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 01-Jul-2021 01:11:33 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P00505/2_msa/P00505_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P00505/3_mltree/P00505 --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/P00505/2_msa/P00505_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 408 sites

WARNING: Sequences tr_A0A0E1RYH2_A0A0E1RYH2_COCIM_246410 and tr_A0A0J6Y314_A0A0J6Y314_COCIT_404692 are exactly identical!
WARNING: Sequences tr_G2WTY5_G2WTY5_VERDV_498257 and tr_C9SFD1_C9SFD1_VERA1_526221 are exactly identical!
WARNING: Sequences tr_B8N0W2_B8N0W2_ASPFN_332952 and tr_A0A1S9DLB0_A0A1S9DLB0_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179UG89_A0A179UG89_BLAGS_559298 and tr_C5GFQ6_C5GFQ6_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2QB89_H2QB89_PANTR_9598 and tr_A0A2R9CP09_A0A2R9CP09_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FHT8_F9FHT8_FUSOF_660025 and tr_A0A0D2Y8Q5_A0A0D2Y8Q5_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FHT8_F9FHT8_FUSOF_660025 and tr_N4UVM0_N4UVM0_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FHT8_F9FHT8_FUSOF_660025 and tr_X0CPX9_X0CPX9_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FHT8_F9FHT8_FUSOF_660025 and tr_A0A2H3GLS0_A0A2H3GLS0_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A0E0FTF9_A0A0E0FTF9_ORYNI_4536 and tr_A0A0E0C803_A0A0E0C803_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0FTF9_A0A0E0FTF9_ORYNI_4536 and tr_A0A0D3EUA0_A0A0D3EUA0_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0HS68_A0A0E0HS68_ORYNI_4536 and tr_B8B3J3_B8B3J3_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0HS68_A0A0E0HS68_ORYNI_4536 and tr_A0A0E0PYY5_A0A0E0PYY5_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0HS68_A0A0E0HS68_ORYNI_4536 and tr_A0A0E0AAQ0_A0A0E0AAQ0_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A2QJA6_A2QJA6_ASPNC_425011 and tr_G3Y9K0_G3Y9K0_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QJA6_A2QJA6_ASPNC_425011 and tr_A0A319AGH6_A0A319AGH6_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XKC7_G7XKC7_ASPKW_1033177 and tr_A0A100IBA4_A0A100IBA4_ASPNG_5061 are exactly identical!
WARNING: Sequences tr_G7XKC7_G7XKC7_ASPKW_1033177 and tr_A0A146FLD4_A0A146FLD4_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A2WVA6_A2WVA6_ORYSI_39946 and sp_P37833_AATC_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_F4P813_F4P813_BATDJ_684364 and tr_A0A177WTW7_A0A177WTW7_BATDE_403673 are exactly identical!
WARNING: Sequences tr_I1NYU4_I1NYU4_ORYGL_4538 and tr_A0A0D3F2W4_A0A0D3F2W4_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_F9X0A1_F9X0A1_ZYMTI_336722 and tr_A0A1X7RFM5_A0A1X7RFM5_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_V2Y889_V2Y889_MONRO_1381753 and tr_A0A0W0G2L4_A0A0W0G2L4_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A015IAS2_A0A015IAS2_9GLOM_1432141 and tr_A0A2I1FUY0_A0A2I1FUY0_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A015IAS2_A0A015IAS2_9GLOM_1432141 and tr_U9UM73_U9UM73_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A067E4R5_A0A067E4R5_CITSI_2711 and tr_V4WD80_V4WD80_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067E4R5_A0A067E4R5_CITSI_2711 and tr_A0A2H5PVG6_A0A2H5PVG6_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A096NJ44_A0A096NJ44_PAPAN_9555 and tr_A0A0D9QXD3_A0A0D9QXD3_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096NJ44_A0A096NJ44_PAPAN_9555 and tr_A0A2K6D1U2_A0A2K6D1U2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A094GPD8_A0A094GPD8_9PEZI_1420912 and tr_A0A1B8GG43_A0A1B8GG43_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0D2U7V0_A0A0D2U7V0_GOSRA_29730 and tr_A0A1U8IX63_A0A1U8IX63_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0F8X9G7_A0A0F8X9G7_9EURO_308745 and tr_A0A2T5M6W1_A0A2T5M6W1_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0G4PS48_A0A0G4PS48_PENCA_1429867 and tr_A0A101MP43_A0A101MP43_9EURO_48697 are exactly identical!
WARNING: Sequences tr_A0A0G4PS48_A0A0G4PS48_PENCA_1429867 and tr_A0A1V6NN60_A0A1V6NN60_9EURO_60169 are exactly identical!
WARNING: Sequences tr_A0A0G4PS48_A0A0G4PS48_PENCA_1429867 and tr_A0A1V6RAY0_A0A1V6RAY0_9EURO_60172 are exactly identical!
WARNING: Sequences tr_A0A0C9M2G9_A0A0C9M2G9_9FUNG_91626 and tr_A0A168H9M0_A0A168H9M0_MUCCL_747725 are exactly identical!
WARNING: Sequences tr_A0A0V0S074_A0A0V0S074_9BILA_6336 and tr_A0A0V0V027_A0A0V0V027_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V0S074_A0A0V0S074_9BILA_6336 and tr_A0A0V1KZD0_A0A0V1KZD0_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0S074_A0A0V0S074_9BILA_6336 and tr_A0A0V1NPI7_A0A0V1NPI7_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0S074_A0A0V0S074_9BILA_6336 and tr_A0A0V0T9Z8_A0A0V0T9Z8_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A164UQA8_A0A164UQA8_9HOMO_1314777 and tr_A0A166IHG4_A0A166IHG4_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1S3ZLW1_A0A1S3ZLW1_TOBAC_4097 and tr_A0A1U7YVS5_A0A1U7YVS5_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4CNP0_A0A1S4CNP0_TOBAC_4097 and tr_A0A1U7XJU6_A0A1U7XJU6_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1F5LEQ9_A0A1F5LEQ9_9EURO_1835702 and tr_A0A1V6PW85_A0A1V6PW85_9EURO_416450 are exactly identical!
WARNING: Sequences tr_A0A1U8HBT5_A0A1U8HBT5_CAPAN_4072 and tr_A0A2G3C192_A0A2G3C192_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2V5JF26_A0A2V5JF26_9EURO_1450541 and tr_A0A2V5HDW9_A0A2V5HDW9_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 46

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/P00505/3_mltree/P00505.raxml.reduced.phy

Alignment comprises 1 partitions and 408 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 408 / 408
Gaps: 1.23 %
Invariant sites: 1.72 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P00505/3_mltree/P00505.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 / 204 / 16320
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -515745.575606] Initial branch length optimization
[00:00:06 -444992.957935] Model parameter optimization (eps = 10.000000)
[00:00:51 -444401.319441] AUTODETECT spr round 1 (radius: 5)
[00:03:57 -301256.392344] AUTODETECT spr round 2 (radius: 10)
[00:07:14 -222220.856797] AUTODETECT spr round 3 (radius: 15)
[00:10:45 -184694.213145] AUTODETECT spr round 4 (radius: 20)
[00:15:02 -170861.072322] AUTODETECT spr round 5 (radius: 25)
[00:20:29 -166517.542382] SPR radius for FAST iterations: 25 (autodetect)
[00:20:29 -166517.542382] Model parameter optimization (eps = 3.000000)
[00:20:55 -166377.548407] FAST spr round 1 (radius: 25)
[00:24:42 -146594.084122] FAST spr round 2 (radius: 25)
[00:27:20 -145686.501847] FAST spr round 3 (radius: 25)
[00:29:37 -145591.227229] FAST spr round 4 (radius: 25)
[00:31:41 -145581.255489] FAST spr round 5 (radius: 25)
[00:33:40 -145575.027728] FAST spr round 6 (radius: 25)
[00:35:37 -145568.256579] FAST spr round 7 (radius: 25)
[00:37:30 -145568.256572] Model parameter optimization (eps = 1.000000)
[00:37:43 -145565.810545] SLOW spr round 1 (radius: 5)
[00:40:38 -145519.833768] SLOW spr round 2 (radius: 5)
[00:43:16 -145519.109216] SLOW spr round 3 (radius: 5)
[00:45:49 -145519.109213] SLOW spr round 4 (radius: 10)
[00:48:28 -145516.610632] SLOW spr round 5 (radius: 5)
[00:51:51 -145507.151708] SLOW spr round 6 (radius: 5)
[00:54:46 -145505.540335] SLOW spr round 7 (radius: 5)
[00:57:28 -145505.540204] SLOW spr round 8 (radius: 10)
[01:00:08 -145504.449036] SLOW spr round 9 (radius: 5)
[01:03:29 -145504.256466] SLOW spr round 10 (radius: 5)
[01:06:23 -145504.256463] SLOW spr round 11 (radius: 10)
[01:09:07 -145504.256463] SLOW spr round 12 (radius: 15)
[01:13:25 -145504.256463] SLOW spr round 13 (radius: 20)
[01:15:55] [worker #2] ML tree search #3, logLikelihood: -145532.323383
[01:20:04 -145504.256463] SLOW spr round 14 (radius: 25)
[01:24:36] [worker #1] ML tree search #2, logLikelihood: -145503.447655
[01:28:52 -145504.256463] Model parameter optimization (eps = 0.100000)

[01:28:58] [worker #0] ML tree search #1, logLikelihood: -145504.230896

[01:28:58 -512285.403964] Initial branch length optimization
[01:29:04 -442602.455851] Model parameter optimization (eps = 10.000000)
[01:29:48 -442009.685629] AUTODETECT spr round 1 (radius: 5)
[01:32:55 -305886.139716] AUTODETECT spr round 2 (radius: 10)
[01:36:15 -217060.287343] AUTODETECT spr round 3 (radius: 15)
[01:39:54 -175663.848704] AUTODETECT spr round 4 (radius: 20)
[01:44:09 -165020.917485] AUTODETECT spr round 5 (radius: 25)
[01:48:31 -163403.758774] SPR radius for FAST iterations: 25 (autodetect)
[01:48:31 -163403.758774] Model parameter optimization (eps = 3.000000)
[01:48:53 -163244.338937] FAST spr round 1 (radius: 25)
[01:52:25 -146188.093954] FAST spr round 2 (radius: 25)
[01:55:03 -145588.844246] FAST spr round 3 (radius: 25)
[01:57:18 -145570.561062] FAST spr round 4 (radius: 25)
[01:59:17 -145570.561025] Model parameter optimization (eps = 1.000000)
[01:59:30 -145563.181098] SLOW spr round 1 (radius: 5)
[02:02:33 -145517.821449] SLOW spr round 2 (radius: 5)
[02:05:19 -145511.213572] SLOW spr round 3 (radius: 5)
[02:07:57 -145510.903187] SLOW spr round 4 (radius: 5)
[02:10:30 -145510.903184] SLOW spr round 5 (radius: 10)
[02:13:07 -145509.782729] SLOW spr round 6 (radius: 5)
[02:16:29 -145509.270852] SLOW spr round 7 (radius: 5)
[02:19:24 -145509.270851] SLOW spr round 8 (radius: 10)
[02:22:07 -145509.270851] SLOW spr round 9 (radius: 15)
[02:26:27 -145509.270851] SLOW spr round 10 (radius: 20)
[02:28:51] [worker #2] ML tree search #6, logLikelihood: -145491.226862
[02:32:42 -145509.270851] SLOW spr round 11 (radius: 25)
[02:40:04] [worker #1] ML tree search #5, logLikelihood: -145514.643914
[02:40:50 -145509.270851] Model parameter optimization (eps = 0.100000)

[02:41:02] [worker #0] ML tree search #4, logLikelihood: -145508.960755

[02:41:02 -513788.506708] Initial branch length optimization
[02:41:08 -443989.332115] Model parameter optimization (eps = 10.000000)
[02:42:00 -443417.893858] AUTODETECT spr round 1 (radius: 5)
[02:45:07 -308111.685255] AUTODETECT spr round 2 (radius: 10)
[02:48:26 -218853.064142] AUTODETECT spr round 3 (radius: 15)
[02:51:56 -177177.262200] AUTODETECT spr round 4 (radius: 20)
[02:56:02 -168613.589107] AUTODETECT spr round 5 (radius: 25)
[03:00:49 -166706.049672] SPR radius for FAST iterations: 25 (autodetect)
[03:00:49 -166706.049672] Model parameter optimization (eps = 3.000000)
[03:01:18 -166516.965104] FAST spr round 1 (radius: 25)
[03:05:01 -146353.164349] FAST spr round 2 (radius: 25)
[03:07:34 -145660.641361] FAST spr round 3 (radius: 25)
[03:09:57 -145590.405629] FAST spr round 4 (radius: 25)
[03:11:58 -145588.794657] FAST spr round 5 (radius: 25)
[03:13:55 -145588.794613] Model parameter optimization (eps = 1.000000)
[03:14:05 -145585.980563] SLOW spr round 1 (radius: 5)
[03:17:01 -145538.992692] SLOW spr round 2 (radius: 5)
[03:19:47 -145527.232624] SLOW spr round 3 (radius: 5)
[03:22:24 -145526.744185] SLOW spr round 4 (radius: 5)
[03:24:58 -145526.744129] SLOW spr round 5 (radius: 10)
[03:27:36 -145526.728586] SLOW spr round 6 (radius: 15)
[03:31:58 -145526.728586] SLOW spr round 7 (radius: 20)
[03:38:15 -145526.728586] SLOW spr round 8 (radius: 25)
[03:46:19 -145526.728586] Model parameter optimization (eps = 0.100000)

[03:46:24] [worker #0] ML tree search #7, logLikelihood: -145526.701560

[03:46:24 -514784.114552] Initial branch length optimization
[03:46:29 -445669.378190] Model parameter optimization (eps = 10.000000)
[03:47:18 -445064.041230] AUTODETECT spr round 1 (radius: 5)
[03:50:22 -310156.008328] AUTODETECT spr round 2 (radius: 10)
[03:53:42 -225401.920367] AUTODETECT spr round 3 (radius: 15)
[03:56:18] [worker #1] ML tree search #8, logLikelihood: -145526.232491
[03:57:15 -181124.808612] AUTODETECT spr round 4 (radius: 20)
[03:59:23] [worker #2] ML tree search #9, logLikelihood: -145526.731033
[04:01:08 -168496.817832] AUTODETECT spr round 5 (radius: 25)
[04:06:14 -166124.412015] SPR radius for FAST iterations: 25 (autodetect)
[04:06:15 -166124.412015] Model parameter optimization (eps = 3.000000)
[04:06:40 -165927.246140] FAST spr round 1 (radius: 25)
[04:10:14 -146426.896801] FAST spr round 2 (radius: 25)
[04:12:53 -145648.614533] FAST spr round 3 (radius: 25)
[04:15:10 -145606.056303] FAST spr round 4 (radius: 25)
[04:17:15 -145586.441239] FAST spr round 5 (radius: 25)
[04:19:12 -145586.441197] Model parameter optimization (eps = 1.000000)
[04:19:20 -145585.972353] SLOW spr round 1 (radius: 5)
[04:22:16 -145543.999433] SLOW spr round 2 (radius: 5)
[04:24:59 -145537.789243] SLOW spr round 3 (radius: 5)
[04:27:34 -145537.789146] SLOW spr round 4 (radius: 10)
[04:30:11 -145520.961202] SLOW spr round 5 (radius: 5)
[04:33:36 -145516.877502] SLOW spr round 6 (radius: 5)
[04:36:33 -145515.913691] SLOW spr round 7 (radius: 5)
[04:39:16 -145515.913687] SLOW spr round 8 (radius: 10)
[04:41:53 -145515.913687] SLOW spr round 9 (radius: 15)
[04:46:14 -145515.913687] SLOW spr round 10 (radius: 20)
[04:52:36 -145515.913687] SLOW spr round 11 (radius: 25)
[05:01:02 -145515.913687] Model parameter optimization (eps = 0.100000)

[05:01:11] [worker #0] ML tree search #10, logLikelihood: -145515.805037

[05:01:11 -514936.975809] Initial branch length optimization
[05:01:17 -444208.874783] Model parameter optimization (eps = 10.000000)
[05:02:00 -443580.103427] AUTODETECT spr round 1 (radius: 5)
[05:05:05 -309225.840660] AUTODETECT spr round 2 (radius: 10)
[05:08:27 -210706.714802] AUTODETECT spr round 3 (radius: 15)
[05:12:11 -178394.496798] AUTODETECT spr round 4 (radius: 20)
[05:15:38] [worker #2] ML tree search #12, logLikelihood: -145508.001261
[05:16:42 -166696.578903] AUTODETECT spr round 5 (radius: 25)
[05:23:11 -165223.615128] SPR radius for FAST iterations: 25 (autodetect)
[05:23:11 -165223.615128] Model parameter optimization (eps = 3.000000)
[05:23:17 -165222.010132] FAST spr round 1 (radius: 25)
[05:26:54 -146570.096694] FAST spr round 2 (radius: 25)
[05:28:37] [worker #1] ML tree search #11, logLikelihood: -145553.540519
[05:29:36 -145809.825502] FAST spr round 3 (radius: 25)
[05:31:54 -145768.795033] FAST spr round 4 (radius: 25)
[05:33:58 -145762.696953] FAST spr round 5 (radius: 25)
[05:35:56 -145761.873820] FAST spr round 6 (radius: 25)
[05:37:51 -145761.873819] Model parameter optimization (eps = 1.000000)
[05:38:16 -145600.698301] SLOW spr round 1 (radius: 5)
[05:41:06 -145550.056616] SLOW spr round 2 (radius: 5)
[05:43:50 -145541.467342] SLOW spr round 3 (radius: 5)
[05:46:34 -145537.606393] SLOW spr round 4 (radius: 5)
[05:49:08 -145537.606357] SLOW spr round 5 (radius: 10)
[05:51:48 -145532.722678] SLOW spr round 6 (radius: 5)
[05:55:18 -145528.271667] SLOW spr round 7 (radius: 5)
[05:58:14 -145528.249057] SLOW spr round 8 (radius: 10)
[06:01:00 -145525.568133] SLOW spr round 9 (radius: 5)
[06:04:23 -145522.789622] SLOW spr round 10 (radius: 5)
[06:07:17 -145522.789377] SLOW spr round 11 (radius: 10)
[06:10:01 -145522.658574] SLOW spr round 12 (radius: 5)
[06:13:29 -145518.394105] SLOW spr round 13 (radius: 5)
[06:16:23 -145518.214579] SLOW spr round 14 (radius: 5)
[06:19:03 -145518.214558] SLOW spr round 15 (radius: 10)
[06:21:42 -145518.214558] SLOW spr round 16 (radius: 15)
[06:26:06 -145518.214558] SLOW spr round 17 (radius: 20)
[06:26:18] [worker #2] ML tree search #15, logLikelihood: -145536.873037
[06:32:28 -145518.214558] SLOW spr round 18 (radius: 25)
[06:40:51 -145518.214558] Model parameter optimization (eps = 0.100000)

[06:41:00] [worker #0] ML tree search #13, logLikelihood: -145518.087055

[06:41:01 -513439.682275] Initial branch length optimization
[06:41:05 -443927.741152] Model parameter optimization (eps = 10.000000)
[06:42:10 -443333.793695] AUTODETECT spr round 1 (radius: 5)
[06:45:13 -300347.159794] AUTODETECT spr round 2 (radius: 10)
[06:48:39 -208445.351602] AUTODETECT spr round 3 (radius: 15)
[06:52:13 -177375.433446] AUTODETECT spr round 4 (radius: 20)
[06:56:38 -166944.962956] AUTODETECT spr round 5 (radius: 25)
[07:01:25 -165942.138938] SPR radius for FAST iterations: 25 (autodetect)
[07:01:25 -165942.138938] Model parameter optimization (eps = 3.000000)
[07:01:47 -165812.627410] FAST spr round 1 (radius: 25)
[07:04:18] [worker #1] ML tree search #14, logLikelihood: -145516.665972
[07:05:19 -146479.438638] FAST spr round 2 (radius: 25)
[07:07:59 -145612.718787] FAST spr round 3 (radius: 25)
[07:10:12 -145591.815728] FAST spr round 4 (radius: 25)
[07:12:12 -145591.815711] Model parameter optimization (eps = 1.000000)
[07:12:31 -145571.630554] SLOW spr round 1 (radius: 5)
[07:15:30 -145519.509765] SLOW spr round 2 (radius: 5)
[07:18:22 -145509.725966] SLOW spr round 3 (radius: 5)
[07:21:09 -145503.173090] SLOW spr round 4 (radius: 5)
[07:23:46 -145502.008339] SLOW spr round 5 (radius: 5)
[07:26:21 -145502.008317] SLOW spr round 6 (radius: 10)
[07:29:02 -145501.783893] SLOW spr round 7 (radius: 5)
[07:32:29 -145501.783806] SLOW spr round 8 (radius: 10)
[07:35:31 -145501.783806] SLOW spr round 9 (radius: 15)
[07:39:47 -145501.783806] SLOW spr round 10 (radius: 20)
[07:46:41 -145501.783806] SLOW spr round 11 (radius: 25)
[07:53:29] [worker #2] ML tree search #18, logLikelihood: -145504.308089
[07:55:25 -145501.783806] Model parameter optimization (eps = 0.100000)

[07:55:35] [worker #0] ML tree search #16, logLikelihood: -145501.569485

[07:55:35 -512851.954123] Initial branch length optimization
[07:55:41 -443846.348094] Model parameter optimization (eps = 10.000000)
[07:56:30 -443225.133376] AUTODETECT spr round 1 (radius: 5)
[07:59:42 -307195.738598] AUTODETECT spr round 2 (radius: 10)
[08:02:56 -220167.124670] AUTODETECT spr round 3 (radius: 15)
[08:06:22 -186052.880692] AUTODETECT spr round 4 (radius: 20)
[08:10:33 -170914.016860] AUTODETECT spr round 5 (radius: 25)
[08:15:29 -168726.320068] SPR radius for FAST iterations: 25 (autodetect)
[08:15:29 -168726.320068] Model parameter optimization (eps = 3.000000)
[08:15:51 -168559.795197] FAST spr round 1 (radius: 25)
[08:19:31 -146947.132642] FAST spr round 2 (radius: 25)
[08:22:05 -145804.106691] FAST spr round 3 (radius: 25)
[08:22:08] [worker #1] ML tree search #17, logLikelihood: -145505.354569
[08:24:30 -145671.273588] FAST spr round 4 (radius: 25)
[08:26:40 -145659.777167] FAST spr round 5 (radius: 25)
[08:28:39 -145653.982752] FAST spr round 6 (radius: 25)
[08:30:33 -145653.982747] Model parameter optimization (eps = 1.000000)
[08:30:53 -145622.495666] SLOW spr round 1 (radius: 5)
[08:33:52 -145577.945324] SLOW spr round 2 (radius: 5)
[08:36:39 -145561.901124] SLOW spr round 3 (radius: 5)
[08:39:22 -145558.418345] SLOW spr round 4 (radius: 5)
[08:41:57 -145554.700202] SLOW spr round 5 (radius: 5)
[08:44:30 -145554.700133] SLOW spr round 6 (radius: 10)
[08:47:10 -145544.446147] SLOW spr round 7 (radius: 5)
[08:50:39 -145540.029390] SLOW spr round 8 (radius: 5)
[08:53:39 -145537.402992] SLOW spr round 9 (radius: 5)
[08:56:24 -145537.402873] SLOW spr round 10 (radius: 10)
[08:59:04 -145537.116219] SLOW spr round 11 (radius: 5)
[09:02:33 -145528.617863] SLOW spr round 12 (radius: 5)
[09:05:31 -145528.617744] SLOW spr round 13 (radius: 10)
[09:08:15 -145528.617744] SLOW spr round 14 (radius: 15)
[09:12:34 -145528.617744] SLOW spr round 15 (radius: 20)
[09:19:03 -145528.617744] SLOW spr round 16 (radius: 25)
[09:26:10] [worker #1] ML tree search #20, logLikelihood: -145483.077675
[09:27:45 -145528.617744] Model parameter optimization (eps = 0.100000)

[09:27:54] [worker #0] ML tree search #19, logLikelihood: -145528.577974


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.266401,0.326768) (0.295206,0.621846) (0.203433,0.868163) (0.234960,2.352583) 
   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: -145483.077675

AIC score: 294976.155349 / AICc score: 8339036.155349 / BIC score: 303018.746034
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=408).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 75 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P00505/3_mltree/P00505.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P00505/3_mltree/P00505.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P00505/3_mltree/P00505.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P00505/3_mltree/P00505.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P00505/3_mltree/P00505.raxml.log

Analysis started: 01-Jul-2021 01:11:33 / finished: 01-Jul-2021 10:39:28

Elapsed time: 34074.579 seconds