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 02-Jul-2021 11:10:42 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P36507/2_msa/P36507_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P36507/3_mltree/P36507 --seed 2 --threads 5 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P36507/2_msa/P36507_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 350 sites WARNING: Sequences tr_F1NYZ2_F1NYZ2_CHICK_9031 and sp_Q90891_MP2K2_CHICK_9031 are exactly identical! WARNING: Sequences tr_F1NYZ2_F1NYZ2_CHICK_9031 and tr_A0A226N322_A0A226N322_CALSU_9009 are exactly identical! WARNING: Sequences tr_F1NYZ2_F1NYZ2_CHICK_9031 and tr_A0A226NS89_A0A226NS89_COLVI_9014 are exactly identical! WARNING: Sequences tr_Q5ZIF0_Q5ZIF0_CHICK_9031 and tr_A0A0Q3MA74_A0A0Q3MA74_AMAAE_12930 are exactly identical! WARNING: Sequences tr_Q5ZIF0_Q5ZIF0_CHICK_9031 and tr_A0A2I0MD87_A0A2I0MD87_COLLI_8932 are exactly identical! WARNING: Sequences tr_M3XMR0_M3XMR0_MUSPF_9669 and tr_A0A2Y9K7U5_A0A2Y9K7U5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_E3RVE1_E3RVE1_PYRTT_861557 and tr_B2VYQ3_B2VYQ3_PYRTR_426418 are exactly identical! WARNING: Sequences tr_E3RVE1_E3RVE1_PYRTT_861557 and tr_A0A2W1DGX9_A0A2W1DGX9_9PLEO_45151 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_G3QM92_G3QM92_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_A0A2I3RF04_A0A2I3RF04_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_H0XE68_H0XE68_OTOGA_30611 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and sp_Q02750_MP2K1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_A0A1D5QKD3_A0A1D5QKD3_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_U3CZR8_U3CZR8_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_A0A287BK75_A0A287BK75_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_Q0VD16_Q0VD16_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_L5K149_L5K149_PTEAL_9402 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_A0A2I3LF26_A0A2I3LF26_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_A0A0D9RL74_A0A0D9RL74_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_A0A2K5YWG9_A0A2K5YWG9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_A0A2R9A4U3_A0A2R9A4U3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_A0A2Y9FRV8_A0A2Y9FRV8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2I3GXI0_A0A2I3GXI0_NOMLE_61853 and tr_A0A383YTE9_A0A383YTE9_BALAS_310752 are exactly identical! WARNING: Sequences tr_J3KH83_J3KH83_COCIM_246410 and tr_E9DJ21_E9DJ21_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3KH83_J3KH83_COCIM_246410 and tr_A0A0J6Y042_A0A0J6Y042_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QTA9_B6QTA9_TALMQ_441960 and tr_A0A093XVT7_A0A093XVT7_TALMA_1077442 are exactly identical! WARNING: Sequences tr_G3QPY6_G3QPY6_GORGO_9595 and tr_H2NNK7_H2NNK7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QPY6_G3QPY6_GORGO_9595 and tr_H2Q9P0_H2Q9P0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QPY6_G3QPY6_GORGO_9595 and sp_Q13163_MP2K5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QPY6_G3QPY6_GORGO_9595 and tr_G7P8W8_G7P8W8_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QPY6_G3QPY6_GORGO_9595 and tr_A0A0D9RLR5_A0A0D9RLR5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3QPY6_G3QPY6_GORGO_9595 and tr_A0A2R9BFH4_A0A2R9BFH4_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R0F2_G3R0F2_GORGO_9595 and tr_K7BYT0_K7BYT0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R0F2_G3R0F2_GORGO_9595 and sp_P36507_MP2K2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G2XEP1_G2XEP1_VERDV_498257 and tr_A0A0G4M3P2_A0A0G4M3P2_9PEZI_100787 are exactly identical! WARNING: Sequences tr_B8PBQ2_B8PBQ2_POSPM_561896 and tr_A0A1X6NCZ1_A0A1X6NCZ1_9APHY_670580 are exactly identical! WARNING: Sequences tr_V5ILY0_V5ILY0_NEUCR_367110 and tr_G4UGY5_G4UGY5_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8NV54_B8NV54_ASPFN_332952 and tr_Q2U560_Q2U560_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NV54_B8NV54_ASPFN_332952 and tr_A0A0F0IIS8_A0A0F0IIS8_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8NV54_B8NV54_ASPFN_332952 and tr_A0A1S9DIH8_A0A1S9DIH8_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_B8NV54_B8NV54_ASPFN_332952 and tr_A0A2G7FI34_A0A2G7FI34_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A179V300_A0A179V300_BLAGS_559298 and tr_C5GMH6_C5GMH6_AJEDR_559297 are exactly identical! WARNING: Sequences tr_J9P5W6_J9P5W6_CANLF_9615 and tr_M3X621_M3X621_FELCA_9685 are exactly identical! WARNING: Sequences tr_J9P5W6_J9P5W6_CANLF_9615 and tr_A0A2U3XED8_A0A2U3XED8_LEPWE_9713 are exactly identical! WARNING: Sequences tr_J9P5W6_J9P5W6_CANLF_9615 and tr_A0A384DIG4_A0A384DIG4_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3RWN9_A0A2I3RWN9_PANTR_9598 and tr_A0A2R9CJT9_A0A2R9CJT9_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FS15_F9FS15_FUSOF_660025 and tr_W7LXC3_W7LXC3_GIBM7_334819 are exactly identical! WARNING: Sequences tr_F9FS15_F9FS15_FUSOF_660025 and tr_A0A0D2XNJ1_A0A0D2XNJ1_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FS15_F9FS15_FUSOF_660025 and tr_S0E1J8_S0E1J8_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_F9FS15_F9FS15_FUSOF_660025 and tr_N4TJD5_N4TJD5_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FS15_F9FS15_FUSOF_660025 and tr_X0CA42_X0CA42_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FS15_F9FS15_FUSOF_660025 and tr_A0A2H3T3Q6_A0A2H3T3Q6_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FS15_F9FS15_FUSOF_660025 and tr_A0A2H3HE94_A0A2H3HE94_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F9FS15_F9FS15_FUSOF_660025 and tr_A0A2K0WBF0_A0A2K0WBF0_GIBNY_42673 are exactly identical! WARNING: Sequences tr_F9FS15_F9FS15_FUSOF_660025 and tr_A0A365MYD3_A0A365MYD3_GIBIN_948311 are exactly identical! WARNING: Sequences tr_E9EWM2_E9EWM2_METRA_655844 and tr_A0A0D9NSQ6_A0A0D9NSQ6_METAN_1291518 are exactly identical! WARNING: Sequences tr_E9DXG6_E9DXG6_METAQ_655827 and tr_A0A0B4H5F2_A0A0B4H5F2_METMF_1276143 are exactly identical! WARNING: Sequences tr_J5JXF7_J5JXF7_BEAB2_655819 and tr_A0A0A2W2Q7_A0A0A2W2Q7_BEABA_1245745 are exactly identical! WARNING: Sequences tr_J5JXF7_J5JXF7_BEAB2_655819 and tr_A0A2N6NR94_A0A2N6NR94_BEABA_176275 are exactly identical! WARNING: Sequences tr_A0A3B5QDC0_A0A3B5QDC0_XIPMA_8083 and tr_A0A087X7K5_A0A087X7K5_POEFO_48698 are exactly identical! WARNING: Sequences tr_M3ZMS8_M3ZMS8_XIPMA_8083 and tr_A0A087XR80_A0A087XR80_POEFO_48698 are exactly identical! WARNING: Sequences tr_A1D8B8_A1D8B8_NEOFI_331117 and tr_A0A0S7DQX4_A0A0S7DQX4_9EURO_293939 are exactly identical! WARNING: Sequences tr_A1D8B8_A1D8B8_NEOFI_331117 and tr_A0A2I1C1T5_A0A2I1C1T5_9EURO_1392255 are exactly identical! WARNING: Sequences tr_A2QXY7_A2QXY7_ASPNC_425011 and tr_G3YC00_G3YC00_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QXY7_A2QXY7_ASPNC_425011 and tr_A0A319B0F3_A0A319B0F3_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XFF6_G7XFF6_ASPKW_1033177 and tr_A0A146FRM4_A0A146FRM4_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XFF6_G7XFF6_ASPKW_1033177 and tr_A0A317UZ94_A0A317UZ94_9EURO_1448314 are exactly identical! WARNING: Sequences tr_E5SMI4_E5SMI4_TRISP_6334 and tr_A0A0V1D8C8_A0A0V1D8C8_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5SMI4_E5SMI4_TRISP_6334 and tr_A0A0V0VUV9_A0A0V0VUV9_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5SMI4_E5SMI4_TRISP_6334 and tr_A0A0V1L227_A0A0V1L227_9BILA_6335 are exactly identical! WARNING: Sequences tr_E5SMI4_E5SMI4_TRISP_6334 and tr_A0A0V0ZJR7_A0A0V0ZJR7_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5SMI4_E5SMI4_TRISP_6334 and tr_A0A0V1P2Z7_A0A0V1P2Z7_9BILA_92180 are exactly identical! WARNING: Sequences tr_E5SMI4_E5SMI4_TRISP_6334 and tr_A0A0V0TSP9_A0A0V0TSP9_9BILA_144512 are exactly identical! WARNING: Sequences tr_H0ZGH0_H0ZGH0_TAEGU_59729 and tr_A0A218V0K5_A0A218V0K5_9PASE_299123 are exactly identical! WARNING: Sequences tr_Q66JE6_Q66JE6_XENTR_8364 and tr_A0A1L8H157_A0A1L8H157_XENLA_8355 are exactly identical! WARNING: Sequences tr_G2XXL3_G2XXL3_BOTF4_999810 and tr_M7TCE6_M7TCE6_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SHL8_F2SHL8_TRIRC_559305 and tr_A0A178F049_A0A178F049_TRIRU_5551 are exactly identical! WARNING: Sequences tr_B3RSG6_B3RSG6_TRIAD_10228 and tr_A0A369SHN9_A0A369SHN9_9METZ_287889 are exactly identical! WARNING: Sequences tr_L0PB47_L0PB47_PNEJ8_1209962 and tr_A0A0W4ZK10_A0A0W4ZK10_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_L2FV46_L2FV46_COLFN_1213859 and tr_T0JTE7_T0JTE7_COLGC_1237896 are exactly identical! WARNING: Sequences tr_M2SSB8_M2SSB8_COCSN_665912 and tr_M2TIQ4_M2TIQ4_COCH5_701091 are exactly identical! WARNING: Sequences tr_M2SSB8_M2SSB8_COCSN_665912 and tr_W6Y8M6_W6Y8M6_COCCA_930089 are exactly identical! WARNING: Sequences tr_A0A015L4Y7_A0A015L4Y7_9GLOM_1432141 and tr_A0A2I1F2S9_A0A2I1F2S9_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A044VHT2_A0A044VHT2_ONCVO_6282 and tr_A0A182EP24_A0A182EP24_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0D9REF2_A0A0D9REF2_CHLSB_60711 and tr_A0A2K6E3R4_A0A2K6E3R4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0M9WFU6_A0A0M9WFU6_9EURO_229535 and tr_A0A1V6QQY6_A0A1V6QQY6_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A0A1N618_A0A0A1N618_9FUNG_58291 and tr_A0A2G4T0D2_A0A2G4T0D2_9FUNG_1340429 are exactly identical! WARNING: Sequences tr_A0A151M8T8_A0A151M8T8_ALLMI_8496 and tr_A0A1U7S241_A0A1U7S241_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151M8Y0_A0A151M8Y0_ALLMI_8496 and tr_A0A1U7RAB7_A0A1U7RAB7_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091J0R2_A0A091J0R2_EGRGA_188379 and tr_A0A0A0A8U2_A0A0A0A8U2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091J0R2_A0A091J0R2_EGRGA_188379 and tr_A0A091ILW0_A0A091ILW0_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091JSD5_A0A091JSD5_EGRGA_188379 and tr_A0A091VII9_A0A091VII9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JSD5_A0A091JSD5_EGRGA_188379 and tr_A0A087R4C5_A0A087R4C5_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JSD5_A0A091JSD5_EGRGA_188379 and tr_A0A093HEM6_A0A093HEM6_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091JSD5_A0A091JSD5_EGRGA_188379 and tr_A0A091WT72_A0A091WT72_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JSD5_A0A091JSD5_EGRGA_188379 and tr_A0A099ZWJ2_A0A099ZWJ2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JSD5_A0A091JSD5_EGRGA_188379 and tr_A0A093GI41_A0A093GI41_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091VJ65_A0A091VJ65_NIPNI_128390 and tr_A0A093HEM4_A0A093HEM4_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A093JVU6_A0A093JVU6_STRCA_441894 and tr_A0A099ZS38_A0A099ZS38_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091H484_A0A091H484_9AVES_55661 and tr_A0A091IIC6_A0A091IIC6_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A2I0MD82_A0A2I0MD82_COLLI_8932 and tr_A0A1V4JE59_A0A1V4JE59_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0D2CBV5_A0A0D2CBV5_9EURO_569365 and tr_A0A178ZGS5_A0A178ZGS5_9EURO_1367422 are exactly identical! WARNING: Sequences tr_A0A0V1MID8_A0A0V1MID8_9BILA_268474 and tr_A0A0V1HHM0_A0A0V1HHM0_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A100IP26_A0A100IP26_ASPNG_5061 and tr_A0A1L9N286_A0A1L9N286_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A166X2H9_A0A166X2H9_9PEZI_708197 and tr_A0A167CAM0_A0A167CAM0_9PEZI_1573173 are exactly identical! WARNING: Sequences tr_A0A164TDC9_A0A164TDC9_9HOMO_1314777 and tr_A0A165ZMR5_A0A165ZMR5_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A194W9B0_A0A194W9B0_9PEZI_105487 and tr_A0A194UY80_A0A194UY80_9PEZI_694573 are exactly identical! WARNING: Sequences tr_A0A1S3T5J0_A0A1S3T5J0_SALSA_8030 and tr_A0A060X622_A0A060X622_ONCMY_8022 are exactly identical! WARNING: Sequences tr_B5X0Y3_B5X0Y3_SALSA_8030 and tr_A0A060XJB7_A0A060XJB7_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1B8B858_A0A1B8B858_FUSPO_36050 and tr_A0A366QZR4_A0A366QZR4_9HYPO_2109339 are exactly identical! WARNING: Sequences tr_A0A2D0QAC2_A0A2D0QAC2_ICTPU_7998 and tr_A0A2D0QB99_A0A2D0QB99_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2G5IDD0_A0A2G5IDD0_CERBT_122368 and tr_A0A2S6CDW7_A0A2S6CDW7_9PEZI_357750 are exactly identical! WARNING: Sequences tr_A0A2G4T721_A0A2G4T721_9FUNG_1340429 and tr_A0A367IXD2_A0A367IXD2_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A2U3VKE8_A0A2U3VKE8_ODORO_9708 and tr_A0A2U3Y596_A0A2U3Y596_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2Y9NWM8_A0A2Y9NWM8_DELLE_9749 and tr_A0A2Y9T0Q8_A0A2Y9T0Q8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2V5I6N9_A0A2V5I6N9_9EURO_1450541 and tr_A0A2V5H1C6_A0A2V5H1C6_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 116 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/P36507/3_mltree/P36507.raxml.reduced.phy Alignment comprises 1 partitions and 350 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 350 / 350 Gaps: 7.47 % Invariant sites: 0.86 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P36507/3_mltree/P36507.raxml.rba Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 350 / 28000 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -474630.349289] Initial branch length optimization [00:00:09 -395133.898849] Model parameter optimization (eps = 10.000000) [00:01:03 -394547.844723] AUTODETECT spr round 1 (radius: 5) [00:05:23 -260387.746928] AUTODETECT spr round 2 (radius: 10) [00:09:53 -191901.053526] AUTODETECT spr round 3 (radius: 15) [00:14:35 -155805.488863] AUTODETECT spr round 4 (radius: 20) [00:19:55 -145927.392469] AUTODETECT spr round 5 (radius: 25) [00:26:07 -133677.755301] SPR radius for FAST iterations: 25 (autodetect) [00:26:07 -133677.755301] Model parameter optimization (eps = 3.000000) [00:26:41 -133609.921456] FAST spr round 1 (radius: 25) [00:31:37 -109542.682505] FAST spr round 2 (radius: 25) [00:35:17 -106485.518757] FAST spr round 3 (radius: 25) [00:38:38 -106298.458484] FAST spr round 4 (radius: 25) [00:41:26 -106286.473832] FAST spr round 5 (radius: 25) [00:43:59 -106286.473167] Model parameter optimization (eps = 1.000000) [00:44:13 -106285.621899] SLOW spr round 1 (radius: 5) [00:48:03 -106259.850079] SLOW spr round 2 (radius: 5) [00:51:29 -106258.293274] SLOW spr round 3 (radius: 5) [00:55:02 -106254.636979] SLOW spr round 4 (radius: 5) [00:58:23 -106254.459828] SLOW spr round 5 (radius: 5) [01:01:42 -106254.459809] SLOW spr round 6 (radius: 10) [01:05:09 -106254.459793] SLOW spr round 7 (radius: 15) [01:10:59 -106254.459777] SLOW spr round 8 (radius: 20) [01:18:55 -106254.459761] SLOW spr round 9 (radius: 25) [01:28:57 -106254.234569] SLOW spr round 10 (radius: 5) [01:33:46 -106254.234552] SLOW spr round 11 (radius: 10) [01:37:38] [worker #4] ML tree search #5, logLikelihood: -105898.952381 [01:38:07 -106254.234536] SLOW spr round 12 (radius: 15) [01:43:32 -106254.234520] SLOW spr round 13 (radius: 20) [01:49:51] [worker #1] ML tree search #2, logLikelihood: -105881.872623 [01:50:59 -106254.234503] SLOW spr round 14 (radius: 25) [01:59:22] [worker #2] ML tree search #3, logLikelihood: -105891.091864 [02:00:35 -106254.234487] Model parameter optimization (eps = 0.100000) [02:00:48] [worker #0] ML tree search #1, logLikelihood: -106254.024986 [02:00:48 -475323.272203] Initial branch length optimization [02:00:57 -397205.666403] Model parameter optimization (eps = 10.000000) [02:01:57 -396455.583028] AUTODETECT spr round 1 (radius: 5) [02:06:15 -250809.809019] AUTODETECT spr round 2 (radius: 10) [02:10:44 -177606.336077] AUTODETECT spr round 3 (radius: 15) [02:15:31 -155549.842450] AUTODETECT spr round 4 (radius: 20) [02:20:57] [worker #3] ML tree search #4, logLikelihood: -105867.650605 [02:20:59 -148081.004806] AUTODETECT spr round 5 (radius: 25) [02:27:55 -131882.135613] SPR radius for FAST iterations: 25 (autodetect) [02:27:55 -131882.135613] Model parameter optimization (eps = 3.000000) [02:28:22 -131838.703796] FAST spr round 1 (radius: 25) [02:33:13 -106870.012123] FAST spr round 2 (radius: 25) [02:36:38 -106001.685306] FAST spr round 3 (radius: 25) [02:39:35 -105921.149858] FAST spr round 4 (radius: 25) [02:42:14 -105917.691093] FAST spr round 5 (radius: 25) [02:44:40 -105917.690719] Model parameter optimization (eps = 1.000000) [02:45:00 -105912.390667] SLOW spr round 1 (radius: 5) [02:48:29 -105884.867585] SLOW spr round 2 (radius: 5) [02:51:51 -105884.784564] SLOW spr round 3 (radius: 10) [02:55:16 -105884.784496] SLOW spr round 4 (radius: 15) [03:01:29 -105883.566682] SLOW spr round 5 (radius: 5) [03:06:05 -105883.566210] SLOW spr round 6 (radius: 10) [03:10:06 -105883.566200] SLOW spr round 7 (radius: 15) [03:15:13] [worker #4] ML tree search #10, logLikelihood: -105889.054669 [03:15:37 -105883.335552] SLOW spr round 8 (radius: 5) [03:20:13 -105883.335543] SLOW spr round 9 (radius: 10) [03:21:13] [worker #1] ML tree search #7, logLikelihood: -105894.538015 [03:24:20 -105883.335533] SLOW spr round 10 (radius: 15) [03:30:03 -105883.335524] SLOW spr round 11 (radius: 20) [03:38:59 -105883.335514] SLOW spr round 12 (radius: 25) [03:48:51] [worker #2] ML tree search #8, logLikelihood: -105898.196039 [03:50:04 -105883.335505] Model parameter optimization (eps = 0.100000) [03:50:21] [worker #0] ML tree search #6, logLikelihood: -105882.343390 [03:50:21 -475274.631565] Initial branch length optimization [03:50:29 -396477.507113] Model parameter optimization (eps = 10.000000) [03:51:41 -395836.907056] AUTODETECT spr round 1 (radius: 5) [03:55:57 -260745.494177] AUTODETECT spr round 2 (radius: 10) [04:00:32 -187649.358530] AUTODETECT spr round 3 (radius: 15) [04:05:29 -149896.460876] AUTODETECT spr round 4 (radius: 20) [04:10:59 -131167.466675] AUTODETECT spr round 5 (radius: 25) [04:16:49 -126413.501430] SPR radius for FAST iterations: 25 (autodetect) [04:16:49 -126413.501430] Model parameter optimization (eps = 3.000000) [04:17:22 -126385.149752] FAST spr round 1 (radius: 25) [04:22:00 -106757.601825] FAST spr round 2 (radius: 25) [04:25:21 -105984.720265] FAST spr round 3 (radius: 25) [04:28:24 -105908.495014] FAST spr round 4 (radius: 25) [04:31:00 -105907.468821] FAST spr round 5 (radius: 25) [04:33:27 -105907.468786] Model parameter optimization (eps = 1.000000) [04:33:46 -105905.506935] SLOW spr round 1 (radius: 5) [04:37:21 -105883.915562] SLOW spr round 2 (radius: 5) [04:40:51 -105880.722254] SLOW spr round 3 (radius: 5) [04:41:47] [worker #3] ML tree search #9, logLikelihood: -105876.556145 [04:44:15 -105880.721960] SLOW spr round 4 (radius: 10) [04:47:36 -105880.721941] SLOW spr round 5 (radius: 15) [04:53:27 -105880.179577] SLOW spr round 6 (radius: 5) [04:58:07 -105880.179528] SLOW spr round 7 (radius: 10) [05:02:13 -105880.179512] SLOW spr round 8 (radius: 15) [05:07:40 -105880.179497] SLOW spr round 9 (radius: 20) [05:15:53 -105880.179476] SLOW spr round 10 (radius: 25) [05:17:47] [worker #1] ML tree search #12, logLikelihood: -105885.729938 [05:20:08] [worker #2] ML tree search #13, logLikelihood: -105889.441207 [05:26:22 -105880.179462] Model parameter optimization (eps = 0.100000) [05:26:31] [worker #0] ML tree search #11, logLikelihood: -105880.146905 [05:26:31 -479294.040733] Initial branch length optimization [05:26:41 -398927.841846] Model parameter optimization (eps = 10.000000) [05:27:40 -398223.534524] AUTODETECT spr round 1 (radius: 5) [05:31:44 -255445.212911] AUTODETECT spr round 2 (radius: 10) [05:35:57 -193116.384882] AUTODETECT spr round 3 (radius: 15) [05:37:25] [worker #4] ML tree search #15, logLikelihood: -105882.210248 [05:40:42 -154251.595650] AUTODETECT spr round 4 (radius: 20) [05:46:12 -129136.796968] AUTODETECT spr round 5 (radius: 25) [05:52:43 -124646.604478] SPR radius for FAST iterations: 25 (autodetect) [05:52:43 -124646.604478] Model parameter optimization (eps = 3.000000) [05:53:20 -124592.150173] FAST spr round 1 (radius: 25) [05:57:44 -106986.784686] FAST spr round 2 (radius: 25) [06:01:01 -106029.034089] FAST spr round 3 (radius: 25) [06:03:55 -105956.323739] FAST spr round 4 (radius: 25) [06:06:35 -105942.984013] FAST spr round 5 (radius: 25) [06:09:03 -105936.092615] FAST spr round 6 (radius: 25) [06:11:26 -105936.092220] Model parameter optimization (eps = 1.000000) [06:11:43 -105933.095126] SLOW spr round 1 (radius: 5) [06:12:00] [worker #3] ML tree search #14, logLikelihood: -105876.371831 [06:15:08 -105903.395854] SLOW spr round 2 (radius: 5) [06:18:29 -105899.798291] SLOW spr round 3 (radius: 5) [06:21:42 -105899.798191] SLOW spr round 4 (radius: 10) [06:25:07 -105896.649853] SLOW spr round 5 (radius: 5) [06:29:29 -105893.981300] SLOW spr round 6 (radius: 5) [06:33:14 -105893.822116] SLOW spr round 7 (radius: 5) [06:36:44 -105893.819939] SLOW spr round 8 (radius: 10) [06:40:11 -105890.605470] SLOW spr round 9 (radius: 5) [06:44:37 -105890.137130] SLOW spr round 10 (radius: 5) [06:48:24 -105890.135686] SLOW spr round 11 (radius: 10) [06:51:52 -105890.135645] SLOW spr round 12 (radius: 15) [06:57:28 -105890.135603] SLOW spr round 13 (radius: 20) [07:05:29 -105889.605999] SLOW spr round 14 (radius: 5) [07:07:45] [worker #2] ML tree search #18, logLikelihood: -105908.598764 [07:09:08] [worker #4] ML tree search #20, logLikelihood: -105899.551016 [07:10:12 -105889.605954] SLOW spr round 15 (radius: 10) [07:14:21 -105889.358845] SLOW spr round 16 (radius: 5) [07:18:24 -105889.324006] SLOW spr round 17 (radius: 10) [07:20:08] [worker #1] ML tree search #17, logLikelihood: -105886.709581 [07:22:05 -105889.323921] SLOW spr round 18 (radius: 15) [07:27:17 -105889.323878] SLOW spr round 19 (radius: 20) [07:35:22 -105889.323835] SLOW spr round 20 (radius: 25) [07:45:59 -105889.323792] Model parameter optimization (eps = 0.100000) [07:46:19] [worker #0] ML tree search #16, logLikelihood: -105888.896902 [07:47:26] [worker #3] ML tree search #19, logLikelihood: -105878.629557 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.174014,0.147375) (0.250486,0.263767) (0.253408,0.802784) (0.322093,2.188355) 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: -105867.650605 AIC score: 215745.301209 / AICc score: 8259805.301209 / BIC score: 223480.457184 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=350). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P36507/3_mltree/P36507.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P36507/3_mltree/P36507.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P36507/3_mltree/P36507.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P36507/3_mltree/P36507.raxml.log Analysis started: 02-Jul-2021 11:10:42 / finished: 02-Jul-2021 18:58:08 Elapsed time: 28046.496 seconds Consumed energy: 2593.619 Wh (= 13 km in an electric car, or 65 km with an e-scooter!)