Mercurial > repos > bgruening > trim_galore

annotate test-data/paired_example_results2.txt @ 7:8352713cf939 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 07148c518916e16602ea26473d00358fe04bc3b6-dirty
author bgruening
date Mon, 25 Jan 2016 04:44:33 -0500
parents 11962ce40855
children b4e39d993fc8
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1
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2 SUMMARISING RUN PARAMETERS
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3 ==========================
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4 Input filename: ./input_mate1
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5 Trimming mode: paired-end
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6 Trim Galore version: 0.4.0
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7 Cutadapt version: 1.8
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8 Quality Phred score cutoff: 20
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9 Quality encoding type selected: ASCII+33
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10 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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11 Maximum trimming error rate: 0.1 (default)
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12 Minimum required adapter overlap (stringency): 1 bp
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13 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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16 This is cutadapt 1.8 with Python 2.7.9
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17 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate1
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18 Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ...
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19 Finished in 0.10 s (1010 us/read; 0.06 M reads/minute).
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21 === Summary ===
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23 Total reads processed: 99
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24 Reads with adapters: 52 (52.5%)
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25 Reads written (passing filters): 99 (100.0%)
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27 Total basepairs processed: 24,849 bp
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28 Quality-trimmed: 205 bp (0.8%)
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29 Total written (filtered): 23,339 bp (93.9%)
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31 === Adapter 1 ===
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33 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.
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35 No. of allowed errors:
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36 0-9 bp: 0; 10-12 bp: 1
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37
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38 Bases preceding removed adapters:
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39 A: 9.6%
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40 C: 38.5%
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41 G: 23.1%
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42 T: 28.8%
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43 none/other: 0.0%
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45 Overview of removed sequences
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46 length count expect max.err error counts
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47 1 11 24.8 0 11
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48 2 5 6.2 0 5
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49 3 3 1.5 0 3
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50 4 3 0.4 0 3
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51 12 1 0.0 1 1
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52 13 2 0.0 1 2
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59 26 2 0.0 1 2
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61 33 1 0.0 1 1
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62 41 2 0.0 1 2
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63 49 1 0.0 1 1
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64 50 1 0.0 1 1
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67 58 2 0.0 1 2
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69 67 2 0.0 1 2
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72 73 1 0.0 1 1
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73 80 1 0.0 1 1
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74 86 1 0.0 1 1
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77 RUN STATISTICS FOR INPUT FILE: ./input_mate1
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78 =============================================
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79 99 sequences processed in total
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82 SUMMARISING RUN PARAMETERS
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83 ==========================
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84 Input filename: ./input_mate2
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85 Trimming mode: paired-end
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86 Trim Galore version: 0.4.0
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87 Cutadapt version: 1.8
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88 Quality Phred score cutoff: 20
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89 Quality encoding type selected: ASCII+33
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90 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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91 Maximum trimming error rate: 0.1 (default)
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92 Minimum required adapter overlap (stringency): 1 bp
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93 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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94
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95
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96 This is cutadapt 1.8 with Python 2.7.9
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97 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate2
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98 Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ...
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99 Finished in 0.10 s (1000 us/read; 0.06 M reads/minute).
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100
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101 === Summary ===
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102
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103 Total reads processed: 100
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104 Reads with adapters: 59 (59.0%)
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105 Reads written (passing filters): 100 (100.0%)
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106
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107 Total basepairs processed: 25,100 bp
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108 Quality-trimmed: 746 bp (3.0%)
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109 Total written (filtered): 23,276 bp (92.7%)
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110
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111 === Adapter 1 ===
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112
6
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113 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times.
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114
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115 No. of allowed errors:
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116 0-9 bp: 0; 10-12 bp: 1
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117
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118 Bases preceding removed adapters:
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119 A: 11.9%
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120 C: 39.0%
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121 G: 8.5%
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122 T: 40.7%
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123 none/other: 0.0%
4
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124
6
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125 Overview of removed sequences
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126 length count expect max.err error counts
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127 1 16 25.0 0 16
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128 2 7 6.2 0 7
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129 3 1 1.6 0 1
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130 4 2 0.4 0 2
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131 6 2 0.0 0 2
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132 9 2 0.0 0 2
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133 10 1 0.0 1 1
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134 13 1 0.0 1 1
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135 14 2 0.0 1 2
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136 15 1 0.0 1 1
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137 16 1 0.0 1 1
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138 17 1 0.0 1 1
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139 19 2 0.0 1 2
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140 21 1 0.0 1 1
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141 25 1 0.0 1 1
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142 30 1 0.0 1 1
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143 32 2 0.0 1 2
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144 34 1 0.0 1 1
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145 36 2 0.0 1 2
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146 38 1 0.0 1 1
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147 40 1 0.0 1 1
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148 41 1 0.0 1 1
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149 42 1 0.0 1 1
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150 43 1 0.0 1 1
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151 49 1 0.0 1 1
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152 51 1 0.0 1 1
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153 56 1 0.0 1 1
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154 57 1 0.0 1 1
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155 60 1 0.0 1 1
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156 67 1 0.0 1 1
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157 80 1 0.0 1 1
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158
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159
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160 RUN STATISTICS FOR INPUT FILE: ./input_mate2
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161 =============================================
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162 100 sequences processed in total
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163
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164 Total number of sequences analysed for the sequence pair length validation: 99
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165
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166 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)