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 04-Jul-2021 01:26:20 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/E9PAV3/2_msa/E9PAV3_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/E9PAV3/3_mltree/E9PAV3 --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/E9PAV3/2_msa/E9PAV3_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 237 sites WARNING: Sequences tr_B4QDH0_B4QDH0_DROSI_7240 and tr_B4HPP3_B4HPP3_DROSE_7238 are exactly identical! WARNING: Sequences tr_B6HGW6_B6HGW6_PENRW_500485 and tr_A0A1V6YZK5_A0A1V6YZK5_PENNA_60175 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and tr_A0A2J8UHH4_A0A2J8UHH4_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and tr_I3MCS9_I3MCS9_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and tr_H0XVE8_H0XVE8_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and tr_G3SUJ8_G3SUJ8_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and tr_G3VH03_G3VH03_SARHA_9305 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and tr_K7GNZ3_K7GNZ3_PIG_9823 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and sp_Q5E9A1_NACA_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and tr_A0A2I2UG75_A0A2I2UG75_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and tr_A0A151PBM4_A0A151PBM4_ALLMI_8496 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and tr_A0A1S3ADG9_A0A1S3ADG9_ERIEU_9365 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and tr_A0A1U8CBH0_A0A1U8CBH0_MESAU_10036 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and tr_A0A2Y9DTB4_A0A2Y9DTB4_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and tr_A0A2Y9ISE6_A0A2Y9ISE6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1NUZ3_G1NUZ3_MYOLU_59463 and tr_A0A384BHD0_A0A384BHD0_URSMA_29073 are exactly identical! WARNING: Sequences sp_Q1DHR3_NACA_COCIM_246410 and tr_E9D325_E9D325_COCPS_443226 are exactly identical! WARNING: Sequences sp_Q1DHR3_NACA_COCIM_246410 and tr_A0A0J6YRD6_A0A0J6YRD6_COCIT_404692 are exactly identical! WARNING: Sequences tr_A0A2I2ZT47_A0A2I2ZT47_GORGO_9595 and tr_A0A2I3TAZ0_A0A2I3TAZ0_PANTR_9598 are exactly identical! WARNING: Sequences tr_C0NHN5_C0NHN5_AJECG_447093 and sp_A6R641_NACA_AJECN_339724 are exactly identical! WARNING: Sequences sp_Q7SI17_NACA_NEUCR_367110 and tr_G4U7F1_G4U7F1_NEUT9_510952 are exactly identical! WARNING: Sequences tr_Q28X82_Q28X82_DROPS_46245 and tr_B4H548_B4H548_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A125YY49_A0A125YY49_TOXGV_432359 and tr_A0A074SZA8_A0A074SZA8_HAMHA_99158 are exactly identical! WARNING: Sequences tr_H2RGB8_H2RGB8_PANTR_9598 and tr_A0A2R8ZCX0_A0A2R8ZCX0_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7DRP9_F7DRP9_HORSE_9796 and tr_W5PR74_W5PR74_SHEEP_9940 are exactly identical! WARNING: Sequences tr_F9FZA4_F9FZA4_FUSOF_660025 and tr_A0A0D2XHH6_A0A0D2XHH6_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FZA4_F9FZA4_FUSOF_660025 and tr_S0E551_S0E551_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9FZA4_F9FZA4_FUSOF_660025 and tr_X0D4Q5_X0D4Q5_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FZA4_F9FZA4_FUSOF_660025 and tr_A0A2H3TYE0_A0A2H3TYE0_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FZA4_F9FZA4_FUSOF_660025 and tr_A0A2K0W3J6_A0A2K0W3J6_GIBNY_42673 are exactly identical! WARNING: Sequences tr_F9FZA4_F9FZA4_FUSOF_660025 and tr_A0A365NFM0_A0A365NFM0_GIBIN_948311 are exactly identical! WARNING: Sequences tr_J4VS23_J4VS23_BEAB2_655819 and tr_A0A0A2WAA2_A0A0A2WAA2_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J4VS23_J4VS23_BEAB2_655819 and tr_A0A167BN43_A0A167BN43_9HYPO_1081107 are exactly identical! WARNING: Sequences tr_J4VS23_J4VS23_BEAB2_655819 and tr_A0A2N6NM59_A0A2N6NM59_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A088AUC4_A0A088AUC4_APIME_7460 and tr_A0A2A3ENP9_A0A2A3ENP9_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A0E0FYK0_A0A0E0FYK0_ORYNI_4536 and tr_I1NV26_I1NV26_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0FYK0_A0A0E0FYK0_ORYNI_4536 and tr_A0A0D9YJU1_A0A0D9YJU1_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0FYK0_A0A0E0FYK0_ORYNI_4536 and tr_Q8RUI4_Q8RUI4_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0HDL8_A0A0E0HDL8_ORYNI_4536 and tr_A2Y3Z4_A2Y3Z4_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0HDL8_A0A0E0HDL8_ORYNI_4536 and tr_I1PV20_I1PV20_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0HDL8_A0A0E0HDL8_ORYNI_4536 and tr_A0A0D3G6X1_A0A0D3G6X1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0HDL8_A0A0E0HDL8_ORYNI_4536 and tr_A0A0D9ZYD7_A0A0D9ZYD7_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0J9XPL1_A0A0J9XPL1_BRUMA_6279 and tr_A0A0N4TJA2_A0A0N4TJA2_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A2XBV9_A2XBV9_ORYSI_39946 and tr_I1P701_I1P701_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2XBV9_A2XBV9_ORYSI_39946 and tr_A0A0D3FD48_A0A0D3FD48_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A2XBV9_A2XBV9_ORYSI_39946 and tr_Q8LMR3_Q8LMR3_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F4P9B2_F4P9B2_BATDJ_684364 and tr_A0A177WWH9_A0A177WWH9_BATDE_403673 are exactly identical! WARNING: Sequences tr_K7F644_K7F644_PELSI_13735 and tr_A0A1S3FP86_A0A1S3FP86_DIPOR_10020 are exactly identical! WARNING: Sequences tr_H0ZZA6_H0ZZA6_TAEGU_59729 and tr_A0A091ED26_A0A091ED26_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZZA6_H0ZZA6_TAEGU_59729 and tr_A0A093Q1K3_A0A093Q1K3_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A0E0CCS7_A0A0E0CCS7_9ORYZ_40149 and tr_A0A0E0N7F4_A0A0E0N7F4_ORYRU_4529 are exactly identical! WARNING: Sequences tr_M4F112_M4F112_BRARP_51351 and tr_A0A078F9H9_A0A078F9H9_BRANA_3708 are exactly identical! WARNING: Sequences tr_M2U523_M2U523_COCH5_701091 and tr_W6XZF8_W6XZF8_COCCA_930089 are exactly identical! WARNING: Sequences tr_V2XCH0_V2XCH0_MONRO_1381753 and tr_A0A0W0F9D5_A0A0W0F9D5_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2R2W9_W2R2W9_PHYPN_761204 and tr_A0A0W8CUV3_A0A0W8CUV3_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2R2W9_W2R2W9_PHYPN_761204 and tr_W2KLD0_W2KLD0_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A067DXU4_A0A067DXU4_CITSI_2711 and tr_V4SXM0_V4SXM0_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067DXU4_A0A067DXU4_CITSI_2711 and tr_A0A2H5PPD9_A0A2H5PPD9_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A067F2E7_A0A067F2E7_CITSI_2711 and tr_V4S886_V4S886_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A2I3MFA1_A0A2I3MFA1_PAPAN_9555 and tr_A0A2K5KZK7_A0A2K5KZK7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MFA1_A0A2I3MFA1_PAPAN_9555 and tr_A0A2K6CDV2_A0A2K6CDV2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3MFA1_A0A2I3MFA1_PAPAN_9555 and tr_A0A2K5YMA2_A0A2K5YMA2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A078IMF0_A0A078IMF0_BRANA_3708 and tr_A0A0D3AE96_A0A0D3AE96_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A094EDX6_A0A094EDX6_9PEZI_1420912 and tr_A0A1B8EAK7_A0A1B8EAK7_9PEZI_1524831 are exactly identical! WARNING: Sequences tr_A0A094EDX6_A0A094EDX6_9PEZI_1420912 and tr_A0A1B8GDP2_A0A1B8GDP2_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A094EDX6_A0A094EDX6_9PEZI_1420912 and tr_A0A1B8C6B0_A0A1B8C6B0_9PEZI_1622147 are exactly identical! WARNING: Sequences tr_A0A094EDX6_A0A094EDX6_9PEZI_1420912 and tr_A0A1B8F8M5_A0A1B8F8M5_9PEZI_1622149 are exactly identical! WARNING: Sequences tr_A0A0A2K2P3_A0A0A2K2P3_PENEN_27334 and tr_A0A0G4P600_A0A0G4P600_PENCA_1429867 are exactly identical! WARNING: Sequences tr_A0A0D2RMT9_A0A0D2RMT9_GOSRA_29730 and tr_A0A1U8NE18_A0A1U8NE18_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2UWR0_A0A0D2UWR0_GOSRA_29730 and tr_A0A1U8KBH3_A0A1U8KBH3_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0K0FXZ7_A0A0K0FXZ7_STRVS_75913 and tr_A0A0N5B7X6_A0A0N5B7X6_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0N0DHC0_A0A0N0DHC0_FUSLA_179993 and sp_Q4I2J8_NACA_GIBZE_229533 are exactly identical! WARNING: Sequences tr_A0A0N0DHC0_A0A0N0DHC0_FUSLA_179993 and tr_A0A2T4GND4_A0A2T4GND4_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A0A1NTH2_A0A0A1NTH2_9FUNG_58291 and tr_A0A367JW68_A0A367JW68_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A091JBT6_A0A091JBT6_EGRGA_188379 and tr_A0A091WHF9_A0A091WHF9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JBT6_A0A091JBT6_EGRGA_188379 and tr_A0A087R7S4_A0A087R7S4_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JBT6_A0A091JBT6_EGRGA_188379 and tr_A0A093HYD0_A0A093HYD0_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091JBT6_A0A091JBT6_EGRGA_188379 and tr_A0A091WDV4_A0A091WDV4_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JBT6_A0A091JBT6_EGRGA_188379 and tr_A0A091G112_A0A091G112_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JBT6_A0A091JBT6_EGRGA_188379 and tr_A0A093GNE1_A0A093GNE1_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091JBT6_A0A091JBT6_EGRGA_188379 and tr_A0A091IYU0_A0A091IYU0_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A093I2N6_A0A093I2N6_STRCA_441894 and tr_A0A0A0AHA0_A0A0A0AHA0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0D2C2F7_A0A0D2C2F7_9EURO_569365 and tr_A0A178ZFV6_A0A178ZFV6_9EURO_1367422 are exactly identical! WARNING: Sequences tr_A0A0V1DF65_A0A0V1DF65_TRIBR_45882 and tr_A0A0V0UEC9_A0A0V0UEC9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A101MQD9_A0A101MQD9_9EURO_48697 and tr_A0A1V6NBP1_A0A1V6NBP1_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A101MQD9_A0A101MQD9_9EURO_48697 and tr_A0A1V6RBD0_A0A1V6RBD0_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A151X349_A0A151X349_9HYME_64791 and tr_A0A151JQV6_A0A151JQV6_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A166XCM3_A0A166XCM3_9PEZI_708197 and tr_A0A162NJZ4_A0A162NJZ4_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_A0A165AJ21_A0A165AJ21_9HOMO_1314777 and tr_A0A166ISM3_A0A166ISM3_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S3ZYK2_A0A1S3ZYK2_TOBAC_4097 and tr_A0A1U7YQF1_A0A1U7YQF1_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4D6N6_A0A1S4D6N6_TOBAC_4097 and tr_A0A1J6JNT9_A0A1J6JNT9_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S4D6N6_A0A1S4D6N6_TOBAC_4097 and tr_A0A1U7XMX6_A0A1U7XMX6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3MHK2_A0A1S3MHK2_SALSA_8030 and tr_C0HAQ3_C0HAQ3_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1V8U6B6_A0A1V8U6B6_9PEZI_1974281 and tr_A0A1V8STF6_A0A1V8STF6_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A226N928_A0A226N928_CALSU_9009 and tr_A0A226NUP0_A0A226NUP0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3CFN7_A0A2H3CFN7_9AGAR_1076256 and tr_A0A284QV28_A0A284QV28_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2H3FAC1_A0A2H3FAC1_9HELO_946125 and tr_A0A2H3FMQ3_A0A2H3FMQ3_9HELO_946125 are exactly identical! WARNING: Sequences tr_A0A2D0PQ66_A0A2D0PQ66_ICTPU_7998 and tr_A0A2D0PRR9_A0A2D0PRR9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PQ66_A0A2D0PQ66_ICTPU_7998 and tr_A0A2D0PTH5_A0A2D0PTH5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A1U8E9V7_A0A1U8E9V7_CAPAN_4072 and tr_A0A2G3BIA6_A0A2G3BIA6_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A1U8FAT4_A0A1U8FAT4_CAPAN_4072 and tr_A0A2G3CXW6_A0A2G3CXW6_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A1U8FFI1_A0A1U8FFI1_CAPAN_4072 and tr_A0A2G3BHC5_A0A2G3BHC5_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2K5LYG7_A0A2K5LYG7_CERAT_9531 and tr_A0A2K5ZK07_A0A2K5ZK07_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K6DAK3_A0A2K6DAK3_MACNE_9545 and tr_A0A2K5XPA0_A0A2K5XPA0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2Y9N015_A0A2Y9N015_DELLE_9749 and tr_A0A2Y9FRZ5_A0A2Y9FRZ5_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 105 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/E9PAV3/3_mltree/E9PAV3.raxml.reduced.phy Alignment comprises 1 partitions and 237 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 237 / 237 Gaps: 20.71 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/E9PAV3/3_mltree/E9PAV3.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 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 237 / 18960 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -261169.958225] Initial branch length optimization [00:00:05 -225483.067886] Model parameter optimization (eps = 10.000000) [00:00:52 -223993.875478] AUTODETECT spr round 1 (radius: 5) [00:04:02 -157662.683938] AUTODETECT spr round 2 (radius: 10) [00:07:21 -119697.476593] AUTODETECT spr round 3 (radius: 15) [00:10:35 -101991.135878] AUTODETECT spr round 4 (radius: 20) [00:14:28 -89734.244996] AUTODETECT spr round 5 (radius: 25) [00:18:51 -87580.072496] SPR radius for FAST iterations: 25 (autodetect) [00:18:51 -87580.072496] Model parameter optimization (eps = 3.000000) [00:19:24 -87388.925328] FAST spr round 1 (radius: 25) [00:23:25 -73972.956558] FAST spr round 2 (radius: 25) [00:26:18 -73142.511834] FAST spr round 3 (radius: 25) [00:28:43 -72436.944158] FAST spr round 4 (radius: 25) [00:31:03 -72318.936806] FAST spr round 5 (radius: 25) [00:33:15 -72304.093982] FAST spr round 6 (radius: 25) [00:35:19 -72304.091088] Model parameter optimization (eps = 1.000000) [00:35:38 -72300.728690] SLOW spr round 1 (radius: 5) [00:38:21 -72286.587823] SLOW spr round 2 (radius: 5) [00:41:02 -72274.299278] SLOW spr round 3 (radius: 5) [00:43:45 -72268.400422] SLOW spr round 4 (radius: 5) [00:46:25 -72268.400273] SLOW spr round 5 (radius: 10) [00:49:09 -72268.400213] SLOW spr round 6 (radius: 15) [00:53:35 -72264.244114] SLOW spr round 7 (radius: 5) [00:56:59 -72264.243936] SLOW spr round 8 (radius: 10) [01:00:07 -72264.243882] SLOW spr round 9 (radius: 15) [01:04:06 -72264.243828] SLOW spr round 10 (radius: 20) [01:10:09 -72264.243777] SLOW spr round 11 (radius: 25) [01:17:26 -72264.243727] Model parameter optimization (eps = 0.100000) [01:17:33] [worker #0] ML tree search #1, logLikelihood: -72264.218590 [01:17:33 -261880.549054] Initial branch length optimization [01:17:38 -225854.404650] Model parameter optimization (eps = 10.000000) [01:18:56 -224300.033788] AUTODETECT spr round 1 (radius: 5) [01:22:03 -155116.379983] AUTODETECT spr round 2 (radius: 10) [01:25:19 -111991.348236] AUTODETECT spr round 3 (radius: 15) [01:28:45 -90762.731057] AUTODETECT spr round 4 (radius: 20) [01:32:46 -84254.653022] AUTODETECT spr round 5 (radius: 25) [01:37:15 -83334.284145] SPR radius for FAST iterations: 25 (autodetect) [01:37:15 -83334.284145] Model parameter optimization (eps = 3.000000) [01:37:44 -83124.753060] FAST spr round 1 (radius: 25) [01:39:32] [worker #1] ML tree search #2, logLikelihood: -72446.596832 [01:41:35 -73054.573022] FAST spr round 2 (radius: 25) [01:44:38 -72683.016408] FAST spr round 3 (radius: 25) [01:47:12 -72656.095156] FAST spr round 4 (radius: 25) [01:49:33 -72652.548741] FAST spr round 5 (radius: 25) [01:51:45] [worker #4] ML tree search #5, logLikelihood: -72842.957770 [01:51:50 -72649.677239] FAST spr round 6 (radius: 25) [01:54:05 -72649.676642] Model parameter optimization (eps = 1.000000) [01:54:22 -72646.741387] SLOW spr round 1 (radius: 5) [01:57:16 -72624.221370] SLOW spr round 2 (radius: 5) [01:59:17] [worker #3] ML tree search #4, logLikelihood: -72257.642123 [02:00:06 -72621.571254] SLOW spr round 3 (radius: 5) [02:02:52 -72621.531029] SLOW spr round 4 (radius: 10) [02:05:36 -72620.967040] SLOW spr round 5 (radius: 5) [02:09:00 -72620.488826] SLOW spr round 6 (radius: 5) [02:11:57 -72620.488692] SLOW spr round 7 (radius: 10) [02:13:15] [worker #2] ML tree search #3, logLikelihood: -72223.198759 [02:14:49 -72620.488615] SLOW spr round 8 (radius: 15) [02:19:04 -72620.488535] SLOW spr round 9 (radius: 20) [02:25:05 -72620.488453] SLOW spr round 10 (radius: 25) [02:32:22 -72620.488369] Model parameter optimization (eps = 0.100000) [02:32:30] [worker #0] ML tree search #6, logLikelihood: -72620.466347 [02:32:30 -261861.189654] Initial branch length optimization [02:32:37 -225290.741394] Model parameter optimization (eps = 10.000000) [02:33:35 -223820.233403] AUTODETECT spr round 1 (radius: 5) [02:36:44 -153924.029164] AUTODETECT spr round 2 (radius: 10) [02:39:56 -113832.804291] AUTODETECT spr round 3 (radius: 15) [02:43:26 -98993.609334] AUTODETECT spr round 4 (radius: 20) [02:47:19 -90221.962779] AUTODETECT spr round 5 (radius: 25) [02:52:09 -86827.274937] SPR radius for FAST iterations: 25 (autodetect) [02:52:09 -86827.274937] Model parameter optimization (eps = 3.000000) [02:52:54 -86612.319080] FAST spr round 1 (radius: 25) [02:56:51 -73276.057354] FAST spr round 2 (radius: 25) [02:59:54 -72391.547343] FAST spr round 3 (radius: 25) [03:02:29 -72313.431251] FAST spr round 4 (radius: 25) [03:04:47 -72304.103670] FAST spr round 5 (radius: 25) [03:06:58 -72302.193332] FAST spr round 6 (radius: 25) [03:09:04 -72302.192401] Model parameter optimization (eps = 1.000000) [03:09:23 -72298.754898] SLOW spr round 1 (radius: 5) [03:12:03 -72278.589886] SLOW spr round 2 (radius: 5) [03:14:40 -72272.501633] SLOW spr round 3 (radius: 5) [03:17:16 -72270.394762] SLOW spr round 4 (radius: 5) [03:19:51 -72270.330827] SLOW spr round 5 (radius: 10) [03:22:38 -72259.487426] SLOW spr round 6 (radius: 5) [03:25:56 -72254.315787] SLOW spr round 7 (radius: 5) [03:28:53 -72253.660342] SLOW spr round 8 (radius: 5) [03:29:03] [worker #2] ML tree search #8, logLikelihood: -72226.769631 [03:31:37 -72253.660169] SLOW spr round 9 (radius: 10) [03:32:31] [worker #4] ML tree search #10, logLikelihood: -72427.544724 [03:34:23 -72251.894752] SLOW spr round 10 (radius: 5) [03:37:39 -72250.873851] SLOW spr round 11 (radius: 5) [03:40:32 -72250.866549] SLOW spr round 12 (radius: 10) [03:43:17 -72250.866472] SLOW spr round 13 (radius: 15) [03:47:37 -72250.679110] SLOW spr round 14 (radius: 5) [03:50:37] [worker #3] ML tree search #9, logLikelihood: -72248.171746 [03:51:03 -72249.297776] SLOW spr round 15 (radius: 5) [03:52:11] [worker #1] ML tree search #7, logLikelihood: -72238.716578 [03:54:04 -72249.297251] SLOW spr round 16 (radius: 10) [03:56:54 -72248.271254] SLOW spr round 17 (radius: 5) [04:00:09 -72248.271174] SLOW spr round 18 (radius: 10) [04:03:11 -72248.271096] SLOW spr round 19 (radius: 15) [04:07:27 -72243.016769] SLOW spr round 20 (radius: 5) [04:10:51 -72243.016475] SLOW spr round 21 (radius: 10) [04:14:02 -72243.016397] SLOW spr round 22 (radius: 15) [04:18:11 -72243.016318] SLOW spr round 23 (radius: 20) [04:24:25 -72240.425930] SLOW spr round 24 (radius: 5) [04:28:00 -72239.000563] SLOW spr round 25 (radius: 5) [04:31:04 -72239.000445] SLOW spr round 26 (radius: 10) [04:33:59 -72239.000365] SLOW spr round 27 (radius: 15) [04:38:15 -72239.000286] SLOW spr round 28 (radius: 20) [04:44:25 -72239.000206] SLOW spr round 29 (radius: 25) [04:52:01 -72239.000126] Model parameter optimization (eps = 0.100000) [04:52:10] [worker #0] ML tree search #11, logLikelihood: -72238.951776 [04:52:10 -261492.957818] Initial branch length optimization [04:52:15 -225257.263449] Model parameter optimization (eps = 10.000000) [04:53:00 -223790.636090] AUTODETECT spr round 1 (radius: 5) [04:56:03 -161212.208284] AUTODETECT spr round 2 (radius: 10) [04:59:25 -118162.648380] AUTODETECT spr round 3 (radius: 15) [05:03:03 -98197.081570] AUTODETECT spr round 4 (radius: 20) [05:07:08 -89458.925894] AUTODETECT spr round 5 (radius: 25) [05:11:53 -86555.594929] SPR radius for FAST iterations: 25 (autodetect) [05:11:53 -86555.594929] Model parameter optimization (eps = 3.000000) [05:12:35 -86246.374296] FAST spr round 1 (radius: 25) [05:14:50] [worker #4] ML tree search #15, logLikelihood: -72415.860552 [05:16:36 -72960.815359] FAST spr round 2 (radius: 25) [05:19:25 -72435.059124] FAST spr round 3 (radius: 25) [05:21:52 -72383.903063] FAST spr round 4 (radius: 25) [05:24:08 -72374.950989] FAST spr round 5 (radius: 25) [05:26:12 -72374.946864] Model parameter optimization (eps = 1.000000) [05:26:38 -72372.443038] SLOW spr round 1 (radius: 5) [05:29:21 -72351.573193] SLOW spr round 2 (radius: 5) [05:32:02 -72343.841280] SLOW spr round 3 (radius: 5) [05:34:42 -72343.388581] SLOW spr round 4 (radius: 5) [05:37:16 -72343.387747] SLOW spr round 5 (radius: 10) [05:40:01 -72340.554557] SLOW spr round 6 (radius: 5) [05:43:29 -72330.383429] SLOW spr round 7 (radius: 5) [05:44:12] [worker #2] ML tree search #13, logLikelihood: -72209.457686 [05:46:26 -72329.312718] SLOW spr round 8 (radius: 5) [05:49:10 -72329.312073] SLOW spr round 9 (radius: 10) [05:51:57 -72329.312067] SLOW spr round 10 (radius: 15) [05:52:37] [worker #3] ML tree search #14, logLikelihood: -72228.668737 [05:56:21 -72329.312066] SLOW spr round 11 (radius: 20) [06:02:31 -72329.312065] SLOW spr round 12 (radius: 25) [06:09:51 -72329.312063] Model parameter optimization (eps = 0.100000) [06:09:58] [worker #0] ML tree search #16, logLikelihood: -72329.288091 [06:51:59] [worker #3] ML tree search #19, logLikelihood: -72380.400630 [07:04:01] [worker #1] ML tree search #12, logLikelihood: -72271.797689 [07:18:55] [worker #4] ML tree search #20, logLikelihood: -72371.855378 [07:35:17] [worker #2] ML tree search #18, logLikelihood: -73250.074069 [08:34:02] [worker #1] ML tree search #17, logLikelihood: -72320.156952 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.194098,0.303383) (0.112113,0.870467) (0.217559,0.426530) (0.476230,1.576399) 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: -72209.457686 AIC score: 148428.915371 / AICc score: 8192488.915371 / BIC score: 155382.375954 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=237). 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/E9PAV3/3_mltree/E9PAV3.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/E9PAV3/3_mltree/E9PAV3.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/E9PAV3/3_mltree/E9PAV3.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/E9PAV3/3_mltree/E9PAV3.raxml.log Analysis started: 04-Jul-2021 01:26:20 / finished: 04-Jul-2021 10:00:23 Elapsed time: 30842.697 seconds Consumed energy: 2227.583 Wh (= 11 km in an electric car, or 56 km with an e-scooter!)