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 30-Jun-2021 17:50:16 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53597/2_msa/P53597_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53597/3_mltree/P53597 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53597/2_msa/P53597_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 280 sites

WARNING: Sequences tr_B4QPY9_B4QPY9_DROSI_7240 and sp_Q94522_SUCA_DROME_7227 are exactly identical!
WARNING: Sequences tr_B4QPY9_B4QPY9_DROSI_7240 and tr_B4HTU6_B4HTU6_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B4QPY9_B4QPY9_DROSI_7240 and tr_A0A1W4W4Q4_A0A1W4W4Q4_DROFC_30025 are exactly identical!
WARNING: Sequences tr_J3K7A7_J3K7A7_COCIM_246410 and tr_A0A0J6Y8M8_A0A0J6Y8M8_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QGB0_B6QGB0_TALMQ_441960 and tr_A0A093VCH9_A0A093VCH9_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_G3QI12_G3QI12_GORGO_9595 and sp_P53597_SUCA_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QI12_G3QI12_GORGO_9595 and tr_A0A2R9AGW1_A0A2R9AGW1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G2X413_G2X413_VERDV_498257 and tr_A0A0G4KR69_A0A0G4KR69_9PEZI_100787 are exactly identical!
WARNING: Sequences sp_Q9P727_SUCA_NEUCR_367110 and tr_G4UF81_G4UF81_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_B5DPQ3_B5DPQ3_DROPS_46245 and tr_B4GS06_B4GS06_DROPE_7234 are exactly identical!
WARNING: Sequences tr_B8NSJ8_B8NSJ8_ASPFN_332952 and tr_Q2UTP9_Q2UTP9_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8NSJ8_B8NSJ8_ASPFN_332952 and tr_A0A1S9D585_A0A1S9D585_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179UKR4_A0A179UKR4_BLAGS_559298 and tr_C5GAY0_C5GAY0_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F9F5M8_F9F5M8_FUSOF_660025 and tr_W7MIE3_W7MIE3_GIBM7_334819 are exactly identical!
WARNING: Sequences tr_F9F5M8_F9F5M8_FUSOF_660025 and tr_A0A0D2XK89_A0A0D2XK89_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9F5M8_F9F5M8_FUSOF_660025 and tr_S0EEE5_S0EEE5_GIBF5_1279085 are exactly identical!
WARNING: Sequences tr_F9F5M8_F9F5M8_FUSOF_660025 and tr_N4U1K5_N4U1K5_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9F5M8_F9F5M8_FUSOF_660025 and tr_X0BZX3_X0BZX3_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9F5M8_F9F5M8_FUSOF_660025 and tr_A0A2H3SX97_A0A2H3SX97_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_F9F5M8_F9F5M8_FUSOF_660025 and tr_A0A2H3HT13_A0A2H3HT13_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_F9F5M8_F9F5M8_FUSOF_660025 and tr_A0A2K0WSS4_A0A2K0WSS4_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_F9F5M8_F9F5M8_FUSOF_660025 and tr_A0A365MYX5_A0A365MYX5_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_E9EXI4_E9EXI4_METRA_655844 and tr_A0A0B4IGT1_A0A0B4IGT1_METMF_1276143 are exactly identical!
WARNING: Sequences tr_E9EXI4_E9EXI4_METRA_655844 and tr_A0A0D9PHV0_A0A0D9PHV0_METAN_1291518 are exactly identical!
WARNING: Sequences tr_C6HPX7_C6HPX7_AJECH_544712 and tr_F0USI1_F0USI1_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_J4UJK7_J4UJK7_BEAB2_655819 and tr_A0A0A2VJE4_A0A0A2VJE4_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_J4UJK7_J4UJK7_BEAB2_655819 and tr_A0A2N6NGD7_A0A2N6NGD7_BEABA_176275 are exactly identical!
WARNING: Sequences tr_K4ASY9_K4ASY9_SOLLC_4081 and sp_Q8GTQ9_SUCA1_SOLLC_4081 are exactly identical!
WARNING: Sequences tr_A0A0E0I2S5_A0A0E0I2S5_ORYNI_4536 and tr_I1QEK6_I1QEK6_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0I2S5_A0A0E0I2S5_ORYNI_4536 and tr_A0A0E0EDI9_A0A0E0EDI9_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0I2S5_A0A0E0I2S5_ORYNI_4536 and tr_A0A0E0QA99_A0A0E0QA99_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0I2S5_A0A0E0I2S5_ORYNI_4536 and tr_A0A0E0ALT3_A0A0E0ALT3_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0I2S5_A0A0E0I2S5_ORYNI_4536 and sp_Q6ZL94_SUCA_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A1CZF5_A1CZF5_NEOFI_331117 and tr_A0A0S7E1N6_A0A0S7E1N6_9EURO_293939 are exactly identical!
WARNING: Sequences tr_A2R9J7_A2R9J7_ASPNC_425011 and tr_G3Y4N4_G3Y4N4_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2R9J7_A2R9J7_ASPNC_425011 and tr_A0A319A4W7_A0A319A4W7_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_A0A1D5QHY3_A0A1D5QHY3_MACMU_9544 and tr_G7PML4_G7PML4_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QHY3_A0A1D5QHY3_MACMU_9544 and tr_A0A096NS38_A0A096NS38_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QHY3_A0A1D5QHY3_MACMU_9544 and tr_A0A2K6BMU4_A0A2K6BMU4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QHY3_A0A1D5QHY3_MACMU_9544 and tr_A0A2K5YA61_A0A2K5YA61_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7XSI8_G7XSI8_ASPKW_1033177 and tr_A0A100IQW4_A0A100IQW4_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7XSI8_G7XSI8_ASPKW_1033177 and tr_A0A146G0B0_A0A146G0B0_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XSI8_G7XSI8_ASPKW_1033177 and tr_A0A1L9N527_A0A1L9N527_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_G7XSI8_G7XSI8_ASPKW_1033177 and tr_A0A317VN01_A0A317VN01_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_F4NVM6_F4NVM6_BATDJ_684364 and tr_A0A177WA53_A0A177WA53_BATDE_403673 are exactly identical!
WARNING: Sequences tr_H0ZKW8_H0ZKW8_TAEGU_59729 and tr_A0A218V913_A0A218V913_9PASE_299123 are exactly identical!
WARNING: Sequences tr_F9XHM3_F9XHM3_ZYMTI_336722 and tr_A0A0F4GTX4_A0A0F4GTX4_9PEZI_1047168 are exactly identical!
WARNING: Sequences tr_F9XHM3_F9XHM3_ZYMTI_336722 and tr_A0A1X7S101_A0A1X7S101_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YRP9_G2YRP9_BOTF4_999810 and tr_M7U328_M7U328_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SPQ7_F2SPQ7_TRIRC_559305 and tr_A0A178F2I8_A0A178F2I8_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_G1L5D4_G1L5D4_AILME_9646 and tr_A0A2U3X0S7_A0A2U3X0S7_ODORO_9708 are exactly identical!
WARNING: Sequences tr_B3SB73_B3SB73_TRIAD_10228 and tr_A0A369SG67_A0A369SG67_9METZ_287889 are exactly identical!
WARNING: Sequences tr_L0PGA8_L0PGA8_PNEJ8_1209962 and tr_A0A0W4ZTH9_A0A0W4ZTH9_PNEJ7_1408657 are exactly identical!
WARNING: Sequences tr_L8G8T6_L8G8T6_PSED2_658429 and tr_A0A094GUB4_A0A094GUB4_9PEZI_1420912 are exactly identical!
WARNING: Sequences tr_L8G8T6_L8G8T6_PSED2_658429 and tr_A0A1B8GI81_A0A1B8GI81_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_M4EIQ0_M4EIQ0_BRARP_51351 and tr_A0A078HSE9_A0A078HSE9_BRANA_3708 are exactly identical!
WARNING: Sequences tr_M7Z323_M7Z323_TRIUA_4572 and tr_A0A3B6AVX5_A0A3B6AVX5_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_V2XW41_V2XW41_MONRO_1381753 and tr_A0A0W0FGS0_A0A0W0FGS0_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2Q9P5_W2Q9P5_PHYPN_761204 and tr_A0A0W8DV71_A0A0W8DV71_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2Q9P5_W2Q9P5_PHYPN_761204 and tr_W2J410_W2J410_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A3B6C3D5_A0A3B6C3D5_WHEAT_4565 and tr_W5C4B7_W5C4B7_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A015J8I2_A0A015J8I2_9GLOM_1432141 and tr_A0A2I1GQ97_A0A2I1GQ97_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A015J8I2_A0A015J8I2_9GLOM_1432141 and tr_U9T1A7_U9T1A7_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A0E0LML8_A0A0E0LML8_ORYPU_4537 and tr_A0A2T7EXT7_A0A2T7EXT7_9POAL_1504633 are exactly identical!
WARNING: Sequences tr_A0A078J9U4_A0A078J9U4_BRANA_3708 and tr_A0A0D3DDD1_A0A0D3DDD1_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0F9XPD3_A0A0F9XPD3_TRIHA_5544 and tr_A0A2T4A2I5_A0A2T4A2I5_TRIHA_983964 are exactly identical!
WARNING: Sequences tr_A0A0F8VKI6_A0A0F8VKI6_9EURO_308745 and tr_A0A2T5M839_A0A2T5M839_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0N0DEU3_A0A0N0DEU3_FUSLA_179993 and tr_A0A1B8B5X5_A0A1B8B5X5_FUSPO_36050 are exactly identical!
WARNING: Sequences tr_A0A0N0DEU3_A0A0N0DEU3_FUSLA_179993 and tr_A0A2L2T527_A0A2L2T527_9HYPO_56646 are exactly identical!
WARNING: Sequences tr_A0A0A1N7S3_A0A0A1N7S3_9FUNG_58291 and tr_A0A2G4T882_A0A2G4T882_9FUNG_1340429 are exactly identical!
WARNING: Sequences tr_W6Y2X8_W6Y2X8_COCCA_930089 and tr_W6YRV1_W6YRV1_COCMI_930090 are exactly identical!
WARNING: Sequences tr_A0A2I0MN30_A0A2I0MN30_COLLI_8932 and tr_A0A1V4JET6_A0A1V4JET6_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V1CCI3_A0A0V1CCI3_TRIBR_45882 and tr_A0A0V0W6B4_A0A0V0W6B4_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1CCI3_A0A0V1CCI3_TRIBR_45882 and tr_A0A0V0V779_A0A0V0V779_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CCI3_A0A0V1CCI3_TRIBR_45882 and tr_A0A0V1LBM8_A0A0V1LBM8_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1CCI3_A0A0V1CCI3_TRIBR_45882 and tr_A0A0V0ZA46_A0A0V0ZA46_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V1CCI3_A0A0V1CCI3_TRIBR_45882 and tr_A0A0V0TBU4_A0A0V0TBU4_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1M9J4_A0A0V1M9J4_9BILA_268474 and tr_A0A0V1HFJ7_A0A0V1HFJ7_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A101MK52_A0A101MK52_9EURO_48697 and tr_A0A1V6NM47_A0A1V6NM47_9EURO_60169 are exactly identical!
WARNING: Sequences tr_A0A162ND76_A0A162ND76_9PEZI_1573173 and tr_A0A1G4BRL3_A0A1G4BRL3_9PEZI_1209926 are exactly identical!
WARNING: Sequences tr_A0A196S6H2_A0A196S6H2_BLAHN_478820 and sp_B3FHT4_SUCA_BLAHN_478820 are exactly identical!
WARNING: Sequences tr_A0A194VI64_A0A194VI64_9PEZI_105487 and tr_A0A194V032_A0A194V032_9PEZI_694573 are exactly identical!
WARNING: Sequences tr_A0A1S3Z6N8_A0A1S3Z6N8_TOBAC_4097 and tr_A0A1J6IR70_A0A1J6IR70_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A1S3ZXY7_A0A1S3ZXY7_TOBAC_4097 and tr_A0A1U7WNS7_A0A1U7WNS7_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4DJ12_A0A1S4DJ12_TOBAC_4097 and tr_A0A1U7WW47_A0A1U7WW47_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3RFI8_A0A1S3RFI8_SALSA_8030 and tr_C0KIP8_C0KIP8_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1B8C426_A0A1B8C426_9PEZI_1622147 and tr_A0A1B8F4I3_A0A1B8F4I3_9PEZI_1622149 are exactly identical!
WARNING: Sequences tr_A0A1F5LVM3_A0A1F5LVM3_9EURO_1835702 and tr_A0A1V6PRG1_A0A1V6PRG1_9EURO_416450 are exactly identical!
WARNING: Sequences tr_A0A1L9WKU7_A0A1L9WKU7_ASPAC_690307 and tr_A0A318Z1Z9_A0A318Z1Z9_9EURO_1450539 are exactly identical!
WARNING: Sequences tr_A0A1V8TWU6_A0A1V8TWU6_9PEZI_1974281 and tr_A0A1V8SWR7_A0A1V8SWR7_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A1V8TWU6_A0A1V8TWU6_9PEZI_1974281 and tr_A0A1V8SZZ0_A0A1V8SZZ0_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A1Y2APD5_A0A1Y2APD5_9FUNG_1754190 and tr_A0A1Y2FMQ2_A0A1Y2FMQ2_9FUNG_1754190 are exactly identical!
WARNING: Sequences tr_A0A226MVF2_A0A226MVF2_CALSU_9009 and tr_A0A226PH54_A0A226PH54_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2V5J2F4_A0A2V5J2F4_9EURO_1450541 and tr_A0A2V5HL43_A0A2V5HL43_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 94

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/P53597/3_mltree/P53597.raxml.reduced.phy

Alignment comprises 1 partitions and 278 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 280 / 278
Gaps: 0.90 %
Invariant sites: 2.86 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53597/3_mltree/P53597.raxml.rba

Parallelization scheme autoconfig: 6 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 / 278 / 22240
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -244931.612299] Initial branch length optimization
[00:00:07 -213210.362000] Model parameter optimization (eps = 10.000000)
[00:00:51 -212938.307406] AUTODETECT spr round 1 (radius: 5)
[00:04:15 -144842.798712] AUTODETECT spr round 2 (radius: 10)
[00:08:15 -107895.941226] AUTODETECT spr round 3 (radius: 15)
[00:12:05 -94301.402507] AUTODETECT spr round 4 (radius: 20)
[00:16:39 -86374.928335] AUTODETECT spr round 5 (radius: 25)
[00:21:44 -81071.129784] SPR radius for FAST iterations: 25 (autodetect)
[00:21:44 -81071.129784] Model parameter optimization (eps = 3.000000)
[00:22:06 -80917.988468] FAST spr round 1 (radius: 25)
[00:26:11 -70129.175897] FAST spr round 2 (radius: 25)
[00:29:05 -69471.311279] FAST spr round 3 (radius: 25)
[00:31:27 -69381.484800] FAST spr round 4 (radius: 25)
[00:33:38 -69369.996761] FAST spr round 5 (radius: 25)
[00:35:36 -69369.994655] Model parameter optimization (eps = 1.000000)
[00:35:45 -69369.521620] SLOW spr round 1 (radius: 5)
[00:38:49 -69352.954811] SLOW spr round 2 (radius: 5)
[00:41:39 -69351.140027] SLOW spr round 3 (radius: 5)
[00:44:21 -69351.139970] SLOW spr round 4 (radius: 10)
[00:47:07 -69346.451853] SLOW spr round 5 (radius: 5)
[00:50:56 -69341.554357] SLOW spr round 6 (radius: 5)
[00:54:06 -69341.281410] SLOW spr round 7 (radius: 5)
[00:56:58 -69341.281343] SLOW spr round 8 (radius: 10)
[00:59:41 -69340.761118] SLOW spr round 9 (radius: 5)
[01:03:16 -69340.761108] SLOW spr round 10 (radius: 10)
[01:06:20 -69339.716874] SLOW spr round 11 (radius: 5)
[01:09:53 -69339.655160] SLOW spr round 12 (radius: 10)
[01:12:52 -69339.655074] SLOW spr round 13 (radius: 15)
[01:17:28 -69339.655069] SLOW spr round 14 (radius: 20)
[01:24:38 -69339.655066] SLOW spr round 15 (radius: 25)
[01:29:24] [worker #5] ML tree search #6, logLikelihood: -69334.746229
[01:33:30 -69339.655062] Model parameter optimization (eps = 0.100000)

[01:33:37] [worker #0] ML tree search #1, logLikelihood: -69339.573438

[01:33:37 -244036.349833] Initial branch length optimization
[01:33:42 -211852.905242] Model parameter optimization (eps = 10.000000)
[01:34:31 -211587.733988] AUTODETECT spr round 1 (radius: 5)
[01:37:51 -147384.076288] AUTODETECT spr round 2 (radius: 10)
[01:41:48 -115128.750528] AUTODETECT spr round 3 (radius: 15)
[01:42:51] [worker #4] ML tree search #5, logLikelihood: -69329.157564
[01:46:07 -96184.187532] AUTODETECT spr round 4 (radius: 20)
[01:46:25] [worker #3] ML tree search #4, logLikelihood: -69302.349554
[01:47:30] [worker #2] ML tree search #3, logLikelihood: -69656.264725
[01:50:32 -85198.027486] AUTODETECT spr round 5 (radius: 25)
[01:55:38 -81228.297598] SPR radius for FAST iterations: 25 (autodetect)
[01:55:38 -81228.297598] Model parameter optimization (eps = 3.000000)
[01:56:06 -81076.350536] FAST spr round 1 (radius: 25)
[02:00:09 -70049.303910] FAST spr round 2 (radius: 25)
[02:03:00 -69473.896906] FAST spr round 3 (radius: 25)
[02:05:29 -69384.335838] FAST spr round 4 (radius: 25)
[02:07:43 -69369.693994] FAST spr round 5 (radius: 25)
[02:09:45 -69367.385852] FAST spr round 6 (radius: 25)
[02:11:43 -69367.385812] Model parameter optimization (eps = 1.000000)
[02:11:53 -69366.604662] SLOW spr round 1 (radius: 5)
[02:14:58 -69350.442179] SLOW spr round 2 (radius: 5)
[02:17:55 -69343.782949] SLOW spr round 3 (radius: 5)
[02:20:41 -69343.487648] SLOW spr round 4 (radius: 5)
[02:23:23 -69343.487258] SLOW spr round 5 (radius: 10)
[02:26:07 -69341.976384] SLOW spr round 6 (radius: 5)
[02:29:55 -69333.824404] SLOW spr round 7 (radius: 5)
[02:33:07 -69330.933344] SLOW spr round 8 (radius: 5)
[02:36:02 -69330.903976] SLOW spr round 9 (radius: 10)
[02:38:47 -69327.099308] SLOW spr round 10 (radius: 5)
[02:42:28 -69326.713172] SLOW spr round 11 (radius: 5)
[02:45:39 -69326.713096] SLOW spr round 12 (radius: 10)
[02:45:47] [worker #1] ML tree search #2, logLikelihood: -69363.784996
[02:48:27 -69326.713094] SLOW spr round 13 (radius: 15)
[02:53:10 -69314.027616] SLOW spr round 14 (radius: 5)
[02:56:58 -69312.805521] SLOW spr round 15 (radius: 5)
[03:00:14 -69312.805213] SLOW spr round 16 (radius: 10)
[03:03:04 -69312.805212] SLOW spr round 17 (radius: 15)
[03:07:43 -69312.805212] SLOW spr round 18 (radius: 20)
[03:14:22 -69312.805212] SLOW spr round 19 (radius: 25)
[03:23:04 -69312.805212] Model parameter optimization (eps = 0.100000)

[03:23:11] [worker #0] ML tree search #7, logLikelihood: -69312.795941

[03:23:11 -244057.881181] Initial branch length optimization
[03:23:18 -212246.970466] Model parameter optimization (eps = 10.000000)
[03:24:09 -212004.819929] AUTODETECT spr round 1 (radius: 5)
[03:27:11] [worker #4] ML tree search #11, logLikelihood: -69348.068738
[03:27:33 -145593.284131] AUTODETECT spr round 2 (radius: 10)
[03:31:27 -111840.014719] AUTODETECT spr round 3 (radius: 15)
[03:32:43] [worker #5] ML tree search #12, logLikelihood: -69330.658814
[03:35:33 -95462.064836] AUTODETECT spr round 4 (radius: 20)
[03:40:40 -84316.098302] AUTODETECT spr round 5 (radius: 25)
[03:45:46 -83500.771791] SPR radius for FAST iterations: 25 (autodetect)
[03:45:46 -83500.771791] Model parameter optimization (eps = 3.000000)
[03:46:12 -83339.129555] FAST spr round 1 (radius: 25)
[03:50:26 -70293.135550] FAST spr round 2 (radius: 25)
[03:52:54] [worker #3] ML tree search #10, logLikelihood: -69327.897737
[03:53:13 -69489.738159] FAST spr round 3 (radius: 25)
[03:55:42 -69418.974851] FAST spr round 4 (radius: 25)
[03:57:52 -69408.295948] FAST spr round 5 (radius: 25)
[03:59:52 -69408.295813] Model parameter optimization (eps = 1.000000)
[04:00:03 -69407.698086] SLOW spr round 1 (radius: 5)
[04:03:08 -69370.789218] SLOW spr round 2 (radius: 5)
[04:06:05 -69364.994613] SLOW spr round 3 (radius: 5)
[04:08:49 -69364.994462] SLOW spr round 4 (radius: 10)
[04:11:38 -69364.487742] SLOW spr round 5 (radius: 5)
[04:15:20 -69364.487285] SLOW spr round 6 (radius: 10)
[04:18:34 -69364.076700] SLOW spr round 7 (radius: 5)
[04:22:11 -69364.025541] SLOW spr round 8 (radius: 10)
[04:25:20 -69363.691054] SLOW spr round 9 (radius: 5)
[04:28:59 -69357.157358] SLOW spr round 10 (radius: 5)
[04:31:16] [worker #2] ML tree search #9, logLikelihood: -69288.834187
[04:32:07 -69357.157344] SLOW spr round 11 (radius: 10)
[04:35:01 -69356.854139] SLOW spr round 12 (radius: 5)
[04:38:42 -69356.524170] SLOW spr round 13 (radius: 5)
[04:41:52 -69356.524130] SLOW spr round 14 (radius: 10)
[04:44:46 -69356.115151] SLOW spr round 15 (radius: 5)
[04:48:30 -69352.190564] SLOW spr round 16 (radius: 5)
[04:51:39 -69352.190557] SLOW spr round 17 (radius: 10)
[04:53:25] [worker #4] ML tree search #17, logLikelihood: -69331.531671
[04:54:37 -69346.644056] SLOW spr round 18 (radius: 5)
[04:55:02] [worker #5] ML tree search #18, logLikelihood: -69305.805515
[04:58:14 -69346.642767] SLOW spr round 19 (radius: 10)
[05:00:04] [worker #3] ML tree search #16, logLikelihood: -69341.806648
[05:01:24 -69346.642738] SLOW spr round 20 (radius: 15)
[05:06:03 -69346.642736] SLOW spr round 21 (radius: 20)
[05:13:30] [worker #1] ML tree search #8, logLikelihood: -69303.749036
[05:13:43 -69346.441398] SLOW spr round 22 (radius: 5)
[05:17:33 -69346.441317] SLOW spr round 23 (radius: 10)
[05:20:57 -69346.441315] SLOW spr round 24 (radius: 15)
[05:25:28 -69346.441314] SLOW spr round 25 (radius: 20)
[05:33:16 -69346.441312] SLOW spr round 26 (radius: 25)
[05:42:40 -69346.441311] Model parameter optimization (eps = 0.100000)

[05:42:58] [worker #0] ML tree search #13, logLikelihood: -69345.233816

[05:42:58 -244981.207854] Initial branch length optimization
[05:43:04 -213454.953561] Model parameter optimization (eps = 10.000000)
[05:43:58 -213157.815145] AUTODETECT spr round 1 (radius: 5)
[05:47:17 -146214.168385] AUTODETECT spr round 2 (radius: 10)
[05:51:10 -109089.868807] AUTODETECT spr round 3 (radius: 15)
[05:55:10 -92823.562722] AUTODETECT spr round 4 (radius: 20)
[05:58:35] [worker #2] ML tree search #15, logLikelihood: -69314.661907
[05:59:41 -81838.633234] AUTODETECT spr round 5 (radius: 25)
[06:04:32 -81094.027401] SPR radius for FAST iterations: 25 (autodetect)
[06:04:32 -81094.027401] Model parameter optimization (eps = 3.000000)
[06:04:57 -80934.174467] FAST spr round 1 (radius: 25)
[06:08:55 -71057.417285] FAST spr round 2 (radius: 25)
[06:11:48 -70093.977092] FAST spr round 3 (radius: 25)
[06:14:22 -69364.903039] FAST spr round 4 (radius: 25)
[06:16:35 -69326.793385] FAST spr round 5 (radius: 25)
[06:18:32 -69322.437623] FAST spr round 6 (radius: 25)
[06:20:26 -69322.437555] Model parameter optimization (eps = 1.000000)
[06:20:38 -69319.347003] SLOW spr round 1 (radius: 5)
[06:23:35 -69309.738925] SLOW spr round 2 (radius: 5)
[06:26:25 -69304.098434] SLOW spr round 3 (radius: 5)
[06:29:11 -69302.636543] SLOW spr round 4 (radius: 5)
[06:31:49 -69301.938774] SLOW spr round 5 (radius: 5)
[06:34:32 -69298.854905] SLOW spr round 6 (radius: 5)
[06:35:55] [worker #1] ML tree search #14, logLikelihood: -69363.592233
[06:37:07 -69298.854619] SLOW spr round 7 (radius: 10)
[06:39:45 -69298.780906] SLOW spr round 8 (radius: 15)
[06:44:52 -69298.780894] SLOW spr round 9 (radius: 20)
[06:51:24 -69298.780889] SLOW spr round 10 (radius: 25)
[06:59:39 -69298.780883] Model parameter optimization (eps = 0.100000)

[06:59:44] [worker #0] ML tree search #19, logLikelihood: -69298.773302

[07:54:25] [worker #1] ML tree search #20, logLikelihood: -69322.016451

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.347931,0.378474) (0.346188,0.525754) (0.198364,1.662525) (0.107517,3.315952) 
   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: -69288.834187

AIC score: 142587.668374 / AICc score: 8186647.668374 / BIC score: 149875.421529
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=280).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 140 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53597/3_mltree/P53597.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53597/3_mltree/P53597.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53597/3_mltree/P53597.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53597/3_mltree/P53597.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P53597/3_mltree/P53597.raxml.log

Analysis started: 30-Jun-2021 17:50:16 / finished: 01-Jul-2021 01:44:42

Elapsed time: 28466.056 seconds

Consumed energy: 2379.924 Wh (= 12 km in an electric car, or 59 km with an e-scooter!)