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 6258R CPU @ 2.70GHz, 56 cores, 187 GB RAM

RAxML-NG was called at 04-Jun-2021 03:53:06 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y345/2_msa/Q9Y345_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y345/3_mltree/Q9Y345 --seed 2 --threads 6 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y345/2_msa/Q9Y345_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 526 sites

WARNING: Sequences tr_B4QI04_B4QI04_DROSI_7240 and sp_Q7K4Y6_DAT_DROME_7227 are exactly identical!
WARNING: Sequences tr_B4QI04_B4QI04_DROSI_7240 and tr_B4HSZ4_B4HSZ4_DROSE_7238 are exactly identical!
WARNING: Sequences sp_P31648_SC6A1_MOUSE_10090 and sp_P23978_SC6A1_RAT_10116 are exactly identical!
WARNING: Sequences sp_Q61327_SC6A3_MOUSE_10090 and sp_P23977_SC6A3_RAT_10116 are exactly identical!
WARNING: Sequences tr_M3XWD3_M3XWD3_MUSPF_9669 and tr_A0A2Y9KT67_A0A2Y9KT67_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3Z0E9_M3Z0E9_MUSPF_9669 and tr_E2RKV9_E2RKV9_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3Z0E9_M3Z0E9_MUSPF_9669 and tr_F1SQA4_F1SQA4_PIG_9823 are exactly identical!
WARNING: Sequences tr_M3Z0E9_M3Z0E9_MUSPF_9669 and tr_A0A2I2UPJ1_A0A2I2UPJ1_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3Z0E9_M3Z0E9_MUSPF_9669 and tr_A0A1U7TXN5_A0A1U7TXN5_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_M3Z0E9_M3Z0E9_MUSPF_9669 and tr_A0A2U3YMF9_A0A2U3YMF9_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2I3HQS5_A0A2I3HQS5_NOMLE_61853 and tr_A0A2I2ZXV3_A0A2I2ZXV3_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3HQS5_A0A2I3HQS5_NOMLE_61853 and tr_H2QRS9_H2QRS9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3HE37_G3HE37_CRIGR_10029 and sp_P58295_SC6A5_RAT_10116 are exactly identical!
WARNING: Sequences tr_G3HE37_G3HE37_CRIGR_10029 and tr_A0A1U8CFY0_A0A1U8CFY0_MESAU_10036 are exactly identical!
WARNING: Sequences tr_A0A2I2ZQY9_A0A2I2ZQY9_GORGO_9595 and sp_P48067_SC6A9_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2ZQY9_A0A2I2ZQY9_GORGO_9595 and tr_A0A2R9CR56_A0A2R9CR56_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_H2PA22_H2PA22_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_H2QM23_H2QM23_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and sp_P30531_SC6A1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_F6WVM8_F6WVM8_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_F6ZPU5_F6ZPU5_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_G7NYT4_G7NYT4_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A096NQ20_A0A096NQ20_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A0D9RC09_A0A0D9RC09_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A2K6A0C9_A0A2K6A0C9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3QDQ1_G3QDQ1_GORGO_9595 and tr_A0A2R9CH47_A0A2R9CH47_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_G1SE03_G1SE03_RABIT_9986 are exactly identical!
WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_F1P8R8_F1P8R8_CANLF_9615 are exactly identical!
WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_F6WCP2_F6WCP2_HORSE_9796 are exactly identical!
WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_F7F7H9_F7F7H9_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A287AMT4_A0A287AMT4_PIG_9823 are exactly identical!
WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_G7PQK0_G7PQK0_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A096NG10_A0A096NG10_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A0D9QYL3_A0A0D9QYL3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A2K5MCU9_A0A2K5MCU9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A2K6ECY9_A0A2K6ECY9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A2K5YI07_A0A2K5YI07_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3QKV5_G3QKV5_GORGO_9595 and tr_A0A2Y9JTR3_A0A2Y9JTR3_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3QR21_G3QR21_GORGO_9595 and tr_A0A2J8MWT0_A0A2J8MWT0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QR21_G3QR21_GORGO_9595 and sp_P23975_SC6A2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QR21_G3QR21_GORGO_9595 and tr_A0A2R9AJ86_A0A2R9AJ86_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1MTI8_G1MTI8_MELGA_9103 and tr_A0A2I0MHT3_A0A2I0MHT3_COLLI_8932 are exactly identical!
WARNING: Sequences tr_G1MTI8_G1MTI8_MELGA_9103 and tr_A0A1V4JPB2_A0A1V4JPB2_PATFA_372326 are exactly identical!
WARNING: Sequences tr_G1MTI8_G1MTI8_MELGA_9103 and tr_A0A226MWW0_A0A226MWW0_CALSU_9009 are exactly identical!
WARNING: Sequences tr_Q291U3_Q291U3_DROPS_46245 and tr_B4GA93_B4GA93_DROPE_7234 are exactly identical!
WARNING: Sequences tr_Q293F9_Q293F9_DROPS_46245 and tr_B4GBK6_B4GBK6_DROPE_7234 are exactly identical!
WARNING: Sequences tr_H2Q3A9_H2Q3A9_PANTR_9598 and sp_Q9Y345_SC6A5_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q3A9_H2Q3A9_PANTR_9598 and tr_A0A2R9AHV1_A0A2R9AHV1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QQL1_H2QQL1_PANTR_9598 and tr_A0A2R8ZUK6_A0A2R8ZUK6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F7FWA1_F7FWA1_MONDO_13616 and tr_G3WUU1_G3WUU1_SARHA_9305 are exactly identical!
WARNING: Sequences tr_W5PDT2_W5PDT2_SHEEP_9940 and tr_F1N5R0_F1N5R0_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A158NPD8_A0A158NPD8_ATTCE_12957 and tr_F4WH84_F4WH84_ACREC_103372 are exactly identical!
WARNING: Sequences tr_A0A158NQQ9_A0A158NQQ9_ATTCE_12957 and tr_F4WBV1_F4WBV1_ACREC_103372 are exactly identical!
WARNING: Sequences tr_A0A1D5QDI0_A0A1D5QDI0_MACMU_9544 and tr_G7NUY2_G7NUY2_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QDI0_A0A1D5QDI0_MACMU_9544 and tr_A0A0D9S7I0_A0A0D9S7I0_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QDI0_A0A1D5QDI0_MACMU_9544 and tr_A0A2K5NQK4_A0A2K5NQK4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5QDI0_A0A1D5QDI0_MACMU_9544 and tr_A0A2K6CLC6_A0A2K6CLC6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5QDI0_A0A1D5QDI0_MACMU_9544 and tr_A0A2K5XLX2_A0A2K5XLX2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7HQF7_F7HQF7_MACMU_9544 and tr_A0A096MXM4_A0A096MXM4_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_H0ZQY1_H0ZQY1_TAEGU_59729 and tr_A0A218V974_A0A218V974_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A9XCH4_A9XCH4_MACFA_9541 and tr_A0A096MN61_A0A096MN61_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A9XCH4_A9XCH4_MACFA_9541 and tr_A0A0D9RXR1_A0A0D9RXR1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A9XCH4_A9XCH4_MACFA_9541 and tr_A0A2K5KJJ7_A0A2K5KJJ7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A9XCH4_A9XCH4_MACFA_9541 and tr_A0A2K6C6Z6_A0A2K6C6Z6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A9XCH4_A9XCH4_MACFA_9541 and tr_A0A2K5Z263_A0A2K5Z263_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F1MZ67_F1MZ67_BOVIN_9913 and sp_P51143_SC6A2_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M3WZR1_M3WZR1_FELCA_9685 and tr_A0A2Y9FHD2_A0A2Y9FHD2_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_M3WZR1_M3WZR1_FELCA_9685 and tr_A0A383ZIE6_A0A383ZIE6_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A087XTR0_A0A087XTR0_POEFO_48698 and tr_A0A087YDV2_A0A087YDV2_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A2I3ME54_A0A2I3ME54_PAPAN_9555 and tr_A0A0D9RGQ5_A0A0D9RGQ5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3ME54_A0A2I3ME54_PAPAN_9555 and tr_A0A2K5MBD5_A0A2K5MBD5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A151NIH4_A0A151NIH4_ALLMI_8496 and tr_A0A1U7SBY4_A0A1U7SBY4_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091UUT5_A0A091UUT5_NIPNI_128390 and tr_A0A087R105_A0A087R105_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091UUT5_A0A091UUT5_NIPNI_128390 and tr_A0A091HNU0_A0A091HNU0_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A091VSV1_A0A091VSV1_NIPNI_128390 and tr_A0A087RH38_A0A087RH38_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091VSV1_A0A091VSV1_NIPNI_128390 and tr_A0A0A0ATB2_A0A0A0ATB2_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A093I2B1_A0A093I2B1_STRCA_441894 and tr_A0A226P2N5_A0A226P2N5_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A1S3IBF4_A0A1S3IBF4_LINUN_7574 and tr_A0A1S3K1M1_A0A1S3K1M1_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3LX61_A0A1S3LX61_SALSA_8030 and tr_A0A060XET8_A0A060XET8_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A226NG47_A0A226NG47_CALSU_9009 and tr_A0A226PF47_A0A226PF47_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226NLT9_A0A226NLT9_CALSU_9009 and tr_A0A226PJ24_A0A226PJ24_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0T468_A0A2D0T468_ICTPU_7998 and tr_A0A2D0T472_A0A2D0T472_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5KZH8_A0A2K5KZH8_CERAT_9531 and tr_A0A2K6BVQ8_A0A2K6BVQ8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2U4B4F4_A0A2U4B4F4_TURTR_9739 and tr_A0A2Y9LN82_A0A2Y9LN82_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 84

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y345/3_mltree/Q9Y345.raxml.reduced.phy

Alignment comprises 1 partitions and 526 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 526 / 526
Gaps: 1.11 %
Invariant sites: 1.90 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y345/3_mltree/Q9Y345.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 / 263 / 21040
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -813699.864932] Initial branch length optimization
[00:00:08 -697862.535110] Model parameter optimization (eps = 10.000000)
[00:01:25 -695838.314565] AUTODETECT spr round 1 (radius: 5)
[00:05:11 -424223.529245] AUTODETECT spr round 2 (radius: 10)
[00:09:47 -293673.004832] AUTODETECT spr round 3 (radius: 15)
[00:14:10 -233999.529263] AUTODETECT spr round 4 (radius: 20)
[00:19:10 -222026.169460] AUTODETECT spr round 5 (radius: 25)
[00:26:31 -210734.961549] SPR radius for FAST iterations: 25 (autodetect)
[00:26:31 -210734.961549] Model parameter optimization (eps = 3.000000)
[00:27:04 -210435.078314] FAST spr round 1 (radius: 25)
[00:30:41 -185522.021941] FAST spr round 2 (radius: 25)
[00:33:27 -184703.724186] FAST spr round 3 (radius: 25)
[00:35:56 -184654.148940] FAST spr round 4 (radius: 25)
[00:38:08 -184653.192116] FAST spr round 5 (radius: 25)
[00:40:19 -184649.657736] FAST spr round 6 (radius: 25)
[00:42:22 -184649.657640] Model parameter optimization (eps = 1.000000)
[00:42:44 -184640.343002] SLOW spr round 1 (radius: 5)
[00:45:46 -184600.557372] SLOW spr round 2 (radius: 5)
[00:48:38 -184596.620739] SLOW spr round 3 (radius: 5)
[00:51:23 -184596.620512] SLOW spr round 4 (radius: 10)
[00:54:21 -184596.620289] SLOW spr round 5 (radius: 15)
[00:59:16 -184596.513249] SLOW spr round 6 (radius: 5)
[01:03:21 -184596.513038] SLOW spr round 7 (radius: 10)
[01:06:49 -184596.512836] SLOW spr round 8 (radius: 15)
[01:11:38 -184596.135642] SLOW spr round 9 (radius: 5)
[01:15:44 -184596.135416] SLOW spr round 10 (radius: 10)
[01:19:12 -184596.135233] SLOW spr round 11 (radius: 15)
[01:23:59 -184596.135056] SLOW spr round 12 (radius: 20)
[01:25:14] [worker #1] ML tree search #2, logLikelihood: -184608.846098
[01:33:23 -184596.134885] SLOW spr round 13 (radius: 25)
[01:37:09] [worker #2] ML tree search #3, logLikelihood: -184612.354286
[01:45:51 -184596.134720] Model parameter optimization (eps = 0.100000)

[01:46:02] [worker #0] ML tree search #1, logLikelihood: -184596.006470

[01:46:03 -818521.803477] Initial branch length optimization
[01:46:13 -696420.668865] Model parameter optimization (eps = 10.000000)
[01:47:18 -694561.078787] AUTODETECT spr round 1 (radius: 5)
[01:51:03 -429253.434195] AUTODETECT spr round 2 (radius: 10)
[01:55:20 -295431.917487] AUTODETECT spr round 3 (radius: 15)
[01:59:42 -237135.367907] AUTODETECT spr round 4 (radius: 20)
[02:04:12 -215453.984265] AUTODETECT spr round 5 (radius: 25)
[02:09:24 -212568.671353] SPR radius for FAST iterations: 25 (autodetect)
[02:09:24 -212568.671353] Model parameter optimization (eps = 3.000000)
[02:09:51 -212377.201250] FAST spr round 1 (radius: 25)
[02:13:37 -185851.786840] FAST spr round 2 (radius: 25)
[02:16:26 -184824.863709] FAST spr round 3 (radius: 25)
[02:18:51 -184685.558301] FAST spr round 4 (radius: 25)
[02:21:03 -184671.816790] FAST spr round 5 (radius: 25)
[02:23:09 -184671.816592] Model parameter optimization (eps = 1.000000)
[02:23:32 -184665.647617] SLOW spr round 1 (radius: 5)
[02:26:30 -184645.343479] SLOW spr round 2 (radius: 5)
[02:29:21 -184634.359880] SLOW spr round 3 (radius: 5)
[02:32:11 -184634.055196] SLOW spr round 4 (radius: 5)
[02:35:02 -184632.605213] SLOW spr round 5 (radius: 5)
[02:37:48 -184632.605049] SLOW spr round 6 (radius: 10)
[02:40:52 -184625.449499] SLOW spr round 7 (radius: 5)
[02:44:03] [worker #1] ML tree search #5, logLikelihood: -184603.452830
[02:44:39 -184624.460431] SLOW spr round 8 (radius: 5)
[02:47:55 -184624.459649] SLOW spr round 9 (radius: 10)
[02:51:00 -184624.459570] SLOW spr round 10 (radius: 15)
[02:55:54 -184624.257471] SLOW spr round 11 (radius: 5)
[02:59:57 -184624.257379] SLOW spr round 12 (radius: 10)
[03:03:26 -184624.257311] SLOW spr round 13 (radius: 15)
[03:08:14 -184624.257245] SLOW spr round 14 (radius: 20)
[03:14:20] [worker #2] ML tree search #6, logLikelihood: -184609.248547
[03:17:47 -184623.488542] SLOW spr round 15 (radius: 5)
[03:21:52 -184623.488490] SLOW spr round 16 (radius: 10)
[03:25:22 -184623.488442] SLOW spr round 17 (radius: 15)
[03:30:09 -184623.488396] SLOW spr round 18 (radius: 20)
[03:39:44 -184623.488351] SLOW spr round 19 (radius: 25)
[03:52:23 -184623.488309] Model parameter optimization (eps = 0.100000)

[03:52:34] [worker #0] ML tree search #4, logLikelihood: -184623.338741

[03:52:34 -816527.842650] Initial branch length optimization
[03:52:41 -697010.995495] Model parameter optimization (eps = 10.000000)
[03:53:42 -695230.354280] AUTODETECT spr round 1 (radius: 5)
[03:57:21 -427333.999211] AUTODETECT spr round 2 (radius: 10)
[04:01:31 -301683.692999] AUTODETECT spr round 3 (radius: 15)
[04:06:11 -251030.466959] AUTODETECT spr round 4 (radius: 20)
[04:10:52 -219636.530637] AUTODETECT spr round 5 (radius: 25)
[04:16:20 -216248.363594] SPR radius for FAST iterations: 25 (autodetect)
[04:16:20 -216248.363594] Model parameter optimization (eps = 3.000000)
[04:16:56 -216018.012758] FAST spr round 1 (radius: 25)
[04:17:41] [worker #1] ML tree search #8, logLikelihood: -184625.350456
[04:20:49 -186146.718347] FAST spr round 2 (radius: 25)
[04:23:41 -184807.363259] FAST spr round 3 (radius: 25)
[04:26:15 -184682.556181] FAST spr round 4 (radius: 25)
[04:28:25 -184682.133943] FAST spr round 5 (radius: 25)
[04:30:30 -184682.133764] Model parameter optimization (eps = 1.000000)
[04:30:49 -184680.486575] SLOW spr round 1 (radius: 5)
[04:33:50 -184622.613556] SLOW spr round 2 (radius: 5)
[04:36:52 -184608.431916] SLOW spr round 3 (radius: 5)
[04:39:38 -184608.431497] SLOW spr round 4 (radius: 10)
[04:41:45] [worker #2] ML tree search #9, logLikelihood: -184610.088076
[04:42:38 -184604.336163] SLOW spr round 5 (radius: 5)
[04:46:22 -184604.336053] SLOW spr round 6 (radius: 10)
[04:49:36 -184604.335959] SLOW spr round 7 (radius: 15)
[04:54:31 -184603.567003] SLOW spr round 8 (radius: 5)
[04:58:33 -184603.566936] SLOW spr round 9 (radius: 10)
[05:01:58 -184603.566870] SLOW spr round 10 (radius: 15)
[05:06:46 -184603.566808] SLOW spr round 11 (radius: 20)
[05:16:09 -184603.566749] SLOW spr round 12 (radius: 25)
[05:28:50 -184603.566692] Model parameter optimization (eps = 0.100000)

[05:28:58] [worker #0] ML tree search #7, logLikelihood: -184603.494872

[05:28:58 -817792.850557] Initial branch length optimization
[05:29:10 -696971.966528] Model parameter optimization (eps = 10.000000)
[05:30:08 -695060.028704] AUTODETECT spr round 1 (radius: 5)
[05:33:51 -410335.119311] AUTODETECT spr round 2 (radius: 10)
[05:38:06 -279246.973737] AUTODETECT spr round 3 (radius: 15)
[05:42:02 -229595.268979] AUTODETECT spr round 4 (radius: 20)
[05:43:58] [worker #1] ML tree search #11, logLikelihood: -184607.417006
[05:46:47 -217525.073206] AUTODETECT spr round 5 (radius: 25)
[05:52:27 -213262.176042] SPR radius for FAST iterations: 25 (autodetect)
[05:52:27 -213262.176042] Model parameter optimization (eps = 3.000000)
[05:52:57 -213022.788082] FAST spr round 1 (radius: 25)
[05:56:45 -185708.236395] FAST spr round 2 (radius: 25)
[05:59:29 -184724.719848] FAST spr round 3 (radius: 25)
[06:02:01 -184659.260341] FAST spr round 4 (radius: 25)
[06:04:06 -184650.359175] FAST spr round 5 (radius: 25)
[06:06:08 -184648.302576] FAST spr round 6 (radius: 25)
[06:08:07 -184648.302551] Model parameter optimization (eps = 1.000000)
[06:08:29 -184641.367714] SLOW spr round 1 (radius: 5)
[06:11:27 -184605.405806] SLOW spr round 2 (radius: 5)
[06:14:07 -184604.439192] SLOW spr round 3 (radius: 5)
[06:15:48] [worker #2] ML tree search #12, logLikelihood: -184596.309279
[06:16:44 -184604.439018] SLOW spr round 4 (radius: 10)
[06:19:38 -184604.061104] SLOW spr round 5 (radius: 5)
[06:23:14 -184604.060907] SLOW spr round 6 (radius: 10)
[06:26:24 -184604.060753] SLOW spr round 7 (radius: 15)
[06:31:07 -184603.042398] SLOW spr round 8 (radius: 5)
[06:35:10 -184596.950664] SLOW spr round 9 (radius: 5)
[06:38:31 -184596.950511] SLOW spr round 10 (radius: 10)
[06:41:34 -184596.950384] SLOW spr round 11 (radius: 15)
[06:46:17 -184596.950263] SLOW spr round 12 (radius: 20)
[06:55:33 -184596.950146] SLOW spr round 13 (radius: 25)
[06:58:50] [worker #1] ML tree search #14, logLikelihood: -184606.849282
[07:07:54 -184596.950033] Model parameter optimization (eps = 0.100000)

[07:08:06] [worker #0] ML tree search #10, logLikelihood: -184596.729336

[07:08:06 -820529.545940] Initial branch length optimization
[07:08:16 -700380.479010] Model parameter optimization (eps = 10.000000)
[07:09:12 -698502.999044] AUTODETECT spr round 1 (radius: 5)
[07:12:48 -431588.555850] AUTODETECT spr round 2 (radius: 10)
[07:16:57 -296840.974898] AUTODETECT spr round 3 (radius: 15)
[07:21:12 -234836.212087] AUTODETECT spr round 4 (radius: 20)
[07:25:29 -217803.260894] AUTODETECT spr round 5 (radius: 25)
[07:30:50 -209822.797942] SPR radius for FAST iterations: 25 (autodetect)
[07:30:50 -209822.797942] Model parameter optimization (eps = 3.000000)
[07:31:19 -209581.738485] FAST spr round 1 (radius: 25)
[07:34:46 -186206.305243] FAST spr round 2 (radius: 25)
[07:37:22] [worker #2] ML tree search #15, logLikelihood: -184601.284054
[07:37:27 -184737.138897] FAST spr round 3 (radius: 25)
[07:39:47 -184689.783020] FAST spr round 4 (radius: 25)
[07:41:54 -184676.109800] FAST spr round 5 (radius: 25)
[07:43:55 -184676.109679] Model parameter optimization (eps = 1.000000)
[07:44:07 -184674.730987] SLOW spr round 1 (radius: 5)
[07:47:09 -184615.065024] SLOW spr round 2 (radius: 5)
[07:49:57 -184609.705805] SLOW spr round 3 (radius: 5)
[07:52:41 -184609.036445] SLOW spr round 4 (radius: 5)
[07:55:22 -184609.036213] SLOW spr round 5 (radius: 10)
[07:58:15 -184608.837444] SLOW spr round 6 (radius: 5)
[08:01:54 -184608.837223] SLOW spr round 7 (radius: 10)
[08:05:08 -184608.837021] SLOW spr round 8 (radius: 15)
[08:09:49 -184608.836826] SLOW spr round 9 (radius: 20)
[08:18:43 -184608.836637] SLOW spr round 10 (radius: 25)
[08:23:23] [worker #1] ML tree search #17, logLikelihood: -184598.614377
[08:30:44 -184608.836454] Model parameter optimization (eps = 0.100000)

[08:30:51] [worker #0] ML tree search #13, logLikelihood: -184608.817381

[08:30:51 -818045.124426] Initial branch length optimization
[08:31:00 -696437.421463] Model parameter optimization (eps = 10.000000)
[08:31:56 -694445.013423] AUTODETECT spr round 1 (radius: 5)
[08:35:34 -433552.467653] AUTODETECT spr round 2 (radius: 10)
[08:39:47 -296588.927324] AUTODETECT spr round 3 (radius: 15)
[08:44:15 -238901.544084] AUTODETECT spr round 4 (radius: 20)
[08:49:31 -214168.370577] AUTODETECT spr round 5 (radius: 25)
[08:52:34] [worker #2] ML tree search #18, logLikelihood: -184616.716919
[08:55:24 -211341.970750] SPR radius for FAST iterations: 25 (autodetect)
[08:55:24 -211341.970750] Model parameter optimization (eps = 3.000000)
[08:55:35 -211336.716078] FAST spr round 1 (radius: 25)
[08:59:15 -186223.386012] FAST spr round 2 (radius: 25)
[09:02:01 -184917.018449] FAST spr round 3 (radius: 25)
[09:04:18 -184858.214080] FAST spr round 4 (radius: 25)
[09:06:27 -184843.172711] FAST spr round 5 (radius: 25)
[09:08:29 -184840.724769] FAST spr round 6 (radius: 25)
[09:10:27 -184840.724070] Model parameter optimization (eps = 1.000000)
[09:10:52 -184668.867099] SLOW spr round 1 (radius: 5)
[09:13:46 -184616.378508] SLOW spr round 2 (radius: 5)
[09:16:28 -184610.374535] SLOW spr round 3 (radius: 5)
[09:19:05 -184610.374131] SLOW spr round 4 (radius: 10)
[09:21:57 -184609.040216] SLOW spr round 5 (radius: 5)
[09:25:33 -184607.581263] SLOW spr round 6 (radius: 5)
[09:28:37 -184607.579096] SLOW spr round 7 (radius: 10)
[09:31:34 -184607.578717] SLOW spr round 8 (radius: 15)
[09:36:08 -184607.578576] SLOW spr round 9 (radius: 20)
[09:44:19 -184607.578483] SLOW spr round 10 (radius: 25)
[09:52:09] [worker #1] ML tree search #20, logLikelihood: -184599.736193
[09:56:13 -184607.578402] Model parameter optimization (eps = 0.100000)

[09:56:20] [worker #0] ML tree search #16, logLikelihood: -184607.492685

[09:56:20 -822318.588977] Initial branch length optimization
[09:56:27 -703633.203683] Model parameter optimization (eps = 10.000000)
[09:57:20 -701687.330685] AUTODETECT spr round 1 (radius: 5)
[10:00:57 -426174.813474] AUTODETECT spr round 2 (radius: 10)
[10:04:55 -291456.334665] AUTODETECT spr round 3 (radius: 15)
[10:09:07 -232467.170735] AUTODETECT spr round 4 (radius: 20)
[10:13:59 -216640.037950] AUTODETECT spr round 5 (radius: 25)
[10:19:37 -213062.741604] SPR radius for FAST iterations: 25 (autodetect)
[10:19:37 -213062.741604] Model parameter optimization (eps = 3.000000)
[10:20:02 -212814.732672] FAST spr round 1 (radius: 25)
[10:23:40 -185910.452356] FAST spr round 2 (radius: 25)
[10:26:25 -184714.439942] FAST spr round 3 (radius: 25)
[10:28:50 -184680.038941] FAST spr round 4 (radius: 25)
[10:31:00 -184673.652653] FAST spr round 5 (radius: 25)
[10:33:01 -184673.652097] Model parameter optimization (eps = 1.000000)
[10:33:24 -184665.168062] SLOW spr round 1 (radius: 5)
[10:36:11 -184624.035872] SLOW spr round 2 (radius: 5)
[10:38:58 -184621.986787] SLOW spr round 3 (radius: 5)
[10:41:39 -184621.986444] SLOW spr round 4 (radius: 10)
[10:44:31 -184621.692984] SLOW spr round 5 (radius: 5)
[10:48:03 -184621.692836] SLOW spr round 6 (radius: 10)
[10:51:10 -184621.692704] SLOW spr round 7 (radius: 15)
[10:55:48 -184621.692577] SLOW spr round 8 (radius: 20)
[11:04:40 -184621.692455] SLOW spr round 9 (radius: 25)
[11:16:43 -184621.692337] Model parameter optimization (eps = 0.100000)

[11:16:56] [worker #0] ML tree search #19, logLikelihood: -184621.545615


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.268364,0.393324) (0.379199,0.573370) (0.274533,1.555661) (0.077904,3.208355) 
   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: -184596.006470

AIC score: 373202.012939 / AICc score: 8417262.012939 / BIC score: 381753.941871
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=526).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y345/3_mltree/Q9Y345.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y345/3_mltree/Q9Y345.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y345/3_mltree/Q9Y345.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9Y345/3_mltree/Q9Y345.raxml.log

Analysis started: 04-Jun-2021 03:53:06 / finished: 04-Jun-2021 15:10:02

Elapsed time: 40616.371 seconds

Consumed energy: 3483.400 Wh (= 17 km in an electric car, or 87 km with an e-scooter!)