Mercurial > repos > bgruening > trim_galore

annotate test-data/paired_example_results2.txt @ 16:cd7e644cae1d draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
author bgruening
date Fri, 08 Oct 2021 09:57:52 +0000
parents 084bbd8ba7b8
children
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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: 0.6.7
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7 Cutadapt version: 3.4
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8 Python version: could not detect
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9 Number of cores used for trimming: 4
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10 Quality Phred score cutoff: 20
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11 Quality encoding type selected: ASCII+33
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12 Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
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13 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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14 Maximum trimming error rate: 0.1 (default)
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15 Minimum required adapter overlap (stringency): 1 bp
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16 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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19 This is cutadapt 3.4 with Python 3.9.6
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20 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
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21 Processing reads on 4 cores in single-end mode ...
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22 Finished in 0.01 s (117 µs/read; 0.51 M reads/minute).
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24 === Summary ===
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26 Total reads processed: 99
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27 Reads with adapters: 52 (52.5%)
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28 Reads written (passing filters): 99 (100.0%)
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29
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30 Total basepairs processed: 24,849 bp
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31 Quality-trimmed: 205 bp (0.8%)
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32 Total written (filtered): 23,339 bp (93.9%)
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34 === Adapter 1 ===
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36 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times
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38 No. of allowed errors:
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39 1-9 bp: 0; 10-12 bp: 1
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40
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41 Bases preceding removed adapters:
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42 A: 9.6%
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43 C: 38.5%
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44 G: 23.1%
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45 T: 28.8%
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46 none/other: 0.0%
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47
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48 Overview of removed sequences
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49 length count expect max.err error counts
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50 1 11 24.8 0 11
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51 2 5 6.2 0 5
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52 3 3 1.5 0 3
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53 4 3 0.4 0 3
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54 12 1 0.0 1 1
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55 13 2 0.0 1 2
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56 14 1 0.0 1 1
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57 16 1 0.0 1 1
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58 17 1 0.0 1 0 1
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59 20 2 0.0 1 2
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60 21 1 0.0 1 1
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61 24 1 0.0 1 1
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62 26 2 0.0 1 2
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63 31 1 0.0 1 1
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64 33 1 0.0 1 1
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65 41 2 0.0 1 2
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66 49 1 0.0 1 1
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72 67 2 0.0 1 2
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74 69 1 0.0 1 1
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75 73 1 0.0 1 1
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76 80 1 0.0 1 1
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77 86 1 0.0 1 1
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78
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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: 0.6.7
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89 Cutadapt version: 3.4
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90 Python version: could not detect
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91 Number of cores used for trimming: 4
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92 Quality Phred score cutoff: 20
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93 Quality encoding type selected: ASCII+33
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94 Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
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95 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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96 Maximum trimming error rate: 0.1 (default)
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97 Minimum required adapter overlap (stringency): 1 bp
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98 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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99
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100
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101 This is cutadapt 3.4 with Python 3.9.6
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102 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
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103 Processing reads on 4 cores in single-end mode ...
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104 Finished in 0.03 s (256 µs/read; 0.23 M reads/minute).
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106 === Summary ===
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107
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108 Total reads processed: 99
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109 Reads with adapters: 58 (58.6%)
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110 Reads written (passing filters): 99 (100.0%)
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111
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112 Total basepairs processed: 24,849 bp
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113 Quality-trimmed: 745 bp (3.0%)
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114 Total written (filtered): 23,035 bp (92.7%)
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115
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116 === Adapter 1 ===
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117
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118 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times
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119
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120 No. of allowed errors:
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121 1-9 bp: 0; 10-12 bp: 1
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122
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123 Bases preceding removed adapters:
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124 A: 12.1%
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125 C: 37.9%
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126 G: 8.6%
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127 T: 41.4%
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128 none/other: 0.0%
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129
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130 Overview of removed sequences
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131 length count expect max.err error counts
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132 1 16 24.8 0 16
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133 2 7 6.2 0 7
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134 3 1 1.5 0 1
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135 4 2 0.4 0 2
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136 6 2 0.0 0 2
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137 9 1 0.0 0 1
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138 10 1 0.0 1 1
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139 13 1 0.0 1 1
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140 14 2 0.0 1 2
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141 15 1 0.0 1 1
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142 16 1 0.0 1 1
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143 17 1 0.0 1 1
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144 19 2 0.0 1 2
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145 21 1 0.0 1 1
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146 25 1 0.0 1 1
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147 30 1 0.0 1 1
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148 32 2 0.0 1 2
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149 34 1 0.0 1 1
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150 36 2 0.0 1 2
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151 38 1 0.0 1 1
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152 40 1 0.0 1 1
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153 41 1 0.0 1 1
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154 42 1 0.0 1 1
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155 43 1 0.0 1 1
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156 49 1 0.0 1 1
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157 51 1 0.0 1 1
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158 56 1 0.0 1 1
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159 57 1 0.0 1 1
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160 60 1 0.0 1 1
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161 67 1 0.0 1 1
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162 80 1 0.0 1 1
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163
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164 RUN STATISTICS FOR INPUT FILE: input_2.fastq
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165 =============================================
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166 99 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%)