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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 03-Jul-2021 17:04:57 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/2_msa/P52848_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/3_mltree/P52848 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/2_msa/P52848_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 382 sites WARNING: Sequences tr_A0A2R8Q2T8_A0A2R8Q2T8_DANRE_7955 and tr_E7F825_E7F825_DANRE_7955 are exactly identical! WARNING: Sequences tr_A0A1D5P4U9_A0A1D5P4U9_CHICK_9031 and tr_A0A226MVT5_A0A226MVT5_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5P4U9_A0A1D5P4U9_CHICK_9031 and tr_A0A226P8F4_A0A226P8F4_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q673U1_HS3S2_MOUSE_10090 and sp_Q80W66_HS3S2_RAT_10116 are exactly identical! WARNING: Sequences tr_M3YQQ9_M3YQQ9_MUSPF_9669 and tr_A0A2Y9IKZ5_A0A2Y9IKZ5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_A0A2J8U159_A0A2J8U159_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_F7IAJ7_F7IAJ7_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_G7P3M0_G7P3M0_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_A0A096MX52_A0A096MX52_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_A0A2K5L8U9_A0A2K5L8U9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_A0A2K6BWI1_A0A2K6BWI1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_A0A2K5XKT5_A0A2K5XKT5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3QFL4_G3QFL4_GORGO_9595 and tr_A0A2R8ZRJ5_A0A2R8ZRJ5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QTP6_G3QTP6_GORGO_9595 and tr_G7N251_G7N251_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QTP6_G3QTP6_GORGO_9595 and tr_A0A096P4L1_A0A096P4L1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QTP6_G3QTP6_GORGO_9595 and tr_A0A2K5MRU1_A0A2K5MRU1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QTP6_G3QTP6_GORGO_9595 and tr_A0A2K6BWF2_A0A2K6BWF2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QTP6_G3QTP6_GORGO_9595 and tr_A0A2K5Z088_A0A2K5Z088_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and tr_H2QAR3_H2QAR3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and sp_Q9Y278_HS3S2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and tr_A0A096NHD6_A0A096NHD6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and tr_A0A0D9R3M4_A0A0D9R3M4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and tr_A0A2K5N5Q6_A0A2K5N5Q6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and tr_A0A2K6CDE8_A0A2K6CDE8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RFC1_G3RFC1_GORGO_9595 and tr_A0A2R9B8Q8_A0A2R9B8Q8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SKG0_G3SKG0_GORGO_9595 and tr_H2QQ28_H2QQ28_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SKG0_G3SKG0_GORGO_9595 and tr_A0A2R9AL62_A0A2R9AL62_PANPA_9597 are exactly identical! WARNING: Sequences tr_E2RBI5_E2RBI5_CANLF_9615 and tr_A0A384CHE7_A0A384CHE7_URSMA_29073 are exactly identical! WARNING: Sequences tr_F6XY50_F6XY50_CANLF_9615 and tr_F6SPQ2_F6SPQ2_HORSE_9796 are exactly identical! WARNING: Sequences tr_H2QQ27_H2QQ27_PANTR_9598 and tr_A0A2R9BTR9_A0A2R9BTR9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R584_H2R584_PANTR_9598 and tr_A0A2R9AYT7_A0A2R9AYT7_PANPA_9597 are exactly identical! WARNING: Sequences tr_M4A4T6_M4A4T6_XIPMA_8083 and tr_A0A087Y103_A0A087Y103_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NK09_A0A158NK09_ATTCE_12957 and tr_A0A195B3X9_A0A195B3X9_9HYME_520822 are exactly identical! WARNING: Sequences sp_P52848_NDST1_HUMAN_9606 and tr_F7GSZ9_F7GSZ9_MACMU_9544 are exactly identical! WARNING: Sequences sp_P52848_NDST1_HUMAN_9606 and tr_G7P8P9_G7P8P9_MACFA_9541 are exactly identical! WARNING: Sequences sp_P52848_NDST1_HUMAN_9606 and tr_A0A0D9RG83_A0A0D9RG83_CHLSB_60711 are exactly identical! WARNING: Sequences sp_P52848_NDST1_HUMAN_9606 and tr_A0A2K5LGQ2_A0A2K5LGQ2_CERAT_9531 are exactly identical! WARNING: Sequences sp_P52848_NDST1_HUMAN_9606 and tr_A0A2K6CHB2_A0A2K6CHB2_MACNE_9545 are exactly identical! WARNING: Sequences sp_P52848_NDST1_HUMAN_9606 and tr_A0A2K5ZMK8_A0A2K5ZMK8_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7DZJ3_F7DZJ3_MACMU_9544 and tr_A0A096MX80_A0A096MX80_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DZJ3_F7DZJ3_MACMU_9544 and tr_A0A2K5NHZ7_A0A2K5NHZ7_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DZJ3_F7DZJ3_MACMU_9544 and tr_A0A2K5YXZ7_A0A2K5YXZ7_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HFM8_F7HFM8_MACMU_9544 and tr_G7P653_G7P653_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HFM8_F7HFM8_MACMU_9544 and tr_A0A2K6CK99_A0A2K6CK99_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZFK1_H0ZFK1_TAEGU_59729 and tr_A0A091EAX4_A0A091EAX4_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZFK1_H0ZFK1_TAEGU_59729 and tr_A0A093PIZ9_A0A093PIZ9_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZNZ3_H0ZNZ3_TAEGU_59729 and tr_A0A218UX55_A0A218UX55_9PASE_299123 are exactly identical! WARNING: Sequences tr_F4W426_F4W426_ACREC_103372 and tr_A0A195DWC5_A0A195DWC5_9HYME_471704 are exactly identical! WARNING: Sequences tr_D2H9J8_D2H9J8_AILME_9646 and tr_A0A384BYL3_A0A384BYL3_URSMA_29073 are exactly identical! WARNING: Sequences tr_B3S367_B3S367_TRIAD_10228 and tr_A0A369RY91_A0A369RY91_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A044TS16_A0A044TS16_ONCVO_6282 and tr_A0A182E006_A0A182E006_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096MY37_A0A096MY37_PAPAN_9555 and tr_A0A2K5L8W4_A0A2K5L8W4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MYQ6_A0A096MYQ6_PAPAN_9555 and tr_A0A2K5LUT4_A0A2K5LUT4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MYQ6_A0A096MYQ6_PAPAN_9555 and tr_A0A2K5YYW3_A0A2K5YYW3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096P2Z1_A0A096P2Z1_PAPAN_9555 and tr_A0A0D9R9H6_A0A0D9R9H6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096P2Z1_A0A096P2Z1_PAPAN_9555 and tr_A0A2K5P3K2_A0A2K5P3K2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0N0BIQ6_A0A0N0BIQ6_9HYME_166423 and tr_A0A2A3EGP8_A0A2A3EGP8_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A091UKI3_A0A091UKI3_NIPNI_128390 and tr_A0A0A0ANY3_A0A0A0ANY3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091V5G6_A0A091V5G6_NIPNI_128390 and tr_A0A0A0AZE7_A0A0A0AZE7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091V5G6_A0A091V5G6_NIPNI_128390 and tr_A0A2I0MA77_A0A2I0MA77_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091V5G6_A0A091V5G6_NIPNI_128390 and tr_A0A1V4KVX8_A0A1V4KVX8_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A087QYU7_A0A087QYU7_APTFO_9233 and tr_A0A1V4KJD4_A0A1V4KJD4_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V1CKS7_A0A0V1CKS7_TRIBR_45882 and tr_A0A0V0WDB8_A0A0V0WDB8_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CKS7_A0A0V1CKS7_TRIBR_45882 and tr_A0A0V1L028_A0A0V1L028_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A151X1F8_A0A151X1F8_9HYME_64791 and tr_A0A195EUE6_A0A195EUE6_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A151X1F8_A0A151X1F8_9HYME_64791 and tr_A0A195CJT5_A0A195CJT5_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A2U4A8M0_A0A2U4A8M0_TURTR_9739 and tr_A0A2Y9PB65_A0A2Y9PB65_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A8M0_A0A2U4A8M0_TURTR_9739 and tr_A0A2Y9SUA7_A0A2Y9SUA7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4A8M6_A0A2U4A8M6_TURTR_9739 and tr_A0A2Y9PEE9_A0A2Y9PEE9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3W465_A0A2U3W465_ODORO_9708 and tr_A0A2U3YC72_A0A2U3YC72_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 70 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/3_mltree/P52848.raxml.reduced.phy Alignment comprises 1 partitions and 382 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 382 / 382 Gaps: 14.85 % Invariant sites: 0.26 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/3_mltree/P52848.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 / 191 / 15280 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -550048.591775] Initial branch length optimization [00:00:06 -439403.025349] Model parameter optimization (eps = 10.000000) [00:00:55 -438495.337678] AUTODETECT spr round 1 (radius: 5) [00:04:00 -277402.200066] AUTODETECT spr round 2 (radius: 10) [00:07:19 -206830.470083] AUTODETECT spr round 3 (radius: 15) [00:10:38 -161822.468521] AUTODETECT spr round 4 (radius: 20) [00:14:16 -137259.252151] AUTODETECT spr round 5 (radius: 25) [00:19:52 -130550.966316] SPR radius for FAST iterations: 25 (autodetect) [00:19:52 -130550.966316] Model parameter optimization (eps = 3.000000) [00:20:21 -130295.331858] FAST spr round 1 (radius: 25) [00:23:42 -109050.754721] FAST spr round 2 (radius: 25) [00:26:27 -105232.480691] FAST spr round 3 (radius: 25) [00:28:55 -104605.828645] FAST spr round 4 (radius: 25) [00:31:14 -104562.991428] FAST spr round 5 (radius: 25) [00:33:16 -104557.185000] FAST spr round 6 (radius: 25) [00:35:15 -104546.981527] FAST spr round 7 (radius: 25) [00:37:10 -104543.030645] FAST spr round 8 (radius: 25) [00:39:05 -104535.383306] FAST spr round 9 (radius: 25) [00:40:59 -104535.382445] Model parameter optimization (eps = 1.000000) [00:41:15 -104533.592925] SLOW spr round 1 (radius: 5) [00:43:54 -104509.065132] SLOW spr round 2 (radius: 5) [00:46:26 -104507.934538] SLOW spr round 3 (radius: 5) [00:48:54 -104507.922204] SLOW spr round 4 (radius: 10) [00:51:25 -104507.556369] SLOW spr round 5 (radius: 5) [00:54:32 -104507.556019] SLOW spr round 6 (radius: 10) [00:57:25 -104507.556018] SLOW spr round 7 (radius: 15) [01:01:10 -104507.556017] SLOW spr round 8 (radius: 20) [01:07:03 -104507.556017] SLOW spr round 9 (radius: 25) [01:14:31 -104507.556016] Model parameter optimization (eps = 0.100000) [01:14:41] [worker #0] ML tree search #1, logLikelihood: -104507.418494 [01:14:41 -550817.445546] Initial branch length optimization [01:14:49 -439105.046007] Model parameter optimization (eps = 10.000000) [01:15:37 -438174.398801] AUTODETECT spr round 1 (radius: 5) [01:18:34 -274167.560403] AUTODETECT spr round 2 (radius: 10) [01:21:45 -197066.106084] AUTODETECT spr round 3 (radius: 15) [01:23:51] [worker #2] ML tree search #3, logLikelihood: -104519.119906 [01:24:07] [worker #1] ML tree search #2, logLikelihood: -104507.657986 [01:24:55 -160656.592102] AUTODETECT spr round 4 (radius: 20) [01:28:40 -141338.104720] AUTODETECT spr round 5 (radius: 25) [01:32:57 -128617.429552] SPR radius for FAST iterations: 25 (autodetect) [01:32:57 -128617.429552] Model parameter optimization (eps = 3.000000) [01:33:25 -128368.980414] FAST spr round 1 (radius: 25) [01:36:55 -106648.653839] FAST spr round 2 (radius: 25) [01:39:40 -104721.634402] FAST spr round 3 (radius: 25) [01:41:56 -104555.882381] FAST spr round 4 (radius: 25) [01:44:01 -104546.930890] FAST spr round 5 (radius: 25) [01:45:58 -104546.930828] Model parameter optimization (eps = 1.000000) [01:46:14 -104544.076902] SLOW spr round 1 (radius: 5) [01:48:50 -104522.782612] SLOW spr round 2 (radius: 5) [01:51:27 -104518.285498] SLOW spr round 3 (radius: 5) [01:54:00 -104517.915873] SLOW spr round 4 (radius: 5) [01:56:28 -104517.915862] SLOW spr round 5 (radius: 10) [01:59:00 -104517.915857] SLOW spr round 6 (radius: 15) [02:03:05 -104508.329103] SLOW spr round 7 (radius: 5) [02:06:21 -104508.328941] SLOW spr round 8 (radius: 10) [02:09:25 -104506.940828] SLOW spr round 9 (radius: 5) [02:12:26 -104506.940687] SLOW spr round 10 (radius: 10) [02:15:15 -104506.940668] SLOW spr round 11 (radius: 15) [02:19:02 -104506.940666] SLOW spr round 12 (radius: 20) [02:24:49 -104506.940665] SLOW spr round 13 (radius: 25) [02:32:06 -104506.940663] Model parameter optimization (eps = 0.100000) [02:32:17] [worker #0] ML tree search #4, logLikelihood: -104506.770569 [02:32:17 -548687.435806] Initial branch length optimization [02:32:22 -437759.116432] Model parameter optimization (eps = 10.000000) [02:33:08 -436807.026443] AUTODETECT spr round 1 (radius: 5) [02:36:08 -273561.186728] AUTODETECT spr round 2 (radius: 10) [02:36:26] [worker #1] ML tree search #5, logLikelihood: -104504.396604 [02:39:22 -195684.605791] AUTODETECT spr round 3 (radius: 15) [02:42:39 -151254.678008] AUTODETECT spr round 4 (radius: 20) [02:45:52] [worker #2] ML tree search #6, logLikelihood: -104516.918249 [02:46:24 -136408.788129] AUTODETECT spr round 5 (radius: 25) [02:51:29 -127579.770668] SPR radius for FAST iterations: 25 (autodetect) [02:51:29 -127579.770668] Model parameter optimization (eps = 3.000000) [02:52:01 -127297.457674] FAST spr round 1 (radius: 25) [02:55:42 -105933.728516] FAST spr round 2 (radius: 25) [02:58:17 -104702.229329] FAST spr round 3 (radius: 25) [03:00:33 -104602.785190] FAST spr round 4 (radius: 25) [03:02:38 -104601.131930] FAST spr round 5 (radius: 25) [03:04:37 -104601.129801] Model parameter optimization (eps = 1.000000) [03:04:55 -104597.435261] SLOW spr round 1 (radius: 5) [03:07:32 -104545.683555] SLOW spr round 2 (radius: 5) [03:10:09 -104534.451481] SLOW spr round 3 (radius: 5) [03:12:44 -104527.419051] SLOW spr round 4 (radius: 5) [03:15:13 -104526.270475] SLOW spr round 5 (radius: 5) [03:17:40 -104526.270452] SLOW spr round 6 (radius: 10) [03:20:13 -104525.793021] SLOW spr round 7 (radius: 5) [03:23:22 -104525.792964] SLOW spr round 8 (radius: 10) [03:26:16 -104525.792954] SLOW spr round 9 (radius: 15) [03:30:05 -104525.311416] SLOW spr round 10 (radius: 5) [03:33:24 -104525.311406] SLOW spr round 11 (radius: 10) [03:36:28 -104525.311396] SLOW spr round 12 (radius: 15) [03:36:52] [worker #1] ML tree search #8, logLikelihood: -104507.901959 [03:40:13 -104525.311387] SLOW spr round 13 (radius: 20) [03:46:22 -104525.311377] SLOW spr round 14 (radius: 25) [03:52:44] [worker #2] ML tree search #9, logLikelihood: -104526.843986 [03:53:56 -104525.311368] Model parameter optimization (eps = 0.100000) [03:54:02] [worker #0] ML tree search #7, logLikelihood: -104525.268666 [03:54:03 -552326.035023] Initial branch length optimization [03:54:09 -442885.531905] Model parameter optimization (eps = 10.000000) [03:55:08 -442016.468734] AUTODETECT spr round 1 (radius: 5) [03:58:09 -272691.936219] AUTODETECT spr round 2 (radius: 10) [04:01:25 -202075.508238] AUTODETECT spr round 3 (radius: 15) [04:04:34 -151678.680160] AUTODETECT spr round 4 (radius: 20) [04:08:56 -126759.190144] AUTODETECT spr round 5 (radius: 25) [04:13:23 -123783.880088] SPR radius for FAST iterations: 25 (autodetect) [04:13:23 -123783.880088] Model parameter optimization (eps = 3.000000) [04:13:46 -123560.568946] FAST spr round 1 (radius: 25) [04:17:08 -105710.390706] FAST spr round 2 (radius: 25) [04:19:40 -104677.323737] FAST spr round 3 (radius: 25) [04:21:57 -104562.071411] FAST spr round 4 (radius: 25) [04:24:04 -104548.448560] FAST spr round 5 (radius: 25) [04:26:04 -104542.077879] FAST spr round 6 (radius: 25) [04:28:01 -104538.601854] FAST spr round 7 (radius: 25) [04:29:57 -104536.961222] FAST spr round 8 (radius: 25) [04:31:52 -104536.961018] Model parameter optimization (eps = 1.000000) [04:32:08 -104532.910535] SLOW spr round 1 (radius: 5) [04:34:43 -104516.062036] SLOW spr round 2 (radius: 5) [04:37:18 -104513.268131] SLOW spr round 3 (radius: 5) [04:39:50 -104511.361449] SLOW spr round 4 (radius: 5) [04:42:17 -104511.360811] SLOW spr round 5 (radius: 10) [04:44:49 -104511.360679] SLOW spr round 6 (radius: 15) [04:48:59 -104511.360628] SLOW spr round 7 (radius: 20) [04:54:52 -104511.360607] SLOW spr round 8 (radius: 25) [05:02:32 -104511.360597] Model parameter optimization (eps = 0.100000) [05:02:38] [worker #0] ML tree search #10, logLikelihood: -104511.323251 [05:02:39 -552128.539614] Initial branch length optimization [05:02:46 -438473.034356] Model parameter optimization (eps = 10.000000) [05:03:27 -437561.933826] AUTODETECT spr round 1 (radius: 5) [05:06:30 -278811.831736] AUTODETECT spr round 2 (radius: 10) [05:09:39 -196195.560611] AUTODETECT spr round 3 (radius: 15) [05:13:01 -149806.227619] AUTODETECT spr round 4 (radius: 20) [05:15:12] [worker #2] ML tree search #12, logLikelihood: -104520.922405 [05:16:48 -134385.742683] AUTODETECT spr round 5 (radius: 25) [05:19:11] [worker #1] ML tree search #11, logLikelihood: -104515.882051 [05:21:22 -128872.632119] SPR radius for FAST iterations: 25 (autodetect) [05:21:22 -128872.632119] Model parameter optimization (eps = 3.000000) [05:21:54 -128508.195266] FAST spr round 1 (radius: 25) [05:25:11 -105879.969548] FAST spr round 2 (radius: 25) [05:27:42 -104690.071573] FAST spr round 3 (radius: 25) [05:29:59 -104614.177870] FAST spr round 4 (radius: 25) [05:32:08 -104592.429045] FAST spr round 5 (radius: 25) [05:34:09 -104589.573119] FAST spr round 6 (radius: 25) [05:36:07 -104587.524445] FAST spr round 7 (radius: 25) [05:38:04 -104584.944085] FAST spr round 8 (radius: 25) [05:40:00 -104584.944060] Model parameter optimization (eps = 1.000000) [05:40:17 -104580.741143] SLOW spr round 1 (radius: 5) [05:42:53 -104542.527076] SLOW spr round 2 (radius: 5) [05:45:28 -104541.276017] SLOW spr round 3 (radius: 5) [05:48:00 -104541.275164] SLOW spr round 4 (radius: 10) [05:50:34 -104541.091395] SLOW spr round 5 (radius: 5) [05:53:42 -104541.091386] SLOW spr round 6 (radius: 10) [05:56:38 -104541.091383] SLOW spr round 7 (radius: 15) [06:00:25 -104540.445029] SLOW spr round 8 (radius: 5) [06:03:44 -104540.445026] SLOW spr round 9 (radius: 10) [06:06:48 -104540.445024] SLOW spr round 10 (radius: 15) [06:10:32 -104540.445023] SLOW spr round 11 (radius: 20) [06:16:23 -104540.445021] SLOW spr round 12 (radius: 25) [06:16:42] [worker #1] ML tree search #14, logLikelihood: -104504.289101 [06:23:41 -104540.445020] Model parameter optimization (eps = 0.100000) [06:23:50] [worker #0] ML tree search #13, logLikelihood: -104540.338646 [06:23:50 -549545.059930] Initial branch length optimization [06:23:56 -438083.702777] Model parameter optimization (eps = 10.000000) [06:24:43 -437096.773168] AUTODETECT spr round 1 (radius: 5) [06:27:44 -278695.088409] AUTODETECT spr round 2 (radius: 10) [06:31:14 -199304.294711] AUTODETECT spr round 3 (radius: 15) [06:34:44 -164099.431118] AUTODETECT spr round 4 (radius: 20) [06:38:41 -143399.673481] AUTODETECT spr round 5 (radius: 25) [06:43:04 -134199.690726] SPR radius for FAST iterations: 25 (autodetect) [06:43:04 -134199.690726] Model parameter optimization (eps = 3.000000) [06:43:38 -133935.930008] FAST spr round 1 (radius: 25) [06:47:14 -105870.560588] FAST spr round 2 (radius: 25) [06:49:57 -104684.259872] FAST spr round 3 (radius: 25) [06:52:13 -104553.985699] FAST spr round 4 (radius: 25) [06:54:19 -104550.736991] FAST spr round 5 (radius: 25) [06:56:17 -104550.735422] Model parameter optimization (eps = 1.000000) [06:56:32 -104547.689909] SLOW spr round 1 (radius: 5) [06:59:13 -104520.135535] SLOW spr round 2 (radius: 5) [07:01:51 -104513.949335] SLOW spr round 3 (radius: 5) [07:04:27 -104512.140188] SLOW spr round 4 (radius: 5) [07:06:59 -104512.123840] SLOW spr round 5 (radius: 10) [07:09:33 -104510.557909] SLOW spr round 6 (radius: 5) [07:12:47 -104502.492787] SLOW spr round 7 (radius: 5) [07:15:35 -104502.492584] SLOW spr round 8 (radius: 10) [07:18:16 -104501.012911] SLOW spr round 9 (radius: 5) [07:21:20 -104501.012864] SLOW spr round 10 (radius: 10) [07:23:51] [worker #2] ML tree search #15, logLikelihood: -104510.988730 [07:24:11 -104501.012853] SLOW spr round 11 (radius: 15) [07:27:56 -104501.012844] SLOW spr round 12 (radius: 20) [07:34:02 -104501.012835] SLOW spr round 13 (radius: 25) [07:41:54 -104501.012826] Model parameter optimization (eps = 0.100000) [07:42:04] [worker #0] ML tree search #16, logLikelihood: -104500.828214 [07:42:04 -552408.166645] Initial branch length optimization [07:42:10 -440507.904281] Model parameter optimization (eps = 10.000000) [07:42:51 -439615.069410] AUTODETECT spr round 1 (radius: 5) [07:45:54 -277400.016946] AUTODETECT spr round 2 (radius: 10) [07:49:10 -193097.455040] AUTODETECT spr round 3 (radius: 15) [07:52:38 -138893.099872] AUTODETECT spr round 4 (radius: 20) [07:56:28 -126470.437770] AUTODETECT spr round 5 (radius: 25) [08:01:02 -124531.347400] SPR radius for FAST iterations: 25 (autodetect) [08:01:02 -124531.347400] Model parameter optimization (eps = 3.000000) [08:01:29 -124305.824463] FAST spr round 1 (radius: 25) [08:05:04 -105849.317236] FAST spr round 2 (radius: 25) [08:06:19] [worker #1] ML tree search #17, logLikelihood: -104522.864726 [08:07:45 -104706.212741] FAST spr round 3 (radius: 25) [08:10:02 -104605.246189] FAST spr round 4 (radius: 25) [08:12:06 -104601.116258] FAST spr round 5 (radius: 25) [08:14:05 -104601.115923] Model parameter optimization (eps = 1.000000) [08:14:20 -104598.156199] SLOW spr round 1 (radius: 5) [08:17:00 -104566.644099] SLOW spr round 2 (radius: 5) [08:19:39 -104563.790056] SLOW spr round 3 (radius: 5) [08:22:13 -104563.789504] SLOW spr round 4 (radius: 10) [08:24:49 -104558.237384] SLOW spr round 5 (radius: 5) [08:26:47] [worker #2] ML tree search #18, logLikelihood: -104504.136899 [08:28:03 -104555.911940] SLOW spr round 6 (radius: 5) [08:30:53 -104555.848920] SLOW spr round 7 (radius: 10) [08:33:35 -104555.848916] SLOW spr round 8 (radius: 15) [08:37:35 -104555.330333] SLOW spr round 9 (radius: 5) [08:40:54 -104555.330324] SLOW spr round 10 (radius: 10) [08:44:00 -104555.330323] SLOW spr round 11 (radius: 15) [08:47:49 -104555.330322] SLOW spr round 12 (radius: 20) [08:53:59 -104555.330321] SLOW spr round 13 (radius: 25) [09:01:53 -104555.330321] Model parameter optimization (eps = 0.100000) [09:01:59] [worker #0] ML tree search #19, logLikelihood: -104555.282600 [09:18:18] [worker #1] ML tree search #20, logLikelihood: -104507.353712 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.132935,0.284625) (0.233749,0.385871) (0.351250,0.959535) (0.282066,1.896471) 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: -104500.828214 AIC score: 213011.656427 / AICc score: 8257071.656427 / BIC score: 220922.224748 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=382). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 214 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/3_mltree/P52848.raxml.bestTreeCollapsed Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/3_mltree/P52848.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/3_mltree/P52848.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/3_mltree/P52848.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P52848/3_mltree/P52848.raxml.log Analysis started: 03-Jul-2021 17:04:57 / finished: 04-Jul-2021 02:23:16 Elapsed time: 33498.872 seconds