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lasv-s_matched_sle.log
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IQ-TREE multicore version 1.6.5 for Linux 64-bit built May 8 2018
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
Host: simon-XPS-13-9370 (AVX2, FMA3, 15 GB RAM)
Command: iqtree -s lasv-s_matched_sle.mafft.fasta -m GTR+G4 -nt AUTO -pre lasv-s_matched_sle
Seed: 513803 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Tue Aug 14 10:27:04 2018
Kernel: AVX+FMA - auto-detect threads (8 CPU cores detected)
Reading alignment file lasv-s_matched_sle.mafft.fasta ... Fasta format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 72 sequences with 3406 columns, 1351 distinct patterns
1149 parsimony-informative, 205 singleton sites, 2052 constant sites
Gap/Ambiguity Composition p-value
1 G502-S-SLE-2009 0.35% passed 98.47%
2 G1180-S-SLE-2010 0.62% passed 95.24%
3 G2147-S-SLE-2011 0.32% passed 97.12%
4 G610-S-SLE-2009 0.18% passed 85.88%
5 G693-S-SLE-2009 0.21% passed 87.32%
6 G771-S-SLE-2010 0.21% passed 89.18%
7 G1792-S-SLE-2011 0.47% passed 90.83%
8 G2565-S-SLE-2012 0.18% passed 90.70%
9 G1960-S-SLE-2011 0.15% passed 94.63%
10 G2197-S-SLE-2011 0.41% passed 99.45%
11 LM032-S-SLE-2010 1.06% passed 97.74%
12 G636-S-SLE-2009 0.47% passed 96.47%
13 G2315-S-SLE-2012 2.00% passed 95.96%
14 G2903-S-SLE-2012 0.65% passed 95.55%
15 G3206-S-SLE-2012 0.26% passed 99.49%
16 G676-S-SLE-2009 0.15% passed 99.80%
17 G2405-S-SLE-2012 0.44% passed 98.72%
18 G692-S-SLE-2009 0.15% passed 96.41%
19 LM779-S-SLE-2012 0.88% passed 98.47%
20 G1190-S-SLE-2010 0.12% passed 98.69%
21 G2944-S-SLE-2012 0.38% passed 97.28%
22 Z0947-S-SLE-2011 0.26% passed 99.22%
23 Z0948-S-SLE-2011 0.32% passed 99.13%
24 G1727-S-SLE-2011 0.21% passed 99.00%
25 G3148-S-SLE-2012 0.41% passed 99.72%
26 LM765-S-SLE-2012 0.59% passed 99.95%
27 G1647-S-SLE-2011 0.32% passed 99.99%
28 G2295-S-SLE-2012 0.18% passed 97.15%
29 G2587-S-SLE-2012 0.32% passed 96.37%
30 G2280-S-SLE-2012 0.12% passed 99.28%
31 G2612-S-SLE-2012 0.59% passed 99.98%
32 G3016-S-SLE-2012 0.29% passed 96.49%
33 G3106-S-SLE-2012 0.29% passed 96.49%
34 G1774-S-SLE-2011 0.15% passed 99.97%
35 G2222-S-SLE-2011 0.38% passed 99.04%
36 LM395-S-SLE-2009 0.32% passed 95.72%
37 Josiah-S-SLE-1976 0.12% passed 85.20%
38 G2868-S-SLE-2012 0.12% passed 94.47%
39 G2165-S-SLE-2011 0.23% passed 99.17%
40 G2184-S-SLE-2011 0.18% passed 99.63%
41 LM776-S-SLE-2012 0.44% passed 99.87%
42 LM222-S-SLE-2010 1.09% passed 99.67%
43 LM774-S-SLE-2012 0.23% passed 99.84%
44 LM778-S-SLE-2012 0.06% passed 99.70%
45 G808-S-SLE-2010 0.26% passed 96.41%
46 G503-S-SLE-2009 0.26% passed 97.52%
47 G1959-S-SLE-2011 0.12% passed 99.95%
48 G3010-S-SLE-2012 0.12% passed 99.86%
49 G2318-S-SLE-2012 0.47% passed 73.40%
50 G733-S-SLE-2010 0.21% passed 99.02%
51 G1618-S-SLE-2011 0.41% passed 98.27%
52 G1646-S-SLE-2011 0.35% passed 99.41%
53 G2554-S-SLE-2012 0.21% passed 98.07%
54 G2263-S-SLE-2012 0.12% passed 93.36%
55 G2392-S-SLE-2012 0.18% passed 95.66%
56 G3151-S-SLE-2012 0.15% passed 93.94%
57 G3170-S-SLE-2012 0.38% passed 91.48%
58 G3248-S-SLE-2012 0.44% passed 92.15%
59 G3229-S-SLE-2012 0.09% passed 98.20%
60 G2427-S-SLE-2012 1.32% passed 89.01%
61 NL-S-SLE-2000 1.23% passed 95.30%
62 G1442-S-SLE-2011 0.12% passed 98.00%
63 G2259-S-SLE-2012 0.26% passed 92.22%
64 G2723-S-SLE-2012 0.97% passed 94.39%
65 G3278-S-SLE-2012 0.44% passed 99.53%
66 G2557-S-SLE-2012 0.29% passed 98.13%
67 G2615-S-SLE-2012 1.23% passed 95.19%
68 G1529-S-SLE-2011 0.15% passed 91.72%
69 G3234-S-SLE-2012 1.70% passed 51.89%
70 G2363-S-SLE-2012 0.29% passed 99.68%
71 G2141-S-SLE-2011 0.26% passed 98.57%
72 G2431-S-SLE-2012 0.12% passed 96.90%
**** TOTAL 0.40% 0 sequences failed composition chi2 test (p-value<5%; df=3)
NOTE: G3106-S-SLE-2012 is identical to G3016-S-SLE-2012 but kept for subsequent analysis
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.014 seconds
NOTE: 12 MB RAM (0 GB) is required!
Measuring multi-threading efficiency up to 8 CPU cores
Increase to 10 rounds for branch lengths
80 trees examined
Threads: 1 / Time: 8.007 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -54905
Threads: 2 / Time: 5.586 sec / Speedup: 1.433 / Efficiency: 72% / LogL: -54905
Threads: 3 / Time: 3.662 sec / Speedup: 2.187 / Efficiency: 73% / LogL: -54905
Threads: 4 / Time: 3.830 sec / Speedup: 2.091 / Efficiency: 52% / LogL: -54905
Threads: 5 / Time: 6.200 sec / Speedup: 1.291 / Efficiency: 26% / LogL: -54905
BEST NUMBER OF THREADS: 3
Estimate model parameters (epsilon = 0.100)
1. Initial log-likelihood: -33537.427
2. Current log-likelihood: -28982.171
3. Current log-likelihood: -28947.165
4. Current log-likelihood: -28945.942
Optimal log-likelihood: -28945.834
Rate parameters: A-C: 0.75152 A-G: 23.24511 A-T: 1.59407 C-G: 0.56756 C-T: 21.14976 G-T: 1.00000
Base frequencies: A: 0.269 C: 0.233 G: 0.214 T: 0.284
Gamma shape alpha: 0.227
Parameters optimization took 4 rounds (0.925 sec)
Computing ML distances based on estimated model parameters... 0.110 sec
Computing BIONJ tree...
0.003 seconds
Log-likelihood of BIONJ tree: -28952.485
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.032 second
Computing log-likelihood of 98 initial trees ... 1.925 seconds
Current best score: -28944.512
Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -28941.846
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 3: -28941.429
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 9: -28940.756
Iteration 10 / LogL: -28942.068 / Time: 0h:0m:32s
Iteration 20 / LogL: -28941.650 / Time: 0h:0m:33s
Finish initializing candidate tree set (6)
Current best tree score: -28940.756 / CPU time: 5.055
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 23: -28940.561
Iteration 30 / LogL: -28940.563 / Time: 0h:0m:35s (0h:1m:54s left)
Iteration 40 / LogL: -28940.563 / Time: 0h:0m:37s (0h:1m:20s left)
Iteration 50 / LogL: -28942.424 / Time: 0h:0m:40s (0h:0m:59s left)
UPDATE BEST LOG-LIKELIHOOD: -28940.561
Iteration 60 / LogL: -28940.759 / Time: 0h:0m:42s (0h:0m:45s left)
UPDATE BEST LOG-LIKELIHOOD: -28940.561
Iteration 70 / LogL: -28940.561 / Time: 0h:0m:44s (0h:0m:34s left)
Iteration 80 / LogL: -28940.681 / Time: 0h:0m:47s (0h:0m:25s left)
Iteration 90 / LogL: -28940.627 / Time: 0h:0m:49s (0h:0m:18s left)
UPDATE BEST LOG-LIKELIHOOD: -28940.560
Iteration 100 / LogL: -28971.086 / Time: 0h:0m:52s (0h:0m:12s left)
Iteration 110 / LogL: -28940.761 / Time: 0h:0m:54s (0h:0m:6s left)
Iteration 120 / LogL: -28940.759 / Time: 0h:0m:56s (0h:0m:1s left)
TREE SEARCH COMPLETED AFTER 124 ITERATIONS / Time: 0h:0m:57s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -28940.560
Optimal log-likelihood: -28940.560
Rate parameters: A-C: 0.74990 A-G: 23.24497 A-T: 1.57965 C-G: 0.56578 C-T: 21.15055 G-T: 1.00000
Base frequencies: A: 0.269 C: 0.233 G: 0.214 T: 0.284
Gamma shape alpha: 0.227
Parameters optimization took 1 rounds (0.057 sec)
BEST SCORE FOUND : -28940.560
Total tree length: 1.624
Total number of iterations: 124
CPU time used for tree search: 85.498 sec (0h:1m:25s)
Wall-clock time used for tree search: 29.064 sec (0h:0m:29s)
Total CPU time used: 166.878 sec (0h:2m:46s)
Total wall-clock time used: 57.452 sec (0h:0m:57s)
Analysis results written to:
IQ-TREE report: lasv-s_matched_sle.iqtree
Maximum-likelihood tree: lasv-s_matched_sle.treefile
Likelihood distances: lasv-s_matched_sle.mldist
Screen log file: lasv-s_matched_sle.log
Date and Time: Tue Aug 14 10:28:02 2018