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

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

RAxML-NG was called at 16-Jul-2021 04:18:23 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q92994/2_msa/Q92994_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q92994/3_mltree/Q92994 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q92994/2_msa/Q92994_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 411 sites

WARNING: Sequences tr_J3KBD7_J3KBD7_COCIM_246410 and tr_E9CXJ1_E9CXJ1_COCPS_443226 are exactly identical!
WARNING: Sequences tr_B6Q5D7_B6Q5D7_TALMQ_441960 and tr_A0A093VDK4_A0A093VDK4_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_H2NMF7_H2NMF7_PONAB_9601 and sp_Q92994_TF3B_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2NMF7_H2NMF7_PONAB_9601 and tr_A0A2R9ARC9_A0A2R9ARC9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_Q7RY40_Q7RY40_NEUCR_367110 and tr_G4UJW3_G4UJW3_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_J4VZP3_J4VZP3_BEAB2_655819 and tr_A0A0A2VFL8_A0A0A2VFL8_BEABA_1245745 are exactly identical!
WARNING: Sequences tr_J4VZP3_J4VZP3_BEAB2_655819 and tr_A0A2N6N9S1_A0A2N6N9S1_BEABA_176275 are exactly identical!
WARNING: Sequences tr_A0A088AD90_A0A088AD90_APIME_7460 and tr_A0A2A3EDV7_A0A2A3EDV7_APICC_94128 are exactly identical!
WARNING: Sequences tr_Q2UBV2_Q2UBV2_ASPOR_510516 and tr_A0A1S9DQZ3_A0A1S9DQZ3_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A2QDY3_A2QDY3_ASPNC_425011 and tr_G3Y0R0_G3Y0R0_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_G7XBU2_G7XBU2_ASPKW_1033177 and tr_A0A146FDD4_A0A146FDD4_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_I1PU91_I1PU91_ORYGL_4538 and tr_Q0DJB2_Q0DJB2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_G2Y4X2_G2Y4X2_BOTF4_999810 and tr_M7URR9_M7URR9_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SY19_F2SY19_TRIRC_559305 and tr_A0A178F7C7_A0A178F7C7_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_L2FM84_L2FM84_COLFN_1213859 and tr_T0KKQ1_T0KKQ1_COLGC_1237896 are exactly identical!
WARNING: Sequences tr_W2QMZ8_W2QMZ8_PHYPN_761204 and tr_A0A0W8CX27_A0A0W8CX27_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QMZ8_W2QMZ8_PHYPN_761204 and tr_W2NY48_W2NY48_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015K738_A0A015K738_9GLOM_1432141 and tr_A0A2H5R1D1_A0A2H5R1D1_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A096NK53_A0A096NK53_PAPAN_9555 and tr_A0A0D9RAZ4_A0A0D9RAZ4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096NK53_A0A096NK53_PAPAN_9555 and tr_A0A2K5NWM7_A0A2K5NWM7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NK53_A0A096NK53_PAPAN_9555 and tr_A0A2K6D166_A0A2K6D166_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A0F0IF65_A0A0F0IF65_ASPPU_1403190 and tr_A0A2G7FL37_A0A2G7FL37_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A0A1P931_A0A0A1P931_9FUNG_58291 and tr_A0A367JWW6_A0A367JWW6_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A0V1CRF6_A0A0V1CRF6_TRIBR_45882 and tr_A0A0V0X170_A0A0V0X170_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1CRF6_A0A0V1CRF6_TRIBR_45882 and tr_A0A0V0V066_A0A0V0V066_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CRF6_A0A0V1CRF6_TRIBR_45882 and tr_A0A0V1L8A7_A0A0V1L8A7_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V1CRF6_A0A0V1CRF6_TRIBR_45882 and tr_A0A0V1NWY8_A0A0V1NWY8_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CRF6_A0A0V1CRF6_TRIBR_45882 and tr_A0A0V0U1F0_A0A0V0U1F0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A100I9H6_A0A100I9H6_ASPNG_5061 and tr_A0A1L9N8G5_A0A1L9N8G5_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A100I9H6_A0A100I9H6_ASPNG_5061 and tr_A0A317UXR7_A0A317UXR7_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_A0A161VW88_A0A161VW88_9PEZI_708197 and tr_A0A167EF03_A0A167EF03_9PEZI_1573173 are exactly identical!
WARNING: Sequences tr_A0A164WLS6_A0A164WLS6_9HOMO_1314777 and tr_A0A166FRZ3_A0A166FRZ3_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1S3XM05_A0A1S3XM05_TOBAC_4097 and tr_A0A1U7XW49_A0A1U7XW49_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3TC53_A0A1S3TC53_VIGRR_3916 and tr_A0A3Q0ENX1_A0A3Q0ENX1_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A1S3TC53_A0A1S3TC53_VIGRR_3916 and tr_A0A3Q0ESZ6_A0A3Q0ESZ6_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A226MXR3_A0A226MXR3_CALSU_9009 and tr_A0A226P742_A0A226P742_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2N5SLL4_A0A2N5SLL4_9BASI_200324 and tr_A0A2N5V7H8_A0A2N5V7H8_9BASI_200324 are exactly identical!
WARNING: Sequences tr_A0A2S7Q6F8_A0A2S7Q6F8_9HELO_2070414 and tr_A0A2S7R078_A0A2S7R078_9HELO_2070412 are exactly identical!
WARNING: Sequences tr_A0A2V5HZK7_A0A2V5HZK7_9EURO_1450541 and tr_A0A2V5HA13_A0A2V5HA13_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 39

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q92994/3_mltree/Q92994.raxml.reduced.phy

Alignment comprises 1 partitions and 411 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 411 / 411
Gaps: 12.11 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q92994/3_mltree/Q92994.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 2 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 / 206 / 16480
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -689924.344063] Initial branch length optimization
[00:00:07 -595703.141719] Model parameter optimization (eps = 10.000000)
[00:00:55 -592780.293208] AUTODETECT spr round 1 (radius: 5)
[00:04:20 -427253.522830] AUTODETECT spr round 2 (radius: 10)
[00:08:14 -318323.025128] AUTODETECT spr round 3 (radius: 15)
[00:12:14 -271466.539632] AUTODETECT spr round 4 (radius: 20)
[00:16:58 -246822.549293] AUTODETECT spr round 5 (radius: 25)
[00:22:28 -245988.550304] SPR radius for FAST iterations: 25 (autodetect)
[00:22:28 -245988.550304] Model parameter optimization (eps = 3.000000)
[00:23:01 -245888.511624] FAST spr round 1 (radius: 25)
[00:27:45 -219678.130581] FAST spr round 2 (radius: 25)
[00:31:02 -218504.871194] FAST spr round 3 (radius: 25)
[00:33:53 -218392.791089] FAST spr round 4 (radius: 25)
[00:36:25 -218385.609545] FAST spr round 5 (radius: 25)
[00:38:51 -218385.608697] Model parameter optimization (eps = 1.000000)
[00:39:11 -218382.815383] SLOW spr round 1 (radius: 5)
[00:42:32 -218336.259613] SLOW spr round 2 (radius: 5)
[00:45:50 -218333.884213] SLOW spr round 3 (radius: 5)
[00:48:54 -218333.882951] SLOW spr round 4 (radius: 10)
[00:52:05 -218333.702038] SLOW spr round 5 (radius: 5)
[00:55:56 -218333.700390] SLOW spr round 6 (radius: 10)
[01:01:17 -218333.700101] SLOW spr round 7 (radius: 15)
[01:07:06 -218333.050967] SLOW spr round 8 (radius: 5)
[01:11:18 -218333.050522] SLOW spr round 9 (radius: 10)
[01:15:17 -218333.050373] SLOW spr round 10 (radius: 15)
[01:20:59 -218333.050277] SLOW spr round 11 (radius: 20)
[01:30:28 -218333.050200] SLOW spr round 12 (radius: 25)
[01:41:40 -218333.050132] Model parameter optimization (eps = 0.100000)

[01:41:57] [worker #0] ML tree search #1, logLikelihood: -218332.748643

[01:41:57 -685032.192186] Initial branch length optimization
[01:42:04 -590119.851002] Model parameter optimization (eps = 10.000000)
[01:42:50 -587402.376109] AUTODETECT spr round 1 (radius: 5)
[01:46:14 -433100.498511] AUTODETECT spr round 2 (radius: 10)
[01:50:06 -319190.543976] AUTODETECT spr round 3 (radius: 15)
[01:52:29] [worker #2] ML tree search #3, logLikelihood: -218349.197094
[01:54:08 -259803.916944] AUTODETECT spr round 4 (radius: 20)
[01:59:36 -247521.636350] AUTODETECT spr round 5 (radius: 25)
[02:09:57 -246397.364300] SPR radius for FAST iterations: 25 (autodetect)
[02:09:57 -246397.364300] Model parameter optimization (eps = 3.000000)
[02:10:27 -246343.893418] FAST spr round 1 (radius: 25)
[02:18:03 -219397.980729] FAST spr round 2 (radius: 25)
[02:23:49 -218505.802864] FAST spr round 3 (radius: 25)
[02:24:27] [worker #1] ML tree search #2, logLikelihood: -218339.799438
[02:28:49 -218432.081591] FAST spr round 4 (radius: 25)
[02:33:08 -218426.254124] FAST spr round 5 (radius: 25)
[02:37:05 -218426.253691] Model parameter optimization (eps = 1.000000)
[02:37:34 -218422.077297] SLOW spr round 1 (radius: 5)
[02:43:25 -218357.346412] SLOW spr round 2 (radius: 5)
[02:49:08 -218349.458411] SLOW spr round 3 (radius: 5)
[02:54:45 -218343.959254] SLOW spr round 4 (radius: 5)
[03:00:08 -218341.181215] SLOW spr round 5 (radius: 5)
[03:05:40 -218341.180626] SLOW spr round 6 (radius: 10)
[03:11:26 -218340.759903] SLOW spr round 7 (radius: 5)
[03:18:30 -218339.900342] SLOW spr round 8 (radius: 5)
[03:24:20 -218339.899802] SLOW spr round 9 (radius: 10)
[03:28:58 -218339.746456] SLOW spr round 10 (radius: 5)
[03:32:48 -218339.746232] SLOW spr round 11 (radius: 10)
[03:36:24 -218339.746205] SLOW spr round 12 (radius: 15)
[03:41:59 -218339.746183] SLOW spr round 13 (radius: 20)
[03:48:10] [worker #2] ML tree search #6, logLikelihood: -218337.675345
[03:51:02 -218339.746162] SLOW spr round 14 (radius: 25)
[04:08:47 -218339.746142] Model parameter optimization (eps = 0.100000)

[04:09:08] [worker #0] ML tree search #4, logLikelihood: -218338.541100

[04:09:08 -685217.029731] Initial branch length optimization
[04:09:13 -592781.136730] Model parameter optimization (eps = 10.000000)
[04:10:10 -589994.948951] AUTODETECT spr round 1 (radius: 5)
[04:15:58 -432071.846800] AUTODETECT spr round 2 (radius: 10)
[04:22:23 -327460.927318] AUTODETECT spr round 3 (radius: 15)
[04:26:26 -278622.546464] AUTODETECT spr round 4 (radius: 20)
[04:30:58 -256063.175717] AUTODETECT spr round 5 (radius: 25)
[04:36:41 -251871.038759] SPR radius for FAST iterations: 25 (autodetect)
[04:36:41 -251871.038759] Model parameter optimization (eps = 3.000000)
[04:37:05 -251794.057177] FAST spr round 1 (radius: 25)
[04:42:02 -219320.089334] FAST spr round 2 (radius: 25)
[04:45:58 -218471.513929] FAST spr round 3 (radius: 25)
[04:48:33] [worker #1] ML tree search #5, logLikelihood: -218347.590329
[04:49:38 -218418.862958] FAST spr round 4 (radius: 25)
[04:52:32 -218413.112505] FAST spr round 5 (radius: 25)
[04:55:12 -218413.112033] Model parameter optimization (eps = 1.000000)
[04:55:36 -218410.649481] SLOW spr round 1 (radius: 5)
[04:59:43 -218358.602197] SLOW spr round 2 (radius: 5)
[05:03:44 -218356.127005] SLOW spr round 3 (radius: 5)
[05:07:34 -218356.125979] SLOW spr round 4 (radius: 10)
[05:11:21 -218354.300593] SLOW spr round 5 (radius: 5)
[05:15:50 -218350.854447] SLOW spr round 6 (radius: 5)
[05:19:43 -218350.853818] SLOW spr round 7 (radius: 10)
[05:23:36 -218349.287503] SLOW spr round 8 (radius: 5)
[05:27:59 -218346.109370] SLOW spr round 9 (radius: 5)
[05:31:55 -218346.108871] SLOW spr round 10 (radius: 10)
[05:35:42 -218345.954902] SLOW spr round 11 (radius: 5)
[05:40:17 -218345.502708] SLOW spr round 12 (radius: 5)
[05:43:58 -218345.496816] SLOW spr round 13 (radius: 10)
[05:47:44 -218345.496240] SLOW spr round 14 (radius: 15)
[05:54:15 -218345.060715] SLOW spr round 15 (radius: 5)
[05:58:48 -218343.124617] SLOW spr round 16 (radius: 5)
[06:02:41 -218342.770939] SLOW spr round 17 (radius: 5)
[06:06:21 -218342.770722] SLOW spr round 18 (radius: 10)
[06:09:47 -218342.770697] SLOW spr round 19 (radius: 15)
[06:16:13 -218342.770685] SLOW spr round 20 (radius: 20)
[06:26:07 -218342.770674] SLOW spr round 21 (radius: 25)
[06:27:58] [worker #1] ML tree search #8, logLikelihood: -218347.719973
[06:29:12] [worker #2] ML tree search #9, logLikelihood: -218343.911029
[06:38:47 -218342.770664] Model parameter optimization (eps = 0.100000)

[06:39:07] [worker #0] ML tree search #7, logLikelihood: -218342.543214

[06:39:07 -690259.729282] Initial branch length optimization
[06:39:20 -596548.264517] Model parameter optimization (eps = 10.000000)
[06:40:12 -593865.232627] AUTODETECT spr round 1 (radius: 5)
[06:44:22 -436859.541877] AUTODETECT spr round 2 (radius: 10)
[06:49:59 -338802.005572] AUTODETECT spr round 3 (radius: 15)
[06:55:54 -286846.597826] AUTODETECT spr round 4 (radius: 20)
[07:02:17 -263290.939805] AUTODETECT spr round 5 (radius: 25)
[07:08:57 -259295.009790] SPR radius for FAST iterations: 25 (autodetect)
[07:08:57 -259295.009790] Model parameter optimization (eps = 3.000000)
[07:09:26 -259238.657653] FAST spr round 1 (radius: 25)
[07:15:16 -220380.434666] FAST spr round 2 (radius: 25)
[07:18:46 -218490.402051] FAST spr round 3 (radius: 25)
[07:21:42 -218425.614216] FAST spr round 4 (radius: 25)
[07:24:58 -218411.641299] FAST spr round 5 (radius: 25)
[07:27:38 -218411.540673] FAST spr round 6 (radius: 25)
[07:30:33 -218411.539888] Model parameter optimization (eps = 1.000000)
[07:30:59 -218405.007545] SLOW spr round 1 (radius: 5)
[07:35:19 -218349.265164] SLOW spr round 2 (radius: 5)
[07:39:05 -218346.421151] SLOW spr round 3 (radius: 5)
[07:42:30 -218346.418914] SLOW spr round 4 (radius: 10)
[07:46:06 -218344.907438] SLOW spr round 5 (radius: 5)
[07:51:18 -218343.581182] SLOW spr round 6 (radius: 5)
[07:55:37 -218343.580224] SLOW spr round 7 (radius: 10)
[07:59:30 -218343.557708] SLOW spr round 8 (radius: 15)
[08:08:00 -218340.108975] SLOW spr round 9 (radius: 5)
[08:15:44 -218340.100858] SLOW spr round 10 (radius: 10)
[08:20:57 -218332.232144] SLOW spr round 11 (radius: 5)
[08:25:50 -218331.622849] SLOW spr round 12 (radius: 5)
[08:29:50 -218331.622546] SLOW spr round 13 (radius: 10)
[08:31:07] [worker #2] ML tree search #12, logLikelihood: -218345.774004
[08:34:23 -218331.622443] SLOW spr round 14 (radius: 15)
[08:41:43 -218331.622363] SLOW spr round 15 (radius: 20)
[08:53:49 -218331.622288] SLOW spr round 16 (radius: 25)
[08:54:43] [worker #1] ML tree search #11, logLikelihood: -218327.329458
[09:08:03 -218331.622217] Model parameter optimization (eps = 0.100000)

[09:11:39] [worker #0] ML tree search #10, logLikelihood: -218330.736905

[09:11:39 -691168.585768] Initial branch length optimization
[09:11:54 -597904.677420] Model parameter optimization (eps = 10.000000)
[09:13:30 -595226.495148] AUTODETECT spr round 1 (radius: 5)
[09:18:01 -446555.044929] AUTODETECT spr round 2 (radius: 10)
[09:21:59 -340063.085928] AUTODETECT spr round 3 (radius: 15)
[09:26:02 -281244.676055] AUTODETECT spr round 4 (radius: 20)
[09:31:03 -256334.454880] AUTODETECT spr round 5 (radius: 25)
[09:37:22 -253718.853874] SPR radius for FAST iterations: 25 (autodetect)
[09:37:22 -253718.853874] Model parameter optimization (eps = 3.000000)
[09:37:51 -253667.262413] FAST spr round 1 (radius: 25)
[09:43:01 -219386.590133] FAST spr round 2 (radius: 25)
[09:46:39 -218482.549523] FAST spr round 3 (radius: 25)
[09:49:31 -218427.076042] FAST spr round 4 (radius: 25)
[09:52:09 -218420.691324] FAST spr round 5 (radius: 25)
[09:54:35 -218419.973926] FAST spr round 6 (radius: 25)
[09:56:57 -218419.876013] Model parameter optimization (eps = 1.000000)
[09:57:16 -218415.252193] SLOW spr round 1 (radius: 5)
[10:00:38 -218355.388003] SLOW spr round 2 (radius: 5)
[10:03:53 -218355.137133] SLOW spr round 3 (radius: 5)
[10:07:00 -218355.136966] SLOW spr round 4 (radius: 10)
[10:10:18 -218354.737589] SLOW spr round 5 (radius: 5)
[10:14:12 -218354.737497] SLOW spr round 6 (radius: 10)
[10:18:00 -218354.737449] SLOW spr round 7 (radius: 15)
[10:23:49 -218354.737409] SLOW spr round 8 (radius: 20)
[10:25:47] [worker #2] ML tree search #15, logLikelihood: -218346.714414
[10:33:16 -218354.737375] SLOW spr round 9 (radius: 25)
[10:42:06] [worker #1] ML tree search #14, logLikelihood: -218341.351485
[10:44:43 -218354.737345] Model parameter optimization (eps = 0.100000)

[10:44:50] [worker #0] ML tree search #13, logLikelihood: -218354.705974

[10:44:50 -688367.697058] Initial branch length optimization
[10:44:58 -595760.201143] Model parameter optimization (eps = 10.000000)
[10:45:58 -592930.102392] AUTODETECT spr round 1 (radius: 5)
[10:49:30 -440749.877090] AUTODETECT spr round 2 (radius: 10)
[10:53:24 -339609.783865] AUTODETECT spr round 3 (radius: 15)
[10:57:16 -301653.856065] AUTODETECT spr round 4 (radius: 20)
[11:02:14 -260367.096551] AUTODETECT spr round 5 (radius: 25)
[11:07:14 -254958.800355] SPR radius for FAST iterations: 25 (autodetect)
[11:07:14 -254958.800355] Model parameter optimization (eps = 3.000000)
[11:07:41 -254849.925992] FAST spr round 1 (radius: 25)
[11:12:50 -220290.246186] FAST spr round 2 (radius: 25)
[11:16:25 -218669.252494] FAST spr round 3 (radius: 25)
[11:19:33 -218477.921559] FAST spr round 4 (radius: 25)
[11:22:17 -218450.256849] FAST spr round 5 (radius: 25)
[11:24:45 -218435.878789] FAST spr round 6 (radius: 25)
[11:27:08 -218435.778394] FAST spr round 7 (radius: 25)
[11:29:30 -218435.777259] Model parameter optimization (eps = 1.000000)
[11:29:53 -218432.170675] SLOW spr round 1 (radius: 5)
[11:33:23 -218392.608959] SLOW spr round 2 (radius: 5)
[11:36:47 -218372.992694] SLOW spr round 3 (radius: 5)
[11:39:56 -218372.992127] SLOW spr round 4 (radius: 10)
[11:43:28 -218361.139241] SLOW spr round 5 (radius: 5)
[11:47:30 -218355.893681] SLOW spr round 6 (radius: 5)
[11:51:05 -218352.910763] SLOW spr round 7 (radius: 5)
[11:54:22 -218352.910670] SLOW spr round 8 (radius: 10)
[11:57:44 -218352.910662] SLOW spr round 9 (radius: 15)
[12:04:13 -218352.910660] SLOW spr round 10 (radius: 20)
[12:14:18 -218352.910660] SLOW spr round 11 (radius: 25)
[12:20:12] [worker #1] ML tree search #17, logLikelihood: -218354.960513
[12:21:25] [worker #2] ML tree search #18, logLikelihood: -218331.183288
[12:27:09 -218352.910660] Model parameter optimization (eps = 0.100000)

[12:27:20] [worker #0] ML tree search #16, logLikelihood: -218352.856787

[12:27:20 -687476.416455] Initial branch length optimization
[12:27:29 -594565.056024] Model parameter optimization (eps = 10.000000)
[12:28:10 -591902.879159] AUTODETECT spr round 1 (radius: 5)
[12:31:34 -439930.322595] AUTODETECT spr round 2 (radius: 10)
[12:35:21 -323871.060855] AUTODETECT spr round 3 (radius: 15)
[12:39:12 -284307.186972] AUTODETECT spr round 4 (radius: 20)
[12:43:51 -268759.742601] AUTODETECT spr round 5 (radius: 25)
[12:49:01 -258293.969481] SPR radius for FAST iterations: 25 (autodetect)
[12:49:01 -258293.969481] Model parameter optimization (eps = 3.000000)
[12:49:30 -258244.621925] FAST spr round 1 (radius: 25)
[12:54:45 -220560.583268] FAST spr round 2 (radius: 25)
[12:58:33 -218569.777752] FAST spr round 3 (radius: 25)
[13:01:35 -218471.523841] FAST spr round 4 (radius: 25)
[13:04:09 -218463.055457] FAST spr round 5 (radius: 25)
[13:06:32 -218462.744369] FAST spr round 6 (radius: 25)
[13:08:51 -218462.740953] Model parameter optimization (eps = 1.000000)
[13:09:10 -218451.238542] SLOW spr round 1 (radius: 5)
[13:12:42 -218382.886787] SLOW spr round 2 (radius: 5)
[13:16:04 -218374.375334] SLOW spr round 3 (radius: 5)
[13:19:12 -218372.725885] SLOW spr round 4 (radius: 5)
[13:22:17 -218372.725815] SLOW spr round 5 (radius: 10)
[13:25:31 -218372.226590] SLOW spr round 6 (radius: 5)
[13:29:32 -218369.027002] SLOW spr round 7 (radius: 5)
[13:33:05 -218364.220922] SLOW spr round 8 (radius: 5)
[13:36:20 -218363.933700] SLOW spr round 9 (radius: 5)
[13:39:29 -218363.933310] SLOW spr round 10 (radius: 10)
[13:42:48 -218363.536833] SLOW spr round 11 (radius: 5)
[13:46:44 -218363.536712] SLOW spr round 12 (radius: 10)
[13:50:26 -218363.372869] SLOW spr round 13 (radius: 5)
[13:54:14 -218363.361073] SLOW spr round 14 (radius: 10)
[13:57:50 -218363.358506] SLOW spr round 15 (radius: 15)
[14:03:33 -218363.357899] SLOW spr round 16 (radius: 20)
[14:12:39 -218352.650457] SLOW spr round 17 (radius: 5)
[14:16:52 -218352.511522] SLOW spr round 18 (radius: 5)
[14:20:28 -218352.510384] SLOW spr round 19 (radius: 10)
[14:23:56 -218352.510021] SLOW spr round 20 (radius: 15)
[14:29:44 -218352.509878] SLOW spr round 21 (radius: 20)
[14:38:42 -218352.509800] SLOW spr round 22 (radius: 25)
[14:49:35 -218352.509742] Model parameter optimization (eps = 0.100000)

[14:49:49] [worker #0] ML tree search #19, logLikelihood: -218352.250899

[14:50:00] [worker #1] ML tree search #20, logLikelihood: -218344.425402

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.173466,0.324403) (0.198857,0.372902) (0.369426,0.932911) (0.258250,2.032646) 
   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: -218327.329458

AIC score: 440664.658916 / AICc score: 8484724.658916 / BIC score: 448721.938311
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=411).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 1 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q92994/3_mltree/Q92994.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q92994/3_mltree/Q92994.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q92994/3_mltree/Q92994.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q92994/3_mltree/Q92994.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q92994/3_mltree/Q92994.raxml.log

Analysis started: 16-Jul-2021 04:18:23 / finished: 16-Jul-2021 19:08:23

Elapsed time: 53400.305 seconds