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 16:28:40 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16389/2_msa/P16389_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16389/3_mltree/P16389 --seed 2 --threads 6 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16389/2_msa/P16389_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 519 sites WARNING: Sequences tr_F1P5Y9_F1P5Y9_CHICK_9031 and tr_A0A226MDZ7_A0A226MDZ7_CALSU_9009 are exactly identical! WARNING: Sequences sp_Q7T199_KCA10_CHICK_9031 and tr_A0A226PYF8_A0A226PYF8_COLVI_9014 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_G1NRG0_G1NRG0_MELGA_9103 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_U3KJP7_U3KJP7_FICAL_59894 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_R0L1C6_R0L1C6_ANAPL_8839 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091F1M2_A0A091F1M2_CORBR_85066 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091JJF6_A0A091JJF6_EGRGA_188379 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091WS81_A0A091WS81_NIPNI_128390 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A093HKM6_A0A093HKM6_STRCA_441894 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091V9H0_A0A091V9H0_OPIHO_30419 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A091G9V4_A0A091G9V4_9AVES_55661 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A0A0AYN4_A0A0A0AYN4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A2I0M055_A0A2I0M055_COLLI_8932 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A1V4KWW4_A0A1V4KWW4_PATFA_372326 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A226NIE9_A0A226NIE9_CALSU_9009 are exactly identical! WARNING: Sequences tr_Q7T1A0_Q7T1A0_CHICK_9031 and tr_A0A226PWN8_A0A226PWN8_COLVI_9014 are exactly identical! WARNING: Sequences sp_P63141_KCNA2_MOUSE_10090 and sp_P63142_KCNA2_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Z613_M3Z613_MUSPF_9669 and tr_A0A2Y9KVM7_A0A2Y9KVM7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z617_M3Z617_MUSPF_9669 and tr_F1PKN8_F1PKN8_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z617_M3Z617_MUSPF_9669 and tr_A0A2U3WVM7_A0A2U3WVM7_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z865_M3Z865_MUSPF_9669 and tr_A0A2Y9IZ48_A0A2Y9IZ48_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z868_M3Z868_MUSPF_9669 and tr_A0A2U3XN43_A0A2U3XN43_LEPWE_9713 are exactly identical! WARNING: Sequences sp_Q28527_KCNA4_MUSPF_9669 and tr_A0A2Y9JQR5_A0A2Y9JQR5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1NZA6_G1NZA6_MYOLU_59463 and tr_F6XE18_F6XE18_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1NZA6_G1NZA6_MYOLU_59463 and tr_I3NB95_I3NB95_ICTTR_43179 are exactly identical! WARNING: Sequences tr_A0A2I2YQ40_A0A2I2YQ40_GORGO_9595 and sp_P17658_KCNA6_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_H2Q593_H2Q593_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_F7DS72_F7DS72_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_A0A096N578_A0A096N578_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_A0A0D9SCZ1_A0A0D9SCZ1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_A0A2K5KMH7_A0A2K5KMH7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_A0A2K6AM91_A0A2K6AM91_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_A0A2K5XFR1_A0A2K5XFR1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3S108_G3S108_GORGO_9595 and tr_A0A2R8ZFZ7_A0A2R8ZFZ7_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q5REB6_Q5REB6_PONAB_9601 and sp_P22459_KCNA4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_Q5REB6_Q5REB6_PONAB_9601 and tr_F7IQA3_F7IQA3_CALJA_9483 are exactly identical! WARNING: Sequences tr_Q5REB6_Q5REB6_PONAB_9601 and tr_A0A0D9SD86_A0A0D9SD86_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2R7L1_H2R7L1_PANTR_9598 and tr_A0A2R8ZAS1_A0A2R8ZAS1_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5PQ46_W5PQ46_SHEEP_9940 and sp_P16389_KCNA2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_W5PQ46_W5PQ46_SHEEP_9940 and tr_F1MKB0_F1MKB0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5PQ46_W5PQ46_SHEEP_9940 and tr_A0A2R8ZH38_A0A2R8ZH38_PANPA_9597 are exactly identical! WARNING: Sequences tr_M4B0C1_M4B0C1_XIPMA_8083 and tr_A0A087YSG6_A0A087YSG6_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A087ZXP3_A0A087ZXP3_APIME_7460 and tr_A0A2A3EI71_A0A2A3EI71_APICC_94128 are exactly identical! WARNING: Sequences tr_H0XWH0_H0XWH0_OTOGA_30611 and tr_G7MIG1_G7MIG1_MACMU_9544 are exactly identical! WARNING: Sequences tr_H0XWH0_H0XWH0_OTOGA_30611 and tr_G7NW44_G7NW44_MACFA_9541 are exactly identical! WARNING: Sequences tr_H0XWH0_H0XWH0_OTOGA_30611 and tr_A0A0D9SAD5_A0A0D9SAD5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H0XWH0_H0XWH0_OTOGA_30611 and tr_A0A1S3GEU1_A0A1S3GEU1_DIPOR_10020 are exactly identical! WARNING: Sequences tr_A0A1D5R5K7_A0A1D5R5K7_MACMU_9544 and tr_A0A096N545_A0A096N545_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5R5K7_A0A1D5R5K7_MACMU_9544 and tr_A0A0D9SCZ0_A0A0D9SCZ0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5R5K7_A0A1D5R5K7_MACMU_9544 and tr_A0A2K5KLX0_A0A2K5KLX0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5R5K7_A0A1D5R5K7_MACMU_9544 and tr_A0A2K6B6G7_A0A2K6B6G7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5RG75_A0A1D5RG75_MACMU_9544 and tr_A0A0D9S345_A0A0D9S345_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5RG75_A0A1D5RG75_MACMU_9544 and tr_A0A2K6CQL3_A0A2K6CQL3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6ZSH4_F6ZSH4_MACMU_9544 and tr_A0A2K5L382_A0A2K5L382_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HL26_F7HL26_MACMU_9544 and tr_G7NW43_G7NW43_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HL26_F7HL26_MACMU_9544 and tr_A0A2K6B581_A0A2K6B581_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_U3KKD6_U3KKD6_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_A0A093GUI1_A0A093GUI1_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0ZNY9_H0ZNY9_TAEGU_59729 and tr_A0A218UFS4_A0A218UFS4_9PASE_299123 are exactly identical! WARNING: Sequences tr_A8WP18_A8WP18_CAEBR_6238 and tr_A0A2G5UUI2_A0A2G5UUI2_9PELO_1611254 are exactly identical! WARNING: Sequences tr_B4M6S3_B4M6S3_DROVI_7244 and tr_B4L2A7_B4L2A7_DROMO_7230 are exactly identical! WARNING: Sequences tr_A0A096NBR8_A0A096NBR8_PAPAN_9555 and tr_A0A2K5M8R4_A0A2K5M8R4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NBR8_A0A096NBR8_PAPAN_9555 and tr_A0A2K5XAS5_A0A2K5XAS5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3MQT4_A0A2I3MQT4_PAPAN_9555 and tr_A0A2K5KWS6_A0A2K5KWS6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091JLB9_A0A091JLB9_EGRGA_188379 and tr_A0A091VNW3_A0A091VNW3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JLB9_A0A091JLB9_EGRGA_188379 and tr_A0A091V6V6_A0A091V6V6_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JLB9_A0A091JLB9_EGRGA_188379 and tr_A0A0A0AVN4_A0A0A0AVN4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JQX9_A0A091JQX9_EGRGA_188379 and tr_A0A091VQM5_A0A091VQM5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091XL48_A0A091XL48_OPIHO_30419 and tr_A0A099ZVZ5_A0A099ZVZ5_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0M047_A0A2I0M047_COLLI_8932 and tr_A0A1V4KX76_A0A1V4KX76_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0MKC3_A0A2I0MKC3_COLLI_8932 and tr_A0A1V4K8E8_A0A1V4K8E8_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0S043_A0A0V0S043_9BILA_6336 and tr_A0A0V0WDR1_A0A0V0WDR1_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V0S043_A0A0V0S043_9BILA_6336 and tr_A0A0V1LNM2_A0A0V1LNM2_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0S043_A0A0V0S043_9BILA_6336 and tr_A0A0V1NZG4_A0A0V1NZG4_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1E1F0_A0A0V1E1F0_TRIPS_6337 and tr_A0A0V1N354_A0A0V1N354_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A0V1E1F0_A0A0V1E1F0_TRIPS_6337 and tr_A0A0V1H589_A0A0V1H589_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A226NI43_A0A226NI43_CALSU_9009 and tr_A0A226PWX2_A0A226PWX2_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5KNT8_A0A2K5KNT8_CERAT_9531 and tr_A0A2K5XWN5_A0A2K5XWN5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3V2M1_A0A2U3V2M1_TURTR_9739 and tr_A0A2Y9P953_A0A2Y9P953_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V2M1_A0A2U3V2M1_TURTR_9739 and tr_A0A2Y9EPE4_A0A2Y9EPE4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3WF14_A0A2U3WF14_ODORO_9708 and tr_A0A2U3XN46_A0A2U3XN46_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3X4T2_A0A2U3X4T2_ODORO_9708 and tr_A0A2U3Y7L2_A0A2U3Y7L2_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 82 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/P16389/3_mltree/P16389.raxml.reduced.phy Alignment comprises 1 partitions and 519 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 519 / 519 Gaps: 14.37 % Invariant sites: 0.19 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16389/3_mltree/P16389.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 260 / 20800 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -506672.117982] Initial branch length optimization [00:00:07 -418027.030142] Model parameter optimization (eps = 10.000000) [00:01:40 -416615.385811] AUTODETECT spr round 1 (radius: 5) [00:05:16 -296425.964962] AUTODETECT spr round 2 (radius: 10) [00:09:25 -223862.734043] AUTODETECT spr round 3 (radius: 15) [00:14:18 -182440.100227] AUTODETECT spr round 4 (radius: 20) [00:19:01 -171271.987898] AUTODETECT spr round 5 (radius: 25) [00:26:28 -161115.599974] SPR radius for FAST iterations: 25 (autodetect) [00:26:28 -161115.599974] Model parameter optimization (eps = 3.000000) [00:27:09 -160909.088270] FAST spr round 1 (radius: 25) [00:31:27 -143306.012448] FAST spr round 2 (radius: 25) [00:34:30 -142620.680811] FAST spr round 3 (radius: 25) [00:37:12 -142478.963429] FAST spr round 4 (radius: 25) [00:39:37 -142460.208260] FAST spr round 5 (radius: 25) [00:41:52 -142457.378287] FAST spr round 6 (radius: 25) [00:44:03 -142457.378285] Model parameter optimization (eps = 1.000000) [00:44:29 -142446.538666] SLOW spr round 1 (radius: 5) [00:47:39 -142421.926983] SLOW spr round 2 (radius: 5) [00:50:42 -142415.104163] SLOW spr round 3 (radius: 5) [00:53:42 -142415.037802] SLOW spr round 4 (radius: 10) [00:56:47 -142413.841811] SLOW spr round 5 (radius: 5) [01:00:40 -142413.488632] SLOW spr round 6 (radius: 5) [01:03:58 -142412.903816] SLOW spr round 7 (radius: 5) [01:06:59 -142412.903767] SLOW spr round 8 (radius: 10) [01:09:59 -142412.903767] SLOW spr round 9 (radius: 15) [01:15:27 -142412.782639] SLOW spr round 10 (radius: 5) [01:19:22 -142412.782621] SLOW spr round 11 (radius: 10) [01:23:01 -142412.782621] SLOW spr round 12 (radius: 15) [01:28:07 -142412.782621] SLOW spr round 13 (radius: 20) [01:40:03 -142412.782621] SLOW spr round 14 (radius: 25) [01:40:27] [worker #1] ML tree search #2, logLikelihood: -142404.969676 [01:55:13 -142412.782621] Model parameter optimization (eps = 0.100000) [01:55:29] [worker #0] ML tree search #1, logLikelihood: -142412.651624 [01:55:29 -506169.519205] Initial branch length optimization [01:55:35 -420937.688816] Model parameter optimization (eps = 10.000000) [01:56:48 -419667.548428] AUTODETECT spr round 1 (radius: 5) [02:00:24 -303429.749656] AUTODETECT spr round 2 (radius: 10) [02:04:32 -214507.676527] AUTODETECT spr round 3 (radius: 15) [02:08:51 -185227.391981] AUTODETECT spr round 4 (radius: 20) [02:14:04 -165987.822709] AUTODETECT spr round 5 (radius: 25) [02:22:21 -162682.369529] SPR radius for FAST iterations: 25 (autodetect) [02:22:21 -162682.369529] Model parameter optimization (eps = 3.000000) [02:23:09 -162474.227256] FAST spr round 1 (radius: 25) [02:27:37 -143230.318216] FAST spr round 2 (radius: 25) [02:30:48 -142516.216791] FAST spr round 3 (radius: 25) [02:33:33 -142456.316386] FAST spr round 4 (radius: 25) [02:35:56 -142448.759894] FAST spr round 5 (radius: 25) [02:38:13 -142438.162769] FAST spr round 6 (radius: 25) [02:40:23 -142436.251215] FAST spr round 7 (radius: 25) [02:42:30 -142436.250548] Model parameter optimization (eps = 1.000000) [02:42:50 -142429.425401] SLOW spr round 1 (radius: 5) [02:45:51 -142405.699969] SLOW spr round 2 (radius: 5) [02:48:51 -142404.873368] SLOW spr round 3 (radius: 5) [02:51:46 -142404.872456] SLOW spr round 4 (radius: 10) [02:53:36] [worker #2] ML tree search #3, logLikelihood: -142419.533077 [02:54:46 -142404.065332] SLOW spr round 5 (radius: 5) [02:58:29 -142404.065235] SLOW spr round 6 (radius: 10) [03:01:56 -142404.065197] SLOW spr round 7 (radius: 15) [03:07:09 -142404.065194] SLOW spr round 8 (radius: 20) [03:19:08 -142404.065192] SLOW spr round 9 (radius: 25) [03:19:49] [worker #1] ML tree search #5, logLikelihood: -142400.465548 [03:34:30 -142404.065190] Model parameter optimization (eps = 0.100000) [03:34:39] [worker #0] ML tree search #4, logLikelihood: -142404.017978 [03:34:39 -508266.771504] Initial branch length optimization [03:34:46 -422487.368871] Model parameter optimization (eps = 10.000000) [03:36:04 -421215.179357] AUTODETECT spr round 1 (radius: 5) [03:39:40 -300834.045419] AUTODETECT spr round 2 (radius: 10) [03:43:46 -223949.995135] AUTODETECT spr round 3 (radius: 15) [03:49:10 -194679.022813] AUTODETECT spr round 4 (radius: 20) [03:54:15 -183865.442650] AUTODETECT spr round 5 (radius: 25) [04:01:01 -171217.312405] SPR radius for FAST iterations: 25 (autodetect) [04:01:01 -171217.312405] Model parameter optimization (eps = 3.000000) [04:01:34 -171083.624799] FAST spr round 1 (radius: 25) [04:06:10 -145049.318472] FAST spr round 2 (radius: 25) [04:09:20 -143005.610248] FAST spr round 3 (radius: 25) [04:11:58 -142531.446673] FAST spr round 4 (radius: 25) [04:14:26 -142468.503317] FAST spr round 5 (radius: 25) [04:16:40 -142466.656751] FAST spr round 6 (radius: 25) [04:18:48 -142466.656123] Model parameter optimization (eps = 1.000000) [04:19:15 -142445.021249] SLOW spr round 1 (radius: 5) [04:22:17 -142417.747591] SLOW spr round 2 (radius: 5) [04:25:16 -142417.468688] SLOW spr round 3 (radius: 5) [04:28:13 -142414.112564] SLOW spr round 4 (radius: 5) [04:31:05 -142414.112418] SLOW spr round 5 (radius: 10) [04:34:04 -142414.112330] SLOW spr round 6 (radius: 15) [04:39:41 -142414.112329] SLOW spr round 7 (radius: 20) [04:51:09 -142414.112328] SLOW spr round 8 (radius: 25) [05:06:09 -142414.112328] Model parameter optimization (eps = 0.100000) [05:06:25] [worker #0] ML tree search #7, logLikelihood: -142414.007601 [05:06:25 -506538.438537] Initial branch length optimization [05:06:32 -418263.533721] Model parameter optimization (eps = 10.000000) [05:07:59 -416913.472437] AUTODETECT spr round 1 (radius: 5) [05:11:34 -299206.641253] AUTODETECT spr round 2 (radius: 10) [05:15:42 -218308.556336] AUTODETECT spr round 3 (radius: 15) [05:20:42 -190136.431883] AUTODETECT spr round 4 (radius: 20) [05:27:06 -166513.755433] AUTODETECT spr round 5 (radius: 25) [05:27:08] [worker #2] ML tree search #6, logLikelihood: -142401.436750 [05:37:20 -162103.857287] SPR radius for FAST iterations: 25 (autodetect) [05:37:20 -162103.857287] Model parameter optimization (eps = 3.000000) [05:38:13 -161884.244100] FAST spr round 1 (radius: 25) [05:42:27] [worker #1] ML tree search #8, logLikelihood: -142400.270035 [05:42:39 -144020.206618] FAST spr round 2 (radius: 25) [05:45:48 -142527.200250] FAST spr round 3 (radius: 25) [05:48:28 -142458.027203] FAST spr round 4 (radius: 25) [05:50:51 -142445.083354] FAST spr round 5 (radius: 25) [05:53:05 -142445.081621] Model parameter optimization (eps = 1.000000) [05:53:29 -142435.721025] SLOW spr round 1 (radius: 5) [05:56:37 -142414.261392] SLOW spr round 2 (radius: 5) [05:59:42 -142412.821955] SLOW spr round 3 (radius: 5) [06:02:44 -142412.821573] SLOW spr round 4 (radius: 10) [06:05:52 -142408.219522] SLOW spr round 5 (radius: 5) [06:09:42 -142408.218908] SLOW spr round 6 (radius: 10) [06:13:09 -142408.218878] SLOW spr round 7 (radius: 15) [06:18:27 -142408.218877] SLOW spr round 8 (radius: 20) [06:30:36 -142408.218877] SLOW spr round 9 (radius: 25) [06:46:10 -142408.218877] Model parameter optimization (eps = 0.100000) [06:46:20] [worker #0] ML tree search #10, logLikelihood: -142408.126377 [06:46:20 -504136.076131] Initial branch length optimization [06:46:29 -418672.450371] Model parameter optimization (eps = 10.000000) [06:47:47 -417428.872466] AUTODETECT spr round 1 (radius: 5) [06:51:22 -294531.898023] AUTODETECT spr round 2 (radius: 10) [06:55:28 -218830.227333] AUTODETECT spr round 3 (radius: 15) [07:00:15 -185680.913204] AUTODETECT spr round 4 (radius: 20) [07:05:21 -166625.861077] AUTODETECT spr round 5 (radius: 25) [07:11:49 -163340.287576] SPR radius for FAST iterations: 25 (autodetect) [07:11:49 -163340.287576] Model parameter optimization (eps = 3.000000) [07:12:31 -163133.599164] FAST spr round 1 (radius: 25) [07:14:29] [worker #2] ML tree search #9, logLikelihood: -142417.055892 [07:16:30 -143397.426848] FAST spr round 2 (radius: 25) [07:19:20 -142539.112218] FAST spr round 3 (radius: 25) [07:21:56 -142481.751655] FAST spr round 4 (radius: 25) [07:24:15 -142471.464900] FAST spr round 5 (radius: 25) [07:26:25 -142471.464562] Model parameter optimization (eps = 1.000000) [07:26:54 -142460.880926] SLOW spr round 1 (radius: 5) [07:29:55 -142430.124350] SLOW spr round 2 (radius: 5) [07:32:57 -142424.051058] SLOW spr round 3 (radius: 5) [07:33:52] [worker #1] ML tree search #11, logLikelihood: -142418.116833 [07:35:59 -142423.869424] SLOW spr round 4 (radius: 5) [07:38:54 -142423.869007] SLOW spr round 5 (radius: 10) [07:41:54 -142423.868940] SLOW spr round 6 (radius: 15) [07:47:29 -142423.868924] SLOW spr round 7 (radius: 20) [07:58:58 -142423.868910] SLOW spr round 8 (radius: 25) [08:13:52 -142423.468286] SLOW spr round 9 (radius: 5) [08:18:03 -142423.467617] SLOW spr round 10 (radius: 10) [08:21:46 -142423.467429] SLOW spr round 11 (radius: 15) [08:26:48 -142423.467361] SLOW spr round 12 (radius: 20) [08:37:56 -142423.467330] SLOW spr round 13 (radius: 25) [08:49:12] [worker #2] ML tree search #12, logLikelihood: -142417.274911 [08:51:09 -142423.467312] Model parameter optimization (eps = 0.100000) [08:51:17] [worker #0] ML tree search #13, logLikelihood: -142423.436624 [08:51:17 -504213.648711] Initial branch length optimization [08:51:24 -419896.877310] Model parameter optimization (eps = 10.000000) [08:53:00 -418647.031454] AUTODETECT spr round 1 (radius: 5) [08:56:33 -306337.585393] AUTODETECT spr round 2 (radius: 10) [09:00:37 -229110.778309] AUTODETECT spr round 3 (radius: 15) [09:05:58 -181909.646128] AUTODETECT spr round 4 (radius: 20) [09:10:47 -166959.236030] AUTODETECT spr round 5 (radius: 25) [09:16:58 -164365.732552] SPR radius for FAST iterations: 25 (autodetect) [09:16:58 -164365.732552] Model parameter optimization (eps = 3.000000) [09:17:33 -164194.617309] FAST spr round 1 (radius: 25) [09:21:59 -144212.089892] FAST spr round 2 (radius: 25) [09:22:34] [worker #1] ML tree search #14, logLikelihood: -142402.960713 [09:25:10 -142473.754024] FAST spr round 3 (radius: 25) [09:27:52 -142441.559902] FAST spr round 4 (radius: 25) [09:30:11 -142440.929759] FAST spr round 5 (radius: 25) [09:32:23 -142440.927195] Model parameter optimization (eps = 1.000000) [09:32:46 -142438.023718] SLOW spr round 1 (radius: 5) [09:35:55 -142412.310728] SLOW spr round 2 (radius: 5) [09:38:58 -142410.208220] SLOW spr round 3 (radius: 5) [09:41:56 -142410.207885] SLOW spr round 4 (radius: 10) [09:44:58 -142408.253260] SLOW spr round 5 (radius: 5) [09:48:42 -142408.253113] SLOW spr round 6 (radius: 10) [09:52:08 -142408.252931] SLOW spr round 7 (radius: 15) [09:57:25 -142408.252920] SLOW spr round 8 (radius: 20) [10:09:39 -142408.252910] SLOW spr round 9 (radius: 25) [10:24:57 -142408.252899] Model parameter optimization (eps = 0.100000) [10:25:05] [worker #0] ML tree search #16, logLikelihood: -142408.225829 [10:25:05 -508313.777831] Initial branch length optimization [10:25:12 -420834.536262] Model parameter optimization (eps = 10.000000) [10:26:44 -419471.208890] AUTODETECT spr round 1 (radius: 5) [10:30:22 -300256.090399] AUTODETECT spr round 2 (radius: 10) [10:33:08] [worker #2] ML tree search #15, logLikelihood: -142410.427289 [10:34:29 -228529.358105] AUTODETECT spr round 3 (radius: 15) [10:40:13 -187514.094793] AUTODETECT spr round 4 (radius: 20) [10:45:58 -165430.664392] AUTODETECT spr round 5 (radius: 25) [10:54:05 -162339.621405] SPR radius for FAST iterations: 25 (autodetect) [10:54:05 -162339.621405] Model parameter optimization (eps = 3.000000) [10:54:39 -162147.935219] FAST spr round 1 (radius: 25) [10:59:06 -143586.513967] FAST spr round 2 (radius: 25) [11:02:12 -142518.984364] FAST spr round 3 (radius: 25) [11:04:47 -142465.791080] FAST spr round 4 (radius: 25) [11:07:05 -142463.525919] FAST spr round 5 (radius: 25) [11:09:18 -142462.466937] FAST spr round 6 (radius: 25) [11:10:59] [worker #1] ML tree search #17, logLikelihood: -142402.044242 [11:11:27 -142462.466297] Model parameter optimization (eps = 1.000000) [11:11:51 -142456.373271] SLOW spr round 1 (radius: 5) [11:14:56 -142427.671089] SLOW spr round 2 (radius: 5) [11:17:59 -142426.200533] SLOW spr round 3 (radius: 5) [11:20:59 -142425.426599] SLOW spr round 4 (radius: 5) [11:23:52 -142425.426443] SLOW spr round 5 (radius: 10) [11:26:55 -142423.471729] SLOW spr round 6 (radius: 5) [11:30:40 -142423.471677] SLOW spr round 7 (radius: 10) [11:34:05 -142423.471674] SLOW spr round 8 (radius: 15) [11:39:27 -142423.471672] SLOW spr round 9 (radius: 20) [11:51:57 -142423.471670] SLOW spr round 10 (radius: 25) [12:06:06] [worker #2] ML tree search #18, logLikelihood: -142412.506208 [12:07:40 -142423.471668] Model parameter optimization (eps = 0.100000) [12:07:49] [worker #0] ML tree search #19, logLikelihood: -142423.461230 [12:40:27] [worker #1] ML tree search #20, logLikelihood: -142410.681631 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.202611,0.214154) (0.217399,0.328706) (0.292628,0.753730) (0.287361,2.312720) 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: -142400.270035 AIC score: 288810.540069 / AICc score: 8332870.540069 / BIC score: 297335.607355 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=519). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 175 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16389/3_mltree/P16389.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16389/3_mltree/P16389.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16389/3_mltree/P16389.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16389/3_mltree/P16389.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P16389/3_mltree/P16389.raxml.log Analysis started: 04-Jul-2021 16:28:40 / finished: 05-Jul-2021 05:09:07 Elapsed time: 45627.675 seconds Consumed energy: 4144.237 Wh (= 21 km in an electric car, or 104 km with an e-scooter!)