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1 #############################################
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2 ###### SICER v1.1 ######
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3 #############################################
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4 Input library directory:
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5 ChIP library:
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6 Output directory:
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7 Species: mm8
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8 Threshold for redundancy allowed for reads: 1
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9 Window size: 200 bps
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10 Fragment size: 150 bps. The shift for reads is half of 150
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11 Effective genome size as a fraction of the reference genome of mm8: 0.740000
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12 Gap size: 600 bps
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13 Evalue for identification of significant islands: 0.01
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14 Preprocess the raw input_bed_file file to remove redundancy with threshold 1...
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15 chr1 Plus reads: 4989 Retained plus reads: 4935 ; Minus reads: 5011 Retained minus reads: 4963
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16 chr2 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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17 chr3 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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18 chr4 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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19 chr5 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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20 chr6 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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21 chr7 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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22 chr8 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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23 chr9 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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24 chr10 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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25 chr11 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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26 chr12 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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27 chr13 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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28 chr14 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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29 chr15 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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30 chr16 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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31 chr17 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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32 chr18 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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33 chr19 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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34 chrX Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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35 chrY Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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36 chrM Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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37 Partion the genome in windows ...
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38 Generate summary files for input_bed_file...
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39 total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0
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40 total tag count in chr2.bed is: 0.0 = 0.0+0.0
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41 total tag count in chr3.bed is: 0.0 = 0.0+0.0
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42 total tag count in chr4.bed is: 0.0 = 0.0+0.0
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43 total tag count in chr5.bed is: 0.0 = 0.0+0.0
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44 total tag count in chr6.bed is: 0.0 = 0.0+0.0
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45 total tag count in chr7.bed is: 0.0 = 0.0+0.0
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46 total tag count in chr8.bed is: 0.0 = 0.0+0.0
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47 total tag count in chr9.bed is: 0.0 = 0.0+0.0
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48 total tag count in chr10.bed is: 0.0 = 0.0+0.0
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49 total tag count in chr11.bed is: 0.0 = 0.0+0.0
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50 total tag count in chr12.bed is: 0.0 = 0.0+0.0
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51 total tag count in chr13.bed is: 0.0 = 0.0+0.0
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52 total tag count in chr14.bed is: 0.0 = 0.0+0.0
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53 total tag count in chr15.bed is: 0.0 = 0.0+0.0
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54 total tag count in chr16.bed is: 0.0 = 0.0+0.0
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55 total tag count in chr17.bed is: 0.0 = 0.0+0.0
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56 total tag count in chr18.bed is: 0.0 = 0.0+0.0
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57 total tag count in chr19.bed is: 0.0 = 0.0+0.0
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58 total tag count in chrX.bed is: 0.0 = 0.0+0.0
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59 total tag count in chrY.bed is: 0.0 = 0.0+0.0
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60 total tag count in chrM.bed is: 0.0 = 0.0+0.0
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61 Normalize summary graph by total redundancy-removed reads per million for input_bed_file ...
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62 Convert the normalized summary graph into wig vstep format...
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63 Find significant islands with E-value 0.01 for input_bed_file...
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64 Species: mm8
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65 Window_size: 200
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66 Gap size: 600
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67 E value is: 0.01
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68 Total read count: 9898.0
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69 Genome Length: 2644093988
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70 Effective genome Length: 1956629551
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71 Window average: 0.0010117398048
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72 Window pvalue: 0.2
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73 Minimum num of tags in a qualified window: 1
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74 Generate the enriched probscore summary graph and filter the summary graph to get rid of ineligible windows
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75 Determine the score threshold from random background
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76 The score threshold is: 21.384
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77 Make and write islands
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78 Total number of islands: 352
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79 Filter reads with identified significant islands for input_bed_file...
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80 Make summary graph with filtered reads for input_bed_file...
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81 total tag count in chr1.bed is: 9654.0 = 4808.0+4846.0
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82 total tag count in chr2.bed is: 0.0 = 0.0+0.0
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83 total tag count in chr3.bed is: 0.0 = 0.0+0.0
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84 total tag count in chr4.bed is: 0.0 = 0.0+0.0
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85 total tag count in chr5.bed is: 0.0 = 0.0+0.0
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86 total tag count in chr6.bed is: 0.0 = 0.0+0.0
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87 total tag count in chr7.bed is: 0.0 = 0.0+0.0
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88 total tag count in chr8.bed is: 0.0 = 0.0+0.0
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89 total tag count in chr9.bed is: 0.0 = 0.0+0.0
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90 total tag count in chr10.bed is: 0.0 = 0.0+0.0
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91 total tag count in chr11.bed is: 0.0 = 0.0+0.0
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92 total tag count in chr12.bed is: 0.0 = 0.0+0.0
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93 total tag count in chr13.bed is: 0.0 = 0.0+0.0
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94 total tag count in chr14.bed is: 0.0 = 0.0+0.0
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95 total tag count in chr15.bed is: 0.0 = 0.0+0.0
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96 total tag count in chr16.bed is: 0.0 = 0.0+0.0
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97 total tag count in chr17.bed is: 0.0 = 0.0+0.0
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98 total tag count in chr18.bed is: 0.0 = 0.0+0.0
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99 total tag count in chr19.bed is: 0.0 = 0.0+0.0
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100 total tag count in chrX.bed is: 0.0 = 0.0+0.0
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101 total tag count in chrY.bed is: 0.0 = 0.0+0.0
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102 total tag count in chrM.bed is: 0.0 = 0.0+0.0
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103 Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million...
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104 Convert the summary graph made with the filtered reads into wig vstep format and normalize by total island-filtered read count per million...
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105 Done!
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106 Additionally, these warnings were reported:
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107 Warning: chr2 reads do not exist in
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108 Warning: chr3 reads do not exist in
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109 Warning: chr4 reads do not exist in
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110 Warning: chr5 reads do not exist in
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111 Warning: chr6 reads do not exist in
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112 Warning: chr7 reads do not exist in
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113 Warning: chr8 reads do not exist in
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114 Warning: chr9 reads do not exist in
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115 Warning: chr10 reads do not exist in
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116 Warning: chr11 reads do not exist in
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117 Warning: chr12 reads do not exist in
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118 Warning: chr13 reads do not exist in
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119 Warning: chr14 reads do not exist in
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120 Warning: chr15 reads do not exist in
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121 Warning: chr16 reads do not exist in
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122 Warning: chr17 reads do not exist in
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123 Warning: chr18 reads do not exist in
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124 Warning: chr19 reads do not exist in
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125 Warning: chrX reads do not exist in
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126 Warning: chrY reads do not exist in
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127 Warning: chrM reads do not exist in
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128 Warning: chr2 reads do not exist in
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129 Warning: chr3 reads do not exist in
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130 Warning: chr4 reads do not exist in
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131 Warning: chr5 reads do not exist in
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132 Warning: chr6 reads do not exist in
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133 Warning: chr7 reads do not exist in
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134 Warning: chr8 reads do not exist in
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135 Warning: chr9 reads do not exist in
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136 Warning: chr10 reads do not exist in
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137 Warning: chr11 reads do not exist in
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138 Warning: chr12 reads do not exist in
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139 Warning: chr13 reads do not exist in
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140 Warning: chr14 reads do not exist in
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141 Warning: chr15 reads do not exist in
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142 Warning: chr16 reads do not exist in
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143 Warning: chr17 reads do not exist in
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144 Warning: chr18 reads do not exist in
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145 Warning: chr19 reads do not exist in
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146 Warning: chrX reads do not exist in
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147 Warning: chrY reads do not exist in
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148 Warning: chrM reads do not exist in
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149 Warning: chr2 reads do not exist in
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150 Warning: chr3 reads do not exist in
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151 Warning: chr4 reads do not exist in
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152 Warning: chr5 reads do not exist in
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153 Warning: chr6 reads do not exist in
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154 Warning: chr7 reads do not exist in
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155 Warning: chr8 reads do not exist in
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156 Warning: chr9 reads do not exist in
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157 Warning: chr10 reads do not exist in
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158 Warning: chr11 reads do not exist in
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159 Warning: chr12 reads do not exist in
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160 Warning: chr13 reads do not exist in
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161 Warning: chr14 reads do not exist in
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162 Warning: chr15 reads do not exist in
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163 Warning: chr16 reads do not exist in
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164 Warning: chr17 reads do not exist in
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165 Warning: chr18 reads do not exist in
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166 Warning: chr19 reads do not exist in
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167 Warning: chrX reads do not exist in
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168 Warning: chrY reads do not exist in
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169 Warning: chrM reads do not exist in
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170 Warning: chr2 reads do not exist in
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171 Warning: chr3 reads do not exist in
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172 Warning: chr4 reads do not exist in
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173 Warning: chr5 reads do not exist in
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174 Warning: chr6 reads do not exist in
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175 Warning: chr7 reads do not exist in
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176 Warning: chr8 reads do not exist in
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177 Warning: chr9 reads do not exist in
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178 Warning: chr10 reads do not exist in
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179 Warning: chr11 reads do not exist in
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180 Warning: chr12 reads do not exist in
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181 Warning: chr13 reads do not exist in
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182 Warning: chr14 reads do not exist in
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183 Warning: chr15 reads do not exist in
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184 Warning: chr16 reads do not exist in
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185 Warning: chr17 reads do not exist in
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186 Warning: chr18 reads do not exist in
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187 Warning: chr19 reads do not exist in
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188 Warning: chrX reads do not exist in
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189 Warning: chrY reads do not exist in
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190 Warning: chrM reads do not exist in
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