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 05-Jul-2021 06:52:13 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92817/2_msa/Q92817_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92817/3_mltree/Q92817 --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/Q92817/2_msa/Q92817_trimmed_msa.fasta
[00:00:00] Loaded alignment with 473 taxa and 228 sites

WARNING: Sequences tr_M3XNC1_M3XNC1_MUSPF_9669 and tr_M3WCK3_M3WCK3_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3XNC1_M3XNC1_MUSPF_9669 and tr_A0A2U3WBB7_A0A2U3WBB7_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3XNC1_M3XNC1_MUSPF_9669 and tr_A0A2Y9KIP9_A0A2Y9KIP9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3XNC1_M3XNC1_MUSPF_9669 and tr_A0A384C9Y0_A0A384C9Y0_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G1RLS6_G1RLS6_NOMLE_61853 and tr_A0A2I2ZCV6_A0A2I2ZCV6_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1RLS6_G1RLS6_NOMLE_61853 and sp_P15924_DESP_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1RLS6_G1RLS6_NOMLE_61853 and tr_A0A2R9AM84_A0A2R9AM84_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3HD94_G3HD94_CRIGR_10029 and tr_F1LMV6_F1LMV6_RAT_10116 are exactly identical!
WARNING: Sequences tr_G3SAE6_G3SAE6_GORGO_9595 and tr_H2QWV3_H2QWV3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3SAE6_G3SAE6_GORGO_9595 and sp_Q15149_PLEC_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3SAE6_G3SAE6_GORGO_9595 and tr_A0A2R9CDC9_A0A2R9CDC9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3SGR6_G3SGR6_GORGO_9595 and tr_H2QDX2_H2QDX2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A1D5R996_A0A1D5R996_MACMU_9544 and tr_G8F406_G8F406_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5R996_A0A1D5R996_MACMU_9544 and tr_A0A096NKT3_A0A096NKT3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5R996_A0A1D5R996_MACMU_9544 and tr_A0A0D9R4Y1_A0A0D9R4Y1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5R996_A0A1D5R996_MACMU_9544 and tr_A0A2K5MBL2_A0A2K5MBL2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5R996_A0A1D5R996_MACMU_9544 and tr_A0A2K6DEV1_A0A2K6DEV1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5R996_A0A1D5R996_MACMU_9544 and tr_A0A2K6A525_A0A2K6A525_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6X5W2_F6X5W2_MACMU_9544 and tr_A0A0D9R924_A0A0D9R924_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6X5W2_F6X5W2_MACMU_9544 and tr_A0A2K5KN25_A0A2K5KN25_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6X5W2_F6X5W2_MACMU_9544 and tr_A0A2K6ATL0_A0A2K6ATL0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6X5W2_F6X5W2_MACMU_9544 and tr_A0A2K5YS76_A0A2K5YS76_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0YVV0_H0YVV0_TAEGU_59729 and tr_U3KFM5_U3KFM5_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0YVV0_H0YVV0_TAEGU_59729 and tr_A0A0A0AGK4_A0A0A0AGK4_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_H0YVV0_H0YVV0_TAEGU_59729 and tr_A0A218UXJ7_A0A218UXJ7_9PASE_299123 are exactly identical!
WARNING: Sequences tr_H2ZEL5_H2ZEL5_CIOSA_51511 and tr_H2ZEN5_H2ZEN5_CIOSA_51511 are exactly identical!
WARNING: Sequences tr_A0A1B8XZD2_A0A1B8XZD2_XENTR_8364 and tr_F7ESM6_F7ESM6_XENTR_8364 are exactly identical!
WARNING: Sequences tr_A0A0D9QY43_A0A0D9QY43_CHLSB_60711 and tr_A0A2K6C4F7_A0A2K6C4F7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A151ND53_A0A151ND53_ALLMI_8496 and tr_A0A1U7RQU3_A0A1U7RQU3_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091VPR2_A0A091VPR2_NIPNI_128390 and tr_A0A0A0A5R8_A0A0A0A5R8_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A087R1U7_A0A087R1U7_APTFO_9233 and tr_A0A091V5M8_A0A091V5M8_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A1S3S3S7_A0A1S3S3S7_SALSA_8030 and tr_A0A1S3S431_A0A1S3S431_SALSA_8030 are exactly identical!
WARNING: Sequences tr_A0A226N0N3_A0A226N0N3_CALSU_9009 and tr_A0A226PNZ7_A0A226PNZ7_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226N7Z8_A0A226N7Z8_CALSU_9009 and tr_A0A226PYP2_A0A226PYP2_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PT23_A0A2D0PT23_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PT29_A0A2D0PT29_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PUI9_A0A2D0PUI9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PUJ2_A0A2D0PUJ2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PUJ7_A0A2D0PUJ7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PUK2_A0A2D0PUK2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PUM4_A0A2D0PUM4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PWA1_A0A2D0PWA1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PWA6_A0A2D0PWA6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PWB1_A0A2D0PWB1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PT18_A0A2D0PT18_ICTPU_7998 and tr_A0A2D0PX51_A0A2D0PX51_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RPP3_A0A2D0RPP3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RPT8_A0A2D0RPT8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RPT9_A0A2D0RPT9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RPW9_A0A2D0RPW9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RQ29_A0A2D0RQ29_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RQ32_A0A2D0RQ32_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RQN1_A0A2D0RQN1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RQP1_A0A2D0RQP1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RQW3_A0A2D0RQW3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RQX2_A0A2D0RQX2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RRC2_A0A2D0RRC2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RRE7_A0A2D0RRE7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RRF7_A0A2D0RRF7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RRG7_A0A2D0RRG7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RRK2_A0A2D0RRK2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RPN8_A0A2D0RPN8_ICTPU_7998 and tr_A0A2D0RRL2_A0A2D0RRL2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T4C8_A0A2D0T4C8_ICTPU_7998 and tr_A0A2D0T582_A0A2D0T582_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 62

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/Q92817/3_mltree/Q92817.raxml.reduced.phy

Alignment comprises 1 partitions and 228 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 228 / 228
Gaps: 8.88 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92817/3_mltree/Q92817.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 473 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 228 / 18240
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -185609.409017] Initial branch length optimization
[00:00:02 -147678.907078] Model parameter optimization (eps = 10.000000)
[00:00:29 -147180.199016] AUTODETECT spr round 1 (radius: 5)
[00:01:15 -84561.487288] AUTODETECT spr round 2 (radius: 10)
[00:02:12 -58475.362507] AUTODETECT spr round 3 (radius: 15)
[00:03:22 -49987.543593] AUTODETECT spr round 4 (radius: 20)
[00:04:47 -48222.114006] AUTODETECT spr round 5 (radius: 25)
[00:06:18 -48156.861805] SPR radius for FAST iterations: 25 (autodetect)
[00:06:18 -48156.861805] Model parameter optimization (eps = 3.000000)
[00:06:36 -47979.324418] FAST spr round 1 (radius: 25)
[00:07:34 -43093.698724] FAST spr round 2 (radius: 25)
[00:08:21 -42904.644437] FAST spr round 3 (radius: 25)
[00:09:01 -42868.376379] FAST spr round 4 (radius: 25)
[00:09:35 -42866.154928] FAST spr round 5 (radius: 25)
[00:10:08 -42866.154819] Model parameter optimization (eps = 1.000000)
[00:10:18 -42863.713544] SLOW spr round 1 (radius: 5)
[00:11:15 -42837.164496] SLOW spr round 2 (radius: 5)
[00:12:11 -42834.782063] SLOW spr round 3 (radius: 5)
[00:13:07 -42833.922546] SLOW spr round 4 (radius: 5)
[00:14:00 -42833.922135] SLOW spr round 5 (radius: 10)
[00:14:52 -42833.717564] SLOW spr round 6 (radius: 5)
[00:16:06 -42833.717563] SLOW spr round 7 (radius: 10)
[00:17:07 -42821.051824] SLOW spr round 8 (radius: 5)
[00:18:23 -42806.405857] SLOW spr round 9 (radius: 5)
[00:19:25 -42806.405114] SLOW spr round 10 (radius: 10)
[00:20:19 -42806.405043] SLOW spr round 11 (radius: 15)
[00:21:54 -42806.405038] SLOW spr round 12 (radius: 20)
[00:24:07 -42806.405038] SLOW spr round 13 (radius: 25)
[00:26:41 -42806.405037] Model parameter optimization (eps = 0.100000)

[00:26:52] [worker #0] ML tree search #1, logLikelihood: -42805.186172

[00:26:52 -182739.259518] Initial branch length optimization
[00:26:54 -146221.854671] Model parameter optimization (eps = 10.000000)
[00:27:18 -145718.745747] AUTODETECT spr round 1 (radius: 5)
[00:28:07 -89066.952864] AUTODETECT spr round 2 (radius: 10)
[00:29:06 -63442.661855] AUTODETECT spr round 3 (radius: 15)
[00:30:19 -53487.537667] AUTODETECT spr round 4 (radius: 20)
[00:31:58 -49932.458311] AUTODETECT spr round 5 (radius: 25)
[00:32:34] [worker #2] ML tree search #3, logLikelihood: -42805.869722
[00:33:56 -49421.075059] SPR radius for FAST iterations: 25 (autodetect)
[00:33:56 -49421.075059] Model parameter optimization (eps = 3.000000)
[00:34:17 -49278.457067] FAST spr round 1 (radius: 25)
[00:35:24 -43093.879691] FAST spr round 2 (radius: 25)
[00:36:13 -42905.038261] FAST spr round 3 (radius: 25)
[00:36:54 -42876.554897] FAST spr round 4 (radius: 25)
[00:37:30 -42876.554338] Model parameter optimization (eps = 1.000000)
[00:37:46 -42860.431030] SLOW spr round 1 (radius: 5)
[00:38:45 -42840.703727] SLOW spr round 2 (radius: 5)
[00:38:55] [worker #4] ML tree search #5, logLikelihood: -42805.915853
[00:39:38 -42823.408846] SLOW spr round 3 (radius: 5)
[00:40:31 -42819.602242] SLOW spr round 4 (radius: 5)
[00:41:20 -42819.601443] SLOW spr round 5 (radius: 10)
[00:42:12 -42817.320157] SLOW spr round 6 (radius: 5)
[00:43:24 -42817.319746] SLOW spr round 7 (radius: 10)
[00:43:25] [worker #3] ML tree search #4, logLikelihood: -42819.421553
[00:44:23 -42817.319676] SLOW spr round 8 (radius: 15)
[00:45:56 -42816.618161] SLOW spr round 9 (radius: 5)
[00:47:12 -42816.618053] SLOW spr round 10 (radius: 10)
[00:48:16 -42814.909686] SLOW spr round 11 (radius: 5)
[00:48:18] [worker #1] ML tree search #2, logLikelihood: -42817.048899
[00:49:25 -42813.355965] SLOW spr round 12 (radius: 5)
[00:50:23 -42805.577119] SLOW spr round 13 (radius: 5)
[00:51:16 -42805.577003] SLOW spr round 14 (radius: 10)
[00:52:08 -42805.576973] SLOW spr round 15 (radius: 15)
[00:53:44 -42805.576973] SLOW spr round 16 (radius: 20)
[00:56:06 -42805.576973] SLOW spr round 17 (radius: 25)
[00:59:00 -42805.576973] Model parameter optimization (eps = 0.100000)

[00:59:07] [worker #0] ML tree search #6, logLikelihood: -42805.379548

[00:59:07 -180796.598057] Initial branch length optimization
[00:59:09 -144877.495691] Model parameter optimization (eps = 10.000000)
[00:59:39 -144427.597458] AUTODETECT spr round 1 (radius: 5)
[01:00:24 -88244.885374] AUTODETECT spr round 2 (radius: 10)
[01:01:20 -62926.773782] AUTODETECT spr round 3 (radius: 15)
[01:02:29 -51847.580016] AUTODETECT spr round 4 (radius: 20)
[01:03:57 -49104.509993] AUTODETECT spr round 5 (radius: 25)
[01:05:28 -48431.205834] SPR radius for FAST iterations: 25 (autodetect)
[01:05:28 -48431.205834] Model parameter optimization (eps = 3.000000)
[01:05:47 -48294.062996] FAST spr round 1 (radius: 25)
[01:06:20] [worker #4] ML tree search #10, logLikelihood: -42805.808988
[01:06:40 -43142.964752] FAST spr round 2 (radius: 25)
[01:07:23 -42857.376184] FAST spr round 3 (radius: 25)
[01:07:29] [worker #2] ML tree search #8, logLikelihood: -42805.985204
[01:08:01 -42848.038932] FAST spr round 4 (radius: 25)
[01:08:36 -42847.316036] FAST spr round 5 (radius: 25)
[01:09:10 -42847.304732] Model parameter optimization (eps = 1.000000)
[01:09:19 -42841.083345] SLOW spr round 1 (radius: 5)
[01:10:14 -42827.912539] SLOW spr round 2 (radius: 5)
[01:10:32] [worker #3] ML tree search #9, logLikelihood: -42818.154324
[01:11:08 -42827.664746] SLOW spr round 3 (radius: 5)
[01:12:04 -42827.664712] SLOW spr round 4 (radius: 10)
[01:12:54 -42827.664708] SLOW spr round 5 (radius: 15)
[01:14:23 -42826.402964] SLOW spr round 6 (radius: 5)
[01:15:20] [worker #1] ML tree search #7, logLikelihood: -42818.699663
[01:15:43 -42824.893847] SLOW spr round 7 (radius: 5)
[01:16:47 -42824.893398] SLOW spr round 8 (radius: 10)
[01:17:40 -42824.893388] SLOW spr round 9 (radius: 15)
[01:19:09 -42824.635436] SLOW spr round 10 (radius: 5)
[01:20:24 -42824.635400] SLOW spr round 11 (radius: 10)
[01:21:25 -42824.635396] SLOW spr round 12 (radius: 15)
[01:22:50 -42824.635395] SLOW spr round 13 (radius: 20)
[01:24:49 -42824.250538] SLOW spr round 14 (radius: 5)
[01:26:06 -42824.171238] SLOW spr round 15 (radius: 10)
[01:27:09 -42824.171073] SLOW spr round 16 (radius: 15)
[01:28:34 -42824.171056] SLOW spr round 17 (radius: 20)
[01:30:38 -42824.171054] SLOW spr round 18 (radius: 25)
[01:32:57 -42824.171054] Model parameter optimization (eps = 0.100000)

[01:33:05] [worker #0] ML tree search #11, logLikelihood: -42823.982498

[01:33:05 -182277.005262] Initial branch length optimization
[01:33:06 -145321.229020] Model parameter optimization (eps = 10.000000)
[01:33:29 -144866.046121] AUTODETECT spr round 1 (radius: 5)
[01:34:15 -87374.369311] AUTODETECT spr round 2 (radius: 10)
[01:34:52] [worker #1] ML tree search #12, logLikelihood: -42808.380260
[01:35:14 -65979.448725] AUTODETECT spr round 3 (radius: 15)
[01:36:28 -54933.882926] AUTODETECT spr round 4 (radius: 20)
[01:37:52 -52334.047472] AUTODETECT spr round 5 (radius: 25)
[01:38:27] [worker #2] ML tree search #13, logLikelihood: -42807.014176
[01:39:26 -51395.328160] SPR radius for FAST iterations: 25 (autodetect)
[01:39:26 -51395.328160] Model parameter optimization (eps = 3.000000)
[01:39:45 -51227.375328] FAST spr round 1 (radius: 25)
[01:40:45] [worker #4] ML tree search #15, logLikelihood: -42817.699795
[01:40:46 -44604.547265] FAST spr round 2 (radius: 25)
[01:41:35] [worker #3] ML tree search #14, logLikelihood: -42804.951731
[01:41:36 -43128.930924] FAST spr round 3 (radius: 25)
[01:42:18 -42893.467037] FAST spr round 4 (radius: 25)
[01:42:56 -42888.176340] FAST spr round 5 (radius: 25)
[01:43:34 -42884.219239] FAST spr round 6 (radius: 25)
[01:44:09 -42884.219162] Model parameter optimization (eps = 1.000000)
[01:44:18 -42881.906472] SLOW spr round 1 (radius: 5)
[01:45:15 -42871.309260] SLOW spr round 2 (radius: 5)
[01:46:09 -42871.305947] SLOW spr round 3 (radius: 10)
[01:47:02 -42871.098379] SLOW spr round 4 (radius: 5)
[01:48:18 -42871.098207] SLOW spr round 5 (radius: 10)
[01:49:20 -42871.098166] SLOW spr round 6 (radius: 15)
[01:50:55 -42836.596804] SLOW spr round 7 (radius: 5)
[01:52:20 -42824.255399] SLOW spr round 8 (radius: 5)
[01:53:30 -42809.623138] SLOW spr round 9 (radius: 5)
[01:54:28 -42809.622739] SLOW spr round 10 (radius: 10)
[01:55:24 -42806.645734] SLOW spr round 11 (radius: 5)
[01:56:38 -42806.643605] SLOW spr round 12 (radius: 10)
[01:57:39 -42806.643232] SLOW spr round 13 (radius: 15)
[01:59:16 -42803.179404] SLOW spr round 14 (radius: 5)
[02:00:36 -42803.178362] SLOW spr round 15 (radius: 10)
[02:01:37 -42803.178243] SLOW spr round 16 (radius: 15)
[02:03:04 -42802.367448] SLOW spr round 17 (radius: 5)
[02:04:02] [worker #3] ML tree search #19, logLikelihood: -42812.873060
[02:04:18 -42802.367400] SLOW spr round 18 (radius: 10)
[02:05:19 -42802.367400] SLOW spr round 19 (radius: 15)
[02:06:46 -42802.367400] SLOW spr round 20 (radius: 20)
[02:08:17] [worker #4] ML tree search #20, logLikelihood: -42801.368589
[02:08:45] [worker #1] ML tree search #17, logLikelihood: -42818.110849
[02:08:55 -42802.367400] SLOW spr round 21 (radius: 25)
[02:11:14 -42802.367400] Model parameter optimization (eps = 0.100000)

[02:11:24] [worker #0] ML tree search #16, logLikelihood: -42801.162610

[02:15:28] [worker #2] ML tree search #18, logLikelihood: -42808.488886

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.171628,0.784868) (0.068987,0.672778) (0.413919,0.721584) (0.345465,1.505807) 
   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: -42801.162610

AIC score: 87500.325219 / AICc score: 1890600.325219 / BIC score: 90754.774221
Free parameters (model + branch lengths): 949

WARNING: Number of free parameters (K=949) is larger than alignment size (n=228).
         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/Q92817/3_mltree/Q92817.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92817/3_mltree/Q92817.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92817/3_mltree/Q92817.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q92817/3_mltree/Q92817.raxml.log

Analysis started: 05-Jul-2021 06:52:13 / finished: 05-Jul-2021 09:07:42

Elapsed time: 8129.036 seconds

Consumed energy: 762.717 Wh (= 4 km in an electric car, or 19 km with an e-scooter!)