Mercurial > repos > bgruening > trim_galore

annotate test-data/paired_collection_example_results3gz.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 Length cut-off for read 1: 35 bp (default)
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16 Length cut-off for read 2: 35 bp (default)
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17 Output file will be GZIP compressed
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19
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20 This is cutadapt 2.4 with Python 3.7.3
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21 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
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22 Processing reads on 1 core in single-end mode ...
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23 Finished in 0.02 s (176 us/read; 0.34 M reads/minute).
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25 === Summary ===
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27 Total reads processed: 99
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28 Reads with adapters: 52 (52.5%)
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29 Reads written (passing filters): 99 (100.0%)
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31 Total basepairs processed: 24,849 bp
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32 Quality-trimmed: 205 bp (0.8%)
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33 Total written (filtered): 23,339 bp (93.9%)
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35 === Adapter 1 ===
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37 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.
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39 No. of allowed errors:
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40 0-9 bp: 0; 10-12 bp: 1
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42 Bases preceding removed adapters:
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43 A: 9.6%
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44 C: 38.5%
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45 G: 23.1%
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46 T: 28.8%
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47 none/other: 0.0%
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49 Overview of removed sequences
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50 length count expect max.err error counts
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51 1 11 24.8 0 11
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52 2 5 6.2 0 5
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53 3 3 1.5 0 3
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54 4 3 0.4 0 3
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55 12 1 0.0 1 1
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56 13 2 0.0 1 2
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58 16 1 0.0 1 1
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66 41 2 0.0 1 2
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71 58 2 0.0 1 2
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78 86 1 0.0 1 1
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80 RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz
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81 =============================================
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82 99 sequences processed in total
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85 SUMMARISING RUN PARAMETERS
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86 ==========================
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87 Input filename: input_2.fastq.gz
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88 Trimming mode: paired-end
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89 Trim Galore version: 0.6.3
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90 Cutadapt version: 2.4
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91 Number of cores used for trimming: 1
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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 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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95 Maximum trimming error rate: 0.1 (default)
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96 Minimum required adapter overlap (stringency): 1 bp
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97 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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98 Length cut-off for read 1: 35 bp (default)
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99 Length cut-off for read 2: 35 bp (default)
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100 Output file will be GZIP compressed
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101
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102
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103 This is cutadapt 2.4 with Python 3.7.3
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104 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
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105 Processing reads on 1 core in single-end mode ...
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106 Finished in 0.02 s (169 us/read; 0.36 M reads/minute).
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107
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108 === Summary ===
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109
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110 Total reads processed: 99
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111 Reads with adapters: 58 (58.6%)
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112 Reads written (passing filters): 99 (100.0%)
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113
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114 Total basepairs processed: 24,849 bp
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115 Quality-trimmed: 745 bp (3.0%)
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116 Total written (filtered): 23,035 bp (92.7%)
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117
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118 === Adapter 1 ===
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119
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120 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.
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121
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122 No. of allowed errors:
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123 0-9 bp: 0; 10-12 bp: 1
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124
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125 Bases preceding removed adapters:
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126 A: 12.1%
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127 C: 37.9%
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128 G: 8.6%
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129 T: 41.4%
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130 none/other: 0.0%
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131
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132 Overview of removed sequences
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133 length count expect max.err error counts
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134 1 16 24.8 0 16
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135 2 7 6.2 0 7
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136 3 1 1.5 0 1
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137 4 2 0.4 0 2
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138 6 2 0.0 0 2
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139 9 1 0.0 0 1
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140 10 1 0.0 1 1
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141 13 1 0.0 1 1
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142 14 2 0.0 1 2
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143 15 1 0.0 1 1
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144 16 1 0.0 1 1
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145 17 1 0.0 1 1
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146 19 2 0.0 1 2
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147 21 1 0.0 1 1
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148 25 1 0.0 1 1
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149 30 1 0.0 1 1
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150 32 2 0.0 1 2
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151 34 1 0.0 1 1
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152 36 2 0.0 1 2
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153 38 1 0.0 1 1
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154 40 1 0.0 1 1
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155 41 1 0.0 1 1
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156 42 1 0.0 1 1
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157 43 1 0.0 1 1
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158 49 1 0.0 1 1
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159 51 1 0.0 1 1
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160 56 1 0.0 1 1
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161 57 1 0.0 1 1
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162 60 1 0.0 1 1
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163 67 1 0.0 1 1
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164 80 1 0.0 1 1
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165
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166 RUN STATISTICS FOR INPUT FILE: input_2.fastq.gz
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167 =============================================
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168 99 sequences processed in total
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169
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170 Total number of sequences analysed for the sequence pair length validation: 99
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171
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172 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)