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 13:02:05 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE67/2_msa/Q8TE67_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE67/3_mltree/Q8TE67 --seed 2 --threads 4 --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 (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE67/2_msa/Q8TE67_trimmed_msa.fasta [00:00:00] Loaded alignment with 844 taxa and 202 sites WARNING: Sequences tr_E2AX91_E2AX91_CAMFO_104421 and tr_F4X4S8_F4X4S8_ACREC_103372 are exactly identical! WARNING: Sequences tr_E2AX91_E2AX91_CAMFO_104421 and tr_A0A151IIB2_A0A151IIB2_9HYME_456900 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_H0WNS4_H0WNS4_OTOGA_30611 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_H0ZP43_H0ZP43_TAEGU_59729 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_U3K8R9_U3K8R9_FICAL_59894 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_U3J5M4_U3J5M4_ANAPL_8839 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A091DJ27_A0A091DJ27_FUKDA_885580 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A0Q3PNI3_A0A0Q3PNI3_AMAAE_12930 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A091F166_A0A091F166_CORBR_85066 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A091JKT0_A0A091JKT0_EGRGA_188379 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A093QF57_A0A093QF57_9PASS_328815 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A091UXD3_A0A091UXD3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A087RKZ0_A0A087RKZ0_APTFO_9233 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A093K3W6_A0A093K3W6_STRCA_441894 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A091XK84_A0A091XK84_OPIHO_30419 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A099ZAA8_A0A099ZAA8_TINGU_94827 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A091G9N1_A0A091G9N1_9AVES_55661 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A0A0B2T4_A0A0A0B2T4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A2I0MUC4_A0A2I0MUC4_COLLI_8932 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A093GBY3_A0A093GBY3_DRYPU_118200 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A091I3Y6_A0A091I3Y6_CALAN_9244 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A1V4JMB1_A0A1V4JMB1_PATFA_372326 are exactly identical! WARNING: Sequences tr_F1NQU9_F1NQU9_CHICK_9031 and tr_A0A2U4AW15_A0A2U4AW15_TURTR_9739 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_M3YFP0_M3YFP0_MUSPF_9669 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_G1P913_G1P913_MYOLU_59463 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_G1NL23_G1NL23_MELGA_9103 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_E2RC09_E2RC09_CANLF_9615 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_F7FG65_F7FG65_MONDO_13616 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_W5PJ18_W5PJ18_SHEEP_9940 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and sp_Q62844_FYN_RAT_10116 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_I3M9M0_I3M9M0_ICTTR_43179 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_A0A286XJ68_A0A286XJ68_CAVPO_10141 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_G5AUN8_G5AUN8_HETGA_10181 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_G3SQT6_G3SQT6_LOXAF_9785 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_G3WAB1_G3WAB1_SARHA_9305 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_F7IB43_F7IB43_CALJA_9483 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and sp_A1Y2K1_FYN_PIG_9823 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_D2H640_D2H640_AILME_9646 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and sp_A0JNB0_FYN_BOVIN_9913 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_M3X148_M3X148_FELCA_9685 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_A0A3Q0E3C6_A0A3Q0E3C6_TARSY_1868482 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_A0A1U7Q8Y9_A0A1U7Q8Y9_MESAU_10036 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_A0A218UXN4_A0A218UXN4_9PASE_299123 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_A0A2U4AW31_A0A2U4AW31_TURTR_9739 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_A0A2U3WDX9_A0A2U3WDX9_ODORO_9708 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_A0A2Y9QVV7_A0A2Y9QVV7_TRIMA_127582 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_A0A2Y9L364_A0A2Y9L364_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_A0A2Y9LLH3_A0A2Y9LLH3_DELLE_9749 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_A0A2Y9S5U4_A0A2Y9S5U4_PHYCD_9755 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_A0A384DBM2_A0A384DBM2_URSMA_29073 are exactly identical! WARNING: Sequences sp_P39688_FYN_MOUSE_10090 and tr_A0A384ATR0_A0A384ATR0_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3Y204_M3Y204_MUSPF_9669 and tr_H2NVZ4_H2NVZ4_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3Y204_M3Y204_MUSPF_9669 and tr_G1SPV2_G1SPV2_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3Y204_M3Y204_MUSPF_9669 and tr_W5PIG2_W5PIG2_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3Y204_M3Y204_MUSPF_9669 and tr_G1LJ17_G1LJ17_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Y204_M3Y204_MUSPF_9669 and tr_A0A2U3WPZ4_A0A2U3WPZ4_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y204_M3Y204_MUSPF_9669 and tr_A0A2U3X8S8_A0A2U3X8S8_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Y204_M3Y204_MUSPF_9669 and tr_A0A2Y9ITB1_A0A2Y9ITB1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y204_M3Y204_MUSPF_9669 and tr_A0A384C1E0_A0A384C1E0_URSMA_29073 are exactly identical! WARNING: Sequences sp_P08630_BTKL_DROME_7227 and tr_B4HYH7_B4HYH7_DROSE_7238 are exactly identical! WARNING: Sequences sp_P08630_BTKL_DROME_7227 and tr_B3MPH0_B3MPH0_DROAN_7217 are exactly identical! WARNING: Sequences tr_Q8IPW1_Q8IPW1_DROME_7227 and tr_B4ID27_B4ID27_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4JDT8_B4JDT8_DROGR_7222 and tr_Q29M84_Q29M84_DROPS_46245 are exactly identical! WARNING: Sequences tr_B4JDT8_B4JDT8_DROGR_7222 and tr_B4G9K9_B4G9K9_DROPE_7234 are exactly identical! WARNING: Sequences tr_B4JDT8_B4JDT8_DROGR_7222 and tr_B4LTX9_B4LTX9_DROVI_7244 are exactly identical! WARNING: Sequences tr_B4JDT8_B4JDT8_DROGR_7222 and tr_B4KF73_B4KF73_DROMO_7230 are exactly identical! WARNING: Sequences tr_B4JDT8_B4JDT8_DROGR_7222 and tr_A0A0M4E7R8_A0A0M4E7R8_DROBS_30019 are exactly identical! WARNING: Sequences tr_A0A2I3HC72_A0A2I3HC72_NOMLE_61853 and tr_G3QYF5_G3QYF5_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HC72_A0A2I3HC72_NOMLE_61853 and tr_G1TA73_G1TA73_RABIT_9986 are exactly identical! WARNING: Sequences tr_A0A2I3HC72_A0A2I3HC72_NOMLE_61853 and tr_A0A2I3SKP4_A0A2I3SKP4_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HC72_A0A2I3HC72_NOMLE_61853 and sp_P06241_FYN_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3HC72_A0A2I3HC72_NOMLE_61853 and tr_G7P3M8_G7P3M8_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3HC72_A0A2I3HC72_NOMLE_61853 and tr_A0A096NW74_A0A096NW74_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HC72_A0A2I3HC72_NOMLE_61853 and tr_A0A0D9RST7_A0A0D9RST7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3HC72_A0A2I3HC72_NOMLE_61853 and tr_A0A3Q0G4K1_A0A3Q0G4K1_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A2I3HC72_A0A2I3HC72_NOMLE_61853 and tr_A0A2K5MDU1_A0A2K5MDU1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3HC72_A0A2I3HC72_NOMLE_61853 and tr_A0A2K6B9D1_A0A2K6B9D1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3HC72_A0A2I3HC72_NOMLE_61853 and tr_A0A2K5YJ25_A0A2K5YJ25_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3HC72_A0A2I3HC72_NOMLE_61853 and tr_A0A2R9B759_A0A2R9B759_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3GXX7_G3GXX7_CRIGR_10029 and sp_P12931_SRC_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3GXX7_G3GXX7_CRIGR_10029 and tr_A0A2R9CBS4_A0A2R9CBS4_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q5R4H4_EPS8_PONAB_9601 and tr_A0A2R9BSG7_A0A2R9BSG7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1NLE0_G1NLE0_MELGA_9103 and tr_A0A226MR21_A0A226MR21_CALSU_9009 are exactly identical! WARNING: Sequences tr_Q29M78_Q29M78_DROPS_46245 and tr_B4G9L5_B4G9L5_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2PZL6_H2PZL6_PANTR_9598 and sp_Q8TE67_ES8L3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F7FRJ2_F7FRJ2_ORNAN_9258 and tr_A0A1U7UVS3_A0A1U7UVS3_TARSY_1868482 are exactly identical! WARNING: Sequences tr_W5QHG1_W5QHG1_SHEEP_9940 and tr_E1BCX9_E1BCX9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F6QQC0_F6QQC0_MACMU_9544 and tr_A0A2K6DQI8_A0A2K6DQI8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H5A6_F7H5A6_MACMU_9544 and tr_G8F3A7_G8F3A7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H5A6_F7H5A6_MACMU_9544 and tr_A0A2K6CQ29_A0A2K6CQ29_MACNE_9545 are exactly identical! WARNING: Sequences tr_E5SRE0_E5SRE0_TRISP_6334 and tr_A0A0V0RXG8_A0A0V0RXG8_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5SRE0_E5SRE0_TRISP_6334 and tr_A0A0V1CKI0_A0A0V1CKI0_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5SRE0_E5SRE0_TRISP_6334 and tr_A0A0V0X1S4_A0A0V0X1S4_9BILA_92179 are exactly identical! WARNING: Sequences tr_E5SRE0_E5SRE0_TRISP_6334 and tr_A0A0V0VJ28_A0A0V0VJ28_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5SRE0_E5SRE0_TRISP_6334 and tr_A0A0V1L9K0_A0A0V1L9K0_9BILA_6335 are exactly identical! WARNING: Sequences tr_E5SRE0_E5SRE0_TRISP_6334 and tr_A0A0V1ACR2_A0A0V1ACR2_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5SRE0_E5SRE0_TRISP_6334 and tr_A0A0V1EG05_A0A0V1EG05_TRIPS_6337 are exactly identical! WARNING: Sequences tr_E5SRE0_E5SRE0_TRISP_6334 and tr_A0A0V1PBA8_A0A0V1PBA8_9BILA_92180 are exactly identical! WARNING: Sequences tr_E5SRE0_E5SRE0_TRISP_6334 and tr_A0A0V0TUN5_A0A0V0TUN5_9BILA_144512 are exactly identical! WARNING: Sequences tr_Q7Q4A9_Q7Q4A9_ANOGA_7165 and tr_A0A084VCV7_A0A084VCV7_ANOSI_74873 are exactly identical! WARNING: Sequences tr_H0ZQ83_H0ZQ83_TAEGU_59729 and tr_A0A218V951_A0A218V951_9PASE_299123 are exactly identical! WARNING: Sequences tr_B4MTJ7_B4MTJ7_DROWI_7260 and tr_A0A1W4V8B2_A0A1W4V8B2_DROFC_30025 are exactly identical! WARNING: Sequences tr_G1LAH8_G1LAH8_AILME_9646 and tr_A0A384DEM3_A0A384DEM3_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A044TAJ8_A0A044TAJ8_ONCVO_6282 and tr_A0A182DZR0_A0A182DZR0_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0A1MZU4_A0A0A1MZU4_9FUNG_58291 and tr_A0A0A1PJX0_A0A0A1PJX0_9FUNG_58291 are exactly identical! WARNING: Sequences tr_A0A0A1PEW6_A0A0A1PEW6_9FUNG_58291 and tr_A0A367K3E4_A0A367K3E4_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A060Y762_A0A060Y762_ONCMY_8022 and tr_A0A060ZEY1_A0A060ZEY1_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A2J7PDR0_A0A2J7PDR0_9NEOP_105785 and tr_A0A2P8XAH7_A0A2P8XAH7_BLAGE_6973 are exactly identical! WARNING: Sequences tr_A0A2U4BHU8_A0A2U4BHU8_TURTR_9739 and tr_A0A2Y9NV44_A0A2Y9NV44_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 109 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/Q8TE67/3_mltree/Q8TE67.raxml.reduced.phy Alignment comprises 1 partitions and 202 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 202 / 202 Gaps: 17.85 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE67/3_mltree/Q8TE67.raxml.rba Parallelization scheme autoconfig: 4 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 844 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 202 / 16160 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -310881.358726] Initial branch length optimization [00:00:04 -250296.297346] Model parameter optimization (eps = 10.000000) [00:00:40 -249264.969609] AUTODETECT spr round 1 (radius: 5) [00:02:51 -177023.171820] AUTODETECT spr round 2 (radius: 10) [00:05:06 -132778.186811] AUTODETECT spr round 3 (radius: 15) [00:07:39 -108597.624630] AUTODETECT spr round 4 (radius: 20) [00:10:22 -94594.368843] AUTODETECT spr round 5 (radius: 25) [00:13:46 -93582.496790] SPR radius for FAST iterations: 25 (autodetect) [00:13:46 -93582.496790] Model parameter optimization (eps = 3.000000) [00:14:15 -93108.085376] FAST spr round 1 (radius: 25) [00:17:10 -79129.947025] FAST spr round 2 (radius: 25) [00:19:21 -78396.154631] FAST spr round 3 (radius: 25) [00:21:11 -78268.226691] FAST spr round 4 (radius: 25) [00:22:49 -78261.929151] FAST spr round 5 (radius: 25) [00:24:22 -78251.413500] FAST spr round 6 (radius: 25) [00:25:52 -78250.412655] FAST spr round 7 (radius: 25) [00:27:21 -78250.401506] Model parameter optimization (eps = 1.000000) [00:27:39 -78245.378780] SLOW spr round 1 (radius: 5) [00:29:42 -78221.425647] SLOW spr round 2 (radius: 5) [00:31:41 -78221.228847] SLOW spr round 3 (radius: 5) [00:33:41 -78220.201956] SLOW spr round 4 (radius: 5) [00:35:40 -78219.663800] SLOW spr round 5 (radius: 5) [00:37:34 -78219.663231] SLOW spr round 6 (radius: 10) [00:39:35 -78219.126194] SLOW spr round 7 (radius: 5) [00:42:06 -78218.588054] SLOW spr round 8 (radius: 5) [00:44:16 -78218.588002] SLOW spr round 9 (radius: 10) [00:46:20 -78218.587995] SLOW spr round 10 (radius: 15) [00:48:25] [worker #1] ML tree search #2, logLikelihood: -78300.181323 [00:49:41 -78218.587991] SLOW spr round 11 (radius: 20) [00:54:33 -78218.587989] SLOW spr round 12 (radius: 25) [01:00:04] [worker #2] ML tree search #3, logLikelihood: -78226.872391 [01:00:26 -78218.587988] Model parameter optimization (eps = 0.100000) [01:00:38] [worker #0] ML tree search #1, logLikelihood: -78218.321379 [01:00:38 -311819.944388] Initial branch length optimization [01:00:42 -250619.631916] Model parameter optimization (eps = 10.000000) [01:01:35 -249518.873373] AUTODETECT spr round 1 (radius: 5) [01:03:45 -184715.951731] AUTODETECT spr round 2 (radius: 10) [01:06:00 -139328.120498] AUTODETECT spr round 3 (radius: 15) [01:08:37 -110079.506188] AUTODETECT spr round 4 (radius: 20) [01:11:22 -97815.369177] AUTODETECT spr round 5 (radius: 25) [01:14:37 -95556.928657] SPR radius for FAST iterations: 25 (autodetect) [01:14:37 -95556.928657] Model parameter optimization (eps = 3.000000) [01:15:03 -95036.967468] FAST spr round 1 (radius: 25) [01:15:14] [worker #3] ML tree search #4, logLikelihood: -78211.639664 [01:17:58 -81856.274999] FAST spr round 2 (radius: 25) [01:20:17 -78763.648940] FAST spr round 3 (radius: 25) [01:22:09 -78294.752209] FAST spr round 4 (radius: 25) [01:23:54 -78264.005773] FAST spr round 5 (radius: 25) [01:25:28 -78257.578944] FAST spr round 6 (radius: 25) [01:26:57 -78257.577270] Model parameter optimization (eps = 1.000000) [01:27:19 -78248.398079] SLOW spr round 1 (radius: 5) [01:29:22 -78221.371061] SLOW spr round 2 (radius: 5) [01:31:22 -78220.763736] SLOW spr round 3 (radius: 5) [01:33:18 -78220.762534] SLOW spr round 4 (radius: 10) [01:35:19 -78219.443606] SLOW spr round 5 (radius: 5) [01:36:54] [worker #1] ML tree search #6, logLikelihood: -78240.335525 [01:37:49 -78219.443290] SLOW spr round 6 (radius: 10) [01:40:01 -78219.443104] SLOW spr round 7 (radius: 15) [01:43:14 -78218.472635] SLOW spr round 8 (radius: 5) [01:45:53 -78218.472436] SLOW spr round 9 (radius: 10) [01:48:12 -78218.472322] SLOW spr round 10 (radius: 15) [01:51:22 -78218.472234] SLOW spr round 11 (radius: 20) [01:54:07] [worker #2] ML tree search #7, logLikelihood: -78229.410771 [01:56:13 -78218.472159] SLOW spr round 12 (radius: 25) [02:02:05 -78218.472089] Model parameter optimization (eps = 0.100000) [02:02:13] [worker #0] ML tree search #5, logLikelihood: -78218.312713 [02:02:13 -309576.839937] Initial branch length optimization [02:02:17 -249906.723141] Model parameter optimization (eps = 10.000000) [02:02:59 -248852.979616] AUTODETECT spr round 1 (radius: 5) [02:05:07 -176482.950368] AUTODETECT spr round 2 (radius: 10) [02:07:22 -134302.874651] AUTODETECT spr round 3 (radius: 15) [02:09:55 -116419.964828] AUTODETECT spr round 4 (radius: 20) [02:13:05 -108528.930254] AUTODETECT spr round 5 (radius: 25) [02:16:39 -98443.710470] SPR radius for FAST iterations: 25 (autodetect) [02:16:39 -98443.710470] Model parameter optimization (eps = 3.000000) [02:17:12 -97900.149881] FAST spr round 1 (radius: 25) [02:20:15 -79407.093452] FAST spr round 2 (radius: 25) [02:22:28 -78405.582581] FAST spr round 3 (radius: 25) [02:24:28 -78266.729685] FAST spr round 4 (radius: 25) [02:26:09 -78257.514524] FAST spr round 5 (radius: 25) [02:27:43 -78256.204186] FAST spr round 6 (radius: 25) [02:29:16 -78253.513297] FAST spr round 7 (radius: 25) [02:30:47 -78251.044834] FAST spr round 8 (radius: 25) [02:31:21] [worker #1] ML tree search #10, logLikelihood: -78217.653973 [02:32:16 -78251.043190] Model parameter optimization (eps = 1.000000) [02:32:32 -78241.914013] SLOW spr round 1 (radius: 5) [02:34:35 -78225.141138] SLOW spr round 2 (radius: 5) [02:36:38 -78221.974929] SLOW spr round 3 (radius: 5) [02:38:35 -78221.957606] SLOW spr round 4 (radius: 10) [02:40:36 -78221.827899] SLOW spr round 5 (radius: 5) [02:43:13 -78211.466096] SLOW spr round 6 (radius: 5) [02:45:27 -78211.465687] SLOW spr round 7 (radius: 10) [02:47:34 -78206.490694] SLOW spr round 8 (radius: 5) [02:50:05 -78206.489341] SLOW spr round 9 (radius: 10) [02:52:18 -78206.489161] SLOW spr round 10 (radius: 15) [02:55:31 -78206.489115] SLOW spr round 11 (radius: 20) [03:00:30 -78205.542215] SLOW spr round 12 (radius: 5) [03:03:12 -78205.542193] SLOW spr round 13 (radius: 10) [03:05:22] [worker #2] ML tree search #11, logLikelihood: -78217.744954 [03:05:35 -78205.542171] SLOW spr round 14 (radius: 15) [03:08:42 -78205.542150] SLOW spr round 15 (radius: 20) [03:12:43] [worker #3] ML tree search #8, logLikelihood: -78230.206157 [03:13:45 -78205.542128] SLOW spr round 16 (radius: 25) [03:19:54 -78205.542106] Model parameter optimization (eps = 0.100000) [03:20:07] [worker #0] ML tree search #9, logLikelihood: -78205.421205 [03:20:08 -309542.092797] Initial branch length optimization [03:20:12 -250773.110765] Model parameter optimization (eps = 10.000000) [03:21:01 -249810.028548] AUTODETECT spr round 1 (radius: 5) [03:23:18 -179360.869422] AUTODETECT spr round 2 (radius: 10) [03:25:41 -130276.431431] AUTODETECT spr round 3 (radius: 15) [03:28:18 -111688.105312] AUTODETECT spr round 4 (radius: 20) [03:28:22] [worker #1] ML tree search #14, logLikelihood: -78208.884098 [03:31:23 -99125.916851] AUTODETECT spr round 5 (radius: 25) [03:34:55 -92942.991179] SPR radius for FAST iterations: 25 (autodetect) [03:34:55 -92942.991179] Model parameter optimization (eps = 3.000000) [03:35:29 -92530.758458] FAST spr round 1 (radius: 25) [03:38:12 -80575.910561] FAST spr round 2 (radius: 25) [03:40:20 -78431.040469] FAST spr round 3 (radius: 25) [03:42:20 -78253.068865] FAST spr round 4 (radius: 25) [03:44:03 -78245.570673] FAST spr round 5 (radius: 25) [03:45:41 -78245.568249] Model parameter optimization (eps = 1.000000) [03:45:58 -78242.713335] SLOW spr round 1 (radius: 5) [03:48:10 -78218.241062] SLOW spr round 2 (radius: 5) [03:50:13 -78217.662064] SLOW spr round 3 (radius: 5) [03:52:10 -78217.577430] SLOW spr round 4 (radius: 10) [03:54:12 -78217.576110] SLOW spr round 5 (radius: 15) [03:57:45 -78217.575516] SLOW spr round 6 (radius: 20) [04:02:57 -78217.575220] SLOW spr round 7 (radius: 25) [04:09:21 -78217.575066] Model parameter optimization (eps = 0.100000) [04:09:29] [worker #0] ML tree search #13, logLikelihood: -78217.516668 [04:09:29 -312103.958480] Initial branch length optimization [04:09:33 -251749.617225] Model parameter optimization (eps = 10.000000) [04:10:12 -250750.699508] AUTODETECT spr round 1 (radius: 5) [04:12:25 -181233.158801] AUTODETECT spr round 2 (radius: 10) [04:14:44 -129216.333777] AUTODETECT spr round 3 (radius: 15) [04:17:19 -103055.845488] AUTODETECT spr round 4 (radius: 20) [04:20:24 -92240.762030] AUTODETECT spr round 5 (radius: 25) [04:24:00 -89045.793568] SPR radius for FAST iterations: 25 (autodetect) [04:24:00 -89045.793568] Model parameter optimization (eps = 3.000000) [04:24:40 -88573.443569] FAST spr round 1 (radius: 25) [04:24:44] [worker #2] ML tree search #15, logLikelihood: -78296.147666 [04:27:24 -78868.366060] FAST spr round 2 (radius: 25) [04:29:21 -78318.870921] FAST spr round 3 (radius: 25) [04:31:06 -78300.420640] FAST spr round 4 (radius: 25) [04:32:43 -78287.029657] FAST spr round 5 (radius: 25) [04:34:14 -78287.024151] Model parameter optimization (eps = 1.000000) [04:34:29 -78283.677127] SLOW spr round 1 (radius: 5) [04:36:31 -78256.014358] SLOW spr round 2 (radius: 5) [04:38:33 -78246.496889] SLOW spr round 3 (radius: 5) [04:39:58] [worker #3] ML tree search #12, logLikelihood: -78225.792535 [04:40:35 -78241.109622] SLOW spr round 4 (radius: 5) [04:42:34 -78241.016278] SLOW spr round 5 (radius: 10) [04:44:24] [worker #1] ML tree search #18, logLikelihood: -78211.031885 [04:44:32 -78241.015266] SLOW spr round 6 (radius: 15) [04:48:07 -78241.014965] SLOW spr round 7 (radius: 20) [04:53:07 -78240.186919] SLOW spr round 8 (radius: 5) [04:55:50 -78240.186837] SLOW spr round 9 (radius: 10) [04:58:15 -78240.186829] SLOW spr round 10 (radius: 15) [05:01:29 -78240.186827] SLOW spr round 11 (radius: 20) [05:06:33 -78240.186827] SLOW spr round 12 (radius: 25) [05:12:47 -78240.186826] Model parameter optimization (eps = 0.100000) [05:12:57] [worker #0] ML tree search #17, logLikelihood: -78239.979264 [05:15:17] [worker #2] ML tree search #19, logLikelihood: -78216.453855 [05:59:14] [worker #3] ML tree search #16, logLikelihood: -78224.111352 [07:12:01] [worker #3] ML tree search #20, logLikelihood: -78218.653102 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.185797,0.869574) (0.111740,0.854303) (0.411691,0.870304) (0.290771,1.322960) 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: -78205.421205 AIC score: 159792.842411 / AICc score: 5882136.842411 / BIC score: 165387.123087 Free parameters (model + branch lengths): 1691 WARNING: Number of free parameters (K=1691) is larger than alignment size (n=202). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 67 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE67/3_mltree/Q8TE67.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE67/3_mltree/Q8TE67.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE67/3_mltree/Q8TE67.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE67/3_mltree/Q8TE67.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8TE67/3_mltree/Q8TE67.raxml.log Analysis started: 07-Jul-2021 13:02:05 / finished: 07-Jul-2021 20:14:08 Elapsed time: 25922.231 seconds Consumed energy: 1808.740 Wh (= 9 km in an electric car, or 45 km with an e-scooter!)