RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 09-Jul-2021 12:34:32 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/2_msa/Q16740_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/3_mltree/Q16740 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/2_msa/Q16740_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 173 sites

WARNING: Sequences tr_B4Q974_B4Q974_DROSI_7240 and tr_B4HWL9_B4HWL9_DROSE_7238 are exactly identical!
WARNING: Sequences sp_O88696_CLPP_MOUSE_10090 and tr_H0XJB3_H0XJB3_OTOGA_30611 are exactly identical!
WARNING: Sequences sp_O88696_CLPP_MOUSE_10090 and tr_H0VPX7_H0VPX7_CAVPO_10141 are exactly identical!
WARNING: Sequences sp_O88696_CLPP_MOUSE_10090 and tr_F6YQ20_F6YQ20_MACMU_9544 are exactly identical!
WARNING: Sequences sp_O88696_CLPP_MOUSE_10090 and tr_U3DUU6_U3DUU6_CALJA_9483 are exactly identical!
WARNING: Sequences sp_O88696_CLPP_MOUSE_10090 and tr_G7PYU1_G7PYU1_MACFA_9541 are exactly identical!
WARNING: Sequences sp_O88696_CLPP_MOUSE_10090 and tr_A0A0A0MWA7_A0A0A0MWA7_PAPAN_9555 are exactly identical!
WARNING: Sequences sp_O88696_CLPP_MOUSE_10090 and tr_A0A091DE98_A0A091DE98_FUKDA_885580 are exactly identical!
WARNING: Sequences sp_O88696_CLPP_MOUSE_10090 and tr_A0A0D9RBE5_A0A0D9RBE5_CHLSB_60711 are exactly identical!
WARNING: Sequences sp_O88696_CLPP_MOUSE_10090 and tr_A0A2K5XNV0_A0A2K5XNV0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_M3Y596_M3Y596_MUSPF_9669 and tr_E2QUV8_E2QUV8_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3Y596_M3Y596_MUSPF_9669 and tr_A0A2U3VKL8_A0A2U3VKL8_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3Y596_M3Y596_MUSPF_9669 and tr_A0A2U3YZM2_A0A2U3YZM2_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3Y596_M3Y596_MUSPF_9669 and tr_A0A2Y9L7S2_A0A2Y9L7S2_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A1B6PM68_A0A1B6PM68_SORBI_4558 and tr_C0PFY0_C0PFY0_MAIZE_4577 are exactly identical!
WARNING: Sequences tr_C5WMG5_C5WMG5_SORBI_4558 and tr_A0A1D6K0D4_A0A1D6K0D4_MAIZE_4577 are exactly identical!
WARNING: Sequences tr_C5WMG5_C5WMG5_SORBI_4558 and tr_A0A2T7CDG7_A0A2T7CDG7_9POAL_1504633 are exactly identical!
WARNING: Sequences tr_C5XY66_C5XY66_SORBI_4558 and tr_A0A368PNT5_A0A368PNT5_SETIT_4555 are exactly identical!
WARNING: Sequences tr_C5XY66_C5XY66_SORBI_4558 and tr_A0A1D6HE45_A0A1D6HE45_MAIZE_4577 are exactly identical!
WARNING: Sequences tr_J3K3S6_J3K3S6_COCIM_246410 and tr_A0A0J6YB72_A0A0J6YB72_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QVS1_B6QVS1_TALMQ_441960 and tr_A0A093VIU2_A0A093VIU2_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2W8W5_B2W8W5_PYRTR_426418 and tr_A0A2W1DEB1_A0A2W1DEB1_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_D8SK56_D8SK56_SELML_88036 and tr_D8T4G2_D8T4G2_SELML_88036 are exactly identical!
WARNING: Sequences tr_C0NAK3_C0NAK3_AJECG_447093 and tr_C6H4K1_C6H4K1_AJECH_544712 are exactly identical!
WARNING: Sequences tr_C0NAK3_C0NAK3_AJECG_447093 and tr_F0UJ43_F0UJ43_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_C0NAK3_C0NAK3_AJECG_447093 and tr_A6R3U3_A6R3U3_AJECN_339724 are exactly identical!
WARNING: Sequences tr_Q1K659_Q1K659_NEUCR_367110 and tr_G4UH24_G4UH24_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_B8N036_B8N036_ASPFN_332952 and tr_A0A1S9DTW5_A0A1S9DTW5_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_B8N036_B8N036_ASPFN_332952 and tr_A0A2G7FW17_A0A2G7FW17_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A179UEG0_A0A179UEG0_BLAGS_559298 and tr_C5GHD3_C5GHD3_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2QF44_H2QF44_PANTR_9598 and sp_Q16740_CLPP_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QF44_H2QF44_PANTR_9598 and tr_A0A2R9CDX0_A0A2R9CDX0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5P8B9_W5P8B9_SHEEP_9940 and tr_A0A286ZRL1_A0A286ZRL1_PIG_9823 are exactly identical!
WARNING: Sequences tr_W5P8B9_W5P8B9_SHEEP_9940 and sp_Q2KHU4_CLPP_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A087ZVI9_A0A087ZVI9_APIME_7460 and tr_A0A2A3ER14_A0A2A3ER14_APICC_94128 are exactly identical!
WARNING: Sequences tr_J3L0C8_J3L0C8_ORYBR_4533 and tr_A0A0D3EMV9_A0A0D3EMV9_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_J3L0C8_J3L0C8_ORYBR_4533 and tr_A0A0D9Y9C7_A0A0D9Y9C7_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_J3LF31_J3LF31_ORYBR_4533 and tr_A0A0E0GA51_A0A0E0GA51_ORYNI_4536 are exactly identical!
WARNING: Sequences tr_J3LF31_J3LF31_ORYBR_4533 and tr_A2X7K2_A2X7K2_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_J3LF31_J3LF31_ORYBR_4533 and tr_A0A0E0CNU6_A0A0E0CNU6_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_J3LF31_J3LF31_ORYBR_4533 and tr_A0A0E0NI67_A0A0E0NI67_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_J3LF31_J3LF31_ORYBR_4533 and tr_A0A0D9YVD6_A0A0D9YVD6_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_J3LF31_J3LF31_ORYBR_4533 and tr_A0A0E0K2Q8_A0A0E0K2Q8_ORYPU_4537 are exactly identical!
WARNING: Sequences tr_J3LF31_J3LF31_ORYBR_4533 and tr_Q6H7I9_Q6H7I9_ORYSJ_39947 are exactly identical!
WARNING: Sequences sp_Q94B60_CLPP4_ARATH_3702 and tr_D7MU32_D7MU32_ARALL_81972 are exactly identical!
WARNING: Sequences sp_Q94B60_CLPP4_ARATH_3702 and tr_R0G7S7_R0G7S7_9BRAS_81985 are exactly identical!
WARNING: Sequences sp_Q94B60_CLPP4_ARATH_3702 and tr_V4N353_V4N353_EUTSA_72664 are exactly identical!
WARNING: Sequences sp_Q9FN42_CLPP2_ARATH_3702 and tr_D7M1N2_D7M1N2_ARALL_81972 are exactly identical!
WARNING: Sequences sp_Q9FN42_CLPP2_ARATH_3702 and tr_R0FBM3_R0FBM3_9BRAS_81985 are exactly identical!
WARNING: Sequences sp_Q9S834_CLPP5_ARATH_3702 and tr_D7KB96_D7KB96_ARALL_81972 are exactly identical!
WARNING: Sequences sp_Q9S834_CLPP5_ARATH_3702 and tr_R0I7Q4_R0I7Q4_9BRAS_81985 are exactly identical!
WARNING: Sequences tr_A0A0E0FM25_A0A0E0FM25_ORYNI_4536 and tr_A2WQJ7_A2WQJ7_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0FM25_A0A0E0FM25_ORYNI_4536 and tr_A0A0E0MX17_A0A0E0MX17_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0FM25_A0A0E0FM25_ORYNI_4536 and tr_Q0JMF9_Q0JMF9_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0GLE2_A0A0E0GLE2_ORYNI_4536 and tr_A0A1D6PC01_A0A1D6PC01_MAIZE_4577 are exactly identical!
WARNING: Sequences tr_A0A0E0GLE2_A0A0E0GLE2_ORYNI_4536 and tr_I1PAM8_I1PAM8_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0GLE2_A0A0E0GLE2_ORYNI_4536 and tr_A0A0E0CZJ5_A0A0E0CZJ5_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0GLE2_A0A0E0GLE2_ORYNI_4536 and tr_A0A0E0NU26_A0A0E0NU26_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0GLE2_A0A0E0GLE2_ORYNI_4536 and tr_A0A0D3FHL4_A0A0D3FHL4_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0GLE2_A0A0E0GLE2_ORYNI_4536 and tr_A0A0D9Z682_A0A0D9Z682_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0GLE2_A0A0E0GLE2_ORYNI_4536 and tr_A0A0D9VT80_A0A0D9VT80_9ORYZ_77586 are exactly identical!
WARNING: Sequences tr_A0A0E0GLE2_A0A0E0GLE2_ORYNI_4536 and tr_Q50LH5_Q50LH5_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0I4B0_A0A0E0I4B0_ORYNI_4536 and tr_A2XVP6_A2XVP6_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0I4B0_A0A0E0I4B0_ORYNI_4536 and tr_I1PN65_I1PN65_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0I4B0_A0A0E0I4B0_ORYNI_4536 and tr_A0A0E0DGD2_A0A0E0DGD2_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0I4B0_A0A0E0I4B0_ORYNI_4536 and tr_A0A0E0PBR6_A0A0E0PBR6_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0I4B0_A0A0E0I4B0_ORYNI_4536 and tr_A0A0D3FY44_A0A0D3FY44_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0I4B0_A0A0E0I4B0_ORYNI_4536 and tr_A0A0D9ZN98_A0A0D9ZN98_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0I4B0_A0A0E0I4B0_ORYNI_4536 and tr_Q0JBL5_Q0JBL5_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A2QER3_A2QER3_ASPNC_425011 and tr_G7XC53_G7XC53_ASPKW_1033177 are exactly identical!
WARNING: Sequences tr_A2QER3_A2QER3_ASPNC_425011 and tr_G3Y1W2_G3Y1W2_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QER3_A2QER3_ASPNC_425011 and tr_A0A117E3R0_A0A117E3R0_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_A2QER3_A2QER3_ASPNC_425011 and tr_A0A146FCV9_A0A146FCV9_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A2QER3_A2QER3_ASPNC_425011 and tr_A0A1L9N8Y2_A0A1L9N8Y2_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A2QER3_A2QER3_ASPNC_425011 and tr_A0A1L9UVF7_A0A1L9UVF7_9EURO_767769 are exactly identical!
WARNING: Sequences tr_A2QER3_A2QER3_ASPNC_425011 and tr_A0A317V8A7_A0A317V8A7_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_A2QER3_A2QER3_ASPNC_425011 and tr_A0A319BAB1_A0A319BAB1_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_B9GST6_B9GST6_POPTR_3694 and tr_B9I9I1_B9I9I1_POPTR_3694 are exactly identical!
WARNING: Sequences tr_E5SSR0_E5SSR0_TRISP_6334 and tr_A0A0V1CK84_A0A0V1CK84_TRIBR_45882 are exactly identical!
WARNING: Sequences tr_E5SSR0_E5SSR0_TRISP_6334 and tr_A0A0V1A3X4_A0A0V1A3X4_9BILA_990121 are exactly identical!
WARNING: Sequences tr_F4X809_F4X809_ACREC_103372 and tr_A0A151WV22_A0A151WV22_9HYME_64791 are exactly identical!
WARNING: Sequences tr_F4X809_F4X809_ACREC_103372 and tr_A0A151JAN7_A0A151JAN7_9HYME_471704 are exactly identical!
WARNING: Sequences tr_G2YH10_G2YH10_BOTF4_999810 and tr_M7TDB8_M7TDB8_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_I1IBV3_I1IBV3_BRADI_15368 and tr_A0A287UBM0_A0A287UBM0_HORVV_112509 are exactly identical!
WARNING: Sequences tr_I1IBV3_I1IBV3_BRADI_15368 and tr_A0A3B6NRW0_A0A3B6NRW0_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_I1IBV3_I1IBV3_BRADI_15368 and tr_A0A3B6PL73_A0A3B6PL73_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_I1JBF6_I1JBF6_SOYBN_3847 and tr_I1L7P0_I1L7P0_SOYBN_3847 are exactly identical!
WARNING: Sequences tr_F2T0R1_F2T0R1_TRIRC_559305 and tr_F2PWW6_F2PWW6_TRIEC_559882 are exactly identical!
WARNING: Sequences tr_B3S3W8_B3S3W8_TRIAD_10228 and tr_A0A369SB16_A0A369SB16_9METZ_287889 are exactly identical!
WARNING: Sequences tr_W7M8T7_W7M8T7_GIBM7_334819 and tr_A0A0D2XKC4_A0A0D2XKC4_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_W7M8T7_W7M8T7_GIBM7_334819 and tr_S0EL23_S0EL23_GIBF5_1279085 are exactly identical!
WARNING: Sequences tr_W7M8T7_W7M8T7_GIBM7_334819 and tr_X0BZT0_X0BZT0_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_W7M8T7_W7M8T7_GIBM7_334819 and tr_A0A2H3SXZ9_A0A2H3SXZ9_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_W7M8T7_W7M8T7_GIBM7_334819 and tr_A0A2K0WSI4_A0A2K0WSI4_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_W7M8T7_W7M8T7_GIBM7_334819 and tr_A0A365MYT8_A0A365MYT8_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_K9G3H0_K9G3H0_PEND2_1170229 and tr_A0A0G4P1P4_A0A0G4P1P4_PENCA_1429867 are exactly identical!
WARNING: Sequences tr_K9G3H0_K9G3H0_PEND2_1170229 and tr_A0A135LA09_A0A135LA09_PENPA_5078 are exactly identical!
WARNING: Sequences tr_K9G3H0_K9G3H0_PEND2_1170229 and tr_A0A1V6S5X6_A0A1V6S5X6_9EURO_29845 are exactly identical!
WARNING: Sequences tr_L8FY85_L8FY85_PSED2_658429 and tr_A0A094DKL7_A0A094DKL7_9PEZI_1420910 are exactly identical!
WARNING: Sequences tr_L8FY85_L8FY85_PSED2_658429 and tr_A0A1B8DRN2_A0A1B8DRN2_9PEZI_1524831 are exactly identical!
WARNING: Sequences tr_L8FY85_L8FY85_PSED2_658429 and tr_A0A1B8C2B0_A0A1B8C2B0_9PEZI_1622147 are exactly identical!
WARNING: Sequences tr_L8FY85_L8FY85_PSED2_658429 and tr_A0A1B8ET58_A0A1B8ET58_9PEZI_1622149 are exactly identical!
WARNING: Sequences tr_A0A287P2X0_A0A287P2X0_HORVV_112509 and tr_A0A3B6HUB7_A0A3B6HUB7_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A287P2X0_A0A287P2X0_HORVV_112509 and tr_A0A3B6IPV3_A0A3B6IPV3_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A287P2X0_A0A287P2X0_HORVV_112509 and tr_A0A3B6JIS0_A0A3B6JIS0_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_M4E8H3_M4E8H3_BRARP_51351 and tr_A0A078HLT6_A0A078HLT6_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4E8H3_M4E8H3_BRARP_51351 and tr_A0A078HN07_A0A078HN07_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4E8H3_M4E8H3_BRARP_51351 and tr_A0A0D3D991_A0A0D3D991_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_M4ENY4_M4ENY4_BRARP_51351 and tr_A0A078FT02_A0A078FT02_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4ENY4_M4ENY4_BRARP_51351 and tr_A0A078IMU5_A0A078IMU5_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4EWZ7_M4EWZ7_BRARP_51351 and tr_A0A078FLD4_A0A078FLD4_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M4EWZ7_M4EWZ7_BRARP_51351 and tr_A0A0D3C753_A0A0D3C753_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_M2TIJ0_M2TIJ0_COCSN_665912 and tr_M2VAH7_M2VAH7_COCH5_701091 are exactly identical!
WARNING: Sequences tr_M2TIJ0_M2TIJ0_COCSN_665912 and tr_W6YAQ1_W6YAQ1_COCCA_930089 are exactly identical!
WARNING: Sequences tr_M2TIJ0_M2TIJ0_COCSN_665912 and tr_W6ZE79_W6ZE79_COCMI_930090 are exactly identical!
WARNING: Sequences tr_W2Q133_W2Q133_PHYPN_761204 and tr_A0A0W8CXU1_A0A0W8CXU1_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2Q133_W2Q133_PHYPN_761204 and tr_W2GHV1_W2GHV1_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015IZL8_A0A015IZL8_9GLOM_1432141 and tr_A0A2I1F3C2_A0A2I1F3C2_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A059JJQ8_A0A059JJQ8_9EURO_1215338 and tr_A0A178EWQ2_A0A178EWQ2_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_A0A067ECH2_A0A067ECH2_CITSI_2711 and tr_V4TGV0_V4TGV0_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067ECH2_A0A067ECH2_CITSI_2711 and tr_A0A2H5P3M7_A0A2H5P3M7_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A067GSQ1_A0A067GSQ1_CITSI_2711 and tr_V4TB07_V4TB07_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067H7P1_A0A067H7P1_CITSI_2711 and tr_V4VWQ3_V4VWQ3_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067H7P1_A0A067H7P1_CITSI_2711 and tr_A0A2H5NXJ8_A0A2H5NXJ8_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A078GA04_A0A078GA04_BRANA_3708 and tr_A0A0D3EGW9_A0A0D3EGW9_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A078JBU9_A0A078JBU9_BRANA_3708 and tr_A0A0D3DDD7_A0A0D3DDD7_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A094EVZ4_A0A094EVZ4_9PEZI_1420912 and tr_A0A1B8GVM9_A0A1B8GVM9_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_W9QCW7_W9QCW7_9ROSA_981085 and tr_A0A200PWE9_A0A200PWE9_9MAGN_56857 are exactly identical!
WARNING: Sequences tr_V4SXW6_V4SXW6_9ROSI_85681 and tr_A0A2H5NUY8_A0A2H5NUY8_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A022S4D2_A0A022S4D2_ERYGU_4155 and tr_A0A1S3X2P4_A0A1S3X2P4_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A022S4D2_A0A022S4D2_ERYGU_4155 and tr_A0A1S4BMH5_A0A1S4BMH5_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A022S4D2_A0A022S4D2_ERYGU_4155 and tr_A0A1S4CH40_A0A1S4CH40_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A022S4D2_A0A022S4D2_ERYGU_4155 and tr_A0A1J6HXP7_A0A1J6HXP7_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A022S4D2_A0A022S4D2_ERYGU_4155 and tr_A0A314LDC7_A0A314LDC7_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A0D9W7C2_A0A0D9W7C2_9ORYZ_77586 and tr_A0A2T7CXP3_A0A2T7CXP3_9POAL_1504633 are exactly identical!
WARNING: Sequences tr_A0A0D2PI23_A0A0D2PI23_GOSRA_29730 and tr_A0A1U8JSG7_A0A1U8JSG7_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0D2PVC1_A0A0D2PVC1_GOSRA_29730 and tr_A0A1U8N9M7_A0A1U8N9M7_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0D2R6I8_A0A0D2R6I8_GOSRA_29730 and tr_A0A1U8IV12_A0A1U8IV12_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0F8WKN6_A0A0F8WKN6_9EURO_308745 and tr_A0A2T5LMP8_A0A2T5LMP8_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0K8LD11_A0A0K8LD11_9EURO_91492 and tr_A0A2I1C2J8_A0A2I1C2J8_9EURO_1392255 are exactly identical!
WARNING: Sequences tr_A0A0L1JF56_A0A0L1JF56_ASPNO_1509407 and tr_A0A1F7ZXS4_A0A1F7ZXS4_9EURO_109264 are exactly identical!
WARNING: Sequences tr_A0A0L9TY38_A0A0L9TY38_PHAAN_3914 and tr_A0A1S3V9C7_A0A1S3V9C7_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A0V0S5L9_A0A0V0S5L9_9BILA_6336 and tr_A0A0V1LHB5_A0A0V1LHB5_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0S5L9_A0A0V0S5L9_9BILA_6336 and tr_A0A0V0UBR5_A0A0V0UBR5_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0VSY6_A0A0V0VSY6_9BILA_181606 and tr_A0A0V1NZH6_A0A0V1NZH6_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A1C3YIK4_A0A1C3YIK4_GIBZE_229533 and tr_A0A2T4H9E7_A0A2T4H9E7_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A166HGS2_A0A166HGS2_DAUCA_79200 and tr_A0A1U8A3B4_A0A1U8A3B4_NELNU_4432 are exactly identical!
WARNING: Sequences tr_A0A1S3XZ22_A0A1S3XZ22_TOBAC_4097 and tr_A0A314LA38_A0A314LA38_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A1S3XZ22_A0A1S3XZ22_TOBAC_4097 and tr_A0A1U7YWQ0_A0A1U7YWQ0_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4A824_A0A1S4A824_TOBAC_4097 and tr_A0A314KHZ5_A0A314KHZ5_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A1S4BBV8_A0A1S4BBV8_TOBAC_4097 and tr_A0A1U7X8P3_A0A1U7X8P3_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1L9WT61_A0A1L9WT61_ASPAC_690307 and tr_A0A319C792_A0A319C792_9EURO_1448315 are exactly identical!
WARNING: Sequences tr_A0A1R3S077_A0A1R3S077_ASPC5_602072 and tr_A0A317VBJ0_A0A317VBJ0_9EURO_1450535 are exactly identical!
WARNING: Sequences tr_A0A1R3S077_A0A1R3S077_ASPC5_602072 and tr_A0A319E3C3_A0A319E3C3_9EURO_1448318 are exactly identical!
WARNING: Sequences tr_A0A1V8TZR0_A0A1V8TZR0_9PEZI_1974281 and tr_A0A1V8UC94_A0A1V8UC94_9PEZI_1974281 are exactly identical!
WARNING: Sequences tr_A0A1V8TZR0_A0A1V8TZR0_9PEZI_1974281 and tr_A0A1V8SRB4_A0A1V8SRB4_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A1Z5TGP9_A0A1Z5TGP9_HORWE_1157616 and tr_A0A1Z5TVS1_A0A1Z5TVS1_HORWE_1157616 are exactly identical!
WARNING: Sequences tr_A0A251TJP2_A0A251TJP2_HELAN_4232 and tr_A0A2J6M109_A0A2J6M109_LACSA_4236 are exactly identical!
WARNING: Sequences tr_A0A251TJP2_A0A251TJP2_HELAN_4232 and tr_A0A103XPG4_A0A103XPG4_CYNCS_59895 are exactly identical!
WARNING: Sequences tr_A0A251TJP2_A0A251TJP2_HELAN_4232 and tr_A0A2U1KQ39_A0A2U1KQ39_ARTAN_35608 are exactly identical!
WARNING: Sequences tr_A0A251TJP2_A0A251TJP2_HELAN_4232 and tr_A0A2U1N9D0_A0A2U1N9D0_ARTAN_35608 are exactly identical!
WARNING: Sequences tr_A0A2H3EEB2_A0A2H3EEB2_ARMGA_47427 and tr_A0A2H3CGQ9_A0A2H3CGQ9_9AGAR_1076256 are exactly identical!
WARNING: Sequences tr_A0A2H3EEB2_A0A2H3EEB2_ARMGA_47427 and tr_A0A284R9F2_A0A284R9F2_9AGAR_47428 are exactly identical!
WARNING: Sequences tr_A0A1U8FF86_A0A1U8FF86_CAPAN_4072 and tr_A0A2G3D2S7_A0A2G3D2S7_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2G5HHU9_A0A2G5HHU9_CERBT_122368 and tr_A0A2I0RL69_A0A2I0RL69_9PEZI_348901 are exactly identical!
WARNING: Sequences tr_A0A2G5HHU9_A0A2G5HHU9_CERBT_122368 and tr_A0A2S6C797_A0A2S6C797_9PEZI_357750 are exactly identical!
WARNING: Sequences tr_A0A2J6PH61_A0A2J6PH61_9HELO_1745343 and tr_A0A2J6R7L7_A0A2J6R7L7_9HELO_1149755 are exactly identical!
WARNING: Sequences tr_A0A2K3QQ70_A0A2K3QQ70_9HYPO_45235 and tr_A0A2S4KPD6_A0A2S4KPD6_9HYPO_94208 are exactly identical!
WARNING: Sequences tr_A0A2P5DGH4_A0A2P5DGH4_TREOI_63057 and tr_A0A2P5CL19_A0A2P5CL19_PARAD_3476 are exactly identical!
WARNING: Sequences tr_A0A2Y9EVC0_A0A2Y9EVC0_PHYCD_9755 and tr_A0A383Z1Y4_A0A383Z1Y4_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 170

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/3_mltree/Q16740.raxml.reduced.phy

Alignment comprises 1 partitions and 172 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 173 / 172
Gaps: 0.96 %
Invariant sites: 4.62 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/3_mltree/Q16740.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 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 172 / 13760
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -222174.518449] Initial branch length optimization
[00:00:03 -192536.222703] Model parameter optimization (eps = 10.000000)
[00:00:35 -191955.421788] AUTODETECT spr round 1 (radius: 5)
[00:03:15 -118865.805618] AUTODETECT spr round 2 (radius: 10)
[00:06:04 -81652.539827] AUTODETECT spr round 3 (radius: 15)
[00:08:54 -65481.160126] AUTODETECT spr round 4 (radius: 20)
[00:12:34 -57382.111106] AUTODETECT spr round 5 (radius: 25)
[00:16:46 -55477.600243] SPR radius for FAST iterations: 25 (autodetect)
[00:16:46 -55477.600243] Model parameter optimization (eps = 3.000000)
[00:17:07 -55459.687931] FAST spr round 1 (radius: 25)
[00:19:47 -47212.200320] FAST spr round 2 (radius: 25)
[00:21:57 -46619.908996] FAST spr round 3 (radius: 25)
[00:23:51 -46595.265632] FAST spr round 4 (radius: 25)
[00:25:35 -46588.892150] FAST spr round 5 (radius: 25)
[00:27:14 -46588.892069] Model parameter optimization (eps = 1.000000)
[00:27:29 -46585.578966] SLOW spr round 1 (radius: 5)
[00:29:50 -46570.033161] SLOW spr round 2 (radius: 5)
[00:32:10 -46565.001564] SLOW spr round 3 (radius: 5)
[00:34:19 -46564.180395] SLOW spr round 4 (radius: 5)
[00:36:26 -46564.180378] SLOW spr round 5 (radius: 10)
[00:38:37 -46562.038815] SLOW spr round 6 (radius: 5)
[00:41:23 -46558.595701] SLOW spr round 7 (radius: 5)
[00:43:49 -46558.595678] SLOW spr round 8 (radius: 10)
[00:46:04 -46558.595678] SLOW spr round 9 (radius: 15)
[00:49:32 -46555.737516] SLOW spr round 10 (radius: 5)
[00:52:24 -46555.737510] SLOW spr round 11 (radius: 10)
[00:54:59 -46555.737510] SLOW spr round 12 (radius: 15)
[00:56:04] [worker #2] ML tree search #3, logLikelihood: -46555.543607
[00:58:20 -46555.737510] SLOW spr round 13 (radius: 20)
[01:03:10 -46555.737510] SLOW spr round 14 (radius: 25)
[01:09:23 -46555.737510] Model parameter optimization (eps = 0.100000)

[01:09:33] [worker #0] ML tree search #1, logLikelihood: -46555.364098

[01:09:33 -222050.489816] Initial branch length optimization
[01:09:37 -192239.295386] Model parameter optimization (eps = 10.000000)
[01:10:56 -191576.558653] AUTODETECT spr round 1 (radius: 5)
[01:11:40] [worker #1] ML tree search #2, logLikelihood: -46534.162203
[01:13:38 -122145.120753] AUTODETECT spr round 2 (radius: 10)
[01:16:27 -82787.008474] AUTODETECT spr round 3 (radius: 15)
[01:19:31 -66632.326313] AUTODETECT spr round 4 (radius: 20)
[01:23:25 -59880.770060] AUTODETECT spr round 5 (radius: 25)
[01:27:12 -57563.153454] SPR radius for FAST iterations: 25 (autodetect)
[01:27:12 -57563.153454] Model parameter optimization (eps = 3.000000)
[01:27:30 -57557.672291] FAST spr round 1 (radius: 25)
[01:30:05 -47661.452385] FAST spr round 2 (radius: 25)
[01:32:09 -46684.351296] FAST spr round 3 (radius: 25)
[01:34:03 -46613.721770] FAST spr round 4 (radius: 25)
[01:35:51 -46584.216412] FAST spr round 5 (radius: 25)
[01:37:34 -46576.093524] FAST spr round 6 (radius: 25)
[01:39:12 -46576.093216] Model parameter optimization (eps = 1.000000)
[01:39:28 -46564.468780] SLOW spr round 1 (radius: 5)
[01:41:48 -46539.016571] SLOW spr round 2 (radius: 5)
[01:44:03 -46531.784328] SLOW spr round 3 (radius: 5)
[01:46:13 -46530.966888] SLOW spr round 4 (radius: 5)
[01:48:20 -46530.736460] SLOW spr round 5 (radius: 5)
[01:50:26 -46530.736457] SLOW spr round 6 (radius: 10)
[01:52:38 -46527.611802] SLOW spr round 7 (radius: 5)
[01:54:06] [worker #2] ML tree search #6, logLikelihood: -46526.837345
[01:55:26 -46523.952203] SLOW spr round 8 (radius: 5)
[01:57:53 -46522.466983] SLOW spr round 9 (radius: 5)
[02:00:08 -46522.466983] SLOW spr round 10 (radius: 10)
[02:02:20 -46522.466983] SLOW spr round 11 (radius: 15)
[02:05:48 -46522.466983] SLOW spr round 12 (radius: 20)
[02:10:14 -46520.419888] SLOW spr round 13 (radius: 5)
[02:12:17] [worker #1] ML tree search #5, logLikelihood: -46535.201847
[02:13:11 -46520.419843] SLOW spr round 14 (radius: 10)
[02:15:49 -46520.419843] SLOW spr round 15 (radius: 15)
[02:19:09 -46519.591783] SLOW spr round 16 (radius: 5)
[02:22:05 -46518.907271] SLOW spr round 17 (radius: 5)
[02:24:37 -46518.729727] SLOW spr round 18 (radius: 5)
[02:26:55 -46518.729710] SLOW spr round 19 (radius: 10)
[02:29:08 -46518.729710] SLOW spr round 20 (radius: 15)
[02:32:38 -46518.281653] SLOW spr round 21 (radius: 5)
[02:35:32 -46518.281596] SLOW spr round 22 (radius: 10)
[02:38:07 -46518.281596] SLOW spr round 23 (radius: 15)
[02:41:28 -46518.281596] SLOW spr round 24 (radius: 20)
[02:46:02 -46518.281596] SLOW spr round 25 (radius: 25)
[02:51:34 -46518.281596] Model parameter optimization (eps = 0.100000)

[02:51:47] [worker #0] ML tree search #4, logLikelihood: -46518.038917

[02:51:47 -222998.220094] Initial branch length optimization
[02:51:51 -192907.604304] Model parameter optimization (eps = 10.000000)
[02:52:30 -192345.253491] AUTODETECT spr round 1 (radius: 5)
[02:55:08 -122580.825454] AUTODETECT spr round 2 (radius: 10)
[02:57:53 -85327.323213] AUTODETECT spr round 3 (radius: 15)
[03:00:45 -71052.624380] AUTODETECT spr round 4 (radius: 20)
[03:04:08 -62171.222594] AUTODETECT spr round 5 (radius: 25)
[03:07:39 -58656.093491] SPR radius for FAST iterations: 25 (autodetect)
[03:07:39 -58656.093491] Model parameter optimization (eps = 3.000000)
[03:08:00 -58620.572085] FAST spr round 1 (radius: 25)
[03:10:46 -47317.241550] FAST spr round 2 (radius: 25)
[03:12:54 -46688.420265] FAST spr round 3 (radius: 25)
[03:14:52 -46578.970243] FAST spr round 4 (radius: 25)
[03:16:39 -46554.956345] FAST spr round 5 (radius: 25)
[03:18:17 -46554.953978] Model parameter optimization (eps = 1.000000)
[03:18:35 -46546.864910] SLOW spr round 1 (radius: 5)
[03:20:53 -46530.198050] SLOW spr round 2 (radius: 5)
[03:23:05 -46527.436385] SLOW spr round 3 (radius: 5)
[03:25:11 -46527.436369] SLOW spr round 4 (radius: 10)
[03:27:18 -46527.436369] SLOW spr round 5 (radius: 15)
[03:30:00] [worker #1] ML tree search #8, logLikelihood: -46513.233343
[03:30:36 -46525.741728] SLOW spr round 6 (radius: 5)
[03:33:27 -46525.741590] SLOW spr round 7 (radius: 10)
[03:35:59 -46525.741586] SLOW spr round 8 (radius: 15)
[03:37:13] [worker #2] ML tree search #9, logLikelihood: -46526.165065
[03:39:03 -46525.741586] SLOW spr round 9 (radius: 20)
[03:43:27 -46525.741586] SLOW spr round 10 (radius: 25)
[03:48:38 -46525.741586] Model parameter optimization (eps = 0.100000)

[03:48:43] [worker #0] ML tree search #7, logLikelihood: -46525.734221

[03:48:43 -222455.627065] Initial branch length optimization
[03:48:46 -192590.454284] Model parameter optimization (eps = 10.000000)
[03:49:30 -191909.831993] AUTODETECT spr round 1 (radius: 5)
[03:52:09 -120465.993647] AUTODETECT spr round 2 (radius: 10)
[03:54:57 -78916.950196] AUTODETECT spr round 3 (radius: 15)
[03:57:57 -67520.586253] AUTODETECT spr round 4 (radius: 20)
[04:01:07 -60479.943514] AUTODETECT spr round 5 (radius: 25)
[04:05:14 -58348.449601] SPR radius for FAST iterations: 25 (autodetect)
[04:05:15 -58348.449601] Model parameter optimization (eps = 3.000000)
[04:05:35 -58335.792007] FAST spr round 1 (radius: 25)
[04:08:18 -47572.052054] FAST spr round 2 (radius: 25)
[04:10:30 -46711.332437] FAST spr round 3 (radius: 25)
[04:12:30 -46600.487366] FAST spr round 4 (radius: 25)
[04:14:20 -46590.689681] FAST spr round 5 (radius: 25)
[04:16:03 -46587.988619] FAST spr round 6 (radius: 25)
[04:17:43 -46587.988509] Model parameter optimization (eps = 1.000000)
[04:17:56 -46585.931072] SLOW spr round 1 (radius: 5)
[04:20:26 -46552.758154] SLOW spr round 2 (radius: 5)
[04:22:51 -46535.780909] SLOW spr round 3 (radius: 5)
[04:25:02 -46535.772927] SLOW spr round 4 (radius: 10)
[04:27:12 -46534.050282] SLOW spr round 5 (radius: 5)
[04:30:02 -46533.673778] SLOW spr round 6 (radius: 5)
[04:32:29 -46533.673775] SLOW spr round 7 (radius: 10)
[04:34:44 -46533.673775] SLOW spr round 8 (radius: 15)
[04:38:03 -46531.850095] SLOW spr round 9 (radius: 5)
[04:38:45] [worker #1] ML tree search #11, logLikelihood: -46534.519448
[04:41:05 -46528.313600] SLOW spr round 10 (radius: 5)
[04:43:36 -46528.197661] SLOW spr round 11 (radius: 5)
[04:45:04] [worker #2] ML tree search #12, logLikelihood: -46534.373288
[04:45:55 -46528.197653] SLOW spr round 12 (radius: 10)
[04:48:07 -46528.197653] SLOW spr round 13 (radius: 15)
[04:51:30 -46528.197653] SLOW spr round 14 (radius: 20)
[04:55:58 -46528.197653] SLOW spr round 15 (radius: 25)
[05:01:25 -46528.197653] Model parameter optimization (eps = 0.100000)

[05:01:41] [worker #0] ML tree search #10, logLikelihood: -46526.231466

[05:01:41 -222757.945898] Initial branch length optimization
[05:01:45 -193501.061708] Model parameter optimization (eps = 10.000000)
[05:02:19 -192839.034306] AUTODETECT spr round 1 (radius: 5)
[05:05:03 -121133.005042] AUTODETECT spr round 2 (radius: 10)
[05:07:52 -80571.549814] AUTODETECT spr round 3 (radius: 15)
[05:10:46 -60289.941557] AUTODETECT spr round 4 (radius: 20)
[05:14:22 -55285.203994] AUTODETECT spr round 5 (radius: 25)
[05:18:51 -54248.380913] SPR radius for FAST iterations: 25 (autodetect)
[05:18:51 -54248.380913] Model parameter optimization (eps = 3.000000)
[05:19:09 -54235.355877] FAST spr round 1 (radius: 25)
[05:21:47 -47033.937178] FAST spr round 2 (radius: 25)
[05:23:58 -46630.073647] FAST spr round 3 (radius: 25)
[05:25:57 -46579.554167] FAST spr round 4 (radius: 25)
[05:27:42 -46570.328119] FAST spr round 5 (radius: 25)
[05:29:23 -46567.737615] FAST spr round 6 (radius: 25)
[05:31:04 -46563.621627] FAST spr round 7 (radius: 25)
[05:32:42 -46563.621277] Model parameter optimization (eps = 1.000000)
[05:32:58 -46557.548705] SLOW spr round 1 (radius: 5)
[05:35:18 -46545.239717] SLOW spr round 2 (radius: 5)
[05:35:22] [worker #1] ML tree search #14, logLikelihood: -46541.194384
[05:37:36 -46542.635718] SLOW spr round 3 (radius: 5)
[05:39:50 -46542.635089] SLOW spr round 4 (radius: 10)
[05:42:03 -46539.832806] SLOW spr round 5 (radius: 5)
[05:44:53 -46539.832749] SLOW spr round 6 (radius: 10)
[05:47:22 -46539.832745] SLOW spr round 7 (radius: 15)
[05:50:40 -46537.604120] SLOW spr round 8 (radius: 5)
[05:53:36 -46537.604090] SLOW spr round 9 (radius: 10)
[05:56:11 -46534.821736] SLOW spr round 10 (radius: 5)
[05:58:56 -46533.590499] SLOW spr round 11 (radius: 5)
[06:01:21 -46533.590481] SLOW spr round 12 (radius: 10)
[06:03:34 -46533.590481] SLOW spr round 13 (radius: 15)
[06:06:59 -46533.590481] SLOW spr round 14 (radius: 20)
[06:08:28] [worker #2] ML tree search #15, logLikelihood: -46553.823667
[06:11:32 -46533.517091] SLOW spr round 15 (radius: 25)
[06:17:10 -46533.517000] Model parameter optimization (eps = 0.100000)

[06:17:22] [worker #0] ML tree search #13, logLikelihood: -46533.244384

[06:17:22 -222464.370130] Initial branch length optimization
[06:17:25 -192365.931227] Model parameter optimization (eps = 10.000000)
[06:17:56 -191766.974935] AUTODETECT spr round 1 (radius: 5)
[06:20:36 -117859.664377] AUTODETECT spr round 2 (radius: 10)
[06:23:25 -83017.539921] AUTODETECT spr round 3 (radius: 15)
[06:26:24 -72448.426829] AUTODETECT spr round 4 (radius: 20)
[06:29:55 -63492.060936] AUTODETECT spr round 5 (radius: 25)
[06:34:03 -57436.814318] SPR radius for FAST iterations: 25 (autodetect)
[06:34:03 -57436.814318] Model parameter optimization (eps = 3.000000)
[06:34:22 -57418.399604] FAST spr round 1 (radius: 25)
[06:36:59 -47305.844093] FAST spr round 2 (radius: 25)
[06:39:04 -46659.015413] FAST spr round 3 (radius: 25)
[06:41:00 -46609.414036] FAST spr round 4 (radius: 25)
[06:42:49 -46591.499490] FAST spr round 5 (radius: 25)
[06:44:29 -46586.918127] FAST spr round 6 (radius: 25)
[06:46:07 -46586.917562] Model parameter optimization (eps = 1.000000)
[06:46:23 -46584.537119] SLOW spr round 1 (radius: 5)
[06:48:44 -46567.845548] SLOW spr round 2 (radius: 5)
[06:50:59 -46560.945255] SLOW spr round 3 (radius: 5)
[06:53:13 -46546.577111] SLOW spr round 4 (radius: 5)
[06:55:26 -46545.250282] SLOW spr round 5 (radius: 5)
[06:57:37 -46542.351925] SLOW spr round 6 (radius: 5)
[06:59:43 -46542.348692] SLOW spr round 7 (radius: 10)
[07:01:52 -46541.911431] SLOW spr round 8 (radius: 5)
[07:04:40 -46540.052158] SLOW spr round 9 (radius: 5)
[07:07:07 -46540.052133] SLOW spr round 10 (radius: 10)
[07:09:21 -46539.008065] SLOW spr round 11 (radius: 5)
[07:09:56] [worker #1] ML tree search #17, logLikelihood: -46513.841298
[07:12:07 -46538.238974] SLOW spr round 12 (radius: 5)
[07:14:32 -46538.238972] SLOW spr round 13 (radius: 10)
[07:16:27] [worker #2] ML tree search #18, logLikelihood: -46506.235075
[07:16:45 -46538.238968] SLOW spr round 14 (radius: 15)
[07:20:13 -46538.238876] SLOW spr round 15 (radius: 20)
[07:24:51 -46538.238876] SLOW spr round 16 (radius: 25)
[07:30:43 -46538.238876] Model parameter optimization (eps = 0.100000)

[07:30:51] [worker #0] ML tree search #16, logLikelihood: -46538.140173

[07:30:51 -220730.511137] Initial branch length optimization
[07:30:54 -191191.613841] Model parameter optimization (eps = 10.000000)
[07:31:38 -190627.755145] AUTODETECT spr round 1 (radius: 5)
[07:34:21 -117952.653152] AUTODETECT spr round 2 (radius: 10)
[07:37:07 -78651.868367] AUTODETECT spr round 3 (radius: 15)
[07:40:02 -64546.799691] AUTODETECT spr round 4 (radius: 20)
[07:43:37 -56350.083321] AUTODETECT spr round 5 (radius: 25)
[07:47:40 -55584.854332] SPR radius for FAST iterations: 25 (autodetect)
[07:47:40 -55584.854332] Model parameter optimization (eps = 3.000000)
[07:47:56 -55576.846733] FAST spr round 1 (radius: 25)
[07:50:24 -47108.799397] FAST spr round 2 (radius: 25)
[07:52:25 -46635.940584] FAST spr round 3 (radius: 25)
[07:54:19 -46578.525288] FAST spr round 4 (radius: 25)
[07:56:04 -46568.294592] FAST spr round 5 (radius: 25)
[07:57:41 -46568.294552] Model parameter optimization (eps = 1.000000)
[07:57:52 -46565.191040] SLOW spr round 1 (radius: 5)
[08:00:13 -46552.155678] SLOW spr round 2 (radius: 5)
[08:02:25 -46550.789151] SLOW spr round 3 (radius: 5)
[08:04:33 -46550.788245] SLOW spr round 4 (radius: 10)
[08:06:42 -46550.133269] SLOW spr round 5 (radius: 5)
[08:09:28 -46550.133254] SLOW spr round 6 (radius: 10)
[08:11:53 -46550.133253] SLOW spr round 7 (radius: 15)
[08:15:09 -46549.287412] SLOW spr round 8 (radius: 5)
[08:18:03 -46547.401556] SLOW spr round 9 (radius: 5)
[08:20:32 -46547.401109] SLOW spr round 10 (radius: 10)
[08:22:47 -46547.401099] SLOW spr round 11 (radius: 15)
[08:26:06 -46547.401099] SLOW spr round 12 (radius: 20)
[08:30:46 -46547.401099] SLOW spr round 13 (radius: 25)
[08:34:03] [worker #1] ML tree search #20, logLikelihood: -46513.566763
[08:36:21 -46547.401099] Model parameter optimization (eps = 0.100000)

[08:36:27] [worker #0] ML tree search #19, logLikelihood: -46547.354566


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.285234,0.297026) (0.385591,0.566783) (0.225371,1.343639) (0.103804,3.794786) 
   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: -46506.235075

AIC score: 97022.470150 / AICc score: 8141082.470150 / BIC score: 103344.819797
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=173).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/3_mltree/Q16740.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/3_mltree/Q16740.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/3_mltree/Q16740.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q16740/3_mltree/Q16740.raxml.log

Analysis started: 09-Jul-2021 12:34:32 / finished: 09-Jul-2021 21:10:59

Elapsed time: 30987.518 seconds