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 14:51:42 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/2_msa/Q7RTP6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/3_mltree/Q7RTP6 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/2_msa/Q7RTP6_trimmed_msa.fasta [00:00:00] Loaded alignment with 972 taxa and 153 sites WARNING: Sequences tr_B4QIY1_B4QIY1_DROSI_7240 and tr_Q9VU34_Q9VU34_DROME_7227 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_M3YNS9_M3YNS9_MUSPF_9669 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_G1S7F1_G1S7F1_NOMLE_61853 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_C3Z6G9_C3Z6G9_BRAFL_7739 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_G3UTB3_G3UTB3_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_F6RAZ0_F6RAZ0_HORSE_9796 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_I3JL20_I3JL20_ORENI_8128 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_H1A0F7_H1A0F7_TAEGU_59729 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_F4WHF4_F4WHF4_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_F6T0F6_F6T0F6_XENTR_8364 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_F7DU62_F7DU62_XENTR_8364 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_G7PH71_G7PH71_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_U3IMX5_U3IMX5_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_W5M924_W5M924_LEPOC_7918 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_A0A151NIK5_A0A151NIK5_ALLMI_8496 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_A0A091IPS9_A0A091IPS9_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_A0A093JZM9_A0A093JZM9_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_A0A091XWV9_A0A091XWV9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_A0A091GGW7_A0A091GGW7_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_A0A0A0A5V0_A0A0A0A5V0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_A0A060VPK4_A0A060VPK4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_A0A060WBB8_A0A060WBB8_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_A0A060YHR1_A0A060YHR1_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1D5P142_A0A1D5P142_CHICK_9031 and tr_A0A2U3YEK9_A0A2U3YEK9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_E1BXR9_E1BXR9_CHICK_9031 and tr_G1NL95_G1NL95_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1BXR9_E1BXR9_CHICK_9031 and tr_A0A091JF32_A0A091JF32_EGRGA_188379 are exactly identical! WARNING: Sequences tr_E1BXR9_E1BXR9_CHICK_9031 and tr_A0A0A0A2N2_A0A0A0A2N2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_E1BXR9_E1BXR9_CHICK_9031 and tr_A0A093GVJ0_A0A093GVJ0_DRYPU_118200 are exactly identical! WARNING: Sequences sp_Q8BGT6_MILK1_MOUSE_10090 and sp_D3ZQL6_MILK1_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_G1R8P5_G1R8P5_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_A0A2I2Z1Q0_A0A2I2Z1Q0_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_F1Q0K3_F1Q0K3_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_A0A2I3TBJ7_A0A2I3TBJ7_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and sp_Q7RTP6_MICA3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_A0A1D5Q5P4_A0A1D5Q5P4_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_A0A096NVY8_A0A096NVY8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_A0A0D9RP54_A0A0D9RP54_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_A0A1U7TST4_A0A1U7TST4_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_A0A2K5LG92_A0A2K5LG92_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_A0A2K6E3P3_A0A2K6E3P3_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_A0A2K6A5U2_A0A2K6A5U2_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_A0A2R9BKP9_A0A2R9BKP9_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_A0A2U3WED3_A0A2U3WED3_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z341_M3Z341_MUSPF_9669 and tr_A0A2Y9KWB7_A0A2Y9KWB7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3H501_G3H501_CRIGR_10029 and tr_I3MF47_I3MF47_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G3H501_G3H501_CRIGR_10029 and tr_H0W0A9_H0W0A9_CAVPO_10141 are exactly identical! WARNING: Sequences tr_G3H501_G3H501_CRIGR_10029 and tr_A0A1S3F8J5_A0A1S3F8J5_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G3H501_G3H501_CRIGR_10029 and tr_A0A3Q0CUP9_A0A3Q0CUP9_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3HQ83_G3HQ83_CRIGR_10029 and tr_A0A3Q0CDG2_A0A3Q0CDG2_MESAU_10036 are exactly identical! WARNING: Sequences tr_B2VU57_B2VU57_PYRTR_426418 and tr_A0A177DJR3_A0A177DJR3_ALTAL_5599 are exactly identical! WARNING: Sequences tr_G3R1U8_G3R1U8_GORGO_9595 and tr_A0A1D5Q6B2_A0A1D5Q6B2_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3R1U8_G3R1U8_GORGO_9595 and tr_F7GD65_F7GD65_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3R1U8_G3R1U8_GORGO_9595 and tr_G7PAJ3_G7PAJ3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3R1U8_G3R1U8_GORGO_9595 and tr_A0A096NVL3_A0A096NVL3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3R1U8_G3R1U8_GORGO_9595 and tr_A0A0D9RLY6_A0A0D9RLY6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3R1U8_G3R1U8_GORGO_9595 and tr_A0A1U7UTH0_A0A1U7UTH0_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G3R1U8_G3R1U8_GORGO_9595 and tr_A0A2K5P6T6_A0A2K5P6T6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3R1U8_G3R1U8_GORGO_9595 and tr_A0A2K6E113_A0A2K6E113_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3R1U8_G3R1U8_GORGO_9595 and tr_A0A2K5XVQ9_A0A2K5XVQ9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3RH07_G3RH07_GORGO_9595 and tr_K7CTI8_K7CTI8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RH07_G3RH07_GORGO_9595 and tr_A0A2R8ZU41_A0A2R8ZU41_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2P3K6_H2P3K6_PONAB_9601 and tr_G7PH72_G7PH72_MACFA_9541 are exactly identical! WARNING: Sequences tr_Q29B66_Q29B66_DROPS_46245 and tr_B4GZ14_B4GZ14_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2QLM8_H2QLM8_PANTR_9598 and sp_Q8N3F8_MILK1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QTJ1_H2QTJ1_PANTR_9598 and tr_A0A2R9C120_A0A2R9C120_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6Q881_F6Q881_MONDO_13616 and tr_G3WES5_G3WES5_SARHA_9305 are exactly identical! WARNING: Sequences tr_W5PVW7_W5PVW7_SHEEP_9940 and sp_G3MWR8_MICA3_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G4ZE95_G4ZE95_PHYSP_1094619 and tr_H3GW46_H3GW46_PHYRM_164328 are exactly identical! WARNING: Sequences tr_M3ZTY4_M3ZTY4_XIPMA_8083 and tr_A0A087XT77_A0A087XT77_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NF25_A0A158NF25_ATTCE_12957 and tr_A0A195AUX5_A0A195AUX5_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0C4EPQ7_A0A0C4EPQ7_PUCT1_630390 and tr_E3KQA5_E3KQA5_PUCGT_418459 are exactly identical! WARNING: Sequences sp_O94851_MICA2_HUMAN_9606 and tr_A0A2R9BD02_A0A2R9BD02_PANPA_9597 are exactly identical! WARNING: Sequences tr_D0NML7_D0NML7_PHYIT_403677 and tr_W2QIL9_W2QIL9_PHYPN_761204 are exactly identical! WARNING: Sequences tr_D0NML7_D0NML7_PHYIT_403677 and tr_A0A0W8DJ24_A0A0W8DJ24_PHYNI_4790 are exactly identical! WARNING: Sequences tr_D0NML7_D0NML7_PHYIT_403677 and tr_W2LNG1_W2LNG1_PHYPR_4792 are exactly identical! WARNING: Sequences tr_D0NML7_D0NML7_PHYIT_403677 and tr_A0A329T1V6_A0A329T1V6_9STRA_29920 are exactly identical! WARNING: Sequences tr_D0NQ34_D0NQ34_PHYIT_403677 and tr_D0NRF1_D0NRF1_PHYIT_403677 are exactly identical! WARNING: Sequences tr_F6XVR6_F6XVR6_MACMU_9544 and tr_G7PQP9_G7PQP9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6XVR6_F6XVR6_MACMU_9544 and tr_A0A2I3MTK1_A0A2I3MTK1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6XVR6_F6XVR6_MACMU_9544 and tr_A0A2K5P755_A0A2K5P755_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6XVR6_F6XVR6_MACMU_9544 and tr_A0A2K6CGD9_A0A2K6CGD9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6XVR6_F6XVR6_MACMU_9544 and tr_A0A2K6AI94_A0A2K6AI94_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7H0M9_F7H0M9_MACMU_9544 and tr_G7PQP8_G7PQP8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H0M9_F7H0M9_MACMU_9544 and tr_A0A096N755_A0A096N755_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7H0M9_F7H0M9_MACMU_9544 and tr_A0A2K5ZIW8_A0A2K5ZIW8_MANLE_9568 are exactly identical! WARNING: Sequences tr_E5SLL4_E5SLL4_TRISP_6334 and tr_A0A0V0SBR9_A0A0V0SBR9_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5SLL4_E5SLL4_TRISP_6334 and tr_A0A0V0UTH6_A0A0V0UTH6_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5SLL4_E5SLL4_TRISP_6334 and tr_A0A0V0ZE56_A0A0V0ZE56_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5SLL4_E5SLL4_TRISP_6334 and tr_A0A0V1P1R2_A0A0V1P1R2_9BILA_92180 are exactly identical! WARNING: Sequences tr_E5SLL4_E5SLL4_TRISP_6334 and tr_A0A0V0U8Q0_A0A0V0U8Q0_9BILA_144512 are exactly identical! WARNING: Sequences tr_F4P7B2_F4P7B2_BATDJ_684364 and tr_A0A177WQY6_A0A177WQY6_BATDE_403673 are exactly identical! WARNING: Sequences tr_H0ZQH8_H0ZQH8_TAEGU_59729 and tr_A0A091EDA6_A0A091EDA6_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZQH8_H0ZQH8_TAEGU_59729 and tr_A0A093PDE0_A0A093PDE0_9PASS_328815 are exactly identical! WARNING: Sequences tr_F4WEL3_F4WEL3_ACREC_103372 and tr_A0A195FL19_A0A195FL19_9HYME_34720 are exactly identical! WARNING: Sequences tr_F9XH71_F9XH71_ZYMTI_336722 and tr_A0A0F4GQA5_A0A0F4GQA5_9PEZI_1047168 are exactly identical! WARNING: Sequences tr_F6UPR3_F6UPR3_CIOIN_7719 and tr_V4B317_V4B317_LOTGI_225164 are exactly identical! WARNING: Sequences tr_F2SZ64_F2SZ64_TRIRC_559305 and tr_D4ARD6_D4ARD6_ARTBC_663331 are exactly identical! WARNING: Sequences tr_F2SZ64_F2SZ64_TRIRC_559305 and tr_A0A059IXW0_A0A059IXW0_9EURO_1215338 are exactly identical! WARNING: Sequences tr_F2SZ64_F2SZ64_TRIRC_559305 and tr_A0A178F4W9_A0A178F4W9_TRIRU_5551 are exactly identical! WARNING: Sequences tr_G7P3P2_G7P3P2_MACFA_9541 and tr_A0A2K5LZI1_A0A2K5LZI1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7P3P2_G7P3P2_MACFA_9541 and tr_A0A2K6D6I7_A0A2K6D6I7_MACNE_9545 are exactly identical! WARNING: Sequences sp_F1MF74_MICA2_BOVIN_9913 and tr_H9GW33_H9GW33_BOVIN_9913 are exactly identical! WARNING: Sequences tr_L0P961_L0P961_PNEJ8_1209962 and tr_A0A0W4ZTP2_A0A0W4ZTP2_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_M2SKG6_M2SKG6_COCSN_665912 and tr_M2UVR8_M2UVR8_COCH5_701091 are exactly identical! WARNING: Sequences tr_M2SKG6_M2SKG6_COCSN_665912 and tr_W6Y7S9_W6Y7S9_COCCA_930089 are exactly identical! WARNING: Sequences tr_W2QB95_W2QB95_PHYPN_761204 and tr_A0A0W8BZI2_A0A0W8BZI2_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QB95_W2QB95_PHYPN_761204 and tr_W2LBM5_W2LBM5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QC39_W2QC39_PHYPN_761204 and tr_A0A0W8BZJ1_A0A0W8BZJ1_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QC39_W2QC39_PHYPN_761204 and tr_W2LBL6_W2LBL6_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QC39_W2QC39_PHYPN_761204 and tr_W2LBX4_W2LBX4_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QGS5_W2QGS5_PHYPN_761204 and tr_A0A0W8DIP7_A0A0W8DIP7_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QGS5_W2QGS5_PHYPN_761204 and tr_W2LN75_W2LN75_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015JRG1_A0A015JRG1_9GLOM_1432141 and tr_A0A2I1DU42_A0A2I1DU42_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A015JRG1_A0A015JRG1_9GLOM_1432141 and tr_A0A2H5TTV0_A0A2H5TTV0_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044QUV2_A0A044QUV2_ONCVO_6282 and tr_A0A182ED27_A0A182ED27_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A084QXT2_A0A084QXT2_STAC4_1283841 and tr_A0A084RZ54_A0A084RZ54_STACH_1283842 are exactly identical! WARNING: Sequences tr_A0A096NJZ8_A0A096NJZ8_PAPAN_9555 and tr_A0A0D9R3J2_A0A0D9R3J2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A094EK08_A0A094EK08_9PEZI_1420912 and tr_A0A1B8GA32_A0A1B8GA32_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0D9R681_A0A0D9R681_CHLSB_60711 and tr_A0A2K5M332_A0A2K5M332_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9R681_A0A0D9R681_CHLSB_60711 and tr_A0A2K6E2W3_A0A2K6E2W3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A067CT94_A0A067CT94_SAPPC_695850 and tr_T0R664_T0R664_9STRA_1156394 are exactly identical! WARNING: Sequences tr_A0A151MC07_A0A151MC07_ALLMI_8496 and tr_A0A3Q0H0J4_A0A3Q0H0J4_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0W8DSN6_A0A0W8DSN6_PHYNI_4790 and tr_W2LBN2_W2LBN2_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0D2GUZ1_A0A0D2GUZ1_9EURO_1442368 and tr_A0A0D1ZHZ2_A0A0D1ZHZ2_9EURO_569365 are exactly identical! WARNING: Sequences tr_A0A091UW99_A0A091UW99_NIPNI_128390 and tr_A0A0A0AXV4_A0A0A0AXV4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A093HMH1_A0A093HMH1_STRCA_441894 and tr_A0A099ZDU5_A0A099ZDU5_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A0V0WFQ6_A0A0V0WFQ6_9BILA_92179 and tr_A0A0V1LR59_A0A0V1LR59_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A1S3AAB2_A0A1S3AAB2_ERIEU_9365 and tr_A0A2U4ABS0_A0A2U4ABS0_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A1S3AAB2_A0A1S3AAB2_ERIEU_9365 and tr_A0A2Y9N3S5_A0A2Y9N3S5_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A1S3H1S0_A0A1S3H1S0_LINUN_7574 and tr_A0A1S3ICE4_A0A1S3ICE4_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A226MYI3_A0A226MYI3_CALSU_9009 and tr_A0A226PKB1_A0A226PKB1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RIB7_A0A2D0RIB7_ICTPU_7998 and tr_A0A2D0RIC0_A0A2D0RIC0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RIB7_A0A2D0RIB7_ICTPU_7998 and tr_A0A2D0RIC2_A0A2D0RIC2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RIB7_A0A2D0RIB7_ICTPU_7998 and tr_A0A2D0RJF1_A0A2D0RJF1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RIB7_A0A2D0RIB7_ICTPU_7998 and tr_A0A2D0RJF6_A0A2D0RJF6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RIB7_A0A2D0RIB7_ICTPU_7998 and tr_A0A2D0RK17_A0A2D0RK17_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RIB7_A0A2D0RIB7_ICTPU_7998 and tr_A0A2D0RK22_A0A2D0RK22_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RTA7_A0A2D0RTA7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RTB4_A0A2D0RTB4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RTB9_A0A2D0RTB9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RU88_A0A2D0RU88_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RU96_A0A2D0RU96_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RUU7_A0A2D0RUU7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RUV1_A0A2D0RUV1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTA5_A0A2D0RTA5_ICTPU_7998 and tr_A0A2D0RUV6_A0A2D0RUV6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0S4H8_A0A2D0S4H8_ICTPU_7998 and tr_A0A2D0S4K9_A0A2D0S4K9_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 146 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/Q7RTP6/3_mltree/Q7RTP6.raxml.reduced.phy Alignment comprises 1 partitions and 153 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 153 / 153 Gaps: 19.15 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/3_mltree/Q7RTP6.raxml.rba Parallelization scheme autoconfig: 3 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 972 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 153 / 12240 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -230301.109832] Initial branch length optimization [00:00:02 -190762.067155] Model parameter optimization (eps = 10.000000) [00:00:46 -189573.321425] AUTODETECT spr round 1 (radius: 5) [00:02:53 -139619.957775] AUTODETECT spr round 2 (radius: 10) [00:05:10 -108737.654298] AUTODETECT spr round 3 (radius: 15) [00:07:48 -83785.277253] AUTODETECT spr round 4 (radius: 20) [00:10:38 -74251.243697] AUTODETECT spr round 5 (radius: 25) [00:14:25 -71795.902456] SPR radius for FAST iterations: 25 (autodetect) [00:14:25 -71795.902456] Model parameter optimization (eps = 3.000000) [00:15:08 -71486.529971] FAST spr round 1 (radius: 25) [00:17:48 -61654.946861] FAST spr round 2 (radius: 25) [00:19:53 -60747.339890] FAST spr round 3 (radius: 25) [00:21:45 -60675.535415] FAST spr round 4 (radius: 25) [00:23:27 -60657.789343] FAST spr round 5 (radius: 25) [00:25:04 -60650.351564] FAST spr round 6 (radius: 25) [00:26:36 -60650.351158] Model parameter optimization (eps = 1.000000) [00:26:50 -60647.979144] SLOW spr round 1 (radius: 5) [00:28:35 -60632.377138] SLOW spr round 2 (radius: 5) [00:30:25 -60627.969868] SLOW spr round 3 (radius: 5) [00:32:17 -60624.887274] SLOW spr round 4 (radius: 5) [00:34:08 -60622.796896] SLOW spr round 5 (radius: 5) [00:35:57 -60622.796706] SLOW spr round 6 (radius: 10) [00:37:57 -60618.966371] SLOW spr round 7 (radius: 5) [00:40:14 -60618.710417] SLOW spr round 8 (radius: 5) [00:42:16 -60618.706358] SLOW spr round 9 (radius: 10) [00:44:17 -60618.706330] SLOW spr round 10 (radius: 15) [00:47:18 -60617.997720] SLOW spr round 11 (radius: 5) [00:49:41 -60616.891798] SLOW spr round 12 (radius: 5) [00:51:46 -60616.890629] SLOW spr round 13 (radius: 10) [00:53:47 -60616.890618] SLOW spr round 14 (radius: 15) [00:56:47 -60616.890602] SLOW spr round 15 (radius: 20) [01:01:13 -60615.497696] SLOW spr round 16 (radius: 5) [01:03:37 -60615.497684] SLOW spr round 17 (radius: 10) [01:05:53 -60615.497673] SLOW spr round 18 (radius: 15) [01:08:52 -60602.837782] SLOW spr round 19 (radius: 5) [01:11:14 -60602.837175] SLOW spr round 20 (radius: 10) [01:13:27 -60602.837151] SLOW spr round 21 (radius: 15) [01:16:25 -60602.837139] SLOW spr round 22 (radius: 20) [01:20:53 -60602.837128] SLOW spr round 23 (radius: 25) [01:22:30] [worker #1] ML tree search #2, logLikelihood: -60611.142923 [01:26:46 -60600.109322] SLOW spr round 24 (radius: 5) [01:29:14 -60599.494362] SLOW spr round 25 (radius: 5) [01:31:22 -60599.492443] SLOW spr round 26 (radius: 10) [01:33:26 -60599.489941] SLOW spr round 27 (radius: 15) [01:36:28 -60599.489885] SLOW spr round 28 (radius: 20) [01:40:55 -60599.489864] SLOW spr round 29 (radius: 25) [01:45:23] [worker #2] ML tree search #3, logLikelihood: -60608.996764 [01:46:42 -60599.489852] Model parameter optimization (eps = 0.100000) [01:46:47] [worker #0] ML tree search #1, logLikelihood: -60599.426503 [01:46:47 -230426.108290] Initial branch length optimization [01:46:50 -190611.503798] Model parameter optimization (eps = 10.000000) [01:47:26 -189315.997573] AUTODETECT spr round 1 (radius: 5) [01:49:29 -138136.907589] AUTODETECT spr round 2 (radius: 10) [01:51:43 -100034.704666] AUTODETECT spr round 3 (radius: 15) [01:54:07 -84779.666454] AUTODETECT spr round 4 (radius: 20) [01:57:02 -76535.846003] AUTODETECT spr round 5 (radius: 25) [02:00:22 -75401.800524] SPR radius for FAST iterations: 25 (autodetect) [02:00:22 -75401.800524] Model parameter optimization (eps = 3.000000) [02:00:52 -75113.644160] FAST spr round 1 (radius: 25) [02:03:36 -63817.957307] FAST spr round 2 (radius: 25) [02:05:46 -61717.327982] FAST spr round 3 (radius: 25) [02:07:41 -60853.988214] FAST spr round 4 (radius: 25) [02:09:26 -60661.950447] FAST spr round 5 (radius: 25) [02:11:07 -60630.929207] FAST spr round 6 (radius: 25) [02:12:42 -60629.453044] FAST spr round 7 (radius: 25) [02:14:15 -60629.384540] Model parameter optimization (eps = 1.000000) [02:14:26 -60624.669026] SLOW spr round 1 (radius: 5) [02:16:13 -60611.090464] SLOW spr round 2 (radius: 5) [02:18:03 -60600.607762] SLOW spr round 3 (radius: 5) [02:19:56 -60591.456694] SLOW spr round 4 (radius: 5) [02:21:49 -60591.412429] SLOW spr round 5 (radius: 10) [02:23:49 -60591.039393] SLOW spr round 6 (radius: 5) [02:26:01 -60585.522071] SLOW spr round 7 (radius: 5) [02:27:54 -60585.521859] SLOW spr round 8 (radius: 10) [02:29:51 -60585.521806] SLOW spr round 9 (radius: 15) [02:33:14 -60585.064268] SLOW spr round 10 (radius: 5) [02:35:50 -60585.064144] SLOW spr round 11 (radius: 10) [02:38:22 -60585.064092] SLOW spr round 12 (radius: 15) [02:42:07 -60585.064041] SLOW spr round 13 (radius: 20) [02:47:45 -60583.894279] SLOW spr round 14 (radius: 5) [02:48:07] [worker #1] ML tree search #5, logLikelihood: -60594.720212 [02:50:28 -60583.149776] SLOW spr round 15 (radius: 5) [02:52:53 -60577.733016] SLOW spr round 16 (radius: 5) [02:55:06 -60576.905710] SLOW spr round 17 (radius: 5) [02:57:10 -60576.904460] SLOW spr round 18 (radius: 10) [02:59:23 -60574.307845] SLOW spr round 19 (radius: 5) [03:01:56 -60571.652925] SLOW spr round 20 (radius: 5) [03:04:12 -60571.509279] SLOW spr round 21 (radius: 5) [03:06:17 -60571.508678] SLOW spr round 22 (radius: 10) [03:08:00] [worker #2] ML tree search #6, logLikelihood: -60754.050666 [03:08:28 -60571.508525] SLOW spr round 23 (radius: 15) [03:12:20 -60571.508378] SLOW spr round 24 (radius: 20) [03:18:00 -60571.508232] SLOW spr round 25 (radius: 25) [03:25:15 -60570.591139] SLOW spr round 26 (radius: 5) [03:27:57 -60570.590539] SLOW spr round 27 (radius: 10) [03:30:33 -60570.590287] SLOW spr round 28 (radius: 15) [03:34:14 -60570.590093] SLOW spr round 29 (radius: 20) [03:39:50 -60570.589920] SLOW spr round 30 (radius: 25) [03:47:01 -60570.589754] Model parameter optimization (eps = 0.100000) [03:47:10] [worker #0] ML tree search #4, logLikelihood: -60570.183308 [03:47:10 -230778.543448] Initial branch length optimization [03:47:14 -190721.568997] Model parameter optimization (eps = 10.000000) [03:47:54 -189591.430987] AUTODETECT spr round 1 (radius: 5) [03:50:11 -141243.552902] AUTODETECT spr round 2 (radius: 10) [03:52:44 -102085.768745] AUTODETECT spr round 3 (radius: 15) [03:55:25 -83247.096447] AUTODETECT spr round 4 (radius: 20) [03:58:41 -73392.491001] AUTODETECT spr round 5 (radius: 25) [04:02:22 -70704.859461] SPR radius for FAST iterations: 25 (autodetect) [04:02:22 -70704.859461] Model parameter optimization (eps = 3.000000) [04:02:56 -70431.329863] FAST spr round 1 (radius: 25) [04:05:55 -61313.259293] FAST spr round 2 (radius: 25) [04:08:23 -60693.719533] FAST spr round 3 (radius: 25) [04:10:30 -60640.872030] FAST spr round 4 (radius: 25) [04:12:22 -60636.992062] FAST spr round 5 (radius: 25) [04:14:06 -60636.574023] FAST spr round 6 (radius: 25) [04:15:47 -60636.572595] Model parameter optimization (eps = 1.000000) [04:16:08 -60624.086275] SLOW spr round 1 (radius: 5) [04:18:12 -60600.879815] SLOW spr round 2 (radius: 5) [04:20:17 -60600.297959] SLOW spr round 3 (radius: 5) [04:22:20 -60599.560850] SLOW spr round 4 (radius: 5) [04:24:20 -60599.560736] SLOW spr round 5 (radius: 10) [04:26:31 -60597.411768] SLOW spr round 6 (radius: 5) [04:29:06 -60596.401864] SLOW spr round 7 (radius: 5) [04:31:22 -60596.400637] SLOW spr round 8 (radius: 10) [04:33:39 -60596.400522] SLOW spr round 9 (radius: 15) [04:37:10 -60593.955896] SLOW spr round 10 (radius: 5) [04:37:47] [worker #1] ML tree search #8, logLikelihood: -60579.497085 [04:39:49 -60591.480295] SLOW spr round 11 (radius: 5) [04:41:40] [worker #2] ML tree search #9, logLikelihood: -60575.993082 [04:42:08 -60591.480214] SLOW spr round 12 (radius: 10) [04:44:27 -60591.480134] SLOW spr round 13 (radius: 15) [04:47:58 -60591.480054] SLOW spr round 14 (radius: 20) [04:53:11 -60589.798273] SLOW spr round 15 (radius: 5) [04:55:54 -60589.768877] SLOW spr round 16 (radius: 10) [04:58:30 -60589.767915] SLOW spr round 17 (radius: 15) [05:01:58 -60589.767675] SLOW spr round 18 (radius: 20) [05:07:08 -60589.767568] SLOW spr round 19 (radius: 25) [05:13:49 -60585.708141] SLOW spr round 20 (radius: 5) [05:16:32 -60585.342445] SLOW spr round 21 (radius: 5) [05:18:54 -60585.342285] SLOW spr round 22 (radius: 10) [05:21:15 -60585.342203] SLOW spr round 23 (radius: 15) [05:24:47 -60585.342109] SLOW spr round 24 (radius: 20) [05:29:59 -60585.342030] SLOW spr round 25 (radius: 25) [05:36:38 -60585.341951] Model parameter optimization (eps = 0.100000) [05:36:46] [worker #0] ML tree search #7, logLikelihood: -60585.171161 [05:36:46 -230346.596559] Initial branch length optimization [05:36:50 -191154.393563] Model parameter optimization (eps = 10.000000) [05:37:30 -189864.000861] AUTODETECT spr round 1 (radius: 5) [05:39:47 -139669.866477] AUTODETECT spr round 2 (radius: 10) [05:42:14 -109207.140136] AUTODETECT spr round 3 (radius: 15) [05:44:56 -92852.120262] AUTODETECT spr round 4 (radius: 20) [05:48:13 -77074.430965] AUTODETECT spr round 5 (radius: 25) [05:52:43 -72510.429041] SPR radius for FAST iterations: 25 (autodetect) [05:52:43 -72510.429041] Model parameter optimization (eps = 3.000000) [05:53:25 -72177.728445] FAST spr round 1 (radius: 25) [05:56:32 -61146.588072] FAST spr round 2 (radius: 25) [05:58:56 -60706.673315] FAST spr round 3 (radius: 25) [06:01:03 -60661.012342] FAST spr round 4 (radius: 25) [06:02:55 -60647.844974] FAST spr round 5 (radius: 25) [06:04:39 -60646.262157] FAST spr round 6 (radius: 25) [06:06:20 -60646.261813] Model parameter optimization (eps = 1.000000) [06:06:43 -60626.095131] SLOW spr round 1 (radius: 5) [06:08:41 -60607.307656] SLOW spr round 2 (radius: 5) [06:10:45 -60605.742398] SLOW spr round 3 (radius: 5) [06:12:49 -60605.012731] SLOW spr round 4 (radius: 5) [06:14:50 -60605.012378] SLOW spr round 5 (radius: 10) [06:16:59 -60603.789893] SLOW spr round 6 (radius: 5) [06:19:32 -60603.728794] SLOW spr round 7 (radius: 10) [06:21:52 -60603.728213] SLOW spr round 8 (radius: 15) [06:25:00 -60602.343074] SLOW spr round 9 (radius: 5) [06:27:41 -60602.015204] SLOW spr round 10 (radius: 5) [06:30:03 -60602.014274] SLOW spr round 11 (radius: 10) [06:31:23] [worker #1] ML tree search #11, logLikelihood: -60598.712606 [06:32:18 -60602.014075] SLOW spr round 12 (radius: 15) [06:35:24 -60602.013925] SLOW spr round 13 (radius: 20) [06:39:48 -60601.059847] SLOW spr round 14 (radius: 5) [06:42:31 -60598.814083] SLOW spr round 15 (radius: 5) [06:44:52 -60598.813552] SLOW spr round 16 (radius: 10) [06:47:07 -60598.813299] SLOW spr round 17 (radius: 15) [06:50:15 -60598.813121] SLOW spr round 18 (radius: 20) [06:50:57] [worker #2] ML tree search #12, logLikelihood: -60565.875761 [06:54:48 -60598.064640] SLOW spr round 19 (radius: 5) [06:57:28 -60598.064400] SLOW spr round 20 (radius: 10) [06:59:56 -60598.064277] SLOW spr round 21 (radius: 15) [07:03:02 -60598.064167] SLOW spr round 22 (radius: 20) [07:07:36 -60598.064059] SLOW spr round 23 (radius: 25) [07:13:25 -60597.804570] SLOW spr round 24 (radius: 5) [07:16:07 -60597.804463] SLOW spr round 25 (radius: 10) [07:18:36 -60597.804356] SLOW spr round 26 (radius: 15) [07:21:43 -60597.804249] SLOW spr round 27 (radius: 20) [07:26:17 -60597.804141] SLOW spr round 28 (radius: 25) [07:32:07 -60597.804032] Model parameter optimization (eps = 0.100000) [07:32:16] [worker #0] ML tree search #10, logLikelihood: -60597.575975 [07:32:16 -230485.999035] Initial branch length optimization [07:32:19 -191955.051755] Model parameter optimization (eps = 10.000000) [07:33:02 -190785.164639] AUTODETECT spr round 1 (radius: 5) [07:35:15 -139669.925680] AUTODETECT spr round 2 (radius: 10) [07:37:43 -104246.208029] AUTODETECT spr round 3 (radius: 15) [07:40:25 -87867.024251] AUTODETECT spr round 4 (radius: 20) [07:43:29 -82611.224676] AUTODETECT spr round 5 (radius: 25) [07:47:03 -74964.143155] SPR radius for FAST iterations: 25 (autodetect) [07:47:03 -74964.143155] Model parameter optimization (eps = 3.000000) [07:47:34 -74601.516551] FAST spr round 1 (radius: 25) [07:50:48 -61649.241689] FAST spr round 2 (radius: 25) [07:53:11 -60811.437002] FAST spr round 3 (radius: 25) [07:55:14 -60654.792327] FAST spr round 4 (radius: 25) [07:57:05 -60633.279865] FAST spr round 5 (radius: 25) [07:58:48 -60632.203383] FAST spr round 6 (radius: 25) [08:00:29 -60631.829858] FAST spr round 7 (radius: 25) [08:02:08 -60631.827672] Model parameter optimization (eps = 1.000000) [08:02:25 -60620.251723] SLOW spr round 1 (radius: 5) [08:04:25 -60595.295103] SLOW spr round 2 (radius: 5) [08:06:27 -60592.822392] SLOW spr round 3 (radius: 5) [08:08:30 -60592.325819] SLOW spr round 4 (radius: 5) [08:10:29 -60592.325127] SLOW spr round 5 (radius: 10) [08:12:40 -60589.685652] SLOW spr round 6 (radius: 5) [08:15:11 -60587.047921] SLOW spr round 7 (radius: 5) [08:17:24 -60587.043845] SLOW spr round 8 (radius: 10) [08:19:40 -60585.341871] SLOW spr round 9 (radius: 5) [08:21:19] [worker #1] ML tree search #14, logLikelihood: -60585.361352 [08:22:07 -60585.338662] SLOW spr round 10 (radius: 10) [08:24:28 -60585.325143] SLOW spr round 11 (radius: 15) [08:27:57 -60584.867172] SLOW spr round 12 (radius: 5) [08:30:32 -60584.866998] SLOW spr round 13 (radius: 10) [08:33:00 -60584.866895] SLOW spr round 14 (radius: 15) [08:36:28 -60584.791015] SLOW spr round 15 (radius: 20) [08:38:53] [worker #2] ML tree search #15, logLikelihood: -60629.985622 [08:41:16 -60580.987872] SLOW spr round 16 (radius: 5) [08:43:36 -60580.983092] SLOW spr round 17 (radius: 10) [08:45:47 -60580.982731] SLOW spr round 18 (radius: 15) [08:48:43 -60580.883823] SLOW spr round 19 (radius: 20) [08:53:55 -60579.663501] SLOW spr round 20 (radius: 5) [08:56:43 -60576.954528] SLOW spr round 21 (radius: 5) [08:59:07 -60576.954402] SLOW spr round 22 (radius: 10) [09:01:28 -60576.954300] SLOW spr round 23 (radius: 15) [09:05:06 -60576.954199] SLOW spr round 24 (radius: 20) [09:10:28 -60576.954101] SLOW spr round 25 (radius: 25) [09:17:33 -60576.669876] SLOW spr round 26 (radius: 5) [09:20:19 -60576.669806] SLOW spr round 27 (radius: 10) [09:22:57 -60576.669737] SLOW spr round 28 (radius: 15) [09:26:30 -60576.669669] SLOW spr round 29 (radius: 20) [09:31:52 -60576.669601] SLOW spr round 30 (radius: 25) [09:38:46 -60576.669532] Model parameter optimization (eps = 0.100000) [09:38:52] [worker #0] ML tree search #13, logLikelihood: -60576.633033 [09:38:53 -232091.344121] Initial branch length optimization [09:38:56 -191785.521965] Model parameter optimization (eps = 10.000000) [09:39:29 -190583.188140] AUTODETECT spr round 1 (radius: 5) [09:41:45 -144402.111494] AUTODETECT spr round 2 (radius: 10) [09:44:14 -109898.925959] AUTODETECT spr round 3 (radius: 15) [09:47:06 -87942.776094] AUTODETECT spr round 4 (radius: 20) [09:50:24 -73620.577971] AUTODETECT spr round 5 (radius: 25) [09:54:10 -71275.917019] SPR radius for FAST iterations: 25 (autodetect) [09:54:10 -71275.917019] Model parameter optimization (eps = 3.000000) [09:54:45 -71053.260981] FAST spr round 1 (radius: 25) [09:57:43 -61718.721705] FAST spr round 2 (radius: 25) [10:00:05 -60893.546298] FAST spr round 3 (radius: 25) [10:02:11 -60805.847693] FAST spr round 4 (radius: 25) [10:04:07 -60773.305001] FAST spr round 5 (radius: 25) [10:05:57 -60764.204666] FAST spr round 6 (radius: 25) [10:07:43 -60760.719805] FAST spr round 7 (radius: 25) [10:09:27 -60760.659616] Model parameter optimization (eps = 1.000000) [10:09:43 -60755.043300] SLOW spr round 1 (radius: 5) [10:11:44 -60740.652460] SLOW spr round 2 (radius: 5) [10:13:49 -60740.011884] SLOW spr round 3 (radius: 5) [10:15:50 -60740.008507] SLOW spr round 4 (radius: 10) [10:18:02 -60738.145224] SLOW spr round 5 (radius: 5) [10:20:33 -60738.144993] SLOW spr round 6 (radius: 10) [10:22:56 -60738.144856] SLOW spr round 7 (radius: 15) [10:26:19 -60736.985444] SLOW spr round 8 (radius: 5) [10:27:01] [worker #2] ML tree search #18, logLikelihood: -60605.450118 [10:28:57 -60736.985126] SLOW spr round 9 (radius: 10) [10:31:23 -60736.985028] SLOW spr round 10 (radius: 15) [10:34:51 -60736.984932] SLOW spr round 11 (radius: 20) [10:35:41] [worker #1] ML tree search #17, logLikelihood: -60583.068456 [10:40:07 -60736.466173] SLOW spr round 12 (radius: 5) [10:42:49 -60734.001762] SLOW spr round 13 (radius: 5) [10:45:09 -60734.000060] SLOW spr round 14 (radius: 10) [10:47:26 -60733.999048] SLOW spr round 15 (radius: 15) [10:50:58 -60733.998441] SLOW spr round 16 (radius: 20) [10:56:15 -60733.998065] SLOW spr round 17 (radius: 25) [11:02:42 -60718.874533] SLOW spr round 18 (radius: 5) [11:05:32 -60642.452326] SLOW spr round 19 (radius: 5) [11:07:58 -60637.047953] SLOW spr round 20 (radius: 5) [11:10:09 -60637.047730] SLOW spr round 21 (radius: 10) [11:12:22 -60637.047570] SLOW spr round 22 (radius: 15) [11:15:50 -60637.047430] SLOW spr round 23 (radius: 20) [11:20:55 -60636.924979] SLOW spr round 24 (radius: 5) [11:23:33 -60636.924612] SLOW spr round 25 (radius: 10) [11:26:01 -60636.791820] SLOW spr round 26 (radius: 5) [11:28:26 -60636.789474] SLOW spr round 27 (radius: 10) [11:30:43 -60636.788559] SLOW spr round 28 (radius: 15) [11:34:09 -60636.788193] SLOW spr round 29 (radius: 20) [11:39:15 -60636.787985] SLOW spr round 30 (radius: 25) [11:45:39 -60636.452151] SLOW spr round 31 (radius: 5) [11:48:22 -60636.404236] SLOW spr round 32 (radius: 10) [11:50:54 -60636.402133] SLOW spr round 33 (radius: 15) [11:54:19 -60636.401783] SLOW spr round 34 (radius: 20) [11:59:27 -60636.401650] SLOW spr round 35 (radius: 25) [12:05:52 -60636.401518] Model parameter optimization (eps = 0.100000) [12:06:00] [worker #0] ML tree search #16, logLikelihood: -60636.302649 [12:06:00 -231624.141198] Initial branch length optimization [12:06:03 -191219.796689] Model parameter optimization (eps = 10.000000) [12:06:51 -189952.899049] AUTODETECT spr round 1 (radius: 5) [12:09:07 -139790.438999] AUTODETECT spr round 2 (radius: 10) [12:11:27 -107838.164696] AUTODETECT spr round 3 (radius: 15) [12:14:11 -86872.301864] AUTODETECT spr round 4 (radius: 20) [12:17:23 -77006.755820] AUTODETECT spr round 5 (radius: 25) [12:20:45 -74033.739083] SPR radius for FAST iterations: 25 (autodetect) [12:20:45 -74033.739083] Model parameter optimization (eps = 3.000000) [12:21:24 -73706.200936] FAST spr round 1 (radius: 25) [12:24:38 -62103.954856] FAST spr round 2 (radius: 25) [12:27:08 -60873.035937] FAST spr round 3 (radius: 25) [12:29:14 -60649.275995] FAST spr round 4 (radius: 25) [12:31:10 -60643.167402] FAST spr round 5 (radius: 25) [12:31:27] [worker #1] ML tree search #20, logLikelihood: -60617.951760 [12:32:57 -60643.049611] FAST spr round 6 (radius: 25) [12:34:47 -60643.047969] Model parameter optimization (eps = 1.000000) [12:35:04 -60638.042295] SLOW spr round 1 (radius: 5) [12:37:07 -60627.271122] SLOW spr round 2 (radius: 5) [12:39:13 -60625.034418] SLOW spr round 3 (radius: 5) [12:41:16 -60625.028200] SLOW spr round 4 (radius: 10) [12:43:30 -60621.870941] SLOW spr round 5 (radius: 5) [12:46:03 -60619.192106] SLOW spr round 6 (radius: 5) [12:48:19 -60619.191048] SLOW spr round 7 (radius: 10) [12:50:34 -60619.190350] SLOW spr round 8 (radius: 15) [12:53:50 -60618.281336] SLOW spr round 9 (radius: 5) [12:56:30 -60617.864543] SLOW spr round 10 (radius: 5) [12:58:55 -60614.756507] SLOW spr round 11 (radius: 5) [13:01:06 -60614.756120] SLOW spr round 12 (radius: 10) [13:03:17 -60614.755995] SLOW spr round 13 (radius: 15) [13:06:31 -60613.371370] SLOW spr round 14 (radius: 5) [13:09:09 -60613.370818] SLOW spr round 15 (radius: 10) [13:11:37 -60613.370684] SLOW spr round 16 (radius: 15) [13:14:46 -60612.998638] SLOW spr round 17 (radius: 5) [13:17:24 -60612.998478] SLOW spr round 18 (radius: 10) [13:19:54 -60612.473442] SLOW spr round 19 (radius: 5) [13:22:20 -60612.473317] SLOW spr round 20 (radius: 10) [13:24:40 -60612.473191] SLOW spr round 21 (radius: 15) [13:27:52 -60612.473017] SLOW spr round 22 (radius: 20) [13:32:20 -60611.759727] SLOW spr round 23 (radius: 5) [13:35:02 -60611.759551] SLOW spr round 24 (radius: 10) [13:37:35 -60611.759401] SLOW spr round 25 (radius: 15) [13:40:45 -60611.759274] SLOW spr round 26 (radius: 20) [13:45:13 -60611.759148] SLOW spr round 27 (radius: 25) [13:50:40 -60611.759022] Model parameter optimization (eps = 0.100000) [13:50:45] [worker #0] ML tree search #19, logLikelihood: -60611.740289 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.204317,0.690114) (0.103493,0.531764) (0.428722,0.870251) (0.263469,1.635370) 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: -60565.875761 AIC score: 125025.751521 / AICc score: 7710537.751521 / BIC score: 130926.014154 Free parameters (model + branch lengths): 1947 WARNING: Number of free parameters (K=1947) is larger than alignment size (n=153). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 1 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/3_mltree/Q7RTP6.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/3_mltree/Q7RTP6.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/3_mltree/Q7RTP6.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/3_mltree/Q7RTP6.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7RTP6/3_mltree/Q7RTP6.raxml.log Analysis started: 04-Jul-2021 14:51:42 / finished: 05-Jul-2021 04:42:28 Elapsed time: 49846.135 seconds Consumed energy: 4303.392 Wh (= 22 km in an electric car, or 108 km with an e-scooter!)