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 03-Jul-2021 16:40:49 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/2_msa/Q7L5A8_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/3_mltree/Q7L5A8 --seed 2 --threads 4 --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 (4 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/2_msa/Q7L5A8_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 199 sites

WARNING: Sequences tr_J3KAL8_J3KAL8_COCIM_246410 and tr_A0A0J6YK01_A0A0J6YK01_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QBT3_B6QBT3_TALMQ_441960 and tr_A0A093UUJ7_A0A093UUJ7_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2WJL3_B2WJL3_PYRTR_426418 and tr_A0A2W1HNE1_A0A2W1HNE1_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_G2XAB5_G2XAB5_VERDV_498257 and tr_A0A0G4KXE4_A0A0G4KXE4_9PEZI_100787 are exactly identical!
WARNING: Sequences tr_Q7RW89_Q7RW89_NEUCR_367110 and tr_G4UTT3_G4UTT3_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_B8MZ70_B8MZ70_ASPFN_332952 and tr_Q2UQS9_Q2UQS9_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_A0A179UVJ0_A0A179UVJ0_BLAGS_559298 and tr_C5GME5_C5GME5_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2QBI4_H2QBI4_PANTR_9598 and sp_Q7L5A8_FA2H_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QBI4_H2QBI4_PANTR_9598 and tr_A0A2R8ZJK9_A0A2R8ZJK9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FF95_F9FF95_FUSOF_660025 and tr_A0A0D2XVA2_A0A0D2XVA2_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FF95_F9FF95_FUSOF_660025 and tr_N4UAV0_N4UAV0_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FF95_F9FF95_FUSOF_660025 and tr_X0CT35_X0CT35_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FF95_F9FF95_FUSOF_660025 and tr_A0A2H3T082_A0A2H3T082_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_E9F990_E9F990_METRA_655844 and tr_A0A0B4IFD5_A0A0B4IFD5_METMF_1276143 are exactly identical!
WARNING: Sequences tr_E9F990_E9F990_METRA_655844 and tr_A0A0D9P862_A0A0D9P862_METAN_1291518 are exactly identical!
WARNING: Sequences tr_C6HNJ0_C6HNJ0_AJECH_544712 and tr_F0UFR1_F0UFR1_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_C6HNJ0_C6HNJ0_AJECH_544712 and tr_A6QXZ9_A6QXZ9_AJECN_339724 are exactly identical!
WARNING: Sequences tr_J5JKS8_J5JKS8_BEAB2_655819 and tr_A0A0A2VKT6_A0A0A2VKT6_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_J5JKS8_J5JKS8_BEAB2_655819 and tr_A0A2N6NWB1_A0A2N6NWB1_BEABA_176275 are exactly identical!
WARNING: Sequences sp_Q9SUC5_FAH2_ARATH_3702 and tr_D7MFH5_D7MFH5_ARALL_81972 are exactly identical!
WARNING: Sequences tr_A0A0E0ITA6_A0A0E0ITA6_ORYNI_4536 and tr_A2XMJ0_A2XMJ0_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0ITA6_A0A0E0ITA6_ORYNI_4536 and tr_I1PG27_I1PG27_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0ITA6_A0A0E0ITA6_ORYNI_4536 and tr_A0A0E0P224_A0A0E0P224_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0ITA6_A0A0E0ITA6_ORYNI_4536 and tr_A0A0D3FPS3_A0A0D3FPS3_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0ITA6_A0A0E0ITA6_ORYNI_4536 and tr_A0A0D9ZDX2_A0A0D9ZDX2_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A0E0ITA6_A0A0E0ITA6_ORYNI_4536 and tr_Q9AY73_Q9AY73_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A1D1H7_A1D1H7_NEOFI_331117 and tr_A0A2I1C826_A0A2I1C826_9EURO_1392255 are exactly identical!
WARNING: Sequences tr_A2QB78_A2QB78_ASPNC_425011 and tr_A0A319B0Y8_A0A319B0Y8_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F7HMN1_F7HMN1_MACMU_9544 and tr_A0A096MQC2_A0A096MQC2_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7HMN1_F7HMN1_MACMU_9544 and tr_A0A2K5MM77_A0A2K5MM77_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7HMN1_F7HMN1_MACMU_9544 and tr_A0A2K6CP19_A0A2K6CP19_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7XIR1_G7XIR1_ASPKW_1033177 and tr_A0A124BVE4_A0A124BVE4_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7XIR1_G7XIR1_ASPKW_1033177 and tr_A0A1L9N6E3_A0A1L9N6E3_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_G7XIR1_G7XIR1_ASPKW_1033177 and tr_A0A317WGR1_A0A317WGR1_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_B8BN49_B8BN49_ORYSI_39946 and tr_I1R831_I1R831_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_B8BN49_B8BN49_ORYSI_39946 and tr_Q0ILR7_Q0ILR7_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F4NWW7_F4NWW7_BATDJ_684364 and tr_A0A177WHX4_A0A177WHX4_BATDE_403673 are exactly identical!
WARNING: Sequences tr_F9X4R5_F9X4R5_ZYMTI_336722 and tr_A0A0F4GFB7_A0A0F4GFB7_9PEZI_1047168 are exactly identical!
WARNING: Sequences tr_F9X4R5_F9X4R5_ZYMTI_336722 and tr_A0A1X7RL96_A0A1X7RL96_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2YJ67_G2YJ67_BOTF4_999810 and tr_M7TQ20_M7TQ20_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_D7LFK3_D7LFK3_ARALL_81972 and tr_M4CMX6_M4CMX6_BRARP_51351 are exactly identical!
WARNING: Sequences tr_D7LFK3_D7LFK3_ARALL_81972 and tr_M4DZ62_M4DZ62_BRARP_51351 are exactly identical!
WARNING: Sequences tr_D7LFK3_D7LFK3_ARALL_81972 and tr_A0A078G1H8_A0A078G1H8_BRANA_3708 are exactly identical!
WARNING: Sequences tr_D7LFK3_D7LFK3_ARALL_81972 and tr_A0A078GF95_A0A078GF95_BRANA_3708 are exactly identical!
WARNING: Sequences tr_D7LFK3_D7LFK3_ARALL_81972 and tr_V4MH08_V4MH08_EUTSA_72664 are exactly identical!
WARNING: Sequences tr_D7LFK3_D7LFK3_ARALL_81972 and tr_A0A0D3C3S2_A0A0D3C3S2_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_B3RVT2_B3RVT2_TRIAD_10228 and tr_A0A369SKD5_A0A369SKD5_9METZ_287889 are exactly identical!
WARNING: Sequences tr_L2G8D6_L2G8D6_COLFN_1213859 and tr_T0LLV8_T0LLV8_COLGC_1237896 are exactly identical!
WARNING: Sequences tr_M0XFE4_M0XFE4_HORVV_112509 and tr_A0A3B6KCG3_A0A3B6KCG3_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_M4E298_M4E298_BRARP_51351 and tr_A0A0D3B4K0_A0A0D3B4K0_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_S0E0M0_S0E0M0_GIBF5_1279085 and tr_A0A365MJ03_A0A365MJ03_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_U5HJ78_U5HJ78_USTV1_683840 and tr_A0A2X0MLE8_A0A2X0MLE8_9BASI_796604 are exactly identical!
WARNING: Sequences tr_A0A015N7V5_A0A015N7V5_9GLOM_1432141 and tr_A0A2I1G2L9_A0A2I1G2L9_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A015N7V5_A0A015N7V5_9GLOM_1432141 and tr_A0A2H5TAW8_A0A2H5TAW8_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2K6VRR4_A0A2K6VRR4_ONCVO_6282 and tr_A0A182ED95_A0A182ED95_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A0D3HX02_A0A0D3HX02_9ORYZ_65489 and tr_A0A0E0BVI8_A0A0E0BVI8_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A084QRP1_A0A084QRP1_STAC4_1283841 and tr_A0A084S064_A0A084S064_STACH_1283842 are exactly identical!
WARNING: Sequences tr_A0A078I5V5_A0A078I5V5_BRANA_3708 and tr_A0A0D3C122_A0A0D3C122_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A094EQX7_A0A094EQX7_9PEZI_1420912 and tr_A0A1B8G690_A0A1B8G690_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_V4UD48_V4UD48_9ROSI_85681 and tr_A0A2H5N1W2_A0A2H5N1W2_CITUN_55188 are exactly identical!
WARNING: Sequences tr_V4UIH0_V4UIH0_9ROSI_85681 and tr_A0A2H5N120_A0A2H5N120_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0D2SF83_A0A0D2SF83_GOSRA_29730 and tr_A0A1U8JZ39_A0A1U8JZ39_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0F8UW55_A0A0F8UW55_9EURO_308745 and tr_A0A2T5M2W4_A0A2T5M2W4_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0A1N352_A0A0A1N352_9FUNG_58291 and tr_A0A2G4SXI6_A0A2G4SXI6_9FUNG_1340429 are exactly identical!
WARNING: Sequences tr_A0A0A1NBU9_A0A0A1NBU9_9FUNG_58291 and tr_A0A367JHD2_A0A367JHD2_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0A1PEE7_A0A0A1PEE7_9FUNG_58291 and tr_A0A367KCC7_A0A367KCC7_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0V1CQU7_A0A0V1CQU7_TRIBR_45882 and tr_A0A0V0WPW3_A0A0V0WPW3_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1CQU7_A0A0V1CQU7_TRIBR_45882 and tr_A0A0V0VAB9_A0A0V0VAB9_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CQU7_A0A0V1CQU7_TRIBR_45882 and tr_A0A0V1L3T1_A0A0V1L3T1_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1CQU7_A0A0V1CQU7_TRIBR_45882 and tr_A0A0V1P653_A0A0V1P653_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CQU7_A0A0V1CQU7_TRIBR_45882 and tr_A0A0V0TS13_A0A0V0TS13_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0P1BLJ4_A0A0P1BLJ4_9BASI_401625 and tr_A0A316W4Y8_A0A316W4Y8_9BASI_1522189 are exactly identical!
WARNING: Sequences tr_A0A165BJD0_A0A165BJD0_EXIGL_1314781 and tr_A0A165DCP1_A0A165DCP1_EXIGL_1314781 are exactly identical!
WARNING: Sequences tr_A0A1S3XTK4_A0A1S3XTK4_TOBAC_4097 and tr_A0A1U7W494_A0A1U7W494_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3YYM5_A0A1S3YYM5_TOBAC_4097 and sp_P49098_CYB5_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A1S3YYM5_A0A1S3YYM5_TOBAC_4097 and tr_A0A1J6J6L0_A0A1J6J6L0_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A1S3YYM5_A0A1S3YYM5_TOBAC_4097 and tr_A0A1U7XR80_A0A1U7XR80_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4C0I5_A0A1S4C0I5_TOBAC_4097 and tr_A0A1U7YSX0_A0A1U7YSX0_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4CRV3_A0A1S4CRV3_TOBAC_4097 and tr_A0A1U7W897_A0A1U7W897_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1V8V0H6_A0A1V8V0H6_9PEZI_1974281 and tr_A0A1V8SEU2_A0A1V8SEU2_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A1V8V0H6_A0A1V8V0H6_9PEZI_1974281 and tr_A0A1V8T469_A0A1V8T469_9PEZI_1507870 are exactly identical!
WARNING: Sequences tr_A0A226MG67_A0A226MG67_CALSU_9009 and tr_A0A226P2Y1_A0A226P2Y1_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2H3C1H3_A0A2H3C1H3_9AGAR_1076256 and tr_A0A284QYF1_A0A284QYF1_9AGAR_47428 are exactly identical!
WARNING: Sequences tr_A0A2G4T0K4_A0A2G4T0K4_9FUNG_1340429 and tr_A0A367JP08_A0A367JP08_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A2U1LEI3_A0A2U1LEI3_ARTAN_35608 and tr_A0A2U1P7A3_A0A2U1P7A3_ARTAN_35608 are exactly identical!
WARNING: Sequences tr_A0A2Z6QZZ1_A0A2Z6QZZ1_9GLOM_94130 and tr_A0A2Z6R1S7_A0A2Z6R1S7_9GLOM_94130 are exactly identical!
WARNING: Sequences tr_A0A319C5Z1_A0A319C5Z1_9EURO_1448315 and tr_A0A2V5IE95_A0A2V5IE95_9EURO_1450541 are exactly identical!
WARNING: Duplicate sequences found: 87

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/Q7L5A8/3_mltree/Q7L5A8.raxml.reduced.phy

Alignment comprises 1 partitions and 199 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 199 / 199
Gaps: 6.70 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/3_mltree/Q7L5A8.raxml.rba

Parallelization scheme autoconfig: 4 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 / 199 / 15920
[00:00:00] Data distribution: max. searches per worker: 5

Starting ML tree search with 20 distinct starting trees

[00:00:00 -308830.396686] Initial branch length optimization
[00:00:06 -256142.357640] Model parameter optimization (eps = 10.000000)
[00:01:06 -254931.203787] AUTODETECT spr round 1 (radius: 5)
[00:03:49 -188586.418196] AUTODETECT spr round 2 (radius: 10)
[00:06:39 -145725.451419] AUTODETECT spr round 3 (radius: 15)
[00:09:47 -126865.429228] AUTODETECT spr round 4 (radius: 20)
[00:13:35 -114615.945067] AUTODETECT spr round 5 (radius: 25)
[00:17:57 -106505.830565] SPR radius for FAST iterations: 25 (autodetect)
[00:17:57 -106505.830565] Model parameter optimization (eps = 3.000000)
[00:18:34 -106438.060310] FAST spr round 1 (radius: 25)
[00:21:57 -89826.206040] FAST spr round 2 (radius: 25)
[00:24:27 -88932.051088] FAST spr round 3 (radius: 25)
[00:26:35 -88836.845208] FAST spr round 4 (radius: 25)
[00:28:32 -88814.562457] FAST spr round 5 (radius: 25)
[00:30:18 -88814.562005] Model parameter optimization (eps = 1.000000)
[00:30:33 -88808.111258] SLOW spr round 1 (radius: 5)
[00:33:01 -88780.462454] SLOW spr round 2 (radius: 5)
[00:35:24 -88773.353708] SLOW spr round 3 (radius: 5)
[00:37:43 -88769.270553] SLOW spr round 4 (radius: 5)
[00:39:57 -88766.869771] SLOW spr round 5 (radius: 5)
[00:42:10 -88766.869711] SLOW spr round 6 (radius: 10)
[00:44:32 -88751.540542] SLOW spr round 7 (radius: 5)
[00:47:29 -88749.586240] SLOW spr round 8 (radius: 5)
[00:50:02 -88749.586187] SLOW spr round 9 (radius: 10)
[00:52:21 -88749.272700] SLOW spr round 10 (radius: 5)
[00:55:19 -88745.237348] SLOW spr round 11 (radius: 5)
[00:57:53 -88744.638188] SLOW spr round 12 (radius: 5)
[01:00:15 -88744.637365] SLOW spr round 13 (radius: 10)
[01:02:32 -88744.637301] SLOW spr round 14 (radius: 15)
[01:06:27 -88744.637275] SLOW spr round 15 (radius: 20)
[01:12:00 -88744.637261] SLOW spr round 16 (radius: 25)
[01:19:18 -88744.637253] Model parameter optimization (eps = 0.100000)

[01:19:30] [worker #0] ML tree search #1, logLikelihood: -88744.385829

[01:19:30 -307390.355708] Initial branch length optimization
[01:19:33 -254924.384373] Model parameter optimization (eps = 10.000000)
[01:20:27 -253674.728708] AUTODETECT spr round 1 (radius: 5)
[01:23:09 -189750.994469] AUTODETECT spr round 2 (radius: 10)
[01:25:05] [worker #3] ML tree search #4, logLikelihood: -88754.855932
[01:26:04 -143824.837467] AUTODETECT spr round 3 (radius: 15)
[01:29:14 -120583.014758] AUTODETECT spr round 4 (radius: 20)
[01:32:53 -110497.456184] AUTODETECT spr round 5 (radius: 25)
[01:37:01 -105403.465955] SPR radius for FAST iterations: 25 (autodetect)
[01:37:01 -105403.465955] Model parameter optimization (eps = 3.000000)
[01:37:07 -105400.917227] FAST spr round 1 (radius: 25)
[01:40:20 -89985.203653] FAST spr round 2 (radius: 25)
[01:42:48 -89032.600836] FAST spr round 3 (radius: 25)
[01:44:59 -88887.757767] FAST spr round 4 (radius: 25)
[01:46:53 -88878.352358] FAST spr round 5 (radius: 25)
[01:48:42 -88874.092858] FAST spr round 6 (radius: 25)
[01:50:17] [worker #1] ML tree search #2, logLikelihood: -88775.787374
[01:50:27 -88874.089865] Model parameter optimization (eps = 1.000000)
[01:50:48 -88822.091921] SLOW spr round 1 (radius: 5)
[01:53:17 -88768.422905] SLOW spr round 2 (radius: 5)
[01:55:40 -88758.348023] SLOW spr round 3 (radius: 5)
[01:57:58 -88758.028183] SLOW spr round 4 (radius: 5)
[02:00:14 -88758.027090] SLOW spr round 5 (radius: 10)
[02:02:37 -88751.247388] SLOW spr round 6 (radius: 5)
[02:05:33 -88748.693206] SLOW spr round 7 (radius: 5)
[02:06:06] [worker #2] ML tree search #3, logLikelihood: -88720.189136
[02:08:07 -88748.693158] SLOW spr round 8 (radius: 10)
[02:10:32 -88747.638190] SLOW spr round 9 (radius: 5)
[02:13:28 -88746.968734] SLOW spr round 10 (radius: 5)
[02:16:02 -88746.967631] SLOW spr round 11 (radius: 10)
[02:18:27 -88746.967500] SLOW spr round 12 (radius: 15)
[02:22:21 -88744.937719] SLOW spr round 13 (radius: 5)
[02:25:23 -88744.937692] SLOW spr round 14 (radius: 10)
[02:28:05 -88744.937688] SLOW spr round 15 (radius: 15)
[02:31:47 -88744.937687] SLOW spr round 16 (radius: 20)
[02:37:10 -88743.733098] SLOW spr round 17 (radius: 5)
[02:40:14 -88743.589910] SLOW spr round 18 (radius: 5)
[02:42:53 -88743.589840] SLOW spr round 19 (radius: 10)
[02:45:18 -88743.589834] SLOW spr round 20 (radius: 15)
[02:49:03 -88743.589833] SLOW spr round 21 (radius: 20)
[02:54:06 -88743.589833] SLOW spr round 22 (radius: 25)
[02:56:52] [worker #3] ML tree search #8, logLikelihood: -88879.821623
[03:00:31 -88741.836344] SLOW spr round 23 (radius: 5)
[03:03:36 -88741.835906] SLOW spr round 24 (radius: 10)
[03:06:22 -88741.835868] SLOW spr round 25 (radius: 15)
[03:09:57 -88741.835862] SLOW spr round 26 (radius: 20)
[03:15:05 -88741.835861] SLOW spr round 27 (radius: 25)
[03:20:15] [worker #2] ML tree search #7, logLikelihood: -88866.697122
[03:21:28 -88741.835861] Model parameter optimization (eps = 0.100000)

[03:21:37] [worker #0] ML tree search #5, logLikelihood: -88741.725339

[03:21:37 -308523.628176] Initial branch length optimization
[03:21:43 -256757.100182] Model parameter optimization (eps = 10.000000)
[03:22:48 -255513.539776] AUTODETECT spr round 1 (radius: 5)
[03:25:32 -186826.988989] AUTODETECT spr round 2 (radius: 10)
[03:28:27 -146814.099961] AUTODETECT spr round 3 (radius: 15)
[03:31:33 -127425.723372] AUTODETECT spr round 4 (radius: 20)
[03:34:47] [worker #1] ML tree search #6, logLikelihood: -88738.673842
[03:35:08 -118230.396086] AUTODETECT spr round 5 (radius: 25)
[03:39:13 -110348.145582] SPR radius for FAST iterations: 25 (autodetect)
[03:39:14 -110348.145582] Model parameter optimization (eps = 3.000000)
[03:39:40 -110254.329460] FAST spr round 1 (radius: 25)
[03:43:03 -91493.764871] FAST spr round 2 (radius: 25)
[03:45:36 -89029.599707] FAST spr round 3 (radius: 25)
[03:47:51 -88826.383318] FAST spr round 4 (radius: 25)
[03:49:49 -88796.517993] FAST spr round 5 (radius: 25)
[03:51:38 -88791.461494] FAST spr round 6 (radius: 25)
[03:53:24 -88791.459314] Model parameter optimization (eps = 1.000000)
[03:53:33 -88789.246928] SLOW spr round 1 (radius: 5)
[03:56:02 -88765.523104] SLOW spr round 2 (radius: 5)
[03:58:21 -88762.172066] SLOW spr round 3 (radius: 5)
[04:00:38 -88761.343539] SLOW spr round 4 (radius: 5)
[04:02:54 -88761.343474] SLOW spr round 5 (radius: 10)
[04:05:15 -88747.197500] SLOW spr round 6 (radius: 5)
[04:08:13 -88744.416975] SLOW spr round 7 (radius: 5)
[04:10:47 -88744.402429] SLOW spr round 8 (radius: 10)
[04:13:10 -88743.731323] SLOW spr round 9 (radius: 5)
[04:16:05 -88743.730288] SLOW spr round 10 (radius: 10)
[04:17:43] [worker #3] ML tree search #12, logLikelihood: -88757.863683
[04:18:37 -88743.730287] SLOW spr round 11 (radius: 15)
[04:22:30 -88742.275747] SLOW spr round 12 (radius: 5)
[04:25:35 -88742.275704] SLOW spr round 13 (radius: 10)
[04:28:17 -88742.275703] SLOW spr round 14 (radius: 15)
[04:32:06 -88742.275703] SLOW spr round 15 (radius: 20)
[04:38:28 -88742.275703] SLOW spr round 16 (radius: 25)
[04:45:55 -88741.741243] SLOW spr round 17 (radius: 5)
[04:49:05 -88741.412884] SLOW spr round 18 (radius: 5)
[04:51:47 -88741.412416] SLOW spr round 19 (radius: 10)
[04:54:13 -88741.412375] SLOW spr round 20 (radius: 15)
[04:58:11 -88741.381668] SLOW spr round 21 (radius: 20)
[05:04:18 -88741.350017] SLOW spr round 22 (radius: 25)
[05:10:04] [worker #1] ML tree search #10, logLikelihood: -88754.322126
[05:11:43 -88741.348540] Model parameter optimization (eps = 0.100000)

[05:11:45] [worker #0] ML tree search #9, logLikelihood: -88741.348417

[05:11:45 -307211.582499] Initial branch length optimization
[05:11:49 -254188.710298] Model parameter optimization (eps = 10.000000)
[05:12:34 -253145.866337] AUTODETECT spr round 1 (radius: 5)
[05:15:19 -186215.595249] AUTODETECT spr round 2 (radius: 10)
[05:15:23] [worker #2] ML tree search #11, logLikelihood: -88729.882961
[05:18:08 -144083.778364] AUTODETECT spr round 3 (radius: 15)
[05:21:21 -120242.569973] AUTODETECT spr round 4 (radius: 20)
[05:25:17 -105766.972740] AUTODETECT spr round 5 (radius: 25)
[05:29:29 -103820.360848] SPR radius for FAST iterations: 25 (autodetect)
[05:29:29 -103820.360848] Model parameter optimization (eps = 3.000000)
[05:29:38 -103816.799335] FAST spr round 1 (radius: 25)
[05:33:04 -89474.259991] FAST spr round 2 (radius: 25)
[05:35:34 -88973.801755] FAST spr round 3 (radius: 25)
[05:37:43 -88890.634273] FAST spr round 4 (radius: 25)
[05:39:39 -88879.409353] FAST spr round 5 (radius: 25)
[05:41:28 -88869.995191] FAST spr round 6 (radius: 25)
[05:43:15 -88869.146524] FAST spr round 7 (radius: 25)
[05:44:04] [worker #3] ML tree search #16, logLikelihood: -88738.900626
[05:44:59 -88869.146306] Model parameter optimization (eps = 1.000000)
[05:45:19 -88792.533223] SLOW spr round 1 (radius: 5)
[05:47:44 -88762.027460] SLOW spr round 2 (radius: 5)
[05:49:57 -88755.989089] SLOW spr round 3 (radius: 5)
[05:52:08 -88755.987625] SLOW spr round 4 (radius: 10)
[05:54:26 -88746.495655] SLOW spr round 5 (radius: 5)
[05:57:23 -88745.131651] SLOW spr round 6 (radius: 5)
[05:59:56 -88745.130881] SLOW spr round 7 (radius: 10)
[06:02:19 -88743.807254] SLOW spr round 8 (radius: 5)
[06:05:12 -88743.807244] SLOW spr round 9 (radius: 10)
[06:07:35 -88743.807244] SLOW spr round 10 (radius: 15)
[06:11:10 -88743.807244] SLOW spr round 11 (radius: 20)
[06:16:27 -88743.807244] SLOW spr round 12 (radius: 25)
[06:23:28 -88743.807244] Model parameter optimization (eps = 0.100000)

[06:23:33] [worker #0] ML tree search #13, logLikelihood: -88743.790086

[06:23:33 -306503.578324] Initial branch length optimization
[06:23:38 -254343.606100] Model parameter optimization (eps = 10.000000)
[06:24:48] [worker #1] ML tree search #14, logLikelihood: -88740.273038
[06:24:49 -253237.689735] AUTODETECT spr round 1 (radius: 5)
[06:27:37 -186176.672454] AUTODETECT spr round 2 (radius: 10)
[06:30:29 -145519.451737] AUTODETECT spr round 3 (radius: 15)
[06:33:32 -122093.800343] AUTODETECT spr round 4 (radius: 20)
[06:37:29 -106767.111615] AUTODETECT spr round 5 (radius: 25)
[06:42:31 -103648.940099] SPR radius for FAST iterations: 25 (autodetect)
[06:42:31 -103648.940099] Model parameter optimization (eps = 3.000000)
[06:42:36 -103646.537660] FAST spr round 1 (radius: 25)
[06:45:57 -89815.949651] FAST spr round 2 (radius: 25)
[06:48:25 -88974.801521] FAST spr round 3 (radius: 25)
[06:50:33 -88904.860948] FAST spr round 4 (radius: 25)
[06:52:30 -88891.767642] FAST spr round 5 (radius: 25)
[06:54:21 -88886.828611] FAST spr round 6 (radius: 25)
[06:56:07 -88886.828526] Model parameter optimization (eps = 1.000000)
[06:56:13 -88886.604810] SLOW spr round 1 (radius: 5)
[06:58:37 -88847.557277] SLOW spr round 2 (radius: 5)
[07:00:59 -88840.986126] SLOW spr round 3 (radius: 5)
[07:03:22 -88836.593119] SLOW spr round 4 (radius: 5)
[07:05:42 -88834.059963] SLOW spr round 5 (radius: 5)
[07:07:56 -88834.059781] SLOW spr round 6 (radius: 10)
[07:10:19 -88829.306578] SLOW spr round 7 (radius: 5)
[07:11:43] [worker #2] ML tree search #15, logLikelihood: -88756.920051
[07:13:15 -88827.282797] SLOW spr round 8 (radius: 5)
[07:15:50 -88823.417652] SLOW spr round 9 (radius: 5)
[07:18:13 -88823.417594] SLOW spr round 10 (radius: 10)
[07:20:34 -88823.417591] SLOW spr round 11 (radius: 15)
[07:24:50 -88821.383818] SLOW spr round 12 (radius: 5)
[07:27:53 -88821.383809] SLOW spr round 13 (radius: 10)
[07:30:34 -88821.383807] SLOW spr round 14 (radius: 15)
[07:34:33 -88821.383806] SLOW spr round 15 (radius: 20)
[07:37:59] [worker #3] ML tree search #20, logLikelihood: -88746.423019
[07:40:55 -88818.524070] SLOW spr round 16 (radius: 5)
[07:44:07 -88817.904566] SLOW spr round 17 (radius: 5)
[07:46:47 -88817.903490] SLOW spr round 18 (radius: 10)
[07:49:12 -88817.903445] SLOW spr round 19 (radius: 15)
[07:53:20 -88817.495842] SLOW spr round 20 (radius: 5)
[07:56:24 -88815.400955] SLOW spr round 21 (radius: 5)
[07:59:01 -88815.399703] SLOW spr round 22 (radius: 10)
[08:01:24 -88815.399068] SLOW spr round 23 (radius: 15)
[08:05:26 -88815.302291] SLOW spr round 24 (radius: 20)
[08:11:26 -88815.302012] SLOW spr round 25 (radius: 25)
[08:16:20] [worker #1] ML tree search #18, logLikelihood: -88757.592158
[08:19:26 -88814.507030] SLOW spr round 26 (radius: 5)
[08:22:31 -88814.500221] SLOW spr round 27 (radius: 10)
[08:25:17 -88814.500103] SLOW spr round 28 (radius: 15)
[08:29:06 -88814.500091] SLOW spr round 29 (radius: 20)
[08:34:53 -88814.500084] SLOW spr round 30 (radius: 25)
[08:42:23 -88814.500080] Model parameter optimization (eps = 0.100000)

[08:42:30] [worker #0] ML tree search #17, logLikelihood: -88814.224799

[08:44:57] [worker #2] ML tree search #19, logLikelihood: -88723.735632

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.180938,0.489858) (0.446954,0.700135) (0.301762,1.483180) (0.070347,2.144673) 
   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: -88720.189136

AIC score: 181450.378273 / AICc score: 8225510.378273 / BIC score: 188053.454446
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=199).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 100 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/3_mltree/Q7L5A8.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/3_mltree/Q7L5A8.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/3_mltree/Q7L5A8.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/3_mltree/Q7L5A8.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q7L5A8/3_mltree/Q7L5A8.raxml.log

Analysis started: 03-Jul-2021 16:40:49 / finished: 04-Jul-2021 01:25:47

Elapsed time: 31498.055 seconds

Consumed energy: 2757.236 Wh (= 14 km in an electric car, or 69 km with an e-scooter!)