annotate test-data/paired_example_results2gz.txt @ 11:80cd83b11214 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf
author bgruening
date Mon, 24 Apr 2017 14:30:07 -0400
parents b4e39d993fc8
children 084bbd8ba7b8
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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_1.fastq.gz
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5 Trimming mode: paired-end
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6 Trim Galore version: 0.4.3
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7 Cutadapt version: 1.13
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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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14 Output file will be GZIP compressed
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16
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17 This is cutadapt 1.13 with Python 3.5.3
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18 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
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19 Trimming 1 adapter with at most 10.0% errors in single-end mode ...
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20 Finished in 0.01 s (101 us/read; 0.59 M reads/minute).
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22 === Summary ===
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24 Total reads processed: 99
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25 Reads with adapters: 52 (52.5%)
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26 Reads written (passing filters): 99 (100.0%)
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28 Total basepairs processed: 24,849 bp
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29 Quality-trimmed: 205 bp (0.8%)
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30 Total written (filtered): 23,339 bp (93.9%)
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32 === Adapter 1 ===
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34 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.
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36 No. of allowed errors:
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37 0-9 bp: 0; 10-12 bp: 1
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39 Bases preceding removed adapters:
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40 A: 9.6%
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41 C: 38.5%
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42 G: 23.1%
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43 T: 28.8%
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44 none/other: 0.0%
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46 Overview of removed sequences
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47 length count expect max.err error counts
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48 1 11 24.8 0 11
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49 2 5 6.2 0 5
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50 3 3 1.5 0 3
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51 4 3 0.4 0 3
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52 12 1 0.0 1 1
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53 13 2 0.0 1 2
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75 86 1 0.0 1 1
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78 RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz
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79 =============================================
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80 99 sequences processed in total
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83 SUMMARISING RUN PARAMETERS
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84 ==========================
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85 Input filename: input_2.fastq.gz
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86 Trimming mode: paired-end
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87 Trim Galore version: 0.4.3
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88 Cutadapt version: 1.13
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89 Quality Phred score cutoff: 20
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90 Quality encoding type selected: ASCII+33
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91 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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92 Maximum trimming error rate: 0.1 (default)
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93 Minimum required adapter overlap (stringency): 1 bp
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94 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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95 Output file will be GZIP compressed
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96
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97
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98 This is cutadapt 1.13 with Python 3.5.3
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99 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
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100 Trimming 1 adapter with at most 10.0% errors in single-end mode ...
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101 Finished in 0.01 s (100 us/read; 0.60 M reads/minute).
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102
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103 === Summary ===
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104
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105 Total reads processed: 100
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106 Reads with adapters: 59 (59.0%)
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107 Reads written (passing filters): 100 (100.0%)
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108
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109 Total basepairs processed: 25,100 bp
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110 Quality-trimmed: 746 bp (3.0%)
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111 Total written (filtered): 23,276 bp (92.7%)
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112
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113 === Adapter 1 ===
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114
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115 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times.
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116
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117 No. of allowed errors:
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118 0-9 bp: 0; 10-12 bp: 1
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119
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120 Bases preceding removed adapters:
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121 A: 11.9%
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122 C: 39.0%
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123 G: 8.5%
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124 T: 40.7%
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125 none/other: 0.0%
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126
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127 Overview of removed sequences
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128 length count expect max.err error counts
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129 1 16 25.0 0 16
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130 2 7 6.2 0 7
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131 3 1 1.6 0 1
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132 4 2 0.4 0 2
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133 6 2 0.0 0 2
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134 9 2 0.0 0 2
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135 10 1 0.0 1 1
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136 13 1 0.0 1 1
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137 14 2 0.0 1 2
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138 15 1 0.0 1 1
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139 16 1 0.0 1 1
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140 17 1 0.0 1 1
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141 19 2 0.0 1 2
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142 21 1 0.0 1 1
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143 25 1 0.0 1 1
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144 30 1 0.0 1 1
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145 32 2 0.0 1 2
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146 34 1 0.0 1 1
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147 36 2 0.0 1 2
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148 38 1 0.0 1 1
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149 40 1 0.0 1 1
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150 41 1 0.0 1 1
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151 42 1 0.0 1 1
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152 43 1 0.0 1 1
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153 49 1 0.0 1 1
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154 51 1 0.0 1 1
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155 56 1 0.0 1 1
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156 57 1 0.0 1 1
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157 60 1 0.0 1 1
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158 67 1 0.0 1 1
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159 80 1 0.0 1 1
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160
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161
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162 RUN STATISTICS FOR INPUT FILE: input_2.fastq.gz
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163 =============================================
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164 100 sequences processed in total
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165
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166 Total number of sequences analysed for the sequence pair length validation: 99
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167
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168 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)