 7 (radius: 5) [02:18:13 -89996.454433] SLOW spr round 8 (radius: 10) [02:20:54 -89996.454433] SLOW spr round 9 (radius: 15) [02:25:20 -89996.454433] SLOW spr round 10 (radius: 20) [02:32:25 -89996.454433] SLOW spr round 11 (radius: 25) [02:42:11 -89996.454433] Model parameter optimization (eps = 0.100000) [02:42:21] [worker #0] ML tree search #6, logLikelihood: -89996.421783 [02:42:21 -281464.542277] Initial branch length optimization [02:42:27 -245284.973566] Model parameter optimization (eps = 10.000000) [02:43:14 -244310.085321] AUTODETECT spr round 1 (radius: 5) [02:46:12 -179415.594128] AUTODETECT spr round 2 (radius: 10) [02:49:28 -129524.649168] AUTODETECT spr round 3 (radius: 15) [02:53:08 -104171.353641] AUTODETECT spr round 4 (radius: 20) [02:55:41] [worker #2] ML tree search #8, logLikelihood: -90003.938716 [02:57:05 -101957.023581] AUTODETECT spr round 5 (radius: 25) [03:01:28 -101764.584892] SPR radius for FAST iterations: 25 (autodetect) [03:01:28 -101764.584892] Model parameter optimization (eps = 3.000000) [03:01:54 -101713.632958] FAST spr round 1 (radius: 25) [03:05:23 -90568.513067] FAST spr round 2 (radius: 25) [03:08:02 -90163.258009] FAST spr round 3 (radius: 25) [03:10:23 -90078.789715] FAST spr round 4 (radius: 25) [03:12:21 -90070.338164] FAST spr round 5 (radius: 25) [03:14:13 -90070.338125] Model parameter optimization (eps = 1.000000) [03:14:30 -90064.855864] SLOW spr round 1 (radius: 5) [03:17:23 -90036.464527] SLOW spr round 2 (radius: 5) [03:18:55] [worker #1] ML tree search #7, logLikelihood: -90004.180397 [03:20:09 -90028.128081] SLOW spr round 3 (radius: 5) [03:22:44 -90027.065063] SLOW spr round 4 (radius: 5) [03:25:16 -90027.065060] SLOW spr round 5 (radius: 10) [03:27:54 -90025.682808] SLOW spr round 6 (radius: 5) [03:30:43] [worker #3] ML tree search #9, logLikelihood: -90000.733601 [03:31:15 -90025.682588] SLOW spr round 7 (radius: 10) [03:34:11 -90024.706068] SLOW spr round 8 (radius: 5) [03:34:44] [worker #4] ML tree search #10, logLikelihood: -90002.387523 [03:37:29 -90024.554155] SLOW spr round 9 (radius: 5) [03:40:22 -90024.554121] SLOW spr round 10 (radius: 10) [03:43:05 -90023.770609] SLOW spr round 11 (radius: 5) [03:46:26 -90023.766479] SLOW spr round 12 (radius: 10) [03:49:21 -90023.571299] SLOW spr round 13 (radius: 5) [03:52:39 -90023.570505] SLOW spr round 14 (radius: 10) [03:55:34 -90023.570430] SLOW spr round 15 (radius: 15) [03:59:45 -90023.340096] SLOW spr round 16 (radius: 5) [04:03:16 -90023.340081] SLOW spr round 17 (radius: 10) [04:06:22 -90023.340080] SLOW spr round 18 (radius: 15) [04:10:30 -90023.340080] SLOW spr round 19 (radius: 20) [04:17:23 -90023.340079] SLOW spr round 20 (radius: 25) [04:26:18 -90021.596599] SLOW spr round 21 (radius: 5) [04:29:51 -90021.596332] SLOW spr round 22 (radius: 10) [04:33:02 -90021.596324] SLOW spr round 23 (radius: 15) [04:37:07 -90021.410237] SLOW spr round 24 (radius: 5) [04:39:20] [worker #2] ML tree search #13, logLikelihood: -90002.104887 [04:40:42 -90018.853638] SLOW spr round 25 (radius: 5) [04:42:44] [worker #1] ML tree search #12, logLikelihood: -90015.348666 [04:43:44 -90018.853281] SLOW spr round 26 (radius: 10) [04:46:29 -90018.853254] SLOW spr round 27 (radius: 15) [04:50:44 -90016.567904] SLOW spr round 28 (radius: 5) [04:54:15 -90016.567619] SLOW spr round 29 (radius: 10) [04:57:20 -90016.567613] SLOW spr round 30 (radius: 15) [05:01:27 -90016.567612] SLOW spr round 31 (radius: 20) [05:08:19] [worker #3] ML tree search #14, logLikelihood: -90003.500667 [05:08:23 -90016.567612] SLOW spr round 32 (radius: 25) [05:17:30 -90016.567612] Model parameter optimization (eps = 0.100000) [05:17:41] [worker #0] ML tree search #11, logLikelihood: -90016.360151 [05:17:41 -281692.166612] Initial branch length optimization [05:17:49 -246349.902716] Model parameter optimization (eps = 10.000000) [05:18:40 -245359.386109] AUTODETECT spr round 1 (radius: 5) [05:21:52 -177308.227513] AUTODETECT spr round 2 (radius: 10) [05:25:21 -122025.445525] AUTODETECT spr round 3 (radius: 15) [05:28:59 -103716.192827] AUTODETECT spr round 4 (radius: 20) [05:33:38 -100019.850587] AUTODETECT spr round 5 (radius: 25) [05:35:56] [worker #4] ML tree search #15, logLikelihood: -89984.414105 [05:38:36 -99559.366051] SPR radius for FAST iterations: 25 (autodetect) [05:38:36 -99559.366051] Model parameter optimization (eps = 3.000000) [05:39:01 -99497.380953] FAST spr round 1 (radius: 25) [05:42:36 -90604.000507] FAST spr round 2 (radius: 25) [05:45:25 -90145.323191] FAST spr round 3 (radius: 25) [05:47:57 -90084.101985] FAST spr round 4 (radius: 25) [05:50:02 -90084.098681] Model parameter optimization (eps = 1.000000) [05:50:16 -90083.321906] SLOW spr round 1 (radius: 5) [05:53:39 -90038.588584] SLOW spr round 2 (radius: 5) [05:56:49 -90025.790167] SLOW spr round 3 (radius: 5) [05:59:38 -90025.621575] SLOW spr round 4 (radius: 5) [06:02:24 -90025.621523] SLOW spr round 5 (radius: 10) [06:05:16 -90024.255724] SLOW spr round 6 (radius: 5) [06:08:55 -90021.299150] SLOW spr round 7 (radius: 5) [06:12:10 -90019.502491] SLOW spr round 8 (radius: 5) [06:15:08 -90019.021517] SLOW spr round 9 (radius: 5) [06:17:59 -90019.021488] SLOW spr round 10 (radius: 10) [06:20:53 -90018.559916] SLOW spr round 11 (radius: 5) [06:24:35 -90018.429296] SLOW spr round 12 (radius: 5) [06:27:46 -90018.428722] SLOW spr round 13 (radius: 10) [06:30:44 -90018.428717] SLOW spr round 14 (radius: 15) [06:35:25 -90017.111386] SLOW spr round 15 (radius: 5) [06:39:15 -90017.111040] SLOW spr round 16 (radius: 10) [06:40:29] [worker #3] ML tree search #19, logLikelihood: -89995.282296 [06:42:38 -90017.111037] SLOW spr round 17 (radius: 15) [06:47:02 -90017.111037] SLOW spr round 18 (radius: 20) [06:53:23] [worker #2] ML tree search #18, logLikelihood: -89989.075259 [06:53:48 -90017.111037] SLOW spr round 19 (radius: 25) [06:58:01] [worker #1] ML tree search #17, logLikelihood: -89992.706848 [07:02:13 -90017.111037] Model parameter optimization (eps = 0.100000) [07:02:24] [worker #0] ML tree search #16, logLikelihood: -90017.068082 [07:04:29] [worker #4] ML tree search #20, logLikelihood: -90003.609159 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.306673,0.368258) (0.318384,0.654135) (0.193938,1.190769) (0.181006,2.474307) 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: -89980.828864 AIC score: 183639.657728 / AICc score: 6951159.657728 / BIC score: 190229.707440 Free parameters (model + branch lengths): 1839 WARNING: Number of free parameters (K=1839) is larger than alignment size (n=266). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 82 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P38117/3_mltree/P38117.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P38117/3_mltree/P38117.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P38117/3_mltree/P38117.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P38117/3_mltree/P38117.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P38117/3_mltree/P38117.raxml.log Analysis started: 03-Jul-2021 00:21:42 / finished: 03-Jul-2021 07:26:12 Elapsed time: 25470.122 seconds Consumed energy: 2227.899 Wh (= 11 km in an electric car, or 56 km with an e-scooter!)