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 07-Jul-2021 16:57:21 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/2_msa/A6NM62_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/3_mltree/A6NM62 --seed 2 --threads 5 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (5 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/2_msa/A6NM62_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 303 sites

WARNING: Sequences tr_B4QR25_B4QR25_DROSI_7240 and tr_B4HUA8_B4HUA8_DROSE_7238 are exactly identical!
WARNING: Sequences tr_F1NJ43_F1NJ43_CHICK_9031 and tr_G1NR56_G1NR56_MELGA_9103 are exactly identical!
WARNING: Sequences tr_M3XMZ6_M3XMZ6_MUSPF_9669 and tr_A0A2Y9KTF6_A0A2Y9KTF6_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3XSC1_M3XSC1_MUSPF_9669 and tr_A0A2Y9KQX0_A0A2Y9KQX0_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3Z2Z5_M3Z2Z5_MUSPF_9669 and tr_A0A2Y9L9B9_A0A2Y9L9B9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3Z502_M3Z502_MUSPF_9669 and tr_E2QXQ1_E2QXQ1_CANLF_9615 are exactly identical!
WARNING: Sequences tr_G1QTH3_G1QTH3_NOMLE_61853 and tr_G3QK58_G3QK58_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I2ZDA6_A0A2I2ZDA6_GORGO_9595 and tr_A0A2I3RBH3_A0A2I3RBH3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2ZDA6_A0A2I2ZDA6_GORGO_9595 and sp_Q86UN3_R4RL2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2ZSR1_A0A2I2ZSR1_GORGO_9595 and tr_H2NH22_H2NH22_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2ZSR1_A0A2I2ZSR1_GORGO_9595 and tr_H2Q5S1_H2Q5S1_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2ZSR1_A0A2I2ZSR1_GORGO_9595 and sp_Q86SJ2_AMGO2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2ZSR1_A0A2I2ZSR1_GORGO_9595 and tr_A0A2R8ZJY3_A0A2R8ZJY3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3R4K4_G3R4K4_GORGO_9595 and tr_A0A2R9ATN7_A0A2R9ATN7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3S4W5_G3S4W5_GORGO_9595 and tr_H2NK44_H2NK44_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3S4W5_G3S4W5_GORGO_9595 and tr_F7HHZ1_F7HHZ1_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3S4W5_G3S4W5_GORGO_9595 and tr_G7PVK5_G7PVK5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3S4W5_G3S4W5_GORGO_9595 and tr_A0A096N0C7_A0A096N0C7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3S4W5_G3S4W5_GORGO_9595 and tr_A0A0D9SA79_A0A0D9SA79_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3S4W5_G3S4W5_GORGO_9595 and tr_A0A2K6CYS3_A0A2K6CYS3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3S4W5_G3S4W5_GORGO_9595 and tr_A0A2K5XRQ3_A0A2K5XRQ3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3SCU5_G3SCU5_GORGO_9595 and tr_H2R4I2_H2R4I2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3SCU5_G3SCU5_GORGO_9595 and sp_Q8IW52_SLIK4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3SCU5_G3SCU5_GORGO_9595 and tr_A0A2R8ZDQ2_A0A2R8ZDQ2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_C3XWM8_C3XWM8_BRAFL_7739 and tr_C3XWM9_C3XWM9_BRAFL_7739 are exactly identical!
WARNING: Sequences tr_H2NI23_H2NI23_PONAB_9601 and tr_A0A2I3STB8_A0A2I3STB8_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2NI23_H2NI23_PONAB_9601 and tr_G7PI19_G7PI19_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H2NI23_H2NI23_PONAB_9601 and tr_A0A096MVL6_A0A096MVL6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H2NI23_H2NI23_PONAB_9601 and tr_A0A2K5N6I2_A0A2K5N6I2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_H2NI23_H2NI23_PONAB_9601 and tr_A0A2K6E268_A0A2K6E268_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H2NI23_H2NI23_PONAB_9601 and tr_A0A2K5Y3N5_A0A2K5Y3N5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H2NI23_H2NI23_PONAB_9601 and tr_A0A2R9B2G8_A0A2R9B2G8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1TUE2_G1TUE2_RABIT_9986 and tr_I3MXB2_I3MXB2_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_F1PY08_F1PY08_CANLF_9615 and sp_Q5XM32_RXFP2_CANLF_9615 are exactly identical!
WARNING: Sequences tr_H2QAB1_H2QAB1_PANTR_9598 and tr_A0A2R8ZSQ7_A0A2R8ZSQ7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QNL6_H2QNL6_PANTR_9598 and sp_Q6WRI0_IGS10_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QNL6_H2QNL6_PANTR_9598 and tr_A0A2R9AWZ8_A0A2R9AWZ8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7D663_K7D663_PANTR_9598 and sp_Q9BXB1_LGR4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A158NHK6_A0A158NHK6_ATTCE_12957 and tr_A0A195DF71_A0A195DF71_9HYME_471704 are exactly identical!
WARNING: Sequences tr_F6PVH4_F6PVH4_MACMU_9544 and tr_G7NZL8_G7NZL8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6WTX8_F6WTX8_MACMU_9544 and tr_A0A2K6AP53_A0A2K6AP53_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6Y7Q4_F6Y7Q4_MACMU_9544 and tr_A0A2K5N083_A0A2K5N083_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6Y7Q4_F6Y7Q4_MACMU_9544 and tr_A0A2K6BZH9_A0A2K6BZH9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7FJR0_F7FJR0_MACMU_9544 and tr_G7PHN7_G7PHN7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7FJR0_F7FJR0_MACMU_9544 and tr_A0A096NCW5_A0A096NCW5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7FJR0_F7FJR0_MACMU_9544 and tr_A0A2K5L071_A0A2K5L071_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7FJR0_F7FJR0_MACMU_9544 and tr_A0A2K6B1J7_A0A2K6B1J7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7FJR0_F7FJR0_MACMU_9544 and tr_A0A2K5XI35_A0A2K5XI35_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0Z2W0_H0Z2W0_TAEGU_59729 and tr_A0A093Q4I0_A0A093Q4I0_9PASS_328815 are exactly identical!
WARNING: Sequences tr_H0Z2W0_H0Z2W0_TAEGU_59729 and tr_A0A218V3S2_A0A218V3S2_9PASE_299123 are exactly identical!
WARNING: Sequences tr_D2HL61_D2HL61_AILME_9646 and tr_A0A384CZ56_A0A384CZ56_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A0A0MP87_A0A0A0MP87_BOVIN_9913 and sp_F1MLX5_LGR4_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_U3K6U7_U3K6U7_FICAL_59894 and tr_A0A091JQP9_A0A091JQP9_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_R0LS63_R0LS63_ANAPL_8839 and tr_A0A226P5Q8_A0A226P5Q8_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A096MW92_A0A096MW92_PAPAN_9555 and tr_A0A0D9SA21_A0A0D9SA21_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096MW92_A0A096MW92_PAPAN_9555 and tr_A0A2K5NUP1_A0A2K5NUP1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096MW92_A0A096MW92_PAPAN_9555 and tr_A0A2K6B2R1_A0A2K6B2R1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096MW92_A0A096MW92_PAPAN_9555 and tr_A0A2K5XYI5_A0A2K5XYI5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096N8N8_A0A096N8N8_PAPAN_9555 and tr_A0A0D9RNT1_A0A0D9RNT1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3MTY7_A0A2I3MTY7_PAPAN_9555 and tr_A0A2K5KWM3_A0A2K5KWM3_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3MTY7_A0A2I3MTY7_PAPAN_9555 and tr_A0A2K5YJL6_A0A2K5YJL6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A151N7P1_A0A151N7P1_ALLMI_8496 and tr_A0A1U7RS70_A0A1U7RS70_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A0V0RHH3_A0A0V0RHH3_9BILA_6336 and tr_A0A0V1D5Q2_A0A0V1D5Q2_TRIBR_45882 are exactly identical!
WARNING: Sequences tr_A0A0V0RHH3_A0A0V0RHH3_9BILA_6336 and tr_A0A0V1L022_A0A0V1L022_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0RHH3_A0A0V0RHH3_9BILA_6336 and tr_A0A0V0TSJ8_A0A0V0TSJ8_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1S3SV55_A0A1S3SV55_SALSA_8030 and tr_A0A060XWH2_A0A060XWH2_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A2D0REN7_A0A2D0REN7_ICTPU_7998 and tr_A0A2D0REP1_A0A2D0REP1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4A0N3_A0A2U4A0N3_TURTR_9739 and tr_A0A2Y9FE36_A0A2Y9FE36_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U3WIV2_A0A2U3WIV2_ODORO_9708 and tr_A0A2U3X7C0_A0A2U3X7C0_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2U3WKC2_A0A2U3WKC2_ODORO_9708 and tr_A0A2U3XAX6_A0A2U3XAX6_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2Y9NYU1_A0A2Y9NYU1_DELLE_9749 and tr_A0A2Y9EZK7_A0A2Y9EZK7_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 71

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/A6NM62/3_mltree/A6NM62.raxml.reduced.phy

Alignment comprises 1 partitions and 303 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 303 / 303
Gaps: 10.50 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/3_mltree/A6NM62.raxml.rba

Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 303 / 24240
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -616070.829319] Initial branch length optimization
[00:00:08 -506803.809919] Model parameter optimization (eps = 10.000000)
[00:01:08 -504765.818727] AUTODETECT spr round 1 (radius: 5)
[00:05:28 -387204.969105] AUTODETECT spr round 2 (radius: 10)
[00:10:12 -282472.718172] AUTODETECT spr round 3 (radius: 15)
[00:16:00 -221658.426600] AUTODETECT spr round 4 (radius: 20)
[00:21:47 -202578.589459] AUTODETECT spr round 5 (radius: 25)
[00:28:56 -194988.750494] SPR radius for FAST iterations: 25 (autodetect)
[00:28:56 -194988.750494] Model parameter optimization (eps = 3.000000)
[00:29:37 -194492.905369] FAST spr round 1 (radius: 25)
[00:35:41 -175131.464318] FAST spr round 2 (radius: 25)
[00:40:28 -174017.698585] FAST spr round 3 (radius: 25)
[00:44:22 -173853.108770] FAST spr round 4 (radius: 25)
[00:47:54 -173819.171723] FAST spr round 5 (radius: 25)
[00:51:02 -173810.696209] FAST spr round 6 (radius: 25)
[00:53:59 -173810.328860] FAST spr round 7 (radius: 25)
[00:56:49 -173800.100764] FAST spr round 8 (radius: 25)
[00:59:32 -173800.100587] Model parameter optimization (eps = 1.000000)
[00:59:57 -173781.644610] SLOW spr round 1 (radius: 5)
[01:04:03 -173738.916453] SLOW spr round 2 (radius: 5)
[01:07:53 -173732.953304] SLOW spr round 3 (radius: 5)
[01:11:28 -173732.937902] SLOW spr round 4 (radius: 10)
[01:15:23 -173727.629874] SLOW spr round 5 (radius: 5)
[01:19:37 -173715.530203] SLOW spr round 6 (radius: 5)
[01:23:21 -173713.815257] SLOW spr round 7 (radius: 5)
[01:27:01 -173713.811810] SLOW spr round 8 (radius: 10)
[01:30:56 -173708.042549] SLOW spr round 9 (radius: 5)
[01:35:08 -173696.671243] SLOW spr round 10 (radius: 5)
[01:38:54 -173694.653127] SLOW spr round 11 (radius: 5)
[01:42:42 -173692.796954] SLOW spr round 12 (radius: 5)
[01:46:07 -173692.796457] SLOW spr round 13 (radius: 10)
[01:49:47 -173692.796448] SLOW spr round 14 (radius: 15)
[01:57:42 -173692.417936] SLOW spr round 15 (radius: 5)
[02:02:11 -173691.603796] SLOW spr round 16 (radius: 5)
[02:05:57 -173691.603470] SLOW spr round 17 (radius: 10)
[02:09:56 -173691.603465] SLOW spr round 18 (radius: 15)
[02:17:24 -173691.603464] SLOW spr round 19 (radius: 20)
[02:29:45] [worker #2] ML tree search #3, logLikelihood: -173649.888316
[02:30:44 -173691.603464] SLOW spr round 20 (radius: 25)
[02:46:59 -173691.603464] Model parameter optimization (eps = 0.100000)

[02:47:18] [worker #0] ML tree search #1, logLikelihood: -173689.701607

[02:47:18 -613724.056728] Initial branch length optimization
[02:47:25 -507156.092803] Model parameter optimization (eps = 10.000000)
[02:48:28 -505103.131409] AUTODETECT spr round 1 (radius: 5)
[02:52:41 -378269.497634] AUTODETECT spr round 2 (radius: 10)
[02:57:32 -297136.543734] AUTODETECT spr round 3 (radius: 15)
[03:00:19] [worker #1] ML tree search #2, logLikelihood: -173659.109829
[03:03:20 -239762.186288] AUTODETECT spr round 4 (radius: 20)
[03:09:29 -208773.067063] AUTODETECT spr round 5 (radius: 25)
[03:16:57 -197625.752645] SPR radius for FAST iterations: 25 (autodetect)
[03:16:57 -197625.752645] Model parameter optimization (eps = 3.000000)
[03:17:50 -197080.133155] FAST spr round 1 (radius: 25)
[03:23:59 -175020.717266] FAST spr round 2 (radius: 25)
[03:28:27 -173884.481007] FAST spr round 3 (radius: 25)
[03:32:11 -173786.693724] FAST spr round 4 (radius: 25)
[03:35:27 -173769.305781] FAST spr round 5 (radius: 25)
[03:38:20 -173766.651546] FAST spr round 6 (radius: 25)
[03:41:10 -173762.778556] FAST spr round 7 (radius: 25)
[03:43:54 -173762.534412] FAST spr round 8 (radius: 25)
[03:46:33 -173762.532794] Model parameter optimization (eps = 1.000000)
[03:46:54 -173752.327300] SLOW spr round 1 (radius: 5)
[03:50:36 -173694.093749] SLOW spr round 2 (radius: 5)
[03:54:07 -173692.581740] SLOW spr round 3 (radius: 5)
[03:57:37 -173690.463835] SLOW spr round 4 (radius: 5)
[04:01:00 -173690.463391] SLOW spr round 5 (radius: 10)
[04:04:38 -173678.382528] SLOW spr round 6 (radius: 5)
[04:08:44 -173676.138743] SLOW spr round 7 (radius: 5)
[04:12:24 -173676.138417] SLOW spr round 8 (radius: 10)
[04:16:10 -173676.138397] SLOW spr round 9 (radius: 15)
[04:23:34 -173673.187273] SLOW spr round 10 (radius: 5)
[04:27:51 -173671.715643] SLOW spr round 11 (radius: 5)
[04:31:43 -173671.574830] SLOW spr round 12 (radius: 5)
[04:35:27 -173671.574726] SLOW spr round 13 (radius: 10)
[04:39:19 -173670.763109] SLOW spr round 14 (radius: 5)
[04:43:21 -173670.762469] SLOW spr round 15 (radius: 10)
[04:47:40 -173670.762420] SLOW spr round 16 (radius: 15)
[04:55:16 -173670.762411] SLOW spr round 17 (radius: 20)
[05:08:21 -173670.762407] SLOW spr round 18 (radius: 25)
[05:24:06 -173670.762406] Model parameter optimization (eps = 0.100000)

[05:24:21] [worker #0] ML tree search #6, logLikelihood: -173670.529330

[05:24:21 -610749.797290] Initial branch length optimization
[05:24:29 -500989.214010] Model parameter optimization (eps = 10.000000)
[05:25:34 -499019.383020] AUTODETECT spr round 1 (radius: 5)
[05:29:45 -371278.348183] AUTODETECT spr round 2 (radius: 10)
[05:34:16 -279204.557874] AUTODETECT spr round 3 (radius: 15)
[05:39:40 -226201.432666] AUTODETECT spr round 4 (radius: 20)
[05:43:11] [worker #2] ML tree search #8, logLikelihood: -173658.359501
[05:45:06 -201079.492193] AUTODETECT spr round 5 (radius: 25)
[05:51:12 -196889.481898] SPR radius for FAST iterations: 25 (autodetect)
[05:51:12 -196889.481898] Model parameter optimization (eps = 3.000000)
[05:51:48 -196401.402871] FAST spr round 1 (radius: 25)
[05:56:04] [worker #4] ML tree search #5, logLikelihood: -173699.061150
[05:57:41 -174992.538988] FAST spr round 2 (radius: 25)
[06:02:02 -173929.497510] FAST spr round 3 (radius: 25)
[06:05:54 -173770.162549] FAST spr round 4 (radius: 25)
[06:09:10 -173733.854681] FAST spr round 5 (radius: 25)
[06:12:07 -173723.094691] FAST spr round 6 (radius: 25)
[06:14:53 -173719.413413] FAST spr round 7 (radius: 25)
[06:17:35 -173719.412881] Model parameter optimization (eps = 1.000000)
[06:18:05 -173708.983503] SLOW spr round 1 (radius: 5)
[06:21:48 -173675.595036] SLOW spr round 2 (radius: 5)
[06:25:28 -173668.166572] SLOW spr round 3 (radius: 5)
[06:25:41] [worker #1] ML tree search #7, logLikelihood: -173662.332696
[06:29:06 -173661.064745] SLOW spr round 4 (radius: 5)
[06:32:41 -173657.060530] SLOW spr round 5 (radius: 5)
[06:36:20 -173656.665488] SLOW spr round 6 (radius: 5)
[06:39:44 -173656.665120] SLOW spr round 7 (radius: 10)
[06:43:26 -173652.831442] SLOW spr round 8 (radius: 5)
[06:47:42 -173648.467102] SLOW spr round 9 (radius: 5)
[06:51:27 -173648.465986] SLOW spr round 10 (radius: 10)
[06:55:21 -173648.465857] SLOW spr round 11 (radius: 15)
[06:57:31] [worker #3] ML tree search #4, logLikelihood: -173691.638914
[07:02:35 -173646.547405] SLOW spr round 12 (radius: 5)
[07:06:58 -173643.525629] SLOW spr round 13 (radius: 5)
[07:10:50 -173642.941164] SLOW spr round 14 (radius: 5)
[07:14:25 -173641.581989] SLOW spr round 15 (radius: 5)
[07:17:56 -173641.392932] SLOW spr round 16 (radius: 5)
[07:21:23 -173641.392755] SLOW spr round 17 (radius: 10)
[07:25:00 -173641.392738] SLOW spr round 18 (radius: 15)
[07:32:28 -173641.392735] SLOW spr round 19 (radius: 20)
[07:44:19 -173641.392734] SLOW spr round 20 (radius: 25)
[07:59:09 -173641.392734] Model parameter optimization (eps = 0.100000)

[07:59:24] [worker #0] ML tree search #11, logLikelihood: -173640.780315

[07:59:24 -615077.364790] Initial branch length optimization
[07:59:36 -503959.283580] Model parameter optimization (eps = 10.000000)
[08:00:55 -501896.455084] AUTODETECT spr round 1 (radius: 5)
[08:05:05 -385392.126771] AUTODETECT spr round 2 (radius: 10)
[08:09:49 -296319.329713] AUTODETECT spr round 3 (radius: 15)
[08:14:47 -246994.786385] AUTODETECT spr round 4 (radius: 20)
[08:20:51 -208061.026187] AUTODETECT spr round 5 (radius: 25)
[08:26:51 -199762.612204] SPR radius for FAST iterations: 25 (autodetect)
[08:26:51 -199762.612204] Model parameter optimization (eps = 3.000000)
[08:27:29 -199213.491425] FAST spr round 1 (radius: 25)
[08:33:01 -176337.365040] FAST spr round 2 (radius: 25)
[08:37:20 -174085.524611] FAST spr round 3 (radius: 25)
[08:41:09 -173822.685755] FAST spr round 4 (radius: 25)
[08:44:28 -173791.860164] FAST spr round 5 (radius: 25)
[08:47:31 -173776.959726] FAST spr round 6 (radius: 25)
[08:50:28 -173758.689126] FAST spr round 7 (radius: 25)
[08:53:12 -173757.883276] FAST spr round 8 (radius: 25)
[08:55:54 -173757.882816] Model parameter optimization (eps = 1.000000)
[08:56:25 -173739.598167] SLOW spr round 1 (radius: 5)
[09:00:11 -173694.439449] SLOW spr round 2 (radius: 5)
[09:03:53 -173680.893462] SLOW spr round 3 (radius: 5)
[09:07:29 -173675.973194] SLOW spr round 4 (radius: 5)
[09:10:54 -173675.972019] SLOW spr round 5 (radius: 10)
[09:14:32 -173673.168684] SLOW spr round 6 (radius: 5)
[09:18:39 -173671.596537] SLOW spr round 7 (radius: 5)
[09:20:10] [worker #3] ML tree search #9, logLikelihood: -173685.444819
[09:22:03] [worker #4] ML tree search #10, logLikelihood: -173660.204659
[09:22:20 -173671.595510] SLOW spr round 8 (radius: 10)
[09:26:10 -173671.595423] SLOW spr round 9 (radius: 15)
[09:32:56 -173669.249493] SLOW spr round 10 (radius: 5)
[09:37:08 -173669.195079] SLOW spr round 11 (radius: 10)
[09:41:35 -173669.194618] SLOW spr round 12 (radius: 15)
[09:48:12 -173669.194423] SLOW spr round 13 (radius: 20)
[09:59:33 -173669.194253] SLOW spr round 14 (radius: 25)
[10:13:09 -173669.194088] Model parameter optimization (eps = 0.100000)

[10:13:17] [worker #0] ML tree search #16, logLikelihood: -173669.126354

[10:54:26] [worker #1] ML tree search #12, logLikelihood: -173650.198654
[10:59:39] [worker #2] ML tree search #13, logLikelihood: -173680.596471
[11:41:45] [worker #4] ML tree search #15, logLikelihood: -173690.703170
[11:46:53] [worker #3] ML tree search #14, logLikelihood: -173675.778022
[14:04:07] [worker #4] ML tree search #20, logLikelihood: -173673.819407
[15:53:27] [worker #3] ML tree search #19, logLikelihood: -173676.531849
[17:07:56] [worker #1] ML tree search #17, logLikelihood: -173653.213266
[17:28:27] [worker #2] ML tree search #18, logLikelihood: -173705.850838

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.211789,0.420486) (0.161123,0.415565) (0.448836,1.272481) (0.178251,1.530721) 
   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: -173640.780315

AIC score: 351291.560630 / AICc score: 8395351.560630 / BIC score: 358737.594905
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=303).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/3_mltree/A6NM62.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/3_mltree/A6NM62.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/3_mltree/A6NM62.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A6NM62/3_mltree/A6NM62.raxml.log

Analysis started: 07-Jul-2021 16:57:21 / finished: 08-Jul-2021 10:25:49

Elapsed time: 62907.340 seconds

Consumed energy: 3598.350 Wh (= 18 km in an electric car, or 90 km with an e-scooter!)