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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: input_bed_file.bed
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6 Control library: input_control_file.bed
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7 Output directory:
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8 Species: mm8
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9 Threshold for redundancy allowed for chip reads: 1
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10 Threshold for redundancy allowed for control reads: 1
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11 Window size: 200 bps
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12 Fragment size: 150 bps. The shift for reads is half of 150
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13 Effective genome size as a fraction of the reference genome of mm8: 0.740000
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14 Gap size: 600 bps
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15 Evalue for identification of candidate islands that exhibit clustering: 1000
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16 False discovery rate controlling significance: 0.01
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17 Preprocess the raw input_bed_file file to remove redundancy with threshold 1...
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18 chr1 Plus reads: 4989 Retained plus reads: 4935 ; Minus reads: 5011 Retained minus reads: 4963
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19 chr2 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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20 chr3 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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21 chr4 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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22 chr5 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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23 chr6 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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24 chr7 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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25 chr8 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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26 chr9 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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27 chr10 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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28 chr11 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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29 chr12 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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30 chr13 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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31 chr14 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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32 chr15 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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33 chr16 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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34 chr17 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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35 chr18 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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36 chr19 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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37 chrX Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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38 chrY Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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39 chrM Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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40 Preprocess the raw input_control_file file to remove redundancy with threshold 1...
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41 chr1 Plus reads: 4980 Retained plus reads: 4937 ; Minus reads: 5020 Retained minus reads: 4959
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42 chr2 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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43 chr3 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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44 chr4 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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45 chr5 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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46 chr6 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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47 chr7 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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48 chr8 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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49 chr9 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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50 chr10 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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51 chr11 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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52 chr12 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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53 chr13 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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54 chr14 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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55 chr15 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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56 chr16 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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57 chr17 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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58 chr18 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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59 chr19 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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60 chrX Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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61 chrY Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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62 chrM Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
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63 Partion the genome in windows ...
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64 Generate summary files ...
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65 total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0
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66 total tag count in chr2.bed is: 0.0 = 0.0+0.0
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67 total tag count in chr3.bed is: 0.0 = 0.0+0.0
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68 total tag count in chr4.bed is: 0.0 = 0.0+0.0
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69 total tag count in chr5.bed is: 0.0 = 0.0+0.0
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70 total tag count in chr6.bed is: 0.0 = 0.0+0.0
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71 total tag count in chr7.bed is: 0.0 = 0.0+0.0
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72 total tag count in chr8.bed is: 0.0 = 0.0+0.0
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73 total tag count in chr9.bed is: 0.0 = 0.0+0.0
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74 total tag count in chr10.bed is: 0.0 = 0.0+0.0
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75 total tag count in chr11.bed is: 0.0 = 0.0+0.0
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76 total tag count in chr12.bed is: 0.0 = 0.0+0.0
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77 total tag count in chr13.bed is: 0.0 = 0.0+0.0
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78 total tag count in chr14.bed is: 0.0 = 0.0+0.0
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79 total tag count in chr15.bed is: 0.0 = 0.0+0.0
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80 total tag count in chr16.bed is: 0.0 = 0.0+0.0
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81 total tag count in chr17.bed is: 0.0 = 0.0+0.0
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82 total tag count in chr18.bed is: 0.0 = 0.0+0.0
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83 total tag count in chr19.bed is: 0.0 = 0.0+0.0
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84 total tag count in chrX.bed is: 0.0 = 0.0+0.0
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85 total tag count in chrY.bed is: 0.0 = 0.0+0.0
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86 total tag count in chrM.bed is: 0.0 = 0.0+0.0
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87 Normalize summary graph by total island filtered reads per million for input_bed_file ...
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88 Convert the normalized summary graph into wig vstep format...
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89 Find candidate islands exhibiting clustering ...
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90 Species: mm8
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91 Window_size: 200
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92 Gap size: 600
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93 E value is: 1000.0
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94 Total read count: 9898.0
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95 Genome Length: 2644093988
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96 Effective genome Length: 1956629551
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97 Window average: 0.0010117398048
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98 Window pvalue: 0.2
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99 Minimum num of tags in a qualified window: 1
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100 Generate the enriched probscore summary graph and filter the summary graph to get rid of ineligible windows
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101 Determine the score threshold from random background
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102 The score threshold is: 6.898
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103 Make and write islands
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104 Total number of islands: 417
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105 Calculate significance of candidate islands using the control library ...
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106 chip library size 9898.0
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107 control library size 9896.0
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108 Total number of chip reads on islands is: 9811
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109 Total number of control reads on islands is: 8514
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110 Identify significant islands using FDR criterion ...
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111 Given significance 0.01 , there are 184 significant islands
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112 Convert island summary to island bed file of format chr start end ChIP-read-count
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113 Filter reads with identified significant islands...
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114 Make summary graph with filtered reads...
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115 total tag count in chr1.bed is: 4303.0 = 2148.0+2155.0
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116 total tag count in chr2.bed is: 0.0 = 0.0+0.0
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117 total tag count in chr3.bed is: 0.0 = 0.0+0.0
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118 total tag count in chr4.bed is: 0.0 = 0.0+0.0
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119 total tag count in chr5.bed is: 0.0 = 0.0+0.0
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120 total tag count in chr6.bed is: 0.0 = 0.0+0.0
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121 total tag count in chr7.bed is: 0.0 = 0.0+0.0
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122 total tag count in chr8.bed is: 0.0 = 0.0+0.0
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123 total tag count in chr9.bed is: 0.0 = 0.0+0.0
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124 total tag count in chr10.bed is: 0.0 = 0.0+0.0
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125 total tag count in chr11.bed is: 0.0 = 0.0+0.0
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126 total tag count in chr12.bed is: 0.0 = 0.0+0.0
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127 total tag count in chr13.bed is: 0.0 = 0.0+0.0
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128 total tag count in chr14.bed is: 0.0 = 0.0+0.0
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129 total tag count in chr15.bed is: 0.0 = 0.0+0.0
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130 total tag count in chr16.bed is: 0.0 = 0.0+0.0
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131 total tag count in chr17.bed is: 0.0 = 0.0+0.0
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132 total tag count in chr18.bed is: 0.0 = 0.0+0.0
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133 total tag count in chr19.bed is: 0.0 = 0.0+0.0
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134 total tag count in chrX.bed is: 0.0 = 0.0+0.0
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135 total tag count in chrY.bed is: 0.0 = 0.0+0.0
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136 total tag count in chrM.bed is: 0.0 = 0.0+0.0
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137 Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million...
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138 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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139 Done!
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140 Additionally, these warnings were reported:
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141 Warning: chr2 reads do not exist in
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142 Warning: chr3 reads do not exist in
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143 Warning: chr4 reads do not exist in
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144 Warning: chr5 reads do not exist in
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145 Warning: chr6 reads do not exist in
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146 Warning: chr7 reads do not exist in
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147 Warning: chr8 reads do not exist in
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148 Warning: chr9 reads do not exist in
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149 Warning: chr10 reads do not exist in
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150 Warning: chr11 reads do not exist in
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151 Warning: chr12 reads do not exist in
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152 Warning: chr13 reads do not exist in
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153 Warning: chr14 reads do not exist in
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154 Warning: chr15 reads do not exist in
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155 Warning: chr16 reads do not exist in
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156 Warning: chr17 reads do not exist in
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157 Warning: chr18 reads do not exist in
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158 Warning: chr19 reads do not exist in
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159 Warning: chrX reads do not exist in
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160 Warning: chrY reads do not exist in
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161 Warning: chrM reads do not exist in
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162 Warning: chr2 reads do not exist in
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163 Warning: chr3 reads do not exist in
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164 Warning: chr4 reads do not exist in
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165 Warning: chr5 reads do not exist in
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166 Warning: chr6 reads do not exist in
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167 Warning: chr7 reads do not exist in
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168 Warning: chr8 reads do not exist in
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169 Warning: chr9 reads do not exist in
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170 Warning: chr10 reads do not exist in
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171 Warning: chr11 reads do not exist in
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172 Warning: chr12 reads do not exist in
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173 Warning: chr13 reads do not exist in
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174 Warning: chr14 reads do not exist in
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175 Warning: chr15 reads do not exist in
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176 Warning: chr16 reads do not exist in
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177 Warning: chr17 reads do not exist in
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178 Warning: chr18 reads do not exist in
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179 Warning: chr19 reads do not exist in
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180 Warning: chrX reads do not exist in
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181 Warning: chrY reads do not exist in
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182 Warning: chrM reads do not exist in
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183 Warning: chr2 reads do not exist in
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184 Warning: chr3 reads do not exist in
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185 Warning: chr4 reads do not exist in
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186 Warning: chr5 reads do not exist in
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187 Warning: chr6 reads do not exist in
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188 Warning: chr7 reads do not exist in
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189 Warning: chr8 reads do not exist in
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190 Warning: chr9 reads do not exist in
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191 Warning: chr10 reads do not exist in
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192 Warning: chr11 reads do not exist in
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193 Warning: chr12 reads do not exist in
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194 Warning: chr13 reads do not exist in
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195 Warning: chr14 reads do not exist in
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196 Warning: chr15 reads do not exist in
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197 Warning: chr16 reads do not exist in
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198 Warning: chr17 reads do not exist in
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199 Warning: chr18 reads do not exist in
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200 Warning: chr19 reads do not exist in
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201 Warning: chrX reads do not exist in
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202 Warning: chrY reads do not exist in
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203 Warning: chrM reads do not exist in
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204 Warning: chr2 reads do not exist in
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205 Warning: chr3 reads do not exist in
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206 Warning: chr4 reads do not exist in
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207 Warning: chr5 reads do not exist in
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208 Warning: chr6 reads do not exist in
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209 Warning: chr7 reads do not exist in
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210 Warning: chr8 reads do not exist in
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211 Warning: chr9 reads do not exist in
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212 Warning: chr10 reads do not exist in
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213 Warning: chr11 reads do not exist in
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214 Warning: chr12 reads do not exist in
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215 Warning: chr13 reads do not exist in
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216 Warning: chr14 reads do not exist in
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217 Warning: chr15 reads do not exist in
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218 Warning: chr16 reads do not exist in
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219 Warning: chr17 reads do not exist in
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220 Warning: chr18 reads do not exist in
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221 Warning: chr19 reads do not exist in
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222 Warning: chrX reads do not exist in
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223 Warning: chrY reads do not exist in
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224 Warning: chrM reads do not exist in
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225 Warning: chr2 reads do not exist in
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226 Warning: chr3 reads do not exist in
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227 Warning: chr4 reads do not exist in
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228 Warning: chr5 reads do not exist in
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229 Warning: chr6 reads do not exist in
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230 Warning: chr7 reads do not exist in
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231 Warning: chr8 reads do not exist in
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232 Warning: chr9 reads do not exist in
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233 Warning: chr10 reads do not exist in
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234 Warning: chr11 reads do not exist in
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235 Warning: chr12 reads do not exist in
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236 Warning: chr13 reads do not exist in
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237 Warning: chr14 reads do not exist in
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238 Warning: chr15 reads do not exist in
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239 Warning: chr16 reads do not exist in
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240 Warning: chr17 reads do not exist in
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241 Warning: chr18 reads do not exist in
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242 Warning: chr19 reads do not exist in
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243 Warning: chrX reads do not exist in
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244 Warning: chrY reads do not exist in
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245 Warning: chrM reads do not exist in
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246 Warning: chr2 reads do not exist in
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247 Warning: chr3 reads do not exist in
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248 Warning: chr4 reads do not exist in
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249 Warning: chr5 reads do not exist in
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250 Warning: chr6 reads do not exist in
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251 Warning: chr7 reads do not exist in
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252 Warning: chr8 reads do not exist in
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253 Warning: chr9 reads do not exist in
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254 Warning: chr10 reads do not exist in
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255 Warning: chr11 reads do not exist in
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256 Warning: chr12 reads do not exist in
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257 Warning: chr13 reads do not exist in
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258 Warning: chr14 reads do not exist in
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259 Warning: chr15 reads do not exist in
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260 Warning: chr16 reads do not exist in
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261 Warning: chr17 reads do not exist in
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262 Warning: chr18 reads do not exist in
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263 Warning: chr19 reads do not exist in
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264 Warning: chrX reads do not exist in
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265 Warning: chrY reads do not exist in
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266 Warning: chrM reads do not exist in
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267 Warning: chr2 reads do not exist in
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268 Warning: chr3 reads do not exist in
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269 Warning: chr4 reads do not exist in
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270 Warning: chr5 reads do not exist in
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271 Warning: chr6 reads do not exist in
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272 Warning: chr7 reads do not exist in
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273 Warning: chr8 reads do not exist in
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274 Warning: chr9 reads do not exist in
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275 Warning: chr10 reads do not exist in
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276 Warning: chr11 reads do not exist in
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277 Warning: chr12 reads do not exist in
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278 Warning: chr13 reads do not exist in
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279 Warning: chr14 reads do not exist in
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280 Warning: chr15 reads do not exist in
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281 Warning: chr16 reads do not exist in
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282 Warning: chr17 reads do not exist in
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283 Warning: chr18 reads do not exist in
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284 Warning: chr19 reads do not exist in
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285 Warning: chrX reads do not exist in
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286 Warning: chrY reads do not exist in
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287 Warning: chrM reads do not exist in
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