Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_example_results2gz.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
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children 80cd83b11214
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9:1bfc7254232e 10:b4e39d993fc8
1
2 SUMMARISING RUN PARAMETERS
3 ==========================
4 Input filename: input_1.fastq.gz
5 Trimming mode: paired-end
6 Trim Galore version: 0.4.0
7 Cutadapt version: 1.8
8 Quality Phred score cutoff: 20
9 Quality encoding type selected: ASCII+33
10 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
11 Maximum trimming error rate: 0.1 (default)
12 Minimum required adapter overlap (stringency): 1 bp
13 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
14 Output file will be GZIP compressed
15
16
17 This is cutadapt 1.8 with Python 3.5.3
18 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
19 Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ...
20 Finished in 0.10 s (1010 us/read; 0.06 M reads/minute).
21
22 === Summary ===
23
24 Total reads processed: 99
25 Reads with adapters: 52 (52.5%)
26 Reads written (passing filters): 99 (100.0%)
27
28 Total basepairs processed: 24,849 bp
29 Quality-trimmed: 205 bp (0.8%)
30 Total written (filtered): 23,339 bp (93.9%)
31
32 === Adapter 1 ===
33
34 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.
35
36 No. of allowed errors:
37 0-9 bp: 0; 10-12 bp: 1
38
39 Bases preceding removed adapters:
40 A: 9.6%
41 C: 38.5%
42 G: 23.1%
43 T: 28.8%
44 none/other: 0.0%
45
46 Overview of removed sequences
47 length count expect max.err error counts
48 1 11 24.8 0 11
49 2 5 6.2 0 5
50 3 3 1.5 0 3
51 4 3 0.4 0 3
52 12 1 0.0 1 1
53 13 2 0.0 1 2
54 14 1 0.0 1 1
55 16 1 0.0 1 1
56 17 1 0.0 1 0 1
57 20 2 0.0 1 2
58 21 1 0.0 1 1
59 24 1 0.0 1 1
60 26 2 0.0 1 2
61 31 1 0.0 1 1
62 33 1 0.0 1 1
63 41 2 0.0 1 2
64 49 1 0.0 1 1
65 50 1 0.0 1 1
66 54 1 0.0 1 1
67 56 1 0.0 1 1
68 58 2 0.0 1 2
69 60 1 0.0 1 1
70 67 2 0.0 1 2
71 68 1 0.0 1 1
72 69 1 0.0 1 1
73 73 1 0.0 1 1
74 80 1 0.0 1 1
75 86 1 0.0 1 1
76
77
78 RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz
79 =============================================
80 99 sequences processed in total
81
82
83 SUMMARISING RUN PARAMETERS
84 ==========================
85 Input filename: input_2.fastq.gz
86 Trimming mode: paired-end
87 Trim Galore version: 0.4.0
88 Cutadapt version: 1.8
89 Quality Phred score cutoff: 20
90 Quality encoding type selected: ASCII+33
91 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
92 Maximum trimming error rate: 0.1 (default)
93 Minimum required adapter overlap (stringency): 1 bp
94 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
95 Output file will be GZIP compressed
96
97
98 This is cutadapt 1.8 with Python 3.5.3
99 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
100 Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ...
101 Finished in 0.10 s (1000 us/read; 0.06 M reads/minute).
102
103 === Summary ===
104
105 Total reads processed: 100
106 Reads with adapters: 59 (59.0%)
107 Reads written (passing filters): 100 (100.0%)
108
109 Total basepairs processed: 25,100 bp
110 Quality-trimmed: 746 bp (3.0%)
111 Total written (filtered): 23,276 bp (92.7%)
112
113 === Adapter 1 ===
114
115 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times.
116
117 No. of allowed errors:
118 0-9 bp: 0; 10-12 bp: 1
119
120 Bases preceding removed adapters:
121 A: 11.9%
122 C: 39.0%
123 G: 8.5%
124 T: 40.7%
125 none/other: 0.0%
126
127 Overview of removed sequences
128 length count expect max.err error counts
129 1 16 25.0 0 16
130 2 7 6.2 0 7
131 3 1 1.6 0 1
132 4 2 0.4 0 2
133 6 2 0.0 0 2
134 9 2 0.0 0 2
135 10 1 0.0 1 1
136 13 1 0.0 1 1
137 14 2 0.0 1 2
138 15 1 0.0 1 1
139 16 1 0.0 1 1
140 17 1 0.0 1 1
141 19 2 0.0 1 2
142 21 1 0.0 1 1
143 25 1 0.0 1 1
144 30 1 0.0 1 1
145 32 2 0.0 1 2
146 34 1 0.0 1 1
147 36 2 0.0 1 2
148 38 1 0.0 1 1
149 40 1 0.0 1 1
150 41 1 0.0 1 1
151 42 1 0.0 1 1
152 43 1 0.0 1 1
153 49 1 0.0 1 1
154 51 1 0.0 1 1
155 56 1 0.0 1 1
156 57 1 0.0 1 1
157 60 1 0.0 1 1
158 67 1 0.0 1 1
159 80 1 0.0 1 1
160
161
162 RUN STATISTICS FOR INPUT FILE: input_2.fastq.gz
163 =============================================
164 100 sequences processed in total
165
166 Total number of sequences analysed for the sequence pair length validation: 99
167
168 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)