Mercurial > repos > bgruening > trim_galore

annotate test-data/paired_collection_example_results3.txt @ 10:b4e39d993fc8 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
author bgruening
date Thu, 20 Apr 2017 09:14:30 -0400
parents 11962ce40855
children 80cd83b11214
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2 SUMMARISING RUN PARAMETERS
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3 ==========================
10
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4 Input filename: input_1.fastq
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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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14 Length cut-off for read 1: 35 bp (default)
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15 Length cut-off for read 2: 35 bp (default)
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18 This is cutadapt 1.8 with Python 3.5.3
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19 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
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20 Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ...
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21 Finished in 0.10 s (1010 us/read; 0.06 M reads/minute).
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23 === Summary ===
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25 Total reads processed: 99
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26 Reads with adapters: 52 (52.5%)
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27 Reads written (passing filters): 99 (100.0%)
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29 Total basepairs processed: 24,849 bp
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30 Quality-trimmed: 205 bp (0.8%)
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31 Total written (filtered): 23,339 bp (93.9%)
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33 === Adapter 1 ===
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34
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35 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.
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37 No. of allowed errors:
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38 0-9 bp: 0; 10-12 bp: 1
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39
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40 Bases preceding removed adapters:
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41 A: 9.6%
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42 C: 38.5%
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43 G: 23.1%
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44 T: 28.8%
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45 none/other: 0.0%
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47 Overview of removed sequences
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48 length count expect max.err error counts
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49 1 11 24.8 0 11
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50 2 5 6.2 0 5
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51 3 3 1.5 0 3
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52 4 3 0.4 0 3
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58 20 2 0.0 1 2
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64 41 2 0.0 1 2
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74 73 1 0.0 1 1
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75 80 1 0.0 1 1
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76 86 1 0.0 1 1
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79 RUN STATISTICS FOR INPUT FILE: input_1.fastq
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80 =============================================
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81 99 sequences processed in total
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84 SUMMARISING RUN PARAMETERS
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85 ==========================
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86 Input filename: input_2.fastq
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87 Trimming mode: paired-end
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88 Trim Galore version: 0.4.0
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89 Cutadapt version: 1.8
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90 Quality Phred score cutoff: 20
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91 Quality encoding type selected: ASCII+33
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92 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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93 Maximum trimming error rate: 0.1 (default)
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94 Minimum required adapter overlap (stringency): 1 bp
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95 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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96 Length cut-off for read 1: 35 bp (default)
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97 Length cut-off for read 2: 35 bp (default)
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100 This is cutadapt 1.8 with Python 3.5.3
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101 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
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102 Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ...
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103 Finished in 0.10 s (1000 us/read; 0.06 M reads/minute).
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105 === Summary ===
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107 Total reads processed: 100
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108 Reads with adapters: 59 (59.0%)
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109 Reads written (passing filters): 100 (100.0%)
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110
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111 Total basepairs processed: 25,100 bp
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112 Quality-trimmed: 746 bp (3.0%)
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113 Total written (filtered): 23,276 bp (92.7%)
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114
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115 === Adapter 1 ===
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116
6
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117 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times.
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118
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119 No. of allowed errors:
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120 0-9 bp: 0; 10-12 bp: 1
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121
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122 Bases preceding removed adapters:
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123 A: 11.9%
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124 C: 39.0%
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125 G: 8.5%
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126 T: 40.7%
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127 none/other: 0.0%
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128
6
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129 Overview of removed sequences
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130 length count expect max.err error counts
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131 1 16 25.0 0 16
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132 2 7 6.2 0 7
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133 3 1 1.6 0 1
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134 4 2 0.4 0 2
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135 6 2 0.0 0 2
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136 9 2 0.0 0 2
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137 10 1 0.0 1 1
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138 13 1 0.0 1 1
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139 14 2 0.0 1 2
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140 15 1 0.0 1 1
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141 16 1 0.0 1 1
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142 17 1 0.0 1 1
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143 19 2 0.0 1 2
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144 21 1 0.0 1 1
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145 25 1 0.0 1 1
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146 30 1 0.0 1 1
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147 32 2 0.0 1 2
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148 34 1 0.0 1 1
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149 36 2 0.0 1 2
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150 38 1 0.0 1 1
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151 40 1 0.0 1 1
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152 41 1 0.0 1 1
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153 42 1 0.0 1 1
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154 43 1 0.0 1 1
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155 49 1 0.0 1 1
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156 51 1 0.0 1 1
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157 56 1 0.0 1 1
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158 57 1 0.0 1 1
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159 60 1 0.0 1 1
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160 67 1 0.0 1 1
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161 80 1 0.0 1 1
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162
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163
10
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164 RUN STATISTICS FOR INPUT FILE: input_2.fastq
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165 =============================================
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166 100 sequences processed in total
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167
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168 Total number of sequences analysed for the sequence pair length validation: 99
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169
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170 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)