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 16:41:26 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/2_msa/O94822_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/3_mltree/O94822 --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/O94822/2_msa/O94822_trimmed_msa.fasta [00:00:00] Loaded alignment with 816 taxa and 222 sites WARNING: Sequences tr_B4QQU8_B4QQU8_DROSI_7240 and sp_Q9VW09_LTN1_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QQU8_B4QQU8_DROSI_7240 and tr_B4IIM0_B4IIM0_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A1I7Q424_A0A1I7Q424_CHICK_9031 and sp_E1C231_LTN1_CHICK_9031 are exactly identical! WARNING: Sequences tr_A0A1I7Q424_A0A1I7Q424_CHICK_9031 and tr_G1NNU5_G1NNU5_MELGA_9103 are exactly identical! WARNING: Sequences tr_M3XPM4_M3XPM4_MUSPF_9669 and tr_G1T2N2_G1T2N2_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3XPM4_M3XPM4_MUSPF_9669 and tr_F6ZU08_F6ZU08_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3XPM4_M3XPM4_MUSPF_9669 and tr_I3MS74_I3MS74_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3XPM4_M3XPM4_MUSPF_9669 and tr_F7F0V7_F7F0V7_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3XPM4_M3XPM4_MUSPF_9669 and tr_G1LNS1_G1LNS1_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XPM4_M3XPM4_MUSPF_9669 and tr_A0A2U3VHZ1_A0A2U3VHZ1_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XPM4_M3XPM4_MUSPF_9669 and tr_A0A2U3YGR8_A0A2U3YGR8_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A0E0GBE4_A0A0E0GBE4_ORYNI_4536 and tr_A2X8C1_A2X8C1_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GBE4_A0A0E0GBE4_ORYNI_4536 and tr_I1P348_I1P348_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GBE4_A0A0E0GBE4_ORYNI_4536 and tr_A0A0E0CPU0_A0A0E0CPU0_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0GBE4_A0A0E0GBE4_ORYNI_4536 and tr_A0A0E0NJ93_A0A0E0NJ93_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GBE4_A0A0E0GBE4_ORYNI_4536 and tr_A0A0D9YWH0_A0A0D9YWH0_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0GBE4_A0A0E0GBE4_ORYNI_4536 and tr_Q6EPN1_Q6EPN1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A2XR03_A2XR03_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_I1PJL7_I1PJL7_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A0A0E0DBR5_A0A0E0DBR5_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A0A0E0P6A8_A0A0E0P6A8_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A0A0D3FTC8_A0A0D3FTC8_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_A0A0D9ZHS7_A0A0D9ZHS7_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0GY33_A0A0E0GY33_ORYNI_4536 and tr_Q7XT61_Q7XT61_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0H513_A0A0E0H513_ORYNI_4536 and tr_A2XWQ7_A2XWQ7_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0H513_A0A0E0H513_ORYNI_4536 and tr_A0A0E0DHK1_A0A0E0DHK1_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0H513_A0A0E0H513_ORYNI_4536 and tr_A0A0E0PD43_A0A0E0PD43_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0H513_A0A0E0H513_ORYNI_4536 and tr_Q7XQ70_Q7XQ70_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0H564_A0A0E0H564_ORYNI_4536 and tr_A0A0E0PD90_A0A0E0PD90_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0H564_A0A0E0H564_ORYNI_4536 and tr_A0A0D9ZPU0_A0A0D9ZPU0_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F6SDK4_F6SDK4_MACMU_9544 and tr_G7P1M1_G7P1M1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6SDK4_F6SDK4_MACMU_9544 and tr_A0A096N0R6_A0A096N0R6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6SDK4_F6SDK4_MACMU_9544 and tr_A0A0D9R9U2_A0A0D9R9U2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6SDK4_F6SDK4_MACMU_9544 and tr_A0A2K5LGE9_A0A2K5LGE9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6SDK4_F6SDK4_MACMU_9544 and tr_A0A2Y9KRD0_A0A2Y9KRD0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_I1NVS5_I1NVS5_ORYGL_4538 and tr_Q5JNB3_Q5JNB3_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_H0ZTP6_H0ZTP6_TAEGU_59729 and tr_A0A218UJS6_A0A218UJS6_9PASE_299123 are exactly identical! WARNING: Sequences tr_E6R771_E6R771_CRYGW_367775 and tr_A0A095ERQ4_A0A095ERQ4_CRYGR_294750 are exactly identical! WARNING: Sequences tr_A0A0E0N8C7_A0A0E0N8C7_ORYRU_4529 and tr_A0A0D9YKV4_A0A0D9YKV4_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_Q175P4_Q175P4_AEDAE_7159 and tr_Q17IH2_Q17IH2_AEDAE_7159 are exactly identical! WARNING: Sequences tr_M4FAD7_M4FAD7_BRARP_51351 and tr_A0A078JHE4_A0A078JHE4_BRANA_3708 are exactly identical! WARNING: Sequences tr_W2QVZ6_W2QVZ6_PHYPN_761204 and tr_A0A0W8B4U4_A0A0W8B4U4_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A078H6E2_A0A078H6E2_BRANA_3708 and tr_A0A0D3ECD7_A0A0D3ECD7_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078J4X7_A0A078J4X7_BRANA_3708 and tr_A0A0D3DM43_A0A0D3DM43_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078J6E9_A0A078J6E9_BRANA_3708 and tr_A0A0D3B2U4_A0A0D3B2U4_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078JAG8_A0A078JAG8_BRANA_3708 and tr_A0A0D3CJI2_A0A0D3CJI2_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078JC68_A0A078JC68_BRANA_3708 and tr_A0A0D3BNH2_A0A0D3BNH2_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A1S3X9B1_A0A1S3X9B1_TOBAC_4097 and tr_A0A1U7WM19_A0A1U7WM19_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3XAS3_A0A1S3XAS3_TOBAC_4097 and tr_A0A1S3XJS4_A0A1S3XJS4_TOBAC_4097 are exactly identical! WARNING: Sequences tr_A0A1S3XAS3_A0A1S3XAS3_TOBAC_4097 and tr_A0A1J6IX31_A0A1J6IX31_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S3XAS3_A0A1S3XAS3_TOBAC_4097 and tr_A0A1U7YCD9_A0A1U7YCD9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CUW4_A0A1S4CUW4_TOBAC_4097 and tr_A0A1U7YX35_A0A1U7YX35_NICSY_4096 are exactly identical! WARNING: Sequences tr_Q9FQZ7_Q9FQZ7_TOBAC_4097 and tr_A0A1U7YB59_A0A1U7YB59_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1U7U1Q6_A0A1U7U1Q6_TARSY_1868482 and tr_A0A384CYU9_A0A384CYU9_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A251S4V8_A0A251S4V8_HELAN_4232 and tr_A0A251S5C4_A0A251S5C4_HELAN_4232 are exactly identical! WARNING: Sequences tr_A0A251TND3_A0A251TND3_HELAN_4232 and tr_A0A251TPD5_A0A251TPD5_HELAN_4232 are exactly identical! WARNING: Sequences tr_A0A2N5S7L3_A0A2N5S7L3_9BASI_200324 and tr_A0A2N5UAG9_A0A2N5UAG9_9BASI_200324 are exactly identical! WARNING: Sequences tr_A0A2T7CJW4_A0A2T7CJW4_9POAL_1504633 and tr_A0A2T7E507_A0A2T7E507_9POAL_1504633 are exactly identical! WARNING: Duplicate sequences found: 58 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/O94822/3_mltree/O94822.raxml.reduced.phy Alignment comprises 1 partitions and 222 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 222 / 222 Gaps: 22.53 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/3_mltree/O94822.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 816 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 222 / 17760 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -282982.934026] Initial branch length optimization [00:00:05 -236696.429339] Model parameter optimization (eps = 10.000000) [00:00:58 -235930.094805] AUTODETECT spr round 1 (radius: 5) [00:03:14 -185977.848196] AUTODETECT spr round 2 (radius: 10) [00:05:53 -145371.111508] AUTODETECT spr round 3 (radius: 15) [00:08:48 -121618.700929] AUTODETECT spr round 4 (radius: 20) [00:11:55 -113609.400499] AUTODETECT spr round 5 (radius: 25) [00:15:15 -111987.447286] SPR radius for FAST iterations: 25 (autodetect) [00:15:15 -111987.447286] Model parameter optimization (eps = 3.000000) [00:15:39 -111916.003826] FAST spr round 1 (radius: 25) [00:19:08 -98582.074531] FAST spr round 2 (radius: 25) [00:21:38 -98001.072964] FAST spr round 3 (radius: 25) [00:23:48 -97947.791915] FAST spr round 4 (radius: 25) [00:25:33 -97947.008592] FAST spr round 5 (radius: 25) [00:27:13 -97947.006720] Model parameter optimization (eps = 1.000000) [00:27:30 -97944.616481] SLOW spr round 1 (radius: 5) [00:29:54 -97919.320676] SLOW spr round 2 (radius: 5) [00:32:05 -97919.145446] SLOW spr round 3 (radius: 5) [00:34:14 -97919.143825] SLOW spr round 4 (radius: 10) [00:36:31 -97918.721890] SLOW spr round 5 (radius: 5) [00:39:13 -97918.721831] SLOW spr round 6 (radius: 10) [00:41:50 -97918.721815] SLOW spr round 7 (radius: 15) [00:45:41 -97915.049612] SLOW spr round 8 (radius: 5) [00:48:33 -97914.317234] SLOW spr round 9 (radius: 5) [00:51:01 -97914.316755] SLOW spr round 10 (radius: 10) [00:53:33 -97908.482220] SLOW spr round 11 (radius: 5) [00:56:14 -97906.994091] SLOW spr round 12 (radius: 5) [00:58:37 -97906.993878] SLOW spr round 13 (radius: 10) [01:01:02 -97906.993825] SLOW spr round 14 (radius: 15) [01:04:58 -97906.949766] SLOW spr round 15 (radius: 20) [01:10:14 -97906.948453] SLOW spr round 16 (radius: 25) [01:16:18 -97906.948067] Model parameter optimization (eps = 0.100000) [01:16:24] [worker #0] ML tree search #1, logLikelihood: -97906.931898 [01:16:24 -283859.640389] Initial branch length optimization [01:16:29 -237443.471075] Model parameter optimization (eps = 10.000000) [01:17:23 -236702.802441] AUTODETECT spr round 1 (radius: 5) [01:19:38 -183539.945944] AUTODETECT spr round 2 (radius: 10) [01:22:14 -143947.655386] AUTODETECT spr round 3 (radius: 15) [01:25:06 -119707.863454] AUTODETECT spr round 4 (radius: 20) [01:28:18 -110915.508474] AUTODETECT spr round 5 (radius: 25) [01:31:57 -110446.708985] SPR radius for FAST iterations: 25 (autodetect) [01:31:57 -110446.708985] Model parameter optimization (eps = 3.000000) [01:32:21 -110371.102188] FAST spr round 1 (radius: 25) [01:34:21] [worker #3] ML tree search #4, logLikelihood: -97910.547903 [01:36:08 -98548.931778] FAST spr round 2 (radius: 25) [01:38:38 -97998.031325] FAST spr round 3 (radius: 25) [01:40:48 -97962.709413] FAST spr round 4 (radius: 25) [01:42:34 -97960.901871] FAST spr round 5 (radius: 25) [01:42:59] [worker #1] ML tree search #2, logLikelihood: -97902.345129 [01:44:17 -97957.826273] FAST spr round 6 (radius: 25) [01:45:56 -97957.825820] Model parameter optimization (eps = 1.000000) [01:46:17 -97951.705238] SLOW spr round 1 (radius: 5) [01:48:27 -97930.164425] SLOW spr round 2 (radius: 5) [01:50:45 -97924.051220] SLOW spr round 3 (radius: 5) [01:53:06 -97918.822282] SLOW spr round 4 (radius: 5) [01:55:16 -97918.607348] SLOW spr round 5 (radius: 5) [01:57:26 -97918.604658] SLOW spr round 6 (radius: 10) [01:59:49 -97914.260212] SLOW spr round 7 (radius: 5) [02:02:36 -97911.991555] SLOW spr round 8 (radius: 5) [02:03:54] [worker #2] ML tree search #3, logLikelihood: -97900.778299 [02:05:01 -97911.990285] SLOW spr round 9 (radius: 10) [02:07:32 -97911.990133] SLOW spr round 10 (radius: 15) [02:11:49 -97911.990109] SLOW spr round 11 (radius: 20) [02:17:55 -97910.764122] SLOW spr round 12 (radius: 5) [02:20:52 -97910.754110] SLOW spr round 13 (radius: 10) [02:23:47 -97910.754050] SLOW spr round 14 (radius: 15) [02:27:52 -97909.189623] SLOW spr round 15 (radius: 5) [02:30:36 -97909.189618] SLOW spr round 16 (radius: 10) [02:33:24 -97909.189614] SLOW spr round 17 (radius: 15) [02:37:31 -97909.189610] SLOW spr round 18 (radius: 20) [02:43:39 -97909.189606] SLOW spr round 19 (radius: 25) [02:49:36] [worker #3] ML tree search #8, logLikelihood: -97907.877145 [02:50:50 -97909.099183] Model parameter optimization (eps = 0.100000) [02:50:58] [worker #0] ML tree search #5, logLikelihood: -97908.996825 [02:50:58 -284631.968946] Initial branch length optimization [02:51:05 -238149.986354] Model parameter optimization (eps = 10.000000) [02:51:53 -237335.477358] AUTODETECT spr round 1 (radius: 5) [02:54:08 -185202.380563] AUTODETECT spr round 2 (radius: 10) [02:56:44 -150316.401574] AUTODETECT spr round 3 (radius: 15) [02:59:43 -124100.786279] AUTODETECT spr round 4 (radius: 20) [03:02:49 -113845.635979] AUTODETECT spr round 5 (radius: 25) [03:06:22 -112067.959062] SPR radius for FAST iterations: 25 (autodetect) [03:06:23 -112067.959062] Model parameter optimization (eps = 3.000000) [03:06:53 -111948.534277] FAST spr round 1 (radius: 25) [03:10:14 -98372.357470] FAST spr round 2 (radius: 25) [03:12:30 -98003.010538] FAST spr round 3 (radius: 25) [03:14:33 -97962.632806] FAST spr round 4 (radius: 25) [03:16:24 -97953.483558] FAST spr round 5 (radius: 25) [03:18:03 -97952.963647] FAST spr round 6 (radius: 25) [03:19:40 -97952.962855] Model parameter optimization (eps = 1.000000) [03:20:02 -97951.015106] SLOW spr round 1 (radius: 5) [03:22:13 -97933.930031] SLOW spr round 2 (radius: 5) [03:24:23 -97922.412940] SLOW spr round 3 (radius: 5) [03:26:37 -97917.414621] SLOW spr round 4 (radius: 5) [03:28:47 -97917.413823] SLOW spr round 5 (radius: 10) [03:31:07 -97917.017175] SLOW spr round 6 (radius: 5) [03:33:46 -97917.017121] SLOW spr round 7 (radius: 10) [03:36:26 -97917.017098] SLOW spr round 8 (radius: 15) [03:40:27 -97915.456824] SLOW spr round 9 (radius: 5) [03:43:16 -97915.456815] SLOW spr round 10 (radius: 10) [03:45:51] [worker #1] ML tree search #6, logLikelihood: -97892.309428 [03:46:04 -97915.456813] SLOW spr round 11 (radius: 15) [03:50:03 -97915.456812] SLOW spr round 12 (radius: 20) [03:55:45 -97915.456812] SLOW spr round 13 (radius: 25) [04:02:22 -97915.456812] Model parameter optimization (eps = 0.100000) [04:02:32] [worker #0] ML tree search #9, logLikelihood: -97914.979253 [04:02:32 -285130.384760] Initial branch length optimization [04:02:40 -238849.398311] Model parameter optimization (eps = 10.000000) [04:02:51] [worker #3] ML tree search #12, logLikelihood: -97907.383824 [04:03:22 -238051.473893] AUTODETECT spr round 1 (radius: 5) [04:05:39 -182469.345068] AUTODETECT spr round 2 (radius: 10) [04:08:12 -141909.818254] AUTODETECT spr round 3 (radius: 15) [04:11:06 -119077.242188] AUTODETECT spr round 4 (radius: 20) [04:14:23 -109832.641034] AUTODETECT spr round 5 (radius: 25) [04:18:01 -108421.650648] SPR radius for FAST iterations: 25 (autodetect) [04:18:02 -108421.650648] Model parameter optimization (eps = 3.000000) [04:18:29 -108299.216023] FAST spr round 1 (radius: 25) [04:21:59 -98414.941101] FAST spr round 2 (radius: 25) [04:24:27 -97998.665890] FAST spr round 3 (radius: 25) [04:25:09] [worker #2] ML tree search #7, logLikelihood: -97882.471287 [04:26:36 -97967.980175] FAST spr round 4 (radius: 25) [04:28:24 -97961.299546] FAST spr round 5 (radius: 25) [04:30:03 -97961.296664] Model parameter optimization (eps = 1.000000) [04:30:17 -97956.554998] SLOW spr round 1 (radius: 5) [04:32:41 -97927.853180] SLOW spr round 2 (radius: 5) [04:34:58 -97927.079339] SLOW spr round 3 (radius: 5) [04:37:11 -97926.333849] SLOW spr round 4 (radius: 5) [04:39:24 -97926.333543] SLOW spr round 5 (radius: 10) [04:41:45 -97926.333348] SLOW spr round 6 (radius: 15) [04:46:06 -97924.326681] SLOW spr round 7 (radius: 5) [04:48:58 -97924.326420] SLOW spr round 8 (radius: 10) [04:51:47 -97924.326409] SLOW spr round 9 (radius: 15) [04:55:55 -97923.842204] SLOW spr round 10 (radius: 5) [04:58:52 -97919.995289] SLOW spr round 11 (radius: 5) [05:01:21 -97919.993551] SLOW spr round 12 (radius: 10) [05:03:53 -97919.424609] SLOW spr round 13 (radius: 5) [05:06:34 -97919.424152] SLOW spr round 14 (radius: 10) [05:09:14 -97919.424117] SLOW spr round 15 (radius: 15) [05:13:26 -97919.016372] SLOW spr round 16 (radius: 5) [05:16:16 -97919.015553] SLOW spr round 17 (radius: 10) [05:19:06 -97919.015535] SLOW spr round 18 (radius: 15) [05:23:16 -97918.292898] SLOW spr round 19 (radius: 5) [05:26:05 -97918.084884] SLOW spr round 20 (radius: 5) [05:28:33 -97918.084883] SLOW spr round 21 (radius: 10) [05:29:02] [worker #2] ML tree search #11, logLikelihood: -97889.013913 [05:31:04 -97918.084859] SLOW spr round 22 (radius: 15) [05:35:23 -97916.956408] SLOW spr round 23 (radius: 5) [05:37:08] [worker #1] ML tree search #10, logLikelihood: -97901.708503 [05:38:15 -97916.956326] SLOW spr round 24 (radius: 10) [05:41:06 -97916.956322] SLOW spr round 25 (radius: 15) [05:45:15 -97916.956321] SLOW spr round 26 (radius: 20) [05:48:40] [worker #3] ML tree search #16, logLikelihood: -97896.089024 [05:51:12 -97916.956320] SLOW spr round 27 (radius: 25) [05:58:02 -97916.861641] Model parameter optimization (eps = 0.100000) [05:58:10] [worker #0] ML tree search #13, logLikelihood: -97916.756355 [05:58:10 -282843.983372] Initial branch length optimization [05:58:15 -235999.364036] Model parameter optimization (eps = 10.000000) [05:59:07 -235276.501096] AUTODETECT spr round 1 (radius: 5) [06:01:20 -182395.072126] AUTODETECT spr round 2 (radius: 10) [06:03:57 -142806.833905] AUTODETECT spr round 3 (radius: 15) [06:06:47 -121562.119752] AUTODETECT spr round 4 (radius: 20) [06:10:05 -115754.876810] AUTODETECT spr round 5 (radius: 25) [06:13:44 -112316.634741] SPR radius for FAST iterations: 25 (autodetect) [06:13:44 -112316.634741] Model parameter optimization (eps = 3.000000) [06:14:04 -112263.409416] FAST spr round 1 (radius: 25) [06:17:18 -98441.845196] FAST spr round 2 (radius: 25) [06:19:38 -98034.909644] FAST spr round 3 (radius: 25) [06:21:40 -98001.867138] FAST spr round 4 (radius: 25) [06:23:27 -97996.561689] FAST spr round 5 (radius: 25) [06:25:02 -97996.561188] Model parameter optimization (eps = 1.000000) [06:25:17 -97990.840044] SLOW spr round 1 (radius: 5) [06:27:41 -97948.830914] SLOW spr round 2 (radius: 5) [06:30:04 -97938.516503] SLOW spr round 3 (radius: 5) [06:32:16 -97937.777690] SLOW spr round 4 (radius: 5) [06:34:25 -97937.777565] SLOW spr round 5 (radius: 10) [06:36:46 -97930.028705] SLOW spr round 6 (radius: 5) [06:39:28 -97930.028539] SLOW spr round 7 (radius: 10) [06:42:10] [worker #1] ML tree search #14, logLikelihood: -97899.096885 [06:42:10 -97930.028537] SLOW spr round 8 (radius: 15) [06:46:14 -97928.287660] SLOW spr round 9 (radius: 5) [06:49:08 -97925.041353] SLOW spr round 10 (radius: 5) [06:51:38 -97925.039176] SLOW spr round 11 (radius: 10) [06:54:10 -97925.038737] SLOW spr round 12 (radius: 15) [06:58:15 -97925.038604] SLOW spr round 13 (radius: 20) [07:04:07 -97925.038552] SLOW spr round 14 (radius: 25) [07:04:11] [worker #3] ML tree search #20, logLikelihood: -97903.636532 [07:11:21 -97925.038530] Model parameter optimization (eps = 0.100000) [07:11:27] [worker #0] ML tree search #17, logLikelihood: -97925.030462 [07:14:59] [worker #2] ML tree search #15, logLikelihood: -97886.812658 [08:09:03] [worker #1] ML tree search #18, logLikelihood: -97886.073322 [08:41:49] [worker #2] ML tree search #19, logLikelihood: -97894.345408 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.126621,0.322738) (0.189538,0.563989) (0.479266,0.949409) (0.204575,1.941673) 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: -97882.471287 AIC score: 199034.942574 / AICc score: 5548754.942574 / BIC score: 204598.320093 Free parameters (model + branch lengths): 1635 WARNING: Number of free parameters (K=1635) is larger than alignment size (n=222). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 101 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/3_mltree/O94822.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/3_mltree/O94822.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/3_mltree/O94822.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/3_mltree/O94822.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O94822/3_mltree/O94822.raxml.log Analysis started: 04-Jul-2021 16:41:26 / finished: 05-Jul-2021 01:23:16 Elapsed time: 31309.448 seconds Consumed energy: 2450.272 Wh (= 12 km in an electric car, or 61 km with an e-scooter!)