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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 07-Jul-2021 17:45:37 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61978/2_msa/P61978_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61978/3_mltree/P61978 --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/P61978/2_msa/P61978_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 360 sites WARNING: Sequences tr_A0A1D5PXG0_A0A1D5PXG0_CHICK_9031 and tr_U3KDB7_U3KDB7_FICAL_59894 are exactly identical! WARNING: Sequences tr_A0A1D5PXG0_A0A1D5PXG0_CHICK_9031 and tr_A0A1V4KDB9_A0A1V4KDB9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1D5PXG0_A0A1D5PXG0_CHICK_9031 and tr_A0A218V907_A0A218V907_9PASE_299123 are exactly identical! WARNING: Sequences sp_P61979_HNRPK_MOUSE_10090 and tr_M3XSI8_M3XSI8_MUSPF_9669 are exactly identical! WARNING: Sequences sp_P61979_HNRPK_MOUSE_10090 and tr_F6Q4Q1_F6Q4Q1_HORSE_9796 are exactly identical! WARNING: Sequences sp_P61979_HNRPK_MOUSE_10090 and sp_P61980_HNRPK_RAT_10116 are exactly identical! WARNING: Sequences sp_P61979_HNRPK_MOUSE_10090 and sp_P61978_HNRPK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YK15_M3YK15_MUSPF_9669 and tr_H0XN68_H0XN68_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3YK15_M3YK15_MUSPF_9669 and tr_M3WAW2_M3WAW2_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YK15_M3YK15_MUSPF_9669 and tr_A0A1U7TQE7_A0A1U7TQE7_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3YK15_M3YK15_MUSPF_9669 and tr_A0A2U3XK22_A0A2U3XK22_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1R5Y3_G1R5Y3_NOMLE_61853 and tr_A0A2J8TH92_A0A2J8TH92_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R5Y3_G1R5Y3_NOMLE_61853 and tr_K7CGS3_K7CGS3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R5Y3_G1R5Y3_NOMLE_61853 and sp_P57723_PCBP4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R5Y3_G1R5Y3_NOMLE_61853 and tr_F6ZFV1_F6ZFV1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R5Y3_G1R5Y3_NOMLE_61853 and tr_U3BK68_U3BK68_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1R5Y3_G1R5Y3_NOMLE_61853 and tr_G7NZX3_G7NZX3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1R5Y3_G1R5Y3_NOMLE_61853 and tr_A0A0D9RN73_A0A0D9RN73_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R5Y3_G1R5Y3_NOMLE_61853 and tr_A0A2R9BQ64_A0A2R9BQ64_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and sp_Q5R5H8_HNRPK_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_K7C562_K7C562_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_F7EHL0_F7EHL0_ORNAN_9258 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_A0A287CYM1_A0A287CYM1_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_F6VJH6_F6VJH6_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_G5ARM9_G5ARM9_HETGA_10181 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_F7IK44_F7IK44_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_M3WLH7_M3WLH7_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_A0A2I3LSM4_A0A2I3LSM4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_A0A1S3A2R9_A0A1S3A2R9_ERIEU_9365 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_A0A1S3GEV2_A0A1S3GEV2_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_A0A1U7SY96_A0A1U7SY96_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_A0A2K6E9E8_A0A2K6E9E8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_A0A2K6A2W9_A0A2K6A2W9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_A0A2U3WG26_A0A2U3WG26_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_A0A2U3YKL0_A0A2U3YKL0_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_A0A2Y9RAS4_A0A2Y9RAS4_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_A0A2Y9K5B9_A0A2Y9K5B9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1P5R3_G1P5R3_MYOLU_59463 and tr_A0A384CHZ0_A0A384CHZ0_URSMA_29073 are exactly identical! WARNING: Sequences tr_J3KIC5_J3KIC5_COCIM_246410 and tr_E9CUT5_E9CUT5_COCPS_443226 are exactly identical! WARNING: Sequences tr_B6Q3Q9_B6Q3Q9_TALMQ_441960 and tr_A0A093VTI7_A0A093VTI7_TALMA_1077442 are exactly identical! WARNING: Sequences tr_G3RHK3_G3RHK3_GORGO_9595 and tr_A0A2R9CMZ8_A0A2R9CMZ8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G2X1Y4_G2X1Y4_VERDV_498257 and tr_A0A0G4KYP5_A0A0G4KYP5_9PEZI_100787 are exactly identical! WARNING: Sequences tr_G2X1Y4_G2X1Y4_VERDV_498257 and tr_A0A0G4LBD7_A0A0G4LBD7_9PEZI_100787 are exactly identical! WARNING: Sequences tr_C0NCT3_C0NCT3_AJECG_447093 and tr_C6HJL2_C6HJL2_AJECH_544712 are exactly identical! WARNING: Sequences tr_Q7SCU3_Q7SCU3_NEUCR_367110 and tr_G4UAQ0_G4UAQ0_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8N4A8_B8N4A8_ASPFN_332952 and tr_A0A0F0IAB5_A0A0F0IAB5_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8N4A8_B8N4A8_ASPFN_332952 and tr_A0A0L1IUS6_A0A0L1IUS6_ASPNO_1509407 are exactly identical! WARNING: Sequences tr_B8N4A8_B8N4A8_ASPFN_332952 and tr_A0A1F8AF93_A0A1F8AF93_9EURO_109264 are exactly identical! WARNING: Sequences tr_B8N4A8_B8N4A8_ASPFN_332952 and tr_A0A1S9DNF5_A0A1S9DNF5_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8N4A8_B8N4A8_ASPFN_332952 and tr_A0A2G7G8J3_A0A2G7G8J3_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A179URE9_A0A179URE9_BLAGS_559298 and tr_C5GEM8_C5GEM8_AJEDR_559297 are exactly identical! WARNING: Sequences tr_E2RCF9_E2RCF9_CANLF_9615 and tr_W5Q4P4_W5Q4P4_SHEEP_9940 are exactly identical! WARNING: Sequences tr_E2RG64_E2RG64_CANLF_9615 and tr_G1LRM8_G1LRM8_AILME_9646 are exactly identical! WARNING: Sequences tr_E2RG64_E2RG64_CANLF_9615 and tr_A0A2U3WQS7_A0A2U3WQS7_ODORO_9708 are exactly identical! WARNING: Sequences tr_F7BUQ2_F7BUQ2_MONDO_13616 and tr_H0WWD7_H0WWD7_OTOGA_30611 are exactly identical! WARNING: Sequences tr_F7BUQ2_F7BUQ2_MONDO_13616 and tr_G3WXL3_G3WXL3_SARHA_9305 are exactly identical! WARNING: Sequences tr_W5PGN1_W5PGN1_SHEEP_9940 and sp_Q3T0D0_HNRPK_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5PGN1_W5PGN1_SHEEP_9940 and tr_A0A2U4BS49_A0A2U4BS49_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5PGN1_W5PGN1_SHEEP_9940 and tr_A0A2Y9LYR5_A0A2Y9LYR5_DELLE_9749 are exactly identical! WARNING: Sequences tr_W5PGN1_W5PGN1_SHEEP_9940 and tr_A0A2Y9EHJ8_A0A2Y9EHJ8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_W5PGN1_W5PGN1_SHEEP_9940 and tr_A0A383ZPG6_A0A383ZPG6_BALAS_310752 are exactly identical! WARNING: Sequences tr_F9FM75_F9FM75_FUSOF_660025 and tr_N4TNT3_N4TNT3_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FM75_F9FM75_FUSOF_660025 and tr_X0C604_X0C604_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FM75_F9FM75_FUSOF_660025 and tr_A0A2H3STK4_A0A2H3STK4_FUSOX_5507 are exactly identical! WARNING: Sequences tr_J4UWK9_J4UWK9_BEAB2_655819 and tr_A0A0A2W0H3_A0A0A2W0H3_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J4UWK9_J4UWK9_BEAB2_655819 and tr_A0A2N6NF53_A0A2N6NF53_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A3B5Q267_A0A3B5Q267_XIPMA_8083 and tr_A0A087XWF7_A0A087XWF7_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4A162_M4A162_XIPMA_8083 and tr_A0A087YAY0_A0A087YAY0_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A088ATQ8_A0A088ATQ8_APIME_7460 and tr_A0A2A3E5Y9_A0A2A3E5Y9_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NGR9_A0A158NGR9_ATTCE_12957 and tr_F4WZL7_F4WZL7_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NGR9_A0A158NGR9_ATTCE_12957 and tr_A0A195DYH6_A0A195DYH6_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NGR9_A0A158NGR9_ATTCE_12957 and tr_A0A195B7U6_A0A195B7U6_9HYME_520822 are exactly identical! WARNING: Sequences tr_G9NHE2_G9NHE2_HYPAI_452589 and tr_A0A2P4ZI51_A0A2P4ZI51_9HYPO_398673 are exactly identical! WARNING: Sequences tr_A1DFR4_A1DFR4_NEOFI_331117 and tr_A0A0K8LRD5_A0A0K8LRD5_9EURO_91492 are exactly identical! WARNING: Sequences tr_A1DFR4_A1DFR4_NEOFI_331117 and tr_A0A0S7DUH7_A0A0S7DUH7_9EURO_293939 are exactly identical! WARNING: Sequences tr_G7XAA4_G7XAA4_ASPKW_1033177 and tr_A0A100IJD1_A0A100IJD1_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XAA4_G7XAA4_ASPKW_1033177 and tr_A0A1L9N115_A0A1L9N115_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G7XAA4_G7XAA4_ASPKW_1033177 and tr_A0A317WE12_A0A317WE12_9EURO_1448314 are exactly identical! WARNING: Sequences tr_G7XAA4_G7XAA4_ASPKW_1033177 and tr_A0A319AA68_A0A319AA68_9EURO_1450533 are exactly identical! WARNING: Sequences tr_D5GFG0_D5GFG0_TUBMM_656061 and tr_A0A2T6ZM57_A0A2T6ZM57_TUBBO_42251 are exactly identical! WARNING: Sequences tr_F4P806_F4P806_BATDJ_684364 and tr_A0A177WTU8_A0A177WTU8_BATDE_403673 are exactly identical! WARNING: Sequences tr_G2YZH2_G2YZH2_BOTF4_999810 and tr_M7U3D0_M7U3D0_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SK09_F2SK09_TRIRC_559305 and tr_A0A059J8S9_A0A059J8S9_9EURO_1215338 are exactly identical! WARNING: Sequences tr_F2SK09_F2SK09_TRIRC_559305 and tr_A0A178EQ64_A0A178EQ64_TRIRU_5551 are exactly identical! WARNING: Sequences tr_D4AKY3_D4AKY3_ARTBC_663331 and tr_F2PM56_F2PM56_TRIEC_559882 are exactly identical! WARNING: Sequences tr_G3YCV2_G3YCV2_ASPNA_380704 and tr_A0A146F8Y9_A0A146F8Y9_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G3YCV2_G3YCV2_ASPNA_380704 and tr_A0A1L9V1K4_A0A1L9V1K4_9EURO_767769 are exactly identical! WARNING: Sequences tr_A0A0D2X8X3_A0A0D2X8X3_FUSO4_426428 and tr_A0A2H3HZ96_A0A2H3HZ96_FUSOX_327505 are exactly identical! WARNING: Sequences tr_L2G4Z8_L2G4Z8_COLFN_1213859 and tr_T0KMN7_T0KMN7_COLGC_1237896 are exactly identical! WARNING: Sequences tr_L2G7Q2_L2G7Q2_COLFN_1213859 and tr_T0KTQ7_T0KTQ7_COLGC_1237896 are exactly identical! WARNING: Sequences tr_U3JMW2_U3JMW2_FICAL_59894 and tr_U3I5F8_U3I5F8_ANAPL_8839 are exactly identical! WARNING: Sequences tr_S0DIW8_S0DIW8_GIBF5_1279085 and tr_A0A365N397_A0A365N397_GIBIN_948311 are exactly identical! WARNING: Sequences tr_V2XGG9_V2XGG9_MONRO_1381753 and tr_A0A0W0G2K1_A0A0W0G2K1_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A044SNL8_A0A044SNL8_ONCVO_6282 and tr_A0A182E2V7_A0A182E2V7_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A2K6W060_A0A2K6W060_ONCVO_6282 and tr_A0A182E4E1_A0A182E4E1_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0A2LAG0_A0A0A2LAG0_PENIT_40296 and tr_A0A0G4PVH5_A0A0G4PVH5_PENCA_1429867 are exactly identical! WARNING: Sequences tr_A0A0A2LAG0_A0A0A2LAG0_PENIT_40296 and tr_A0A1V6R349_A0A1V6R349_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A0R3WKH6_A0A0R3WKH6_HYDTA_6205 and tr_A0A0R3VUY5_A0A0R3VUY5_TAEAS_60517 are exactly identical! WARNING: Sequences tr_A0A091JB10_A0A091JB10_EGRGA_188379 and tr_A0A091V3K5_A0A091V3K5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JB10_A0A091JB10_EGRGA_188379 and tr_A0A087R3V3_A0A087R3V3_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JB10_A0A091JB10_EGRGA_188379 and tr_A0A091VI62_A0A091VI62_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JB10_A0A091JB10_EGRGA_188379 and tr_A0A0A0AKQ4_A0A0A0AKQ4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091VIW6_A0A091VIW6_NIPNI_128390 and tr_A0A091FRJ4_A0A091FRJ4_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A0V0WTB6_A0A0V0WTB6_9BILA_92179 and tr_A0A0V1KYA6_A0A0V1KYA6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0V6Q5_A0A0V0V6Q5_9BILA_181606 and tr_A0A0V1NKN3_A0A0V1NKN3_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0V6Q5_A0A0V0V6Q5_9BILA_181606 and tr_A0A0V0TCD4_A0A0V0TCD4_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A101MQE0_A0A101MQE0_9EURO_48697 and tr_A0A1V6NBR8_A0A1V6NBR8_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A1S3KTN5_A0A1S3KTN5_SALSA_8030 and tr_A0A060XFA2_A0A060XFA2_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3LSX6_A0A1S3LSX6_SALSA_8030 and tr_A0A060X8N4_A0A060X8N4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1I7UXN8_A0A1I7UXN8_9PELO_1561998 and tr_A0A1I7UXN9_A0A1I7UXN9_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1L9X198_A0A1L9X198_ASPAC_690307 and tr_A0A2V5II28_A0A2V5II28_9EURO_1450541 are exactly identical! WARNING: Sequences tr_A0A2I4CLN0_A0A2I4CLN0_9TELE_52670 and tr_A0A2I4D8L9_A0A2I4D8L9_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A226N1J8_A0A226N1J8_CALSU_9009 and tr_A0A226P8X4_A0A226P8X4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PIX9_A0A2D0PIX9_ICTPU_7998 and tr_A0A2D0PKF7_A0A2D0PKF7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PIX9_A0A2D0PIX9_ICTPU_7998 and tr_A0A2D0PN67_A0A2D0PN67_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QE04_A0A2D0QE04_ICTPU_7998 and tr_A0A2D0QF13_A0A2D0QF13_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R1N2_A0A2D0R1N2_ICTPU_7998 and tr_A0A2D0R1W6_A0A2D0R1W6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R1N7_A0A2D0R1N7_ICTPU_7998 and tr_A0A2D0R1P0_A0A2D0R1P0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R3B4_A0A2D0R3B4_ICTPU_7998 and tr_A0A2D0R419_A0A2D0R419_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R3B9_A0A2D0R3B9_ICTPU_7998 and tr_A0A2D0R424_A0A2D0R424_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2G5HGU1_A0A2G5HGU1_CERBT_122368 and tr_A0A2S6BZM6_A0A2S6BZM6_9PEZI_357750 are exactly identical! WARNING: Sequences tr_A0A2K5NCM1_A0A2K5NCM1_CERAT_9531 and tr_A0A2K6AGE3_A0A2K6AGE3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A317V1D5_A0A317V1D5_9EURO_1450535 and tr_A0A319EW65_A0A319EW65_9EURO_1448318 are exactly identical! WARNING: Duplicate sequences found: 123 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/P61978/3_mltree/P61978.raxml.reduced.phy Alignment comprises 1 partitions and 360 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 360 / 360 Gaps: 20.52 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61978/3_mltree/P61978.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 / 360 / 28800 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -505389.203974] Initial branch length optimization [00:00:09 -415296.850487] Model parameter optimization (eps = 10.000000) [00:01:33 -414279.819169] AUTODETECT spr round 1 (radius: 5) [00:06:30 -242083.838752] AUTODETECT spr round 2 (radius: 10) [00:11:21 -171523.425046] AUTODETECT spr round 3 (radius: 15) [00:16:40 -136498.361216] AUTODETECT spr round 4 (radius: 20) [00:23:28 -125247.896677] AUTODETECT spr round 5 (radius: 25) [00:32:35 -118008.480707] SPR radius for FAST iterations: 25 (autodetect) [00:32:35 -118008.480707] Model parameter optimization (eps = 3.000000) [00:33:26 -117554.472779] FAST spr round 1 (radius: 25) [00:38:56 -103005.168971] FAST spr round 2 (radius: 25) [00:42:54 -102272.036698] FAST spr round 3 (radius: 25) [00:46:25 -102233.187042] FAST spr round 4 (radius: 25) [00:49:43 -102224.207747] FAST spr round 5 (radius: 25) [00:52:46 -102223.537881] FAST spr round 6 (radius: 25) [00:55:43 -102223.537283] Model parameter optimization (eps = 1.000000) [00:56:15 -102204.719577] SLOW spr round 1 (radius: 5) [01:00:22 -102172.044205] SLOW spr round 2 (radius: 5) [01:04:27 -102165.795667] SLOW spr round 3 (radius: 5) [01:08:28 -102164.953698] SLOW spr round 4 (radius: 5) [01:12:25 -102164.953578] SLOW spr round 5 (radius: 10) [01:16:30 -102161.360230] SLOW spr round 6 (radius: 5) [01:21:44 -102161.359376] SLOW spr round 7 (radius: 10) [01:26:16 -102161.359350] SLOW spr round 8 (radius: 15) [01:32:39 -102161.046728] SLOW spr round 9 (radius: 5) [01:38:09 -102157.882336] SLOW spr round 10 (radius: 5) [01:42:49 -102156.926775] SLOW spr round 11 (radius: 5) [01:47:02 -102156.886007] SLOW spr round 12 (radius: 10) [01:51:07 -102156.553541] SLOW spr round 13 (radius: 5) [01:56:09 -102156.553526] SLOW spr round 14 (radius: 10) [02:00:39 -102156.553524] SLOW spr round 15 (radius: 15) [02:07:02 -102156.373796] SLOW spr round 16 (radius: 5) [02:08:49] [worker #2] ML tree search #3, logLikelihood: -102129.786740 [02:12:27 -102156.373769] SLOW spr round 17 (radius: 10) [02:17:16 -102156.373746] SLOW spr round 18 (radius: 15) [02:23:35 -102156.373744] SLOW spr round 19 (radius: 20) [02:32:48 -102156.373743] SLOW spr round 20 (radius: 25) [02:44:18 -102152.811071] SLOW spr round 21 (radius: 5) [02:47:25] [worker #1] ML tree search #2, logLikelihood: -102147.531827 [02:49:51 -102152.811067] SLOW spr round 22 (radius: 10) [02:54:52 -102152.811065] SLOW spr round 23 (radius: 15) [03:00:55] [worker #4] ML tree search #5, logLikelihood: -102140.759555 [03:01:11 -102152.811064] SLOW spr round 24 (radius: 20) [03:02:48] [worker #3] ML tree search #4, logLikelihood: -102245.205208 [03:10:25 -102152.811063] SLOW spr round 25 (radius: 25) [03:21:57 -102152.811061] Model parameter optimization (eps = 0.100000) [03:22:13] [worker #0] ML tree search #1, logLikelihood: -102152.703605 [03:22:13 -502589.508411] Initial branch length optimization [03:22:21 -409399.314657] Model parameter optimization (eps = 10.000000) [03:23:45 -408370.073380] AUTODETECT spr round 1 (radius: 5) [03:28:41 -249499.039631] AUTODETECT spr round 2 (radius: 10) [03:33:41 -181869.393434] AUTODETECT spr round 3 (radius: 15) [03:39:05 -140438.051210] AUTODETECT spr round 4 (radius: 20) [03:45:03 -122281.925344] AUTODETECT spr round 5 (radius: 25) [03:51:29 -117296.652783] SPR radius for FAST iterations: 25 (autodetect) [03:51:29 -117296.652783] Model parameter optimization (eps = 3.000000) [03:52:27 -116974.376728] FAST spr round 1 (radius: 25) [03:57:52 -103393.644462] FAST spr round 2 (radius: 25) [04:02:04 -102253.712446] FAST spr round 3 (radius: 25) [04:05:30 -102212.705355] FAST spr round 4 (radius: 25) [04:07:01] [worker #2] ML tree search #8, logLikelihood: -102152.751905 [04:08:40 -102209.531748] FAST spr round 5 (radius: 25) [04:11:42 -102208.462628] FAST spr round 6 (radius: 25) [04:14:41 -102207.249710] FAST spr round 7 (radius: 25) [04:17:36 -102207.249638] Model parameter optimization (eps = 1.000000) [04:17:57 -102205.443916] SLOW spr round 1 (radius: 5) [04:22:11 -102165.796033] SLOW spr round 2 (radius: 5) [04:26:24 -102156.518792] SLOW spr round 3 (radius: 5) [04:30:32 -102155.910589] SLOW spr round 4 (radius: 5) [04:34:33 -102155.909918] SLOW spr round 5 (radius: 10) [04:38:50 -102152.542066] SLOW spr round 6 (radius: 5) [04:44:16 -102149.668846] SLOW spr round 7 (radius: 5) [04:48:50 -102149.664044] SLOW spr round 8 (radius: 10) [04:49:17] [worker #1] ML tree search #7, logLikelihood: -102129.460772 [04:53:11 -102149.663831] SLOW spr round 9 (radius: 15) [05:00:08 -102149.663613] SLOW spr round 10 (radius: 20) [05:10:14 -102149.663391] SLOW spr round 11 (radius: 25) [05:23:07 -102149.663161] Model parameter optimization (eps = 0.100000) [05:23:32] [worker #0] ML tree search #6, logLikelihood: -102149.137002 [05:23:32 -506793.692269] Initial branch length optimization [05:23:44 -412770.683072] Model parameter optimization (eps = 10.000000) [05:25:18 -411869.912185] AUTODETECT spr round 1 (radius: 5) [05:26:06] [worker #4] ML tree search #10, logLikelihood: -102146.532799 [05:30:22 -244536.864046] AUTODETECT spr round 2 (radius: 10) [05:31:14] [worker #3] ML tree search #9, logLikelihood: -102163.505015 [05:35:22 -177735.198240] AUTODETECT spr round 3 (radius: 15) [05:41:16 -129566.862425] AUTODETECT spr round 4 (radius: 20) [05:47:58 -118617.551574] AUTODETECT spr round 5 (radius: 25) [05:55:49 -117331.920356] SPR radius for FAST iterations: 25 (autodetect) [05:55:49 -117331.920356] Model parameter optimization (eps = 3.000000) [05:56:50 -116883.730473] FAST spr round 1 (radius: 25) [06:02:06 -102943.251592] FAST spr round 2 (radius: 25) [06:06:13 -102362.806392] FAST spr round 3 (radius: 25) [06:09:53 -102278.143873] FAST spr round 4 (radius: 25) [06:13:09 -102258.815449] FAST spr round 5 (radius: 25) [06:16:14 -102257.424584] FAST spr round 6 (radius: 25) [06:17:08] [worker #2] ML tree search #13, logLikelihood: -102381.069411 [06:19:17 -102257.422167] Model parameter optimization (eps = 1.000000) [06:19:47 -102233.283720] SLOW spr round 1 (radius: 5) [06:23:59 -102206.521359] SLOW spr round 2 (radius: 5) [06:28:08 -102204.775136] SLOW spr round 3 (radius: 5) [06:32:14 -102204.774948] SLOW spr round 4 (radius: 10) [06:36:19 -102204.774842] SLOW spr round 5 (radius: 15) [06:39:16] [worker #1] ML tree search #12, logLikelihood: -102296.728405 [06:43:19 -102204.615559] SLOW spr round 6 (radius: 5) [06:48:48 -102204.615528] SLOW spr round 7 (radius: 10) [06:53:35 -102204.615519] SLOW spr round 8 (radius: 15) [07:00:06 -102204.615513] SLOW spr round 9 (radius: 20) [07:05:42] [worker #4] ML tree search #15, logLikelihood: -102313.521114 [07:09:34 -102203.981754] SLOW spr round 10 (radius: 5) [07:15:10 -102203.981591] SLOW spr round 11 (radius: 10) [07:20:06 -102203.981582] SLOW spr round 12 (radius: 15) [07:26:34 -102203.981576] SLOW spr round 13 (radius: 20) [07:36:01 -102203.981571] SLOW spr round 14 (radius: 25) [07:48:13 -102203.045354] SLOW spr round 15 (radius: 5) [07:53:49 -102203.045308] SLOW spr round 16 (radius: 10) [07:58:54 -102203.045265] SLOW spr round 17 (radius: 15) [08:05:21 -102203.045260] SLOW spr round 18 (radius: 20) [08:06:12] [worker #3] ML tree search #14, logLikelihood: -102273.628805 [08:14:52 -102203.045254] SLOW spr round 19 (radius: 25) [08:16:39] [worker #2] ML tree search #18, logLikelihood: -102149.161527 [08:27:07 -102203.045249] Model parameter optimization (eps = 0.100000) [08:27:27] [worker #0] ML tree search #11, logLikelihood: -102202.690485 [08:27:27 -504699.300303] Initial branch length optimization [08:27:35 -412025.927330] Model parameter optimization (eps = 10.000000) [08:29:17 -410952.127603] AUTODETECT spr round 1 (radius: 5) [08:34:12 -237841.125707] AUTODETECT spr round 2 (radius: 10) [08:39:15 -166711.176881] AUTODETECT spr round 3 (radius: 15) [08:44:31 -135076.523128] AUTODETECT spr round 4 (radius: 20) [08:50:43 -122243.439241] AUTODETECT spr round 5 (radius: 25) [08:57:38 -118578.368398] SPR radius for FAST iterations: 25 (autodetect) [08:57:38 -118578.368398] Model parameter optimization (eps = 3.000000) [08:58:22 -118162.066447] FAST spr round 1 (radius: 25) [09:03:45 -103064.427330] FAST spr round 2 (radius: 25) [09:07:39 -102425.658332] FAST spr round 3 (radius: 25) [09:11:05 -102253.765318] FAST spr round 4 (radius: 25) [09:14:17 -102239.624157] FAST spr round 5 (radius: 25) [09:17:15 -102237.489394] FAST spr round 6 (radius: 25) [09:20:06 -102237.408033] Model parameter optimization (eps = 1.000000) [09:20:37 -102224.455370] SLOW spr round 1 (radius: 5) [09:24:40 -102183.112229] SLOW spr round 2 (radius: 5) [09:28:38 -102181.040608] SLOW spr round 3 (radius: 5) [09:32:33 -102180.366997] SLOW spr round 4 (radius: 5) [09:36:17 -102180.366469] SLOW spr round 5 (radius: 10) [09:40:19 -102179.879397] SLOW spr round 6 (radius: 5) [09:40:47] [worker #1] ML tree search #17, logLikelihood: -102252.654879 [09:45:18 -102179.877754] SLOW spr round 7 (radius: 10) [09:49:44 -102179.877615] SLOW spr round 8 (radius: 15) [09:54:20] [worker #4] ML tree search #20, logLikelihood: -102162.689779 [09:56:17 -102177.356909] SLOW spr round 9 (radius: 5) [10:01:32 -102177.356888] SLOW spr round 10 (radius: 10) [10:06:13 -102177.356859] SLOW spr round 11 (radius: 15) [10:12:39 -102177.356853] SLOW spr round 12 (radius: 20) [10:22:40 -102177.356847] SLOW spr round 13 (radius: 25) [10:35:50 -102177.356841] Model parameter optimization (eps = 0.100000) [10:36:12] [worker #0] ML tree search #16, logLikelihood: -102177.072006 [11:34:19] [worker #3] ML tree search #19, logLikelihood: -102151.874437 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.201508,0.529570) (0.089750,0.468791) (0.304929,0.672523) (0.403813,1.600101) 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: -102129.460772 AIC score: 208268.921545 / AICc score: 8252328.921545 / BIC score: 216060.560128 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=360). 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/P61978/3_mltree/P61978.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61978/3_mltree/P61978.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61978/3_mltree/P61978.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P61978/3_mltree/P61978.raxml.log Analysis started: 07-Jul-2021 17:45:37 / finished: 08-Jul-2021 05:19:57 Elapsed time: 41659.917 seconds Consumed energy: 2345.966 Wh (= 12 km in an electric car, or 59 km with an e-scooter!)