Mercurial > repos > bgruening > trim_galore

annotate test-data/paired_example_results2gz.txt @ 15:084bbd8ba7b8 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
author bgruening
date Tue, 30 Jul 2019 06:26:49 -0400
parents 80cd83b11214
children cd7e644cae1d
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b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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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: 0.6.3
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7 Cutadapt version: 2.4
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8 Number of cores used for trimming: 1
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9 Quality Phred score cutoff: 20
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10 Quality encoding type selected: ASCII+33
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11 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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12 Maximum trimming error rate: 0.1 (default)
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13 Minimum required adapter overlap (stringency): 1 bp
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14 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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15 Output file will be GZIP compressed
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17
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18 This is cutadapt 2.4 with Python 3.7.3
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19 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
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20 Processing reads on 1 core in single-end mode ...
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21 Finished in 0.03 s (287 us/read; 0.21 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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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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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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53 12 1 0.0 1 1
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54 13 2 0.0 1 2
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57 17 1 0.0 1 0 1
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69 58 2 0.0 1 2
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71 67 2 0.0 1 2
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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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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: 0.6.3
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88 Cutadapt version: 2.4
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89 Number of cores used for trimming: 1
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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 Output file will be GZIP compressed
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97
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98
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99 This is cutadapt 2.4 with Python 3.7.3
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100 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
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101 Processing reads on 1 core in single-end mode ...
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102 Finished in 0.02 s (170 us/read; 0.35 M reads/minute).
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103
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104 === Summary ===
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105
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106 Total reads processed: 99
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107 Reads with adapters: 58 (58.6%)
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108 Reads written (passing filters): 99 (100.0%)
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109
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110 Total basepairs processed: 24,849 bp
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111 Quality-trimmed: 745 bp (3.0%)
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112 Total written (filtered): 23,035 bp (92.7%)
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113
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114 === Adapter 1 ===
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115
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116 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.
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117
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118 No. of allowed errors:
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119 0-9 bp: 0; 10-12 bp: 1
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120
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121 Bases preceding removed adapters:
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122 A: 12.1%
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123 C: 37.9%
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124 G: 8.6%
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125 T: 41.4%
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126 none/other: 0.0%
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127
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128 Overview of removed sequences
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129 length count expect max.err error counts
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130 1 16 24.8 0 16
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131 2 7 6.2 0 7
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132 3 1 1.5 0 1
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133 4 2 0.4 0 2
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134 6 2 0.0 0 2
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135 9 1 0.0 0 1
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136 10 1 0.0 1 1
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137 13 1 0.0 1 1
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138 14 2 0.0 1 2
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139 15 1 0.0 1 1
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140 16 1 0.0 1 1
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141 17 1 0.0 1 1
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142 19 2 0.0 1 2
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143 21 1 0.0 1 1
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144 25 1 0.0 1 1
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145 30 1 0.0 1 1
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146 32 2 0.0 1 2
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147 34 1 0.0 1 1
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148 36 2 0.0 1 2
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149 38 1 0.0 1 1
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150 40 1 0.0 1 1
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151 41 1 0.0 1 1
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152 42 1 0.0 1 1
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153 43 1 0.0 1 1
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154 49 1 0.0 1 1
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155 51 1 0.0 1 1
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157 57 1 0.0 1 1
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158 60 1 0.0 1 1
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159 67 1 0.0 1 1
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160 80 1 0.0 1 1
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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 99 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%)