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 05-Jul-2021 21:45:33 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P55064/2_msa/P55064_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P55064/3_mltree/P55064 --seed 2 --threads 5 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P55064/2_msa/P55064_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 232 sites WARNING: Sequences tr_B4QBL5_B4QBL5_DROSI_7240 and tr_B4HNI2_B4HNI2_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A1D5P9U9_A0A1D5P9U9_CHICK_9031 and tr_G1NDY2_G1NDY2_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5P9U9_A0A1D5P9U9_CHICK_9031 and tr_A0A226NS40_A0A226NS40_COLVI_9014 are exactly identical! WARNING: Sequences tr_F1NTP3_F1NTP3_CHICK_9031 and tr_G1ND84_G1ND84_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NTP3_F1NTP3_CHICK_9031 and tr_A0A226ND65_A0A226ND65_CALSU_9009 are exactly identical! WARNING: Sequences tr_G1S800_G1S800_NOMLE_61853 and tr_A0A2I3S3K4_A0A2I3S3K4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S800_G1S800_NOMLE_61853 and tr_A0A2R9CFL8_A0A2R9CFL8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QSX6_G3QSX6_GORGO_9595 and tr_H2NH89_H2NH89_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QSX6_G3QSX6_GORGO_9595 and tr_H2Q5W2_H2Q5W2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QSX6_G3QSX6_GORGO_9595 and sp_P55064_AQP5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QSX8_G3QSX8_GORGO_9595 and tr_A0A2R9CJB3_A0A2R9CJB3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R332_G3R332_GORGO_9595 and tr_H2QUD6_H2QUD6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R332_G3R332_GORGO_9595 and sp_P29972_AQP1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R332_G3R332_GORGO_9595 and tr_A0A0D9RQJ5_A0A0D9RQJ5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3R332_G3R332_GORGO_9595 and tr_A0A2R9B319_A0A2R9B319_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R4L3_G3R4L3_GORGO_9595 and tr_H2QED7_H2QED7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R4L3_G3R4L3_GORGO_9595 and sp_P55087_AQP4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R4L3_G3R4L3_GORGO_9595 and tr_A0A1D5RFU8_A0A1D5RFU8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3R4L3_G3R4L3_GORGO_9595 and tr_F7IQC1_F7IQC1_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3R4L3_G3R4L3_GORGO_9595 and tr_G7PWJ7_G7PWJ7_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3R4L3_G3R4L3_GORGO_9595 and tr_A0A0D9RZ01_A0A0D9RZ01_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3R4L3_G3R4L3_GORGO_9595 and tr_A0A2K5NVA4_A0A2K5NVA4_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3R4L3_G3R4L3_GORGO_9595 and tr_A0A2K6A5T4_A0A2K6A5T4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3R4L3_G3R4L3_GORGO_9595 and tr_A0A2R9AJM5_A0A2R9AJM5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RKA2_G3RKA2_GORGO_9595 and tr_H2Q690_H2Q690_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RKA2_G3RKA2_GORGO_9595 and sp_P30301_MIP_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RKA2_G3RKA2_GORGO_9595 and tr_A0A2R9CLF0_A0A2R9CLF0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0A0MPA8_A0A0A0MPA8_CANLF_9615 and sp_A2IBY8_MIP_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A0A0MPA8_A0A0A0MPA8_CANLF_9615 and tr_I3M052_I3M052_ICTTR_43179 are exactly identical! WARNING: Sequences tr_A0A0A0MPA8_A0A0A0MPA8_CANLF_9615 and tr_L5KVQ9_L5KVQ9_PTEAL_9402 are exactly identical! WARNING: Sequences tr_A0A0A0MPA8_A0A0A0MPA8_CANLF_9615 and tr_A0A2U3YBV5_A0A2U3YBV5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_F7FSF9_F7FSF9_MONDO_13616 and tr_G3WQD1_G3WQD1_SARHA_9305 are exactly identical! WARNING: Sequences tr_A0A087ZR22_A0A087ZR22_APIME_7460 and tr_A0A2A3E7I3_A0A2A3E7I3_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NES3_A0A158NES3_ATTCE_12957 and tr_A0A195AV93_A0A195AV93_9HYME_520822 are exactly identical! WARNING: Sequences tr_I3MKS2_I3MKS2_ICTTR_43179 and tr_A0A286XDA1_A0A286XDA1_CAVPO_10141 are exactly identical! WARNING: Sequences tr_A0A0E0GF26_A0A0E0GF26_ORYNI_4536 and tr_I1P5P5_I1P5P5_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GF26_A0A0E0GF26_ORYNI_4536 and sp_Q9SXF8_PIP13_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0IN21_A0A0E0IN21_ORYNI_4536 and tr_A2Z3L2_A2Z3L2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0IN21_A0A0E0IN21_ORYNI_4536 and tr_A0A0E0QUH8_A0A0E0QUH8_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0IN21_A0A0E0IN21_ORYNI_4536 and sp_Q651D5_PIP27_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A1D5QSD8_A0A1D5QSD8_MACMU_9544 and tr_A0A096N7Q5_A0A096N7Q5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5R9F2_A0A1D5R9F2_MACMU_9544 and tr_A0A2K5LNR4_A0A2K5LNR4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5R9F2_A0A1D5R9F2_MACMU_9544 and tr_A0A2K6E5Y4_A0A2K6E5Y4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6RG83_F6RG83_MACMU_9544 and tr_G7PII2_G7PII2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6RG83_F6RG83_MACMU_9544 and tr_A0A096NH11_A0A096NH11_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6RG83_F6RG83_MACMU_9544 and tr_A0A2K5MM40_A0A2K5MM40_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6RG83_F6RG83_MACMU_9544 and tr_A0A2K6C3R6_A0A2K6C3R6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6RG83_F6RG83_MACMU_9544 and tr_A0A2K5YUP4_A0A2K5YUP4_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6W6H1_F6W6H1_MACMU_9544 and tr_A0A096MRJ3_A0A096MRJ3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6W6H1_F6W6H1_MACMU_9544 and tr_A0A2K5MEU2_A0A2K5MEU2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6W6H1_F6W6H1_MACMU_9544 and tr_A0A2K6D532_A0A2K6D532_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6W6H1_F6W6H1_MACMU_9544 and tr_A0A2K5ZUN0_A0A2K5ZUN0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A2XVL4_A2XVL4_ORYSI_39946 and tr_I1PN39_I1PN39_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2XVL4_A2XVL4_ORYSI_39946 and tr_A0A0E0DG74_A0A0E0DG74_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A2XVL4_A2XVL4_ORYSI_39946 and tr_A0A0E0PBN7_A0A0E0PBN7_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2XVL4_A2XVL4_ORYSI_39946 and tr_A0A0D9Y8R6_A0A0D9Y8R6_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A2XVL4_A2XVL4_ORYSI_39946 and sp_Q7XUA6_PIP23_ORYSJ_39947 are exactly identical! WARNING: Sequences sp_Q9ATM4_PIP27_MAIZE_4577 and tr_C6TLJ6_C6TLJ6_SOYBN_3847 are exactly identical! WARNING: Sequences tr_I1QQV2_I1QQV2_ORYGL_4538 and tr_A0A0E0EUF4_A0A0E0EUF4_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_I1QQV2_I1QQV2_ORYGL_4538 and tr_A0A0D3H9I1_A0A0D3H9I1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1QQV2_I1QQV2_ORYGL_4538 and tr_A0A0E0B5X1_A0A0E0B5X1_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_H0YPZ9_H0YPZ9_TAEGU_59729 and tr_A0A218UE79_A0A218UE79_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A287AVU9_A0A287AVU9_PIG_9823 and tr_A0A2Y9SH67_A0A2Y9SH67_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G1M6L3_G1M6L3_AILME_9646 and tr_A0A384C2P8_A0A384C2P8_URSMA_29073 are exactly identical! WARNING: Sequences tr_F2D616_F2D616_HORVV_112509 and tr_A0A3B6QI42_A0A3B6QI42_WHEAT_4565 are exactly identical! WARNING: Sequences tr_M4D528_M4D528_BRARP_51351 and tr_A0A078IUF9_A0A078IUF9_BRANA_3708 are exactly identical! WARNING: Sequences tr_M7ZSV7_M7ZSV7_TRIUA_4572 and tr_A7J2I3_A7J2I3_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A3B6B250_A0A3B6B250_WHEAT_4565 and tr_A7J2I2_A7J2I2_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A3B6B3F7_A0A3B6B3F7_WHEAT_4565 and tr_A0A3B6CCF0_A0A3B6CCF0_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067G0Q4_A0A067G0Q4_CITSI_2711 and tr_V4T6T1_V4T6T1_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067G0Y5_A0A067G0Y5_CITSI_2711 and tr_V4SL90_V4SL90_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067G0Y5_A0A067G0Y5_CITSI_2711 and tr_A0A2H5NDU3_A0A2H5NDU3_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A2I3LZP0_A0A2I3LZP0_PAPAN_9555 and tr_A0A2K5KV99_A0A2K5KV99_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A078FX10_A0A078FX10_BRANA_3708 and tr_A0A0D3BL75_A0A0D3BL75_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A078J2Z4_A0A078J2Z4_BRANA_3708 and tr_A0A0D3DSS2_A0A0D3DSS2_BRAOL_109376 are exactly identical! WARNING: Sequences tr_V5RF58_V5RF58_CUCSA_3659 and tr_A0A1S3BIK5_A0A1S3BIK5_CUCME_3656 are exactly identical! WARNING: Sequences tr_A0A0D2RNH4_A0A0D2RNH4_GOSRA_29730 and tr_Q06Z30_Q06Z30_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2RU25_A0A0D2RU25_GOSRA_29730 and tr_A0A1U8MBS3_A0A1U8MBS3_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2UYW2_A0A0D2UYW2_GOSRA_29730 and tr_A0A0D2UYY4_A0A0D2UYY4_GOSRA_29730 are exactly identical! WARNING: Sequences tr_A0A0D2UYW2_A0A0D2UYW2_GOSRA_29730 and tr_A0A1U8M8B6_A0A1U8M8B6_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2UYW2_A0A0D2UYW2_GOSRA_29730 and tr_G8XV51_G8XV51_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2VCR9_A0A0D2VCR9_GOSRA_29730 and tr_A0A1U8ITU8_A0A1U8ITU8_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2VCR9_A0A0D2VCR9_GOSRA_29730 and tr_A0T2N6_A0T2N6_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0Q3M574_A0A0Q3M574_AMAAE_12930 and tr_A0A091VSW2_A0A091VSW2_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A0Q3M574_A0A0Q3M574_AMAAE_12930 and tr_A0A2I0MRK4_A0A2I0MRK4_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A0Q3M574_A0A0Q3M574_AMAAE_12930 and tr_A0A1V4KN74_A0A1V4KN74_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A093QE54_A0A093QE54_9PASS_328815 and tr_A0A087RED3_A0A087RED3_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A093QE54_A0A093QE54_9PASS_328815 and tr_A0A091W9J1_A0A091W9J1_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A093QE54_A0A093QE54_9PASS_328815 and tr_A0A091G6C2_A0A091G6C2_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A093QE54_A0A093QE54_9PASS_328815 and tr_A0A2I0MVZ8_A0A2I0MVZ8_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A0A0ANK7_A0A0A0ANK7_CHAVO_50402 and tr_A0A218V174_A0A218V174_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A0A8WK03_A0A0A8WK03_TOBAC_4097 and tr_A0A314LEN4_A0A314LEN4_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A0A8WK03_A0A0A8WK03_TOBAC_4097 and tr_A0A1U7XNR4_A0A1U7XNR4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3Z197_A0A1S3Z197_TOBAC_4097 and tr_A0A1U7VBQ9_A0A1U7VBQ9_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4AIM0_A0A1S4AIM0_TOBAC_4097 and tr_A0A1S4DCM5_A0A1S4DCM5_TOBAC_4097 are exactly identical! WARNING: Sequences tr_A0A1S4AIM0_A0A1S4AIM0_TOBAC_4097 and tr_A0A1U7WKC0_A0A1U7WKC0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4C130_A0A1S4C130_TOBAC_4097 and tr_A0A1U7VY47_A0A1U7VY47_NICSY_4096 are exactly identical! WARNING: Sequences tr_Q06BK4_Q06BK4_TOBAC_4097 and tr_A0A1U7WNC6_A0A1U7WNC6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3HWB6_A0A1S3HWB6_LINUN_7574 and tr_A0A1S3HWE8_A0A1S3HWE8_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A251SV72_A0A251SV72_HELAN_4232 and tr_A0A251SW63_A0A251SW63_HELAN_4232 are exactly identical! WARNING: Sequences tr_A0A2D0R8C7_A0A2D0R8C7_ICTPU_7998 and tr_A0A2D0R8D3_A0A2D0R8D3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A1U8E439_A0A1U8E439_CAPAN_4072 and tr_A0A2G3BSX9_A0A2G3BSX9_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A1U8GG90_A0A1U8GG90_CAPAN_4072 and tr_A0A2G3DAL9_A0A2G3DAL9_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2G3AP60_A0A2G3AP60_CAPAN_4072 and tr_A0A2G3BPX8_A0A2G3BPX8_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2K5LEW0_A0A2K5LEW0_CERAT_9531 and tr_A0A2K6BZN0_A0A2K6BZN0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K6DKV2_A0A2K6DKV2_MACNE_9545 and tr_A0A2K6A4I5_A0A2K6A4I5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2P5EG95_A0A2P5EG95_TREOI_63057 and tr_A0A2P5CPB8_A0A2P5CPB8_PARAD_3476 are exactly identical! WARNING: Sequences tr_A0A2U3UZF2_A0A2U3UZF2_TURTR_9739 and tr_A0A2Y9ND35_A0A2Y9ND35_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4AYI7_A0A2U4AYI7_TURTR_9739 and tr_A0A2Y9P949_A0A2Y9P949_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 109 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P55064/3_mltree/P55064.raxml.reduced.phy Alignment comprises 1 partitions and 232 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 232 / 232 Gaps: 3.76 % Invariant sites: 0.43 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P55064/3_mltree/P55064.raxml.rba Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 232 / 18560 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -377488.396140] Initial branch length optimization [00:00:05 -310574.506849] Model parameter optimization (eps = 10.000000) [00:01:04 -310040.467892] AUTODETECT spr round 1 (radius: 5) [00:04:21 -186981.656552] AUTODETECT spr round 2 (radius: 10) [00:08:00 -139104.501783] AUTODETECT spr round 3 (radius: 15) [00:12:06 -118011.629550] AUTODETECT spr round 4 (radius: 20) [00:16:26 -102910.070917] AUTODETECT spr round 5 (radius: 25) [00:21:38 -96755.779549] SPR radius for FAST iterations: 25 (autodetect) [00:21:38 -96755.779549] Model parameter optimization (eps = 3.000000) [00:22:19 -96476.497388] FAST spr round 1 (radius: 25) [00:26:03 -82441.926615] FAST spr round 2 (radius: 25) [00:28:47 -81662.845274] FAST spr round 3 (radius: 25) [00:31:13 -81587.583567] FAST spr round 4 (radius: 25) [00:33:36 -81541.600633] FAST spr round 5 (radius: 25) [00:35:39 -81537.656392] FAST spr round 6 (radius: 25) [00:37:34 -81537.656386] Model parameter optimization (eps = 1.000000) [00:38:07 -81533.155767] SLOW spr round 1 (radius: 5) [00:41:10 -81505.887505] SLOW spr round 2 (radius: 5) [00:43:53 -81502.155128] SLOW spr round 3 (radius: 5) [00:46:38 -81499.846983] SLOW spr round 4 (radius: 5) [00:49:12 -81499.846944] SLOW spr round 5 (radius: 10) [00:51:50 -81495.406824] SLOW spr round 6 (radius: 5) [00:55:19 -81493.790235] SLOW spr round 7 (radius: 5) [00:58:20 -81493.790233] SLOW spr round 8 (radius: 10) [01:01:01 -81493.790233] SLOW spr round 9 (radius: 15) [01:05:12 -81493.491345] SLOW spr round 10 (radius: 5) [01:06:55] [worker #2] ML tree search #3, logLikelihood: -81473.187126 [01:08:58 -81489.928951] SLOW spr round 11 (radius: 5) [01:12:04 -81488.474063] SLOW spr round 12 (radius: 5) [01:14:59 -81483.032711] SLOW spr round 13 (radius: 5) [01:17:43 -81479.757762] SLOW spr round 14 (radius: 5) [01:20:13] [worker #1] ML tree search #2, logLikelihood: -81482.699703 [01:20:23 -81479.757718] SLOW spr round 15 (radius: 10) [01:21:30] [worker #4] ML tree search #5, logLikelihood: -81442.830129 [01:22:52 -81477.615504] SLOW spr round 16 (radius: 5) [01:26:29 -81475.829401] SLOW spr round 17 (radius: 5) [01:29:29 -81474.531212] SLOW spr round 18 (radius: 5) [01:32:18 -81474.531078] SLOW spr round 19 (radius: 10) [01:34:53 -81474.531069] SLOW spr round 20 (radius: 15) [01:35:04] [worker #3] ML tree search #4, logLikelihood: -81466.837381 [01:39:12 -81474.531068] SLOW spr round 21 (radius: 20) [01:45:39 -81474.531068] SLOW spr round 22 (radius: 25) [01:53:43 -81474.531068] Model parameter optimization (eps = 0.100000) [01:53:50] [worker #0] ML tree search #1, logLikelihood: -81474.519917 [01:53:50 -376849.581103] Initial branch length optimization [01:53:58 -310784.899526] Model parameter optimization (eps = 10.000000) [01:54:44 -310281.621538] AUTODETECT spr round 1 (radius: 5) [01:58:03 -179890.395927] AUTODETECT spr round 2 (radius: 10) [02:01:29 -137120.441979] AUTODETECT spr round 3 (radius: 15) [02:05:22 -117872.000561] AUTODETECT spr round 4 (radius: 20) [02:09:51 -108291.712785] AUTODETECT spr round 5 (radius: 25) [02:14:42 -101164.751873] SPR radius for FAST iterations: 25 (autodetect) [02:14:42 -101164.751873] Model parameter optimization (eps = 3.000000) [02:15:11 -100906.966635] FAST spr round 1 (radius: 25) [02:18:53 -83597.470073] FAST spr round 2 (radius: 25) [02:21:36 -82291.928392] FAST spr round 3 (radius: 25) [02:24:08 -81880.195435] FAST spr round 4 (radius: 25) [02:26:21 -81835.205393] FAST spr round 5 (radius: 25) [02:28:25 -81831.394510] FAST spr round 6 (radius: 25) [02:30:27 -81831.394491] Model parameter optimization (eps = 1.000000) [02:30:49 -81828.104798] SLOW spr round 1 (radius: 5) [02:33:42 -81802.204233] SLOW spr round 2 (radius: 5) [02:36:27 -81796.233789] SLOW spr round 3 (radius: 5) [02:39:11 -81795.235106] SLOW spr round 4 (radius: 5) [02:41:55 -81795.234760] SLOW spr round 5 (radius: 10) [02:44:31 -81793.789738] SLOW spr round 6 (radius: 5) [02:47:59 -81792.851249] SLOW spr round 7 (radius: 5) [02:48:31] [worker #2] ML tree search #8, logLikelihood: -81488.812991 [02:51:01 -81792.851249] SLOW spr round 8 (radius: 10) [02:53:44 -81792.851249] SLOW spr round 9 (radius: 15) [02:54:02] [worker #4] ML tree search #10, logLikelihood: -81451.152983 [02:57:46 -81790.199729] SLOW spr round 10 (radius: 5) [03:01:20 -81789.372891] SLOW spr round 11 (radius: 5) [03:04:29 -81789.372821] SLOW spr round 12 (radius: 10) [03:07:10 -81789.372819] SLOW spr round 13 (radius: 15) [03:11:09 -81789.372819] SLOW spr round 14 (radius: 20) [03:16:17 -81789.372819] SLOW spr round 15 (radius: 25) [03:16:34] [worker #3] ML tree search #9, logLikelihood: -81454.632794 [03:22:00 -81742.095448] SLOW spr round 16 (radius: 5) [03:24:44] [worker #1] ML tree search #7, logLikelihood: -81530.507236 [03:25:59 -81694.150652] SLOW spr round 17 (radius: 5) [03:29:12 -81692.830979] SLOW spr round 18 (radius: 5) [03:32:05 -81692.830968] SLOW spr round 19 (radius: 10) [03:34:45 -81692.830968] SLOW spr round 20 (radius: 15) [03:39:03 -81691.690202] SLOW spr round 21 (radius: 5) [03:42:45 -81525.964761] SLOW spr round 22 (radius: 5) [03:45:59 -81514.095807] SLOW spr round 23 (radius: 5) [03:48:52 -81514.095604] SLOW spr round 24 (radius: 10) [03:51:31 -81514.095603] SLOW spr round 25 (radius: 15) [03:55:51 -81514.095603] SLOW spr round 26 (radius: 20) [04:01:39 -81514.095603] SLOW spr round 27 (radius: 25) [04:08:58 -81514.095603] Model parameter optimization (eps = 0.100000) [04:09:13] [worker #0] ML tree search #6, logLikelihood: -81513.894988 [04:09:13 -381716.827988] Initial branch length optimization [04:09:18 -312350.270041] Model parameter optimization (eps = 10.000000) [04:10:00] [worker #2] ML tree search #13, logLikelihood: -81432.403614 [04:10:17 -311847.057341] AUTODETECT spr round 1 (radius: 5) [04:13:46 -189322.093187] AUTODETECT spr round 2 (radius: 10) [04:17:22] [worker #4] ML tree search #15, logLikelihood: -81475.622066 [04:17:32 -139751.726336] AUTODETECT spr round 3 (radius: 15) [04:21:37 -119124.198383] AUTODETECT spr round 4 (radius: 20) [04:26:22 -106209.347495] AUTODETECT spr round 5 (radius: 25) [04:28:47] [worker #3] ML tree search #14, logLikelihood: -81458.003029 [04:30:17] [worker #1] ML tree search #12, logLikelihood: -81498.634296 [04:32:00 -99064.180550] SPR radius for FAST iterations: 25 (autodetect) [04:32:00 -99064.180550] Model parameter optimization (eps = 3.000000) [04:32:32 -98804.884142] FAST spr round 1 (radius: 25) [04:36:23 -82466.848933] FAST spr round 2 (radius: 25) [04:39:04 -81598.215407] FAST spr round 3 (radius: 25) [04:41:25 -81504.218560] FAST spr round 4 (radius: 25) [04:43:36 -81498.758029] FAST spr round 5 (radius: 25) [04:45:31 -81498.755666] Model parameter optimization (eps = 1.000000) [04:45:55 -81481.173046] SLOW spr round 1 (radius: 5) [04:48:52 -81460.819923] SLOW spr round 2 (radius: 5) [04:51:39 -81458.242462] SLOW spr round 3 (radius: 5) [04:54:27 -81458.242346] SLOW spr round 4 (radius: 10) [04:57:05 -81458.242346] SLOW spr round 5 (radius: 15) [05:01:38 -81458.242346] SLOW spr round 6 (radius: 20) [05:08:18 -81458.242346] SLOW spr round 7 (radius: 25) [05:17:10 -81458.242346] Model parameter optimization (eps = 0.100000) [05:17:25] [worker #0] ML tree search #11, logLikelihood: -81457.684184 [05:17:25 -376564.004274] Initial branch length optimization [05:17:30 -309538.168411] Model parameter optimization (eps = 10.000000) [05:18:18 -308985.672502] AUTODETECT spr round 1 (radius: 5) [05:21:37 -193272.795718] AUTODETECT spr round 2 (radius: 10) [05:25:03] [worker #4] ML tree search #20, logLikelihood: -81476.742280 [05:25:18 -138721.521141] AUTODETECT spr round 3 (radius: 15) [05:29:43 -112635.170961] AUTODETECT spr round 4 (radius: 20) [05:33:45 -100369.860494] AUTODETECT spr round 5 (radius: 25) [05:38:33 -96112.931591] SPR radius for FAST iterations: 25 (autodetect) [05:38:33 -96112.931591] Model parameter optimization (eps = 3.000000) [05:39:09 -95861.500944] FAST spr round 1 (radius: 25) [05:42:42 -82383.159116] FAST spr round 2 (radius: 25) [05:45:25 -81547.770216] FAST spr round 3 (radius: 25) [05:47:39 -81499.597271] FAST spr round 4 (radius: 25) [05:49:39] [worker #3] ML tree search #19, logLikelihood: -81453.569735 [05:49:45 -81496.188838] FAST spr round 5 (radius: 25) [05:51:42 -81496.188479] Model parameter optimization (eps = 1.000000) [05:51:57 -81493.591257] SLOW spr round 1 (radius: 5) [05:54:41] [worker #1] ML tree search #17, logLikelihood: -81489.765537 [05:54:51 -81474.093818] SLOW spr round 2 (radius: 5) [05:57:30 -81472.017928] SLOW spr round 3 (radius: 5) [06:00:12 -81472.017758] SLOW spr round 4 (radius: 10) [06:02:46 -81472.017755] SLOW spr round 5 (radius: 15) [06:07:12 -81471.224019] SLOW spr round 6 (radius: 5) [06:10:42 -81470.005095] SLOW spr round 7 (radius: 5) [06:13:38 -81470.005091] SLOW spr round 8 (radius: 10) [06:16:26 -81463.689881] SLOW spr round 9 (radius: 5) [06:19:51 -81452.879861] SLOW spr round 10 (radius: 5) [06:22:46] [worker #2] ML tree search #18, logLikelihood: -81468.384495 [06:22:52 -81446.865553] SLOW spr round 11 (radius: 5) [06:25:29 -81446.865302] SLOW spr round 12 (radius: 10) [06:28:05 -81446.865300] SLOW spr round 13 (radius: 15) [06:32:22 -81446.865300] SLOW spr round 14 (radius: 20) [06:38:42 -81446.865300] SLOW spr round 15 (radius: 25) [06:46:41 -81446.865300] Model parameter optimization (eps = 0.100000) [06:47:02] [worker #0] ML tree search #16, logLikelihood: -81446.511627 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.280345,0.504947) (0.375186,0.724510) (0.249917,1.255827) (0.094552,2.884794) 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: -81432.403614 AIC score: 166874.807228 / AICc score: 8210934.807228 / BIC score: 173785.515658 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=232). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P55064/3_mltree/P55064.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P55064/3_mltree/P55064.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P55064/3_mltree/P55064.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P55064/3_mltree/P55064.raxml.log Analysis started: 05-Jul-2021 21:45:33 / finished: 06-Jul-2021 04:32:35 Elapsed time: 24422.309 seconds Consumed energy: 2101.822 Wh (= 11 km in an electric car, or 53 km with an e-scooter!)