Mercurial > repos > bgruening > trim_galore

annotate test-data/paired_collection_example_results3gz.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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b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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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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cd7e644cae1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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6 Trim Galore version: 0.6.7
cd7e644cae1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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7 Cutadapt version: 3.4
cd7e644cae1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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8 Python version: could not detect
cd7e644cae1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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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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cd7e644cae1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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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)
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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14 Maximum trimming error rate: 0.1 (default)
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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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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17 Length cut-off for read 1: 35 bp (default)
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18 Length cut-off for read 2: 35 bp (default)
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19 Output file will be GZIP compressed
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22 This is cutadapt 3.4 with Python 3.9.6
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23 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
cd7e644cae1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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24 Processing reads on 4 cores in single-end mode ...
cd7e644cae1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
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25 Finished in 0.01 s (129 µs/read; 0.47 M reads/minute).
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27 === Summary ===
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29 Total reads processed: 99
b4e39d993fc8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
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30 Reads with adapters: 52 (52.5%)
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31 Reads written (passing filters): 99 (100.0%)
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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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33 Total basepairs processed: 24,849 bp
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34 Quality-trimmed: 205 bp (0.8%)
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35 Total written (filtered): 23,339 bp (93.9%)
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37 === Adapter 1 ===
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38
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39 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times
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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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41 No. of allowed errors:
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42 1-9 bp: 0; 10-12 bp: 1
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44 Bases preceding removed adapters:
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45 A: 9.6%
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46 C: 38.5%
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47 G: 23.1%
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48 T: 28.8%
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49 none/other: 0.0%
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51 Overview of removed sequences
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52 length count expect max.err error counts
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53 1 11 24.8 0 11
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54 2 5 6.2 0 5
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55 3 3 1.5 0 3
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56 4 3 0.4 0 3
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57 12 1 0.0 1 1
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58 13 2 0.0 1 2
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82 RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz
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83 =============================================
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84 99 sequences processed in total
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87 SUMMARISING RUN PARAMETERS
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88 ==========================
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89 Input filename: input_2.fastq.gz
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90 Trimming mode: paired-end
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91 Trim Galore version: 0.6.7
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92 Cutadapt version: 3.4
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93 Python version: could not detect
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94 Number of cores used for trimming: 4
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95 Quality Phred score cutoff: 20
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96 Quality encoding type selected: ASCII+33
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97 Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
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98 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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99 Maximum trimming error rate: 0.1 (default)
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100 Minimum required adapter overlap (stringency): 1 bp
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101 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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102 Length cut-off for read 1: 35 bp (default)
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103 Length cut-off for read 2: 35 bp (default)
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104 Output file will be GZIP compressed
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105
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106
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107 This is cutadapt 3.4 with Python 3.9.6
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108 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
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109 Processing reads on 4 cores in single-end mode ...
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110 Finished in 0.04 s (395 µs/read; 0.15 M reads/minute).
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111
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112 === Summary ===
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113
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114 Total reads processed: 99
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115 Reads with adapters: 58 (58.6%)
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116 Reads written (passing filters): 99 (100.0%)
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117
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118 Total basepairs processed: 24,849 bp
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119 Quality-trimmed: 745 bp (3.0%)
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120 Total written (filtered): 23,035 bp (92.7%)
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121
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122 === Adapter 1 ===
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123
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124 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times
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125
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126 No. of allowed errors:
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127 1-9 bp: 0; 10-12 bp: 1
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128
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129 Bases preceding removed adapters:
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130 A: 12.1%
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131 C: 37.9%
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132 G: 8.6%
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133 T: 41.4%
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134 none/other: 0.0%
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135
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136 Overview of removed sequences
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137 length count expect max.err error counts
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138 1 16 24.8 0 16
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139 2 7 6.2 0 7
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140 3 1 1.5 0 1
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141 4 2 0.4 0 2
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142 6 2 0.0 0 2
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143 9 1 0.0 0 1
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144 10 1 0.0 1 1
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145 13 1 0.0 1 1
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146 14 2 0.0 1 2
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147 15 1 0.0 1 1
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148 16 1 0.0 1 1
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149 17 1 0.0 1 1
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150 19 2 0.0 1 2
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151 21 1 0.0 1 1
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152 25 1 0.0 1 1
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153 30 1 0.0 1 1
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154 32 2 0.0 1 2
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155 34 1 0.0 1 1
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156 36 2 0.0 1 2
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157 38 1 0.0 1 1
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158 40 1 0.0 1 1
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159 41 1 0.0 1 1
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160 42 1 0.0 1 1
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161 43 1 0.0 1 1
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162 49 1 0.0 1 1
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163 51 1 0.0 1 1
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164 56 1 0.0 1 1
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165 57 1 0.0 1 1
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166 60 1 0.0 1 1
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167 67 1 0.0 1 1
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168 80 1 0.0 1 1
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169
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170 RUN STATISTICS FOR INPUT FILE: input_2.fastq.gz
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171 =============================================
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172 99 sequences processed in total
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173
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174 Total number of sequences analysed for the sequence pair length validation: 99
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175
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176 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)