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author | dave |
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date | Mon, 10 Jun 2019 16:04:10 -0400 |
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[28 May 13:09:56] Pipelign started with sequence file <pipelign-in1.fasta> ================================================================ Program: CD-HIT, V4.8.1 (+OpenMP), May 14 2019, 14:40:47 Command: cd-hit-est -c 0.8 -n 5 -i long.good.fas -o grp -d 0 -T 1 Started: Tue May 28 13:09:56 2019 ================================================================ Output ---------------------------------------------------------------- total seq: 100 longest and shortest : 70 and 70 Total letters: 7000 Sequences have been sorted Approximated minimal memory consumption: Sequence : 0M Buffer : 1 X 12M = 12M Table : 1 X 0M = 0M Miscellaneous : 0M Total : 12M Table limit with the given memory limit: Max number of representatives: 4000000 Max number of word counting entries: 98487020 comparing sequences from 0 to 100 100 finished 84 clusters Approximated maximum memory consumption: 12M writing new database writing clustering information program completed ! Total CPU time 0.04 inputfile = orig 84 x 70 - 70 d outputhat23=1 treein = 0 compacttree = 0 stacksize: 8192 kb generating a scoring matrix for nucleotide (dist=200) ... done All-to-all alignment. 0 / 84 (by thread 0) 10 / 84 (by thread 0) 20 / 84 (by thread 0) 30 / 84 (by thread 0) 40 / 84 (by thread 0) 50 / 84 (by thread 0) 60 / 84 (by thread 0) 70 / 84 (by thread 0) 80 / 84 (by thread 0) tbfast-pair (nuc) Version 7.407 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0 1 thread(s) outputhat23=1 Loading 'hat3.seed' ... done. Writing hat3 for iterative refinement generating a scoring matrix for nucleotide (dist=200) ... done Gap Penalty = -1.53, +0.00, +0.00 tbutree = 1, compacttree = 0 Constructing a UPGMA tree ... 0 / 84 10 / 84 20 / 84 30 / 84 40 / 84 50 / 84 60 / 84 70 / 84 80 / 84 done. Progressive alignment ... STEP 1 /83 (thread 0) STEP 2 /83 (thread 0) STEP 3 /83 (thread 0) STEP 4 /83 (thread 0) STEP 5 /83 (thread 0) STEP 6 /83 (thread 0) STEP 7 /83 (thread 0) STEP 8 /83 (thread 0) STEP 9 /83 (thread 0) STEP 10 /83 (thread 0) STEP 11 /83 (thread 0) Reallocating (by thread 0) ..done. *alloclen = 1159 STEP 12 /83 (thread 0) STEP 13 /83 (thread 0) STEP 14 /83 (thread 0) STEP 15 /83 (thread 0) STEP 16 /83 (thread 0) STEP 17 /83 (thread 0) STEP 18 /83 (thread 0) STEP 19 /83 (thread 0) STEP 20 /83 (thread 0) STEP 21 /83 (thread 0) STEP 22 /83 (thread 0) STEP 23 /83 (thread 0) STEP 24 /83 (thread 0) STEP 25 /83 (thread 0) STEP 26 /83 (thread 0) STEP 27 /83 (thread 0) STEP 28 /83 (thread 0) STEP 29 /83 (thread 0) STEP 30 /83 (thread 0) STEP 31 /83 (thread 0) STEP 32 /83 (thread 0) STEP 33 /83 (thread 0) STEP 34 /83 (thread 0) STEP 35 /83 (thread 0) STEP 36 /83 (thread 0) STEP 37 /83 (thread 0) STEP 38 /83 (thread 0) STEP 39 /83 (thread 0) STEP 40 /83 (thread 0) STEP 41 /83 (thread 0) STEP 42 /83 (thread 0) STEP 43 /83 (thread 0) STEP 44 /83 (thread 0) STEP 45 /83 (thread 0) STEP 46 /83 (thread 0) STEP 47 /83 (thread 0) STEP 48 /83 (thread 0) STEP 49 /83 (thread 0) STEP 50 /83 (thread 0) STEP 51 /83 (thread 0) STEP 52 /83 (thread 0) STEP 53 /83 (thread 0) STEP 54 /83 (thread 0) STEP 55 /83 (thread 0) STEP 56 /83 (thread 0) STEP 57 /83 (thread 0) STEP 58 /83 (thread 0) STEP 59 /83 (thread 0) STEP 60 /83 (thread 0) STEP 61 /83 (thread 0) STEP 62 /83 (thread 0) STEP 63 /83 (thread 0) STEP 64 /83 (thread 0) STEP 65 /83 (thread 0) STEP 66 /83 (thread 0) STEP 67 /83 (thread 0) STEP 68 /83 (thread 0) STEP 69 /83 (thread 0) STEP 70 /83 (thread 0) STEP 71 /83 (thread 0) STEP 72 /83 (thread 0) STEP 73 /83 (thread 0) STEP 74 /83 (thread 0) STEP 75 /83 (thread 0) STEP 76 /83 (thread 0) STEP 77 /83 (thread 0) STEP 78 /83 (thread 0) STEP 79 /83 (thread 0) STEP 80 /83 (thread 0) STEP 81 /83 (thread 0) STEP 82 /83 (thread 0) STEP 83 /83 (thread 0) done. tbfast (nuc) Version 7.407 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 1 thread(s) minimumweight = 0.000010 autosubalignment = 0.000000 nthread = 1 randomseed = 0 blosum 62 / kimura 200 poffset = 0 niter = 1 sueff_global = 0.100000 nadd = 1 Loading 'hat3' ... done. generating a scoring matrix for nucleotide (dist=200) ... done 0 / 84 10 / 84 20 / 84 30 / 84 40 / 84 50 / 84 60 / 84 70 / 84 80 / 84 Segment 1/ 1 1- 271 001-0000-0 (thread 1) identical 001-0000-0 (thread 1) worse 001-0001-1 (thread 1) identical 001-0001-1 (thread 1) worse 001-0002-0 (thread 1) identical 001-0002-0 (thread 1) worse 001-0003-1 (thread 1) identical 001-0004-0 (thread 1) identical 001-0004-0 (thread 1) worse 001-0005-1 (thread 1) identical 001-0005-1 (thread 1) better 001-0006-0 (thread 1) identical 001-0006-0 (thread 1) better 001-0007-1 (thread 1) identical 001-0007-1 (thread 1) worse 001-0008-0 (thread 1) identical 001-0008-0 (thread 1) worse 001-0009-1 (thread 1) identical 001-0009-1 (thread 1) worse 001-0010-0 (thread 1) identical 001-0010-0 (thread 1) worse 001-0011-1 (thread 1) identical 001-0012-0 (thread 1) identical 001-0013-1 (thread 1) identical 001-0013-1 (thread 1) better 001-0014-0 (thread 1) identical 001-0015-1 (thread 1) identical 001-0015-1 (thread 1) worse 001-0016-0 (thread 1) identical 001-0017-1 (thread 1) identical 001-0018-0 (thread 1) identical 001-0018-0 (thread 1) worse 001-0019-1 (thread 1) identical 001-0019-1 (thread 1) better 001-0020-0 (thread 1) identical 001-0020-0 (thread 1) worse 001-0021-1 (thread 1) identical 001-0021-1 (thread 1) better 001-0022-0 (thread 1) identical 001-0023-1 (thread 1) identical 001-0023-1 (thread 1) better 001-0024-0 (thread 1) identical 001-0024-0 (thread 1) worse 001-0025-1 (thread 1) identical 001-0025-1 (thread 1) better 001-0026-0 (thread 1) identical 001-0026-0 (thread 1) better 001-0027-1 (thread 1) identical 001-0027-1 (thread 1) worse 001-0028-0 (thread 1) identical 001-0028-0 (thread 1) worse 001-0029-1 (thread 1) identical 001-0029-1 (thread 1) worse 001-0030-0 (thread 1) identical 001-0030-0 (thread 1) better 001-0031-1 (thread 1) identical 001-0031-1 (thread 1) better 001-0032-0 (thread 1) identical 001-0032-0 (thread 1) worse 001-0033-1 (thread 1) identical 001-0033-1 (thread 1) better 001-0034-0 (thread 1) identical 001-0034-0 (thread 1) better 001-0035-1 (thread 1) identical 001-0035-1 (thread 1) worse 001-0036-0 (thread 1) identical 001-0036-0 (thread 1) worse 001-0037-1 (thread 1) identical 001-0037-1 (thread 1) better 001-0038-0 (thread 1) identical 001-0038-0 (thread 1) better 001-0039-1 (thread 1) identical 001-0039-1 (thread 1) better 001-0040-0 (thread 1) identical 001-0040-0 (thread 1) worse 001-0041-1 (thread 1) identical 001-0041-1 (thread 1) better 001-0042-0 (thread 1) identical 001-0042-0 (thread 1) worse 001-0043-1 (thread 1) identical 001-0043-1 (thread 1) better 001-0044-0 (thread 1) identical 001-0044-0 (thread 1) worse 001-0045-1 (thread 1) identical 001-0045-1 (thread 1) better 001-0046-0 (thread 1) identical 001-0046-0 (thread 1) worse 001-0047-1 (thread 1) identical 001-0047-1 (thread 1) worse 001-0048-0 (thread 1) identical 001-0048-0 (thread 1) worse 001-0049-1 (thread 1) identical 001-0049-1 (thread 1) worse 001-0050-0 (thread 1) identical 001-0050-0 (thread 1) worse 001-0051-1 (thread 1) identical 001-0052-0 (thread 1) identical 001-0052-0 (thread 1) worse 001-0053-1 (thread 1) identical 001-0053-1 (thread 1) worse 001-0054-0 (thread 1) identical 001-0054-0 (thread 1) better 001-0055-1 (thread 1) identical 001-0055-1 (thread 1) better 001-0056-0 (thread 1) identical 001-0056-0 (thread 1) worse 001-0057-1 (thread 1) identical 001-0057-1 (thread 1) worse 001-0058-0 (thread 1) identical 001-0059-1 (thread 1) identical 001-0059-1 (thread 1) better 001-0060-0 (thread 1) identical 001-0060-0 (thread 1) worse 001-0061-1 (thread 1) identical 001-0061-1 (thread 1) worse 001-0062-0 (thread 1) identical 001-0062-0 (thread 1) better 001-0063-1 (thread 1) identical 001-0063-1 (thread 1) worse 001-0064-0 (thread 1) identical 001-0064-0 (thread 1) worse 001-0065-1 (thread 1) identical 001-0065-1 (thread 1) better 001-0066-0 (thread 1) identical 001-0066-0 (thread 1) better 001-0067-1 (thread 1) identical 001-0067-1 (thread 1) better 001-0068-0 (thread 1) identical 001-0068-0 (thread 1) worse 001-0069-1 (thread 1) identical 001-0069-1 (thread 1) worse 001-0070-0 (thread 1) identical 001-0070-0 (thread 1) worse 001-0071-1 (thread 1) identical 001-0071-1 (thread 1) better 001-0072-0 (thread 1) identical 001-0073-1 (thread 1) identical 001-0073-1 (thread 1) better 001-0074-0 (thread 1) identical 001-0074-0 (thread 1) worse 001-0075-1 (thread 1) identical 001-0075-1 (thread 1) better 001-0076-0 (thread 1) identical 001-0076-0 (thread 1) better 001-0077-1 (thread 1) identical 001-0077-1 (thread 1) better 001-0078-0 (thread 1) identical 001-0078-0 (thread 1) worse 001-0079-1 (thread 1) identical 001-0079-1 (thread 1) worse 001-0080-0 (thread 1) identical 001-0080-0 (thread 1) worse 001-0081-1 (thread 1) identical 001-0081-1 (thread 1) worse 001-0082-0 (thread 1) identical 001-0083-1 (thread 1) identical 001-0083-1 (thread 1) better 001-0084-0 (thread 1) identical 001-0084-0 (thread 1) worse 001-0085-1 (thread 1) identical 001-0085-1 (thread 1) worse 001-0086-0 (thread 1) identical 001-0086-0 (thread 1) worse 001-0087-1 (thread 1) identical 001-0088-0 (thread 1) identical 001-0088-0 (thread 1) worse 001-0089-1 (thread 1) identical 001-0089-1 (thread 1) worse 001-0090-0 (thread 1) identical 001-0090-0 (thread 1) better 001-0091-1 (thread 1) identical 001-0091-1 (thread 1) better 001-0092-0 (thread 1) identical 001-0092-0 (thread 1) worse 001-0093-1 (thread 1) identical 001-0093-1 (thread 1) better 001-0094-0 (thread 1) identical 001-0094-0 (thread 1) better 001-0095-1 (thread 1) identical 001-0095-1 (thread 1) better 001-0096-0 (thread 1) identical 001-0096-0 (thread 1) worse 001-0097-1 (thread 1) identical 001-0097-1 (thread 1) worse 001-0098-0 (thread 1) identical 001-0098-0 (thread 1) worse 001-0099-1 (thread 1) identical 001-0099-1 (thread 1) worse 001-0100-0 (thread 1) identical 001-0100-0 (thread 1) worse 001-0101-1 (thread 1) identical 001-0101-1 (thread 1) worse 001-0102-0 (thread 1) identical 001-0103-1 (thread 1) identical 001-0104-0 (thread 1) identical 001-0104-0 (thread 1) worse 001-0105-1 (thread 1) identical 001-0105-1 (thread 1) better 001-0106-0 (thread 1) identical 001-0107-1 (thread 1) identical 001-0108-0 (thread 1) identical 001-0108-0 (thread 1) worse 001-0109-1 (thread 1) identical 001-0109-1 (thread 1) better 001-0110-0 (thread 1) identical 001-0110-0 (thread 1) better 001-0111-1 (thread 1) identical 001-0111-1 (thread 1) better 001-0112-0 (thread 1) identical 001-0113-1 (thread 1) identical 001-0113-1 (thread 1) better 001-0114-0 (thread 1) identical 001-0114-0 (thread 1) worse 001-0115-1 (thread 1) identical 001-0115-1 (thread 1) better 001-0116-0 (thread 1) identical 001-0116-0 (thread 1) worse 001-0117-1 (thread 1) identical 001-0117-1 (thread 1) worse 001-0118-0 (thread 1) identical 001-0118-0 (thread 1) better 001-0119-1 (thread 1) identical 001-0120-0 (thread 1) identical 001-0120-0 (thread 1) worse 001-0121-1 (thread 1) identical 001-0121-1 (thread 1) worse 001-0122-0 (thread 1) identical 001-0122-0 (thread 1) better 001-0123-1 (thread 1) identical 001-0124-0 (thread 1) identical 001-0124-0 (thread 1) better 001-0125-1 (thread 1) identical 001-0125-1 (thread 1) better 001-0126-0 (thread 1) identical 001-0127-1 (thread 1) identical 001-0127-1 (thread 1) worse 001-0128-0 (thread 1) identical 001-0128-0 (thread 1) worse 001-0129-1 (thread 1) identical 001-0129-1 (thread 1) worse 001-0130-0 (thread 1) identical 001-0130-0 (thread 1) better 001-0131-1 (thread 1) identical 001-0131-1 (thread 1) better 001-0132-0 (thread 1) identical 001-0132-0 (thread 1) better 001-0133-1 (thread 1) identical 001-0134-0 (thread 1) identical 001-0134-0 (thread 1) worse 001-0135-1 (thread 1) identical 001-0136-0 (thread 1) identical 001-0137-1 (thread 1) identical 001-0137-1 (thread 1) worse 001-0138-0 (thread 1) identical 001-0138-0 (thread 1) worse 001-0139-1 (thread 1) identical 001-0139-1 (thread 1) better 001-0140-0 (thread 1) identical 001-0141-1 (thread 1) identical 001-0141-1 (thread 1) better 001-0142-0 (thread 1) identical 001-0143-1 (thread 1) identical 001-0143-1 (thread 1) worse 001-0144-0 (thread 1) identical 001-0144-0 (thread 1) worse 001-0145-1 (thread 1) identical 001-0145-1 (thread 1) better 001-0146-0 (thread 1) identical 001-0146-0 (thread 1) better 001-0147-1 (thread 1) identical 001-0147-1 (thread 1) worse 001-0148-0 (thread 1) identical 001-0149-1 (thread 1) identical 001-0149-1 (thread 1) better 001-0150-0 (thread 1) identical 001-0151-1 (thread 1) identical 001-0152-0 (thread 1) identical 001-0153-1 (thread 1) identical 001-0154-0 (thread 1) identical 001-0155-1 (thread 1) identical 001-0156-0 (thread 1) identical 001-0157-1 (thread 1) identical 001-0157-1 (thread 1) worse 001-0158-0 (thread 1) identical 001-0159-1 (thread 1) identical 001-0159-1 (thread 1) worse 001-0160-0 (thread 1) identical 001-0160-0 (thread 1) worse 001-0161-1 (thread 1) identical 001-0161-1 (thread 1) worse 001-0162-0 (thread 1) identical 001-0162-0 (thread 1) worse 001-0163-1 (thread 1) identical 001-0163-1 (thread 1) worse 001-0164-1 (thread 1) identical 001-0164-1 (thread 1) worse Reached 1 done dvtditr (nuc) Version 7.407 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 1 thread(s) Strategy: L-INS-i (Probably most accurate, very slow) Iterative refinement method (<1) with LOCAL pairwise alignment information If unsure which option to use, try 'mafft --auto input > output'. For more information, see 'mafft --help', 'mafft --man' and the mafft page. The default gap scoring scheme has been changed in version 7.110 (2013 Oct). It tends to insert more gaps into gap-rich regions than previous versions. To disable this change, add the --leavegappyregion option. IQ-TREE multicore version 1.6.10 for Linux 64-bit built Mar 21 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: gaius (AVX2, FMA3, 15 GB RAM) Command: iqtree -s clsReps.aln -m GTR+R4 -nt 1 Seed: 50990 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Tue May 28 13:09:57 2019 Kernel: AVX+FMA - 1 threads (8 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 8 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file clsReps.aln ... Fasta format detected Alignment most likely contains DNA/RNA sequences Alignment has 84 sequences with 305 columns, 301 distinct patterns 238 parsimony-informative, 52 singleton sites, 15 constant sites WARNING: Some sequence names are changed as follows: K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1_1_0 -> K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0 K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1_2_1 -> K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1 K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1_3_2 -> K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2 K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1_1_3 -> K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3 K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1_2_4 -> K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4 K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1_1_5 -> K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5 K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1_1_6 -> K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6 K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1_1_7 -> K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7 K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1_2_8 -> K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8 K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1_1_9 -> K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9 K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1_2_10 -> K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10 K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1_2_11 -> K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11 K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1_1_12 -> K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12 K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1_1_13 -> K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13 K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1_1_14 -> K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14 K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1_1_15 -> K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15 K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1_2_16 -> K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16 K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1_1_17 -> K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17 K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1_1_18 -> K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18 K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1_1_19 -> K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19 K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1_2_20 -> K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20 K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1_1_21 -> K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21 K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1_1_22 -> K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22 K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1_1_23 -> K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23 K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1_1_24 -> K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24 K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1_1_25 -> K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25 K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1_1_26 -> K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26 K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1_1_27 -> K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27 K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1_1_28 -> K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28 K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1_2_29 -> K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29 K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1_1_30 -> K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30 K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1_1_31 -> K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31 K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1_1_32 -> K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32 K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1_1_33 -> K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33 K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1_1_34 -> K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34 K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1_1_35 -> K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35 K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1_1_36 -> K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36 K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1_1_37 -> K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37 K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1_2_38 -> K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38 K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1_2_39 -> K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39 K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1_2_40 -> K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40 K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1_1_41 -> K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41 K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1_1_42 -> K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42 K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1_1_43 -> K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43 K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1_1_44 -> K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44 K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1_1_45 -> K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45 K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1_1_46 -> K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46 K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1_1_47 -> K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47 K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1_1_48 -> K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48 K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1_1_49 -> K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49 K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1_1_50 -> K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50 K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1_2_51 -> K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51 K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1_1_52 -> K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52 K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1_1_53 -> K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53 K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1_1_54 -> K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54 K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1_1_55 -> K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55 K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1_1_56 -> K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56 K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1_1_57 -> K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57 K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1_1_58 -> K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58 K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1_1_59 -> K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59 K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1_1_60 -> K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60 K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1_1_61 -> K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61 K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1_1_62 -> K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62 K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1_1_63 -> K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63 K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1_2_64 -> K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64 K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1_1_65 -> K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65 K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1_1_66 -> K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66 K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1_1_67 -> K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67 K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1_1_68 -> K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68 K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1_2_69 -> K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69 K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1_1_70 -> K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70 K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1_1_71 -> K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71 K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1_1_72 -> K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72 K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1_1_73 -> K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73 K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1_1_74 -> K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74 K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1_1_75 -> K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75 K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1_1_76 -> K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76 K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1_1_77 -> K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77 K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1_1_78 -> K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78 K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1_1_79 -> K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79 K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1_1_80 -> K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80 K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1_1_81 -> K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81 K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1_1_82 -> K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82 K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1_1_83 -> K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83 Gap/Ambiguity Composition p-value 1 K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0 77.05% passed 19.90% 2 K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1 77.05% failed 4.53% 3 K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2 77.05% failed 1.21% 4 K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3 77.05% passed 25.36% 5 K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4 77.05% passed 55.86% 6 K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5 77.05% passed 35.72% 7 K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6 77.05% failed 0.71% 8 K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7 77.05% passed 85.58% 9 K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8 77.05% passed 7.28% 10 K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9 77.05% passed 23.71% 11 K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10 77.05% failed 4.76% 12 K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11 77.05% passed 36.06% 13 K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12 77.05% failed 0.72% 14 K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13 77.05% failed 0.74% 15 K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14 77.05% failed 0.54% 16 K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15 77.05% failed 1.66% 17 K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16 77.05% passed 88.47% 18 K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17 77.05% failed 0.11% 19 K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18 77.05% passed 36.61% 20 K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19 77.05% passed 81.18% 21 K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20 77.05% failed 0.00% 22 K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21 77.05% passed 14.75% 23 K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22 77.05% passed 65.23% 24 K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23 77.05% passed 15.67% 25 K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24 77.05% failed 0.02% 26 K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25 77.05% passed 56.52% 27 K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26 77.05% passed 26.05% 28 K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27 77.05% failed 1.57% 29 K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28 77.05% passed 10.98% 30 K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29 77.05% passed 27.02% 31 K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30 77.05% passed 13.08% 32 K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31 77.05% failed 0.03% 33 K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32 77.05% passed 12.47% 34 K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33 77.05% passed 7.89% 35 K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34 77.05% passed 25.36% 36 K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35 77.05% failed 0.48% 37 K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36 77.05% passed 7.92% 38 K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37 77.05% passed 41.51% 39 K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38 77.05% failed 0.24% 40 K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39 77.05% passed 41.06% 41 K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40 77.05% passed 62.06% 42 K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41 77.05% failed 0.00% 43 K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42 77.05% passed 94.90% 44 K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43 77.05% passed 21.68% 45 K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44 77.05% passed 22.88% 46 K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45 77.05% passed 32.28% 47 K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46 77.05% passed 14.89% 48 K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47 77.05% failed 3.69% 49 K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48 77.05% passed 19.81% 50 K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49 77.05% passed 8.95% 51 K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50 77.05% passed 15.20% 52 K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51 77.05% passed 16.44% 53 K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52 77.05% passed 72.71% 54 K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53 77.05% passed 46.60% 55 K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54 77.05% failed 2.49% 56 K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55 77.05% passed 25.92% 57 K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56 77.05% passed 36.75% 58 K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57 77.05% passed 12.72% 59 K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58 77.05% passed 33.57% 60 K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59 77.05% passed 89.40% 61 K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60 77.05% passed 20.77% 62 K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61 77.05% passed 20.83% 63 K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62 77.05% failed 0.48% 64 K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63 77.05% passed 16.69% 65 K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64 77.05% passed 24.64% 66 K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65 77.05% failed 1.23% 67 K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66 77.05% failed 0.65% 68 K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67 77.05% passed 68.90% 69 K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68 77.05% passed 51.19% 70 K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69 77.05% failed 0.60% 71 K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70 77.05% failed 0.10% 72 K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71 77.05% passed 5.03% 73 K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72 77.05% passed 33.28% 74 K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73 77.05% passed 50.17% 75 K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74 77.05% failed 0.26% 76 K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75 77.05% passed 6.77% 77 K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76 77.05% failed 2.37% 78 K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77 77.05% passed 10.04% 79 K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78 77.05% failed 3.16% 80 K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79 77.05% passed 32.98% 81 K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80 77.05% passed 51.70% 82 K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81 77.05% passed 14.88% 83 K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82 77.05% passed 82.25% 84 K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83 77.05% passed 68.89% WARNING: 84 sequences contain more than 50% gaps/ambiguity **** TOTAL 77.05% 26 sequences failed composition chi2 test (p-value<5%; df=3) Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds NOTE: 3 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) 1. Initial log-likelihood: -7393.152 2. Current log-likelihood: -6850.590 3. Current log-likelihood: -6814.795 4. Current log-likelihood: -6812.204 5. Current log-likelihood: -6811.732 6. Current log-likelihood: -6811.618 Optimal log-likelihood: -6811.491 Rate parameters: A-C: 1.16582 A-G: 3.17373 A-T: 0.69428 C-G: 1.33012 C-T: 3.22998 G-T: 1.00000 Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287 Site proportion and rates: (0.080,0.274) (0.303,0.606) (0.379,0.714) (0.238,2.200) Parameters optimization took 6 rounds (0.508 sec) Computing ML distances based on estimated model parameters... 0.032 sec WARNING: Some pairwise ML distances are too long (saturated) Computing BIONJ tree... 0.003 seconds Log-likelihood of BIONJ tree: -6859.680 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 1.076 second Computing log-likelihood of 98 initial trees ... 1.196 seconds Current best score: -6803.399 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -6746.667 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 4: -6743.453 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 8: -6739.399 Iteration 10 / LogL: -6755.382 / Time: 0h:0m:8s Iteration 20 / LogL: -6783.485 / Time: 0h:0m:12s Finish initializing candidate tree set (20) Current best tree score: -6739.399 / CPU time: 11.455 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 24: -6738.697 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 25: -6730.006 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 27: -6728.392 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 29: -6725.172 Iteration 30 / LogL: -6728.632 / Time: 0h:0m:15s (0h:0m:53s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 31: -6723.283 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 37: -6720.321 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 39: -6717.689 Iteration 40 / LogL: -6719.783 / Time: 0h:0m:19s (0h:0m:48s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 41: -6717.333 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 44: -6715.754 Iteration 50 / LogL: -6716.133 / Time: 0h:0m:21s (0h:0m:42s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 56: -6714.598 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 59: -6714.257 Iteration 60 / LogL: -6715.774 / Time: 0h:0m:25s (0h:0m:42s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 66: -6713.872 Iteration 70 / LogL: -6714.239 / Time: 0h:0m:28s (0h:0m:39s left) Iteration 80 / LogL: -6714.049 / Time: 0h:0m:30s (0h:0m:33s left) Iteration 90 / LogL: -6716.076 / Time: 0h:0m:33s (0h:0m:28s left) Iteration 100 / LogL: -6715.577 / Time: 0h:0m:36s (0h:0m:24s left) BETTER TREE FOUND at iteration 105: -6713.864 Iteration 110 / LogL: -6715.309 / Time: 0h:0m:39s (0h:0m:34s left) Iteration 120 / LogL: -6713.877 / Time: 0h:0m:42s (0h:0m:30s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 123: -6712.300 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 126: -6710.985 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 127: -6710.445 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 130: -6709.739 Iteration 130 / LogL: -6709.739 / Time: 0h:0m:45s (0h:0m:35s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 136: -6709.364 Iteration 140 / LogL: -6710.807 / Time: 0h:0m:48s (0h:0m:33s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 142: -6709.294 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 147: -6708.895 Iteration 150 / LogL: -6712.081 / Time: 0h:0m:51s (0h:0m:33s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 160: -6708.749 Iteration 160 / LogL: -6708.749 / Time: 0h:0m:54s (0h:0m:34s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 163: -6708.686 Iteration 170 / LogL: -6710.289 / Time: 0h:0m:57s (0h:0m:31s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 173: -6708.554 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 180: -6708.518 Iteration 180 / LogL: -6708.518 / Time: 0h:1m:0s (0h:0m:33s left) Iteration 190 / LogL: -6709.408 / Time: 0h:1m:3s (0h:0m:30s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 193: -6705.296 BETTER TREE FOUND at iteration 200: -6705.295 Iteration 200 / LogL: -6705.295 / Time: 0h:1m:6s (0h:0m:33s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 202: -6705.270 Iteration 210 / LogL: -6705.378 / Time: 0h:1m:8s (0h:0m:30s left) Iteration 220 / LogL: -6708.516 / Time: 0h:1m:11s (0h:0m:26s left) Iteration 230 / LogL: -6705.293 / Time: 0h:1m:14s (0h:0m:23s left) Iteration 240 / LogL: -6707.618 / Time: 0h:1m:17s (0h:0m:20s left) Iteration 250 / LogL: -6705.961 / Time: 0h:1m:20s (0h:0m:16s left) Iteration 260 / LogL: -6705.327 / Time: 0h:1m:22s (0h:0m:13s left) Iteration 270 / LogL: -6705.292 / Time: 0h:1m:25s (0h:0m:10s left) Iteration 280 / LogL: -6707.215 / Time: 0h:1m:28s (0h:0m:6s left) Iteration 290 / LogL: -6705.310 / Time: 0h:1m:31s (0h:0m:3s left) BETTER TREE FOUND at iteration 293: -6705.270 BETTER TREE FOUND at iteration 295: -6705.269 Iteration 300 / LogL: -6705.416 / Time: 0h:1m:33s (0h:0m:29s left) Iteration 310 / LogL: -6708.491 / Time: 0h:1m:36s (0h:0m:26s left) Iteration 320 / LogL: -6705.394 / Time: 0h:1m:39s (0h:0m:23s left) UPDATE BEST LOG-LIKELIHOOD: -6705.269 Iteration 330 / LogL: -6707.929 / Time: 0h:1m:41s (0h:0m:20s left) Iteration 340 / LogL: -6705.373 / Time: 0h:1m:44s (0h:0m:16s left) Iteration 350 / LogL: -6706.548 / Time: 0h:1m:47s (0h:0m:13s left) Iteration 360 / LogL: -6705.366 / Time: 0h:1m:50s (0h:0m:10s left) Iteration 370 / LogL: -6708.694 / Time: 0h:1m:52s (0h:0m:7s left) Iteration 380 / LogL: -6707.358 / Time: 0h:1m:55s (0h:0m:4s left) Iteration 390 / LogL: -6705.825 / Time: 0h:1m:58s (0h:0m:1s left) TREE SEARCH COMPLETED AFTER 396 ITERATIONS / Time: 0h:1m:59s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -6705.269 Optimal log-likelihood: -6705.266 Rate parameters: A-C: 1.13682 A-G: 3.52293 A-T: 0.74232 C-G: 0.82784 C-T: 3.38691 G-T: 1.00000 Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287 Site proportion and rates: (0.052,0.226) (0.340,0.517) (0.301,0.517) (0.307,2.143) Parameters optimization took 1 rounds (0.062 sec) BEST SCORE FOUND : -6705.266 Total tree length: 81.560 Total number of iterations: 396 CPU time used for tree search: 114.612 sec (0h:1m:54s) Wall-clock time used for tree search: 119.058 sec (0h:1m:59s) Total CPU time used: 115.545 sec (0h:1m:55s) Total wall-clock time used: 120.013 sec (0h:2m:0s) Analysis results written to: IQ-TREE report: clsReps.aln.iqtree Maximum-likelihood tree: clsReps.aln.treefile Likelihood distances: clsReps.aln.mldist Screen log file: clsReps.aln.log Date and Time: Tue May 28 13:11:57 2019 Working... done. Pressed and indexed 84 HMMs (84 names). Models pressed into binary file: pipelign.hmm.h3m SSI index for binary model file: pipelign.hmm.h3i Profiles (MSV part) pressed into: pipelign.hmm.h3f Profiles (remainder) pressed into: pipelign.hmm.h3p Alignment files and HMMs can be found in <files> Long sequence alignments have names <long.xx.aln> HMM file written in <long.xx.hmm> HMM database written in <pipelign.hmm> [28 May 13:12:16] Alignment with long sequences and fragments written in <final.noOrphans.aln> [28 May 13:12:16] <final.noBadSeq.aln> file created