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0
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1
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2 [28 May 13:09:56] Pipelign started with sequence file <pipelign-in1.fasta>
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3 ================================================================
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4 Program: CD-HIT, V4.8.1 (+OpenMP), May 14 2019, 14:40:47
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5 Command: cd-hit-est -c 0.8 -n 5 -i long.good.fas -o grp -d 0
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6 -T 1
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7
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8 Started: Tue May 28 13:09:56 2019
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9 ================================================================
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10 Output
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11 ----------------------------------------------------------------
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12 total seq: 100
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13 longest and shortest : 70 and 70
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14 Total letters: 7000
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15 Sequences have been sorted
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16
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17 Approximated minimal memory consumption:
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18 Sequence : 0M
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19 Buffer : 1 X 12M = 12M
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20 Table : 1 X 0M = 0M
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21 Miscellaneous : 0M
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22 Total : 12M
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23
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24 Table limit with the given memory limit:
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25 Max number of representatives: 4000000
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26 Max number of word counting entries: 98487020
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27
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28
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29 comparing sequences from 0 to 100
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30
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31 100 finished 84 clusters
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32
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33 Approximated maximum memory consumption: 12M
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34 writing new database
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35 writing clustering information
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36 program completed !
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37
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38 Total CPU time 0.04
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39 inputfile = orig
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40 84 x 70 - 70 d
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41 outputhat23=1
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42 treein = 0
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43 compacttree = 0
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44 stacksize: 8192 kb
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45 generating a scoring matrix for nucleotide (dist=200) ... done
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46 All-to-all alignment.
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47 0 / 84 (by thread 0)
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48 10 / 84 (by thread 0)
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49 20 / 84 (by thread 0)
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50 30 / 84 (by thread 0)
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51 40 / 84 (by thread 0)
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52 50 / 84 (by thread 0)
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53 60 / 84 (by thread 0)
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54 70 / 84 (by thread 0)
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55 80 / 84 (by thread 0)
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56 tbfast-pair (nuc) Version 7.407
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57 alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
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58 1 thread(s)
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59
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60 outputhat23=1
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61 Loading 'hat3.seed' ...
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62 done.
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63 Writing hat3 for iterative refinement
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64 generating a scoring matrix for nucleotide (dist=200) ... done
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65 Gap Penalty = -1.53, +0.00, +0.00
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66 tbutree = 1, compacttree = 0
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67 Constructing a UPGMA tree ...
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68
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69 0 / 84
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70 10 / 84
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71 20 / 84
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72 30 / 84
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73 40 / 84
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74 50 / 84
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75 60 / 84
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76 70 / 84
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77 80 / 84
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78 done.
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79
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80 Progressive alignment ...
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81
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82 STEP 1 /83 (thread 0)
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83 STEP 2 /83 (thread 0)
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84 STEP 3 /83 (thread 0)
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85 STEP 4 /83 (thread 0)
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86 STEP 5 /83 (thread 0)
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87 STEP 6 /83 (thread 0)
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88 STEP 7 /83 (thread 0)
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89 STEP 8 /83 (thread 0)
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90 STEP 9 /83 (thread 0)
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91 STEP 10 /83 (thread 0)
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92 STEP 11 /83 (thread 0)
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93 Reallocating (by thread 0) ..done. *alloclen = 1159
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94
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95 STEP 12 /83 (thread 0)
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96 STEP 13 /83 (thread 0)
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97 STEP 14 /83 (thread 0)
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98 STEP 15 /83 (thread 0)
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99 STEP 16 /83 (thread 0)
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100 STEP 17 /83 (thread 0)
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101 STEP 18 /83 (thread 0)
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102 STEP 19 /83 (thread 0)
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103 STEP 20 /83 (thread 0)
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104 STEP 21 /83 (thread 0)
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105 STEP 22 /83 (thread 0)
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106 STEP 23 /83 (thread 0)
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107 STEP 24 /83 (thread 0)
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108 STEP 25 /83 (thread 0)
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109 STEP 26 /83 (thread 0)
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110 STEP 27 /83 (thread 0)
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111 STEP 28 /83 (thread 0)
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112 STEP 29 /83 (thread 0)
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113 STEP 30 /83 (thread 0)
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114 STEP 31 /83 (thread 0)
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115 STEP 32 /83 (thread 0)
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116 STEP 33 /83 (thread 0)
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117 STEP 34 /83 (thread 0)
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118 STEP 35 /83 (thread 0)
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119 STEP 36 /83 (thread 0)
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120 STEP 37 /83 (thread 0)
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121 STEP 38 /83 (thread 0)
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122 STEP 39 /83 (thread 0)
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123 STEP 40 /83 (thread 0)
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124 STEP 41 /83 (thread 0)
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125 STEP 42 /83 (thread 0)
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126 STEP 43 /83 (thread 0)
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127 STEP 44 /83 (thread 0)
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128 STEP 45 /83 (thread 0)
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129 STEP 46 /83 (thread 0)
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130 STEP 47 /83 (thread 0)
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131 STEP 48 /83 (thread 0)
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132 STEP 49 /83 (thread 0)
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133 STEP 50 /83 (thread 0)
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134 STEP 51 /83 (thread 0)
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135 STEP 52 /83 (thread 0)
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136 STEP 53 /83 (thread 0)
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137 STEP 54 /83 (thread 0)
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138 STEP 55 /83 (thread 0)
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139 STEP 56 /83 (thread 0)
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140 STEP 57 /83 (thread 0)
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141 STEP 58 /83 (thread 0)
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142 STEP 59 /83 (thread 0)
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143 STEP 60 /83 (thread 0)
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144 STEP 61 /83 (thread 0)
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145 STEP 62 /83 (thread 0)
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146 STEP 63 /83 (thread 0)
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147 STEP 64 /83 (thread 0)
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148 STEP 65 /83 (thread 0)
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149 STEP 66 /83 (thread 0)
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150 STEP 67 /83 (thread 0)
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151 STEP 68 /83 (thread 0)
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152 STEP 69 /83 (thread 0)
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153 STEP 70 /83 (thread 0)
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154 STEP 71 /83 (thread 0)
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155 STEP 72 /83 (thread 0)
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156 STEP 73 /83 (thread 0)
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157 STEP 74 /83 (thread 0)
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158 STEP 75 /83 (thread 0)
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159 STEP 76 /83 (thread 0)
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160 STEP 77 /83 (thread 0)
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161 STEP 78 /83 (thread 0)
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162 STEP 79 /83 (thread 0)
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163 STEP 80 /83 (thread 0)
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164 STEP 81 /83 (thread 0)
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165 STEP 82 /83 (thread 0)
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166 STEP 83 /83 (thread 0)
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167 done.
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168 tbfast (nuc) Version 7.407
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169 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
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170 1 thread(s)
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171
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172 minimumweight = 0.000010
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173 autosubalignment = 0.000000
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174 nthread = 1
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175 randomseed = 0
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176 blosum 62 / kimura 200
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177 poffset = 0
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178 niter = 1
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179 sueff_global = 0.100000
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180 nadd = 1
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181 Loading 'hat3' ... done.
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182 generating a scoring matrix for nucleotide (dist=200) ... done
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183
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184
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185 0 / 84
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186 10 / 84
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187 20 / 84
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188 30 / 84
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189 40 / 84
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190 50 / 84
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191 60 / 84
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192 70 / 84
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193 80 / 84
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194 Segment 1/ 1 1- 271
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195 001-0000-0 (thread 1) identical
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196 001-0000-0 (thread 1) worse
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197
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198 001-0001-1 (thread 1) identical
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199 001-0001-1 (thread 1) worse
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200
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201 001-0002-0 (thread 1) identical
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202 001-0002-0 (thread 1) worse
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203
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204 001-0003-1 (thread 1) identical
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205
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206 001-0004-0 (thread 1) identical
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207 001-0004-0 (thread 1) worse
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208
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209 001-0005-1 (thread 1) identical
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210 001-0005-1 (thread 1) better
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211
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212 001-0006-0 (thread 1) identical
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213 001-0006-0 (thread 1) better
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214
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215 001-0007-1 (thread 1) identical
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216 001-0007-1 (thread 1) worse
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217
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218 001-0008-0 (thread 1) identical
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219 001-0008-0 (thread 1) worse
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220
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221 001-0009-1 (thread 1) identical
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222 001-0009-1 (thread 1) worse
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223
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224 001-0010-0 (thread 1) identical
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225 001-0010-0 (thread 1) worse
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226
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227 001-0011-1 (thread 1) identical
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228
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229 001-0012-0 (thread 1) identical
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230
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231 001-0013-1 (thread 1) identical
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232 001-0013-1 (thread 1) better
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233
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234 001-0014-0 (thread 1) identical
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235
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236 001-0015-1 (thread 1) identical
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237 001-0015-1 (thread 1) worse
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238
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239 001-0016-0 (thread 1) identical
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240
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241 001-0017-1 (thread 1) identical
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242
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243 001-0018-0 (thread 1) identical
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244 001-0018-0 (thread 1) worse
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245
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246 001-0019-1 (thread 1) identical
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247 001-0019-1 (thread 1) better
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248
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249 001-0020-0 (thread 1) identical
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250 001-0020-0 (thread 1) worse
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251
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252 001-0021-1 (thread 1) identical
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253 001-0021-1 (thread 1) better
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254
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255 001-0022-0 (thread 1) identical
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256
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257 001-0023-1 (thread 1) identical
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258 001-0023-1 (thread 1) better
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259
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260 001-0024-0 (thread 1) identical
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261 001-0024-0 (thread 1) worse
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262
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263 001-0025-1 (thread 1) identical
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264 001-0025-1 (thread 1) better
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265
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266 001-0026-0 (thread 1) identical
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267 001-0026-0 (thread 1) better
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268
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269 001-0027-1 (thread 1) identical
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270 001-0027-1 (thread 1) worse
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271
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272 001-0028-0 (thread 1) identical
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273 001-0028-0 (thread 1) worse
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274
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275 001-0029-1 (thread 1) identical
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276 001-0029-1 (thread 1) worse
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277
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278 001-0030-0 (thread 1) identical
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279 001-0030-0 (thread 1) better
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280
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281 001-0031-1 (thread 1) identical
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282 001-0031-1 (thread 1) better
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283
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284 001-0032-0 (thread 1) identical
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285 001-0032-0 (thread 1) worse
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286
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287 001-0033-1 (thread 1) identical
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288 001-0033-1 (thread 1) better
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289
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290 001-0034-0 (thread 1) identical
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291 001-0034-0 (thread 1) better
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292
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293 001-0035-1 (thread 1) identical
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294 001-0035-1 (thread 1) worse
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295
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296 001-0036-0 (thread 1) identical
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297 001-0036-0 (thread 1) worse
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298
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299 001-0037-1 (thread 1) identical
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300 001-0037-1 (thread 1) better
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301
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302 001-0038-0 (thread 1) identical
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303 001-0038-0 (thread 1) better
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304
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305 001-0039-1 (thread 1) identical
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306 001-0039-1 (thread 1) better
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307
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308 001-0040-0 (thread 1) identical
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309 001-0040-0 (thread 1) worse
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310
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311 001-0041-1 (thread 1) identical
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312 001-0041-1 (thread 1) better
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313
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314 001-0042-0 (thread 1) identical
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315 001-0042-0 (thread 1) worse
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316
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317 001-0043-1 (thread 1) identical
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318 001-0043-1 (thread 1) better
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319
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320 001-0044-0 (thread 1) identical
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321 001-0044-0 (thread 1) worse
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322
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323 001-0045-1 (thread 1) identical
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324 001-0045-1 (thread 1) better
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325
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326 001-0046-0 (thread 1) identical
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327 001-0046-0 (thread 1) worse
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328
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329 001-0047-1 (thread 1) identical
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330 001-0047-1 (thread 1) worse
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331
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332 001-0048-0 (thread 1) identical
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333 001-0048-0 (thread 1) worse
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334
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335 001-0049-1 (thread 1) identical
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336 001-0049-1 (thread 1) worse
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337
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338 001-0050-0 (thread 1) identical
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339 001-0050-0 (thread 1) worse
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340
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341 001-0051-1 (thread 1) identical
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342
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343 001-0052-0 (thread 1) identical
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344 001-0052-0 (thread 1) worse
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345
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346 001-0053-1 (thread 1) identical
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347 001-0053-1 (thread 1) worse
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348
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349 001-0054-0 (thread 1) identical
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350 001-0054-0 (thread 1) better
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351
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352 001-0055-1 (thread 1) identical
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353 001-0055-1 (thread 1) better
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354
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355 001-0056-0 (thread 1) identical
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356 001-0056-0 (thread 1) worse
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357
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358 001-0057-1 (thread 1) identical
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359 001-0057-1 (thread 1) worse
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360
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361 001-0058-0 (thread 1) identical
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362
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363 001-0059-1 (thread 1) identical
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364 001-0059-1 (thread 1) better
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365
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366 001-0060-0 (thread 1) identical
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367 001-0060-0 (thread 1) worse
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368
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369 001-0061-1 (thread 1) identical
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370 001-0061-1 (thread 1) worse
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371
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372 001-0062-0 (thread 1) identical
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373 001-0062-0 (thread 1) better
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374
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375 001-0063-1 (thread 1) identical
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376 001-0063-1 (thread 1) worse
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377
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378 001-0064-0 (thread 1) identical
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379 001-0064-0 (thread 1) worse
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380
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381 001-0065-1 (thread 1) identical
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382 001-0065-1 (thread 1) better
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383
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384 001-0066-0 (thread 1) identical
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385 001-0066-0 (thread 1) better
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386
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387 001-0067-1 (thread 1) identical
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388 001-0067-1 (thread 1) better
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389
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390 001-0068-0 (thread 1) identical
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391 001-0068-0 (thread 1) worse
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392
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393 001-0069-1 (thread 1) identical
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394 001-0069-1 (thread 1) worse
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395
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396 001-0070-0 (thread 1) identical
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397 001-0070-0 (thread 1) worse
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398
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399 001-0071-1 (thread 1) identical
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400 001-0071-1 (thread 1) better
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401
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402 001-0072-0 (thread 1) identical
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403
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404 001-0073-1 (thread 1) identical
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405 001-0073-1 (thread 1) better
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406
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407 001-0074-0 (thread 1) identical
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408 001-0074-0 (thread 1) worse
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409
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410 001-0075-1 (thread 1) identical
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411 001-0075-1 (thread 1) better
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412
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413 001-0076-0 (thread 1) identical
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414 001-0076-0 (thread 1) better
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415
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416 001-0077-1 (thread 1) identical
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417 001-0077-1 (thread 1) better
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418
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419 001-0078-0 (thread 1) identical
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420 001-0078-0 (thread 1) worse
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421
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422 001-0079-1 (thread 1) identical
|
|
|
423 001-0079-1 (thread 1) worse
|
|
|
424
|
|
|
425 001-0080-0 (thread 1) identical
|
|
|
426 001-0080-0 (thread 1) worse
|
|
|
427
|
|
|
428 001-0081-1 (thread 1) identical
|
|
|
429 001-0081-1 (thread 1) worse
|
|
|
430
|
|
|
431 001-0082-0 (thread 1) identical
|
|
|
432
|
|
|
433 001-0083-1 (thread 1) identical
|
|
|
434 001-0083-1 (thread 1) better
|
|
|
435
|
|
|
436 001-0084-0 (thread 1) identical
|
|
|
437 001-0084-0 (thread 1) worse
|
|
|
438
|
|
|
439 001-0085-1 (thread 1) identical
|
|
|
440 001-0085-1 (thread 1) worse
|
|
|
441
|
|
|
442 001-0086-0 (thread 1) identical
|
|
|
443 001-0086-0 (thread 1) worse
|
|
|
444
|
|
|
445 001-0087-1 (thread 1) identical
|
|
|
446
|
|
|
447 001-0088-0 (thread 1) identical
|
|
|
448 001-0088-0 (thread 1) worse
|
|
|
449
|
|
|
450 001-0089-1 (thread 1) identical
|
|
|
451 001-0089-1 (thread 1) worse
|
|
|
452
|
|
|
453 001-0090-0 (thread 1) identical
|
|
|
454 001-0090-0 (thread 1) better
|
|
|
455
|
|
|
456 001-0091-1 (thread 1) identical
|
|
|
457 001-0091-1 (thread 1) better
|
|
|
458
|
|
|
459 001-0092-0 (thread 1) identical
|
|
|
460 001-0092-0 (thread 1) worse
|
|
|
461
|
|
|
462 001-0093-1 (thread 1) identical
|
|
|
463 001-0093-1 (thread 1) better
|
|
|
464
|
|
|
465 001-0094-0 (thread 1) identical
|
|
|
466 001-0094-0 (thread 1) better
|
|
|
467
|
|
|
468 001-0095-1 (thread 1) identical
|
|
|
469 001-0095-1 (thread 1) better
|
|
|
470
|
|
|
471 001-0096-0 (thread 1) identical
|
|
|
472 001-0096-0 (thread 1) worse
|
|
|
473
|
|
|
474 001-0097-1 (thread 1) identical
|
|
|
475 001-0097-1 (thread 1) worse
|
|
|
476
|
|
|
477 001-0098-0 (thread 1) identical
|
|
|
478 001-0098-0 (thread 1) worse
|
|
|
479
|
|
|
480 001-0099-1 (thread 1) identical
|
|
|
481 001-0099-1 (thread 1) worse
|
|
|
482
|
|
|
483 001-0100-0 (thread 1) identical
|
|
|
484 001-0100-0 (thread 1) worse
|
|
|
485
|
|
|
486 001-0101-1 (thread 1) identical
|
|
|
487 001-0101-1 (thread 1) worse
|
|
|
488
|
|
|
489 001-0102-0 (thread 1) identical
|
|
|
490
|
|
|
491 001-0103-1 (thread 1) identical
|
|
|
492
|
|
|
493 001-0104-0 (thread 1) identical
|
|
|
494 001-0104-0 (thread 1) worse
|
|
|
495
|
|
|
496 001-0105-1 (thread 1) identical
|
|
|
497 001-0105-1 (thread 1) better
|
|
|
498
|
|
|
499 001-0106-0 (thread 1) identical
|
|
|
500
|
|
|
501 001-0107-1 (thread 1) identical
|
|
|
502
|
|
|
503 001-0108-0 (thread 1) identical
|
|
|
504 001-0108-0 (thread 1) worse
|
|
|
505
|
|
|
506 001-0109-1 (thread 1) identical
|
|
|
507 001-0109-1 (thread 1) better
|
|
|
508
|
|
|
509 001-0110-0 (thread 1) identical
|
|
|
510 001-0110-0 (thread 1) better
|
|
|
511
|
|
|
512 001-0111-1 (thread 1) identical
|
|
|
513 001-0111-1 (thread 1) better
|
|
|
514
|
|
|
515 001-0112-0 (thread 1) identical
|
|
|
516
|
|
|
517 001-0113-1 (thread 1) identical
|
|
|
518 001-0113-1 (thread 1) better
|
|
|
519
|
|
|
520 001-0114-0 (thread 1) identical
|
|
|
521 001-0114-0 (thread 1) worse
|
|
|
522
|
|
|
523 001-0115-1 (thread 1) identical
|
|
|
524 001-0115-1 (thread 1) better
|
|
|
525
|
|
|
526 001-0116-0 (thread 1) identical
|
|
|
527 001-0116-0 (thread 1) worse
|
|
|
528
|
|
|
529 001-0117-1 (thread 1) identical
|
|
|
530 001-0117-1 (thread 1) worse
|
|
|
531
|
|
|
532 001-0118-0 (thread 1) identical
|
|
|
533 001-0118-0 (thread 1) better
|
|
|
534
|
|
|
535 001-0119-1 (thread 1) identical
|
|
|
536
|
|
|
537 001-0120-0 (thread 1) identical
|
|
|
538 001-0120-0 (thread 1) worse
|
|
|
539
|
|
|
540 001-0121-1 (thread 1) identical
|
|
|
541 001-0121-1 (thread 1) worse
|
|
|
542
|
|
|
543 001-0122-0 (thread 1) identical
|
|
|
544 001-0122-0 (thread 1) better
|
|
|
545
|
|
|
546 001-0123-1 (thread 1) identical
|
|
|
547
|
|
|
548 001-0124-0 (thread 1) identical
|
|
|
549 001-0124-0 (thread 1) better
|
|
|
550
|
|
|
551 001-0125-1 (thread 1) identical
|
|
|
552 001-0125-1 (thread 1) better
|
|
|
553
|
|
|
554 001-0126-0 (thread 1) identical
|
|
|
555
|
|
|
556 001-0127-1 (thread 1) identical
|
|
|
557 001-0127-1 (thread 1) worse
|
|
|
558
|
|
|
559 001-0128-0 (thread 1) identical
|
|
|
560 001-0128-0 (thread 1) worse
|
|
|
561
|
|
|
562 001-0129-1 (thread 1) identical
|
|
|
563 001-0129-1 (thread 1) worse
|
|
|
564
|
|
|
565 001-0130-0 (thread 1) identical
|
|
|
566 001-0130-0 (thread 1) better
|
|
|
567
|
|
|
568 001-0131-1 (thread 1) identical
|
|
|
569 001-0131-1 (thread 1) better
|
|
|
570
|
|
|
571 001-0132-0 (thread 1) identical
|
|
|
572 001-0132-0 (thread 1) better
|
|
|
573
|
|
|
574 001-0133-1 (thread 1) identical
|
|
|
575
|
|
|
576 001-0134-0 (thread 1) identical
|
|
|
577 001-0134-0 (thread 1) worse
|
|
|
578
|
|
|
579 001-0135-1 (thread 1) identical
|
|
|
580
|
|
|
581 001-0136-0 (thread 1) identical
|
|
|
582
|
|
|
583 001-0137-1 (thread 1) identical
|
|
|
584 001-0137-1 (thread 1) worse
|
|
|
585
|
|
|
586 001-0138-0 (thread 1) identical
|
|
|
587 001-0138-0 (thread 1) worse
|
|
|
588
|
|
|
589 001-0139-1 (thread 1) identical
|
|
|
590 001-0139-1 (thread 1) better
|
|
|
591
|
|
|
592 001-0140-0 (thread 1) identical
|
|
|
593
|
|
|
594 001-0141-1 (thread 1) identical
|
|
|
595 001-0141-1 (thread 1) better
|
|
|
596
|
|
|
597 001-0142-0 (thread 1) identical
|
|
|
598
|
|
|
599 001-0143-1 (thread 1) identical
|
|
|
600 001-0143-1 (thread 1) worse
|
|
|
601
|
|
|
602 001-0144-0 (thread 1) identical
|
|
|
603 001-0144-0 (thread 1) worse
|
|
|
604
|
|
|
605 001-0145-1 (thread 1) identical
|
|
|
606 001-0145-1 (thread 1) better
|
|
|
607
|
|
|
608 001-0146-0 (thread 1) identical
|
|
|
609 001-0146-0 (thread 1) better
|
|
|
610
|
|
|
611 001-0147-1 (thread 1) identical
|
|
|
612 001-0147-1 (thread 1) worse
|
|
|
613
|
|
|
614 001-0148-0 (thread 1) identical
|
|
|
615
|
|
|
616 001-0149-1 (thread 1) identical
|
|
|
617 001-0149-1 (thread 1) better
|
|
|
618
|
|
|
619 001-0150-0 (thread 1) identical
|
|
|
620
|
|
|
621 001-0151-1 (thread 1) identical
|
|
|
622
|
|
|
623 001-0152-0 (thread 1) identical
|
|
|
624
|
|
|
625 001-0153-1 (thread 1) identical
|
|
|
626
|
|
|
627 001-0154-0 (thread 1) identical
|
|
|
628
|
|
|
629 001-0155-1 (thread 1) identical
|
|
|
630
|
|
|
631 001-0156-0 (thread 1) identical
|
|
|
632
|
|
|
633 001-0157-1 (thread 1) identical
|
|
|
634 001-0157-1 (thread 1) worse
|
|
|
635
|
|
|
636 001-0158-0 (thread 1) identical
|
|
|
637
|
|
|
638 001-0159-1 (thread 1) identical
|
|
|
639 001-0159-1 (thread 1) worse
|
|
|
640
|
|
|
641 001-0160-0 (thread 1) identical
|
|
|
642 001-0160-0 (thread 1) worse
|
|
|
643
|
|
|
644 001-0161-1 (thread 1) identical
|
|
|
645 001-0161-1 (thread 1) worse
|
|
|
646
|
|
|
647 001-0162-0 (thread 1) identical
|
|
|
648 001-0162-0 (thread 1) worse
|
|
|
649
|
|
|
650 001-0163-1 (thread 1) identical
|
|
|
651 001-0163-1 (thread 1) worse
|
|
|
652
|
|
|
653 001-0164-1 (thread 1) identical
|
|
|
654 001-0164-1 (thread 1) worse
|
|
|
655
|
|
|
656 Reached 1
|
|
|
657 done
|
|
|
658 dvtditr (nuc) Version 7.407
|
|
|
659 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
|
|
|
660 1 thread(s)
|
|
|
661
|
|
|
662
|
|
|
663 Strategy:
|
|
|
664 L-INS-i (Probably most accurate, very slow)
|
|
|
665 Iterative refinement method (<1) with LOCAL pairwise alignment information
|
|
|
666
|
|
|
667 If unsure which option to use, try 'mafft --auto input > output'.
|
|
|
668 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
|
|
|
669
|
|
|
670 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
|
|
|
671 It tends to insert more gaps into gap-rich regions than previous versions.
|
|
|
672 To disable this change, add the --leavegappyregion option.
|
|
|
673
|
|
|
674 IQ-TREE multicore version 1.6.10 for Linux 64-bit built Mar 21 2019
|
|
|
675 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
|
|
|
676 Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
|
|
|
677
|
|
|
678 Host: gaius (AVX2, FMA3, 15 GB RAM)
|
|
|
679 Command: iqtree -s clsReps.aln -m GTR+R4 -nt 1
|
|
|
680 Seed: 50990 (Using SPRNG - Scalable Parallel Random Number Generator)
|
|
|
681 Time: Tue May 28 13:09:57 2019
|
|
|
682 Kernel: AVX+FMA - 1 threads (8 CPU cores detected)
|
|
|
683
|
|
|
684 HINT: Use -nt option to specify number of threads because your CPU has 8 cores!
|
|
|
685 HINT: -nt AUTO will automatically determine the best number of threads to use.
|
|
|
686
|
|
|
687 Reading alignment file clsReps.aln ... Fasta format detected
|
|
|
688 Alignment most likely contains DNA/RNA sequences
|
|
|
689 Alignment has 84 sequences with 305 columns, 301 distinct patterns
|
|
|
690 238 parsimony-informative, 52 singleton sites, 15 constant sites
|
|
|
691 WARNING: Some sequence names are changed as follows:
|
|
|
692 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
|
|
|
693 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
|
|
|
694 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
|
|
|
695 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
|
|
|
696 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
|
|
|
697 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
|
|
|
698 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
|
|
|
699 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
|
|
|
700 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
|
|
|
701 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
|
|
|
702 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
|
|
|
703 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
|
|
|
704 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
|
|
|
705 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
|
|
|
706 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
|
|
|
707 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
|
|
|
708 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
|
|
|
709 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
|
|
|
710 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
|
|
|
711 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
|
|
|
712 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
|
|
|
713 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
|
|
|
714 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
|
|
|
715 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
|
|
|
716 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
|
|
|
717 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
|
|
|
718 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
|
|
|
719 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
|
|
|
720 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
|
|
|
721 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
|
|
|
722 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
|
|
|
723 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
|
|
|
724 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
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725 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
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|
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726 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
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|
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727 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
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728 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
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|
|
729 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
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|
|
730 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
|
|
|
731 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
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|
732 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
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|
733 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
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|
|
734 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
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|
|
735 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
|
|
|
736 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
|
|
|
737 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
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|
|
738 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
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|
|
739 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
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|
|
740 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
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|
|
741 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
|
|
|
742 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
|
|
|
743 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
|
|
|
744 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
|
|
|
745 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
|
|
|
746 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
|
|
|
747 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
|
|
|
748 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
|
|
|
749 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
|
|
|
750 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
|
|
|
751 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
|
|
|
752 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
|
|
|
753 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
|
|
|
754 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
|
|
|
755 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
|
|
|
756 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
|
|
|
757 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
|
|
|
758 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
|
|
|
759 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
|
|
|
760 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
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|
|
761 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
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762 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
|
|
|
763 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
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764 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
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|
|
765 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
|
|
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766 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
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767 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
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|
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768 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
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769 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
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770 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
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771 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
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772 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
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773 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
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774 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
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775 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
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|
|
776
|
|
|
777 Gap/Ambiguity Composition p-value
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778 1 K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0 77.05% passed 19.90%
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779 2 K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1 77.05% failed 4.53%
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780 3 K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2 77.05% failed 1.21%
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781 4 K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3 77.05% passed 25.36%
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782 5 K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4 77.05% passed 55.86%
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|
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783 6 K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5 77.05% passed 35.72%
|
|
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784 7 K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6 77.05% failed 0.71%
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785 8 K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7 77.05% passed 85.58%
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|
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786 9 K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8 77.05% passed 7.28%
|
|
|
787 10 K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9 77.05% passed 23.71%
|
|
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788 11 K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10 77.05% failed 4.76%
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|
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789 12 K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11 77.05% passed 36.06%
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790 13 K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12 77.05% failed 0.72%
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791 14 K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13 77.05% failed 0.74%
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792 15 K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14 77.05% failed 0.54%
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793 16 K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15 77.05% failed 1.66%
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794 17 K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16 77.05% passed 88.47%
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795 18 K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17 77.05% failed 0.11%
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796 19 K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18 77.05% passed 36.61%
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797 20 K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19 77.05% passed 81.18%
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798 21 K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20 77.05% failed 0.00%
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|
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799 22 K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21 77.05% passed 14.75%
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800 23 K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22 77.05% passed 65.23%
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801 24 K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23 77.05% passed 15.67%
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802 25 K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24 77.05% failed 0.02%
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803 26 K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25 77.05% passed 56.52%
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804 27 K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26 77.05% passed 26.05%
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805 28 K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27 77.05% failed 1.57%
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806 29 K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28 77.05% passed 10.98%
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807 30 K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29 77.05% passed 27.02%
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808 31 K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30 77.05% passed 13.08%
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809 32 K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31 77.05% failed 0.03%
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810 33 K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32 77.05% passed 12.47%
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811 34 K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33 77.05% passed 7.89%
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812 35 K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34 77.05% passed 25.36%
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813 36 K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35 77.05% failed 0.48%
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814 37 K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36 77.05% passed 7.92%
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815 38 K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37 77.05% passed 41.51%
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816 39 K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38 77.05% failed 0.24%
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817 40 K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39 77.05% passed 41.06%
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818 41 K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40 77.05% passed 62.06%
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819 42 K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41 77.05% failed 0.00%
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820 43 K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42 77.05% passed 94.90%
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821 44 K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43 77.05% passed 21.68%
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822 45 K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44 77.05% passed 22.88%
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823 46 K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45 77.05% passed 32.28%
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824 47 K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46 77.05% passed 14.89%
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825 48 K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47 77.05% failed 3.69%
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826 49 K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48 77.05% passed 19.81%
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827 50 K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49 77.05% passed 8.95%
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828 51 K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50 77.05% passed 15.20%
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829 52 K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51 77.05% passed 16.44%
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830 53 K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52 77.05% passed 72.71%
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831 54 K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53 77.05% passed 46.60%
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832 55 K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54 77.05% failed 2.49%
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833 56 K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55 77.05% passed 25.92%
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834 57 K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56 77.05% passed 36.75%
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835 58 K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57 77.05% passed 12.72%
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836 59 K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58 77.05% passed 33.57%
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837 60 K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59 77.05% passed 89.40%
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838 61 K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60 77.05% passed 20.77%
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839 62 K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61 77.05% passed 20.83%
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840 63 K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62 77.05% failed 0.48%
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|
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841 64 K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63 77.05% passed 16.69%
|
|
|
842 65 K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64 77.05% passed 24.64%
|
|
|
843 66 K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65 77.05% failed 1.23%
|
|
|
844 67 K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66 77.05% failed 0.65%
|
|
|
845 68 K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67 77.05% passed 68.90%
|
|
|
846 69 K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68 77.05% passed 51.19%
|
|
|
847 70 K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69 77.05% failed 0.60%
|
|
|
848 71 K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70 77.05% failed 0.10%
|
|
|
849 72 K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71 77.05% passed 5.03%
|
|
|
850 73 K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72 77.05% passed 33.28%
|
|
|
851 74 K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73 77.05% passed 50.17%
|
|
|
852 75 K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74 77.05% failed 0.26%
|
|
|
853 76 K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75 77.05% passed 6.77%
|
|
|
854 77 K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76 77.05% failed 2.37%
|
|
|
855 78 K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77 77.05% passed 10.04%
|
|
|
856 79 K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78 77.05% failed 3.16%
|
|
|
857 80 K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79 77.05% passed 32.98%
|
|
|
858 81 K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80 77.05% passed 51.70%
|
|
|
859 82 K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81 77.05% passed 14.88%
|
|
|
860 83 K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82 77.05% passed 82.25%
|
|
|
861 84 K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83 77.05% passed 68.89%
|
|
|
862 WARNING: 84 sequences contain more than 50% gaps/ambiguity
|
|
|
863 **** TOTAL 77.05% 26 sequences failed composition chi2 test (p-value<5%; df=3)
|
|
|
864
|
|
|
865 Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds
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|
|
866
|
|
|
867 NOTE: 3 MB RAM (0 GB) is required!
|
|
|
868 Estimate model parameters (epsilon = 0.100)
|
|
|
869 1. Initial log-likelihood: -7393.152
|
|
|
870 2. Current log-likelihood: -6850.590
|
|
|
871 3. Current log-likelihood: -6814.795
|
|
|
872 4. Current log-likelihood: -6812.204
|
|
|
873 5. Current log-likelihood: -6811.732
|
|
|
874 6. Current log-likelihood: -6811.618
|
|
|
875 Optimal log-likelihood: -6811.491
|
|
|
876 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
|
|
|
877 Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287
|
|
|
878 Site proportion and rates: (0.080,0.274) (0.303,0.606) (0.379,0.714) (0.238,2.200)
|
|
|
879 Parameters optimization took 6 rounds (0.508 sec)
|
|
|
880 Computing ML distances based on estimated model parameters... 0.032 sec
|
|
|
881 WARNING: Some pairwise ML distances are too long (saturated)
|
|
|
882 Computing BIONJ tree...
|
|
|
883 0.003 seconds
|
|
|
884 Log-likelihood of BIONJ tree: -6859.680
|
|
|
885 --------------------------------------------------------------------
|
|
|
886 | INITIALIZING CANDIDATE TREE SET |
|
|
|
887 --------------------------------------------------------------------
|
|
|
888 Generating 98 parsimony trees... 1.076 second
|
|
|
889 Computing log-likelihood of 98 initial trees ... 1.196 seconds
|
|
|
890 Current best score: -6803.399
|
|
|
891
|
|
|
892 Do NNI search on 20 best initial trees
|
|
|
893 Estimate model parameters (epsilon = 0.100)
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|
|
894 BETTER TREE FOUND at iteration 1: -6746.667
|
|
|
895 Estimate model parameters (epsilon = 0.100)
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896 BETTER TREE FOUND at iteration 4: -6743.453
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|
897 Estimate model parameters (epsilon = 0.100)
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898 BETTER TREE FOUND at iteration 8: -6739.399
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899 Iteration 10 / LogL: -6755.382 / Time: 0h:0m:8s
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900 Iteration 20 / LogL: -6783.485 / Time: 0h:0m:12s
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901 Finish initializing candidate tree set (20)
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902 Current best tree score: -6739.399 / CPU time: 11.455
|
|
|
903 Number of iterations: 20
|
|
|
904 --------------------------------------------------------------------
|
|
|
905 | OPTIMIZING CANDIDATE TREE SET |
|
|
|
906 --------------------------------------------------------------------
|
|
|
907 Estimate model parameters (epsilon = 0.100)
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|
|
908 BETTER TREE FOUND at iteration 24: -6738.697
|
|
|
909 Estimate model parameters (epsilon = 0.100)
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|
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910 BETTER TREE FOUND at iteration 25: -6730.006
|
|
|
911 Estimate model parameters (epsilon = 0.100)
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|
|
912 BETTER TREE FOUND at iteration 27: -6728.392
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|
913 Estimate model parameters (epsilon = 0.100)
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914 BETTER TREE FOUND at iteration 29: -6725.172
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|
915 Iteration 30 / LogL: -6728.632 / Time: 0h:0m:15s (0h:0m:53s left)
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916 Estimate model parameters (epsilon = 0.100)
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|
917 BETTER TREE FOUND at iteration 31: -6723.283
|
|
|
918 Estimate model parameters (epsilon = 0.100)
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|
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919 BETTER TREE FOUND at iteration 37: -6720.321
|
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|
920 Estimate model parameters (epsilon = 0.100)
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|
|
921 BETTER TREE FOUND at iteration 39: -6717.689
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|
922 Iteration 40 / LogL: -6719.783 / Time: 0h:0m:19s (0h:0m:48s left)
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923 Estimate model parameters (epsilon = 0.100)
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|
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924 BETTER TREE FOUND at iteration 41: -6717.333
|
|
|
925 Estimate model parameters (epsilon = 0.100)
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|
926 BETTER TREE FOUND at iteration 44: -6715.754
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927 Iteration 50 / LogL: -6716.133 / Time: 0h:0m:21s (0h:0m:42s left)
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928 Estimate model parameters (epsilon = 0.100)
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|
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929 BETTER TREE FOUND at iteration 56: -6714.598
|
|
|
930 Estimate model parameters (epsilon = 0.100)
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|
931 BETTER TREE FOUND at iteration 59: -6714.257
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|
932 Iteration 60 / LogL: -6715.774 / Time: 0h:0m:25s (0h:0m:42s left)
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933 Estimate model parameters (epsilon = 0.100)
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934 BETTER TREE FOUND at iteration 66: -6713.872
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935 Iteration 70 / LogL: -6714.239 / Time: 0h:0m:28s (0h:0m:39s left)
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936 Iteration 80 / LogL: -6714.049 / Time: 0h:0m:30s (0h:0m:33s left)
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937 Iteration 90 / LogL: -6716.076 / Time: 0h:0m:33s (0h:0m:28s left)
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938 Iteration 100 / LogL: -6715.577 / Time: 0h:0m:36s (0h:0m:24s left)
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939 BETTER TREE FOUND at iteration 105: -6713.864
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940 Iteration 110 / LogL: -6715.309 / Time: 0h:0m:39s (0h:0m:34s left)
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941 Iteration 120 / LogL: -6713.877 / Time: 0h:0m:42s (0h:0m:30s left)
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942 Estimate model parameters (epsilon = 0.100)
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943 BETTER TREE FOUND at iteration 123: -6712.300
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|
944 Estimate model parameters (epsilon = 0.100)
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945 BETTER TREE FOUND at iteration 126: -6710.985
|
|
|
946 Estimate model parameters (epsilon = 0.100)
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|
|
947 BETTER TREE FOUND at iteration 127: -6710.445
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|
948 Estimate model parameters (epsilon = 0.100)
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|
|
949 BETTER TREE FOUND at iteration 130: -6709.739
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|
950 Iteration 130 / LogL: -6709.739 / Time: 0h:0m:45s (0h:0m:35s left)
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951 Estimate model parameters (epsilon = 0.100)
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952 BETTER TREE FOUND at iteration 136: -6709.364
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|
953 Iteration 140 / LogL: -6710.807 / Time: 0h:0m:48s (0h:0m:33s left)
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954 Estimate model parameters (epsilon = 0.100)
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|
|
955 BETTER TREE FOUND at iteration 142: -6709.294
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|
956 Estimate model parameters (epsilon = 0.100)
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|
|
957 BETTER TREE FOUND at iteration 147: -6708.895
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|
958 Iteration 150 / LogL: -6712.081 / Time: 0h:0m:51s (0h:0m:33s left)
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959 Estimate model parameters (epsilon = 0.100)
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|
|
960 BETTER TREE FOUND at iteration 160: -6708.749
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|
961 Iteration 160 / LogL: -6708.749 / Time: 0h:0m:54s (0h:0m:34s left)
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962 Estimate model parameters (epsilon = 0.100)
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|
|
963 BETTER TREE FOUND at iteration 163: -6708.686
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964 Iteration 170 / LogL: -6710.289 / Time: 0h:0m:57s (0h:0m:31s left)
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|
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965 Estimate model parameters (epsilon = 0.100)
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|
|
966 BETTER TREE FOUND at iteration 173: -6708.554
|
|
|
967 Estimate model parameters (epsilon = 0.100)
|
|
|
968 BETTER TREE FOUND at iteration 180: -6708.518
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|
969 Iteration 180 / LogL: -6708.518 / Time: 0h:1m:0s (0h:0m:33s left)
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970 Iteration 190 / LogL: -6709.408 / Time: 0h:1m:3s (0h:0m:30s left)
|
|
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971 Estimate model parameters (epsilon = 0.100)
|
|
|
972 BETTER TREE FOUND at iteration 193: -6705.296
|
|
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973 BETTER TREE FOUND at iteration 200: -6705.295
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|
974 Iteration 200 / LogL: -6705.295 / Time: 0h:1m:6s (0h:0m:33s left)
|
|
|
975 Estimate model parameters (epsilon = 0.100)
|
|
|
976 BETTER TREE FOUND at iteration 202: -6705.270
|
|
|
977 Iteration 210 / LogL: -6705.378 / Time: 0h:1m:8s (0h:0m:30s left)
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978 Iteration 220 / LogL: -6708.516 / Time: 0h:1m:11s (0h:0m:26s left)
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979 Iteration 230 / LogL: -6705.293 / Time: 0h:1m:14s (0h:0m:23s left)
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980 Iteration 240 / LogL: -6707.618 / Time: 0h:1m:17s (0h:0m:20s left)
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981 Iteration 250 / LogL: -6705.961 / Time: 0h:1m:20s (0h:0m:16s left)
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982 Iteration 260 / LogL: -6705.327 / Time: 0h:1m:22s (0h:0m:13s left)
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983 Iteration 270 / LogL: -6705.292 / Time: 0h:1m:25s (0h:0m:10s left)
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984 Iteration 280 / LogL: -6707.215 / Time: 0h:1m:28s (0h:0m:6s left)
|
|
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985 Iteration 290 / LogL: -6705.310 / Time: 0h:1m:31s (0h:0m:3s left)
|
|
|
986 BETTER TREE FOUND at iteration 293: -6705.270
|
|
|
987 BETTER TREE FOUND at iteration 295: -6705.269
|
|
|
988 Iteration 300 / LogL: -6705.416 / Time: 0h:1m:33s (0h:0m:29s left)
|
|
|
989 Iteration 310 / LogL: -6708.491 / Time: 0h:1m:36s (0h:0m:26s left)
|
|
|
990 Iteration 320 / LogL: -6705.394 / Time: 0h:1m:39s (0h:0m:23s left)
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|
|
991 UPDATE BEST LOG-LIKELIHOOD: -6705.269
|
|
|
992 Iteration 330 / LogL: -6707.929 / Time: 0h:1m:41s (0h:0m:20s left)
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|
|
993 Iteration 340 / LogL: -6705.373 / Time: 0h:1m:44s (0h:0m:16s left)
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|
|
994 Iteration 350 / LogL: -6706.548 / Time: 0h:1m:47s (0h:0m:13s left)
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|
|
995 Iteration 360 / LogL: -6705.366 / Time: 0h:1m:50s (0h:0m:10s left)
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|
|
996 Iteration 370 / LogL: -6708.694 / Time: 0h:1m:52s (0h:0m:7s left)
|
|
|
997 Iteration 380 / LogL: -6707.358 / Time: 0h:1m:55s (0h:0m:4s left)
|
|
|
998 Iteration 390 / LogL: -6705.825 / Time: 0h:1m:58s (0h:0m:1s left)
|
|
|
999 TREE SEARCH COMPLETED AFTER 396 ITERATIONS / Time: 0h:1m:59s
|
|
|
1000
|
|
|
1001 --------------------------------------------------------------------
|
|
|
1002 | FINALIZING TREE SEARCH |
|
|
|
1003 --------------------------------------------------------------------
|
|
|
1004 Performs final model parameters optimization
|
|
|
1005 Estimate model parameters (epsilon = 0.010)
|
|
|
1006 1. Initial log-likelihood: -6705.269
|
|
|
1007 Optimal log-likelihood: -6705.266
|
|
|
1008 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
|
|
|
1009 Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287
|
|
|
1010 Site proportion and rates: (0.052,0.226) (0.340,0.517) (0.301,0.517) (0.307,2.143)
|
|
|
1011 Parameters optimization took 1 rounds (0.062 sec)
|
|
|
1012 BEST SCORE FOUND : -6705.266
|
|
|
1013 Total tree length: 81.560
|
|
|
1014
|
|
|
1015 Total number of iterations: 396
|
|
|
1016 CPU time used for tree search: 114.612 sec (0h:1m:54s)
|
|
|
1017 Wall-clock time used for tree search: 119.058 sec (0h:1m:59s)
|
|
|
1018 Total CPU time used: 115.545 sec (0h:1m:55s)
|
|
|
1019 Total wall-clock time used: 120.013 sec (0h:2m:0s)
|
|
|
1020
|
|
|
1021 Analysis results written to:
|
|
|
1022 IQ-TREE report: clsReps.aln.iqtree
|
|
|
1023 Maximum-likelihood tree: clsReps.aln.treefile
|
|
|
1024 Likelihood distances: clsReps.aln.mldist
|
|
|
1025 Screen log file: clsReps.aln.log
|
|
|
1026
|
|
|
1027 Date and Time: Tue May 28 13:11:57 2019
|
|
|
1028 Working... done.
|
|
|
1029 Pressed and indexed 84 HMMs (84 names).
|
|
|
1030 Models pressed into binary file: pipelign.hmm.h3m
|
|
|
1031 SSI index for binary model file: pipelign.hmm.h3i
|
|
|
1032 Profiles (MSV part) pressed into: pipelign.hmm.h3f
|
|
|
1033 Profiles (remainder) pressed into: pipelign.hmm.h3p
|
|
|
1034
|
|
|
1035 Alignment files and HMMs can be found in <files>
|
|
|
1036 Long sequence alignments have names <long.xx.aln>
|
|
|
1037 HMM file written in <long.xx.hmm>
|
|
|
1038 HMM database written in <pipelign.hmm>
|
|
|
1039
|
|
|
1040 [28 May 13:12:16] Alignment with long sequences and fragments written in <final.noOrphans.aln>
|
|
|
1041
|
|
|
1042 [28 May 13:12:16] <final.noBadSeq.aln> file created
|
