Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_collection_example_results3gz.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 Length cut-off for read 1: 35 bp (default)
15 Length cut-off for read 2: 35 bp (default)
16 Output file will be GZIP compressed
17
18
19 This is cutadapt 1.8 with Python 3.5.3
20 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
21 Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ...
22 Finished in 0.10 s (1010 us/read; 0.06 M reads/minute).
23
24 === Summary ===
25
26 Total reads processed: 99
27 Reads with adapters: 52 (52.5%)
28 Reads written (passing filters): 99 (100.0%)
29
30 Total basepairs processed: 24,849 bp
31 Quality-trimmed: 205 bp (0.8%)
32 Total written (filtered): 23,339 bp (93.9%)
33
34 === Adapter 1 ===
35
36 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.
37
38 No. of allowed errors:
39 0-9 bp: 0; 10-12 bp: 1
40
41 Bases preceding removed adapters:
42 A: 9.6%
43 C: 38.5%
44 G: 23.1%
45 T: 28.8%
46 none/other: 0.0%
47
48 Overview of removed sequences
49 length count expect max.err error counts
50 1 11 24.8 0 11
51 2 5 6.2 0 5
52 3 3 1.5 0 3
53 4 3 0.4 0 3
54 12 1 0.0 1 1
55 13 2 0.0 1 2
56 14 1 0.0 1 1
57 16 1 0.0 1 1
58 17 1 0.0 1 0 1
59 20 2 0.0 1 2
60 21 1 0.0 1 1
61 24 1 0.0 1 1
62 26 2 0.0 1 2
63 31 1 0.0 1 1
64 33 1 0.0 1 1
65 41 2 0.0 1 2
66 49 1 0.0 1 1
67 50 1 0.0 1 1
68 54 1 0.0 1 1
69 56 1 0.0 1 1
70 58 2 0.0 1 2
71 60 1 0.0 1 1
72 67 2 0.0 1 2
73 68 1 0.0 1 1
74 69 1 0.0 1 1
75 73 1 0.0 1 1
76 80 1 0.0 1 1
77 86 1 0.0 1 1
78
79
80 RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz
81 =============================================
82 99 sequences processed in total
83
84
85 SUMMARISING RUN PARAMETERS
86 ==========================
87 Input filename: input_2.fastq.gz
88 Trimming mode: paired-end
89 Trim Galore version: 0.4.0
90 Cutadapt version: 1.8
91 Quality Phred score cutoff: 20
92 Quality encoding type selected: ASCII+33
93 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
94 Maximum trimming error rate: 0.1 (default)
95 Minimum required adapter overlap (stringency): 1 bp
96 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
97 Length cut-off for read 1: 35 bp (default)
98 Length cut-off for read 2: 35 bp (default)
99 Output file will be GZIP compressed
100
101
102 This is cutadapt 1.8 with Python 3.5.3
103 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
104 Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ...
105 Finished in 0.10 s (1000 us/read; 0.06 M reads/minute).
106
107 === Summary ===
108
109 Total reads processed: 100
110 Reads with adapters: 59 (59.0%)
111 Reads written (passing filters): 100 (100.0%)
112
113 Total basepairs processed: 25,100 bp
114 Quality-trimmed: 746 bp (3.0%)
115 Total written (filtered): 23,276 bp (92.7%)
116
117 === Adapter 1 ===
118
119 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times.
120
121 No. of allowed errors:
122 0-9 bp: 0; 10-12 bp: 1
123
124 Bases preceding removed adapters:
125 A: 11.9%
126 C: 39.0%
127 G: 8.5%
128 T: 40.7%
129 none/other: 0.0%
130
131 Overview of removed sequences
132 length count expect max.err error counts
133 1 16 25.0 0 16
134 2 7 6.2 0 7
135 3 1 1.6 0 1
136 4 2 0.4 0 2
137 6 2 0.0 0 2
138 9 2 0.0 0 2
139 10 1 0.0 1 1
140 13 1 0.0 1 1
141 14 2 0.0 1 2
142 15 1 0.0 1 1
143 16 1 0.0 1 1
144 17 1 0.0 1 1
145 19 2 0.0 1 2
146 21 1 0.0 1 1
147 25 1 0.0 1 1
148 30 1 0.0 1 1
149 32 2 0.0 1 2
150 34 1 0.0 1 1
151 36 2 0.0 1 2
152 38 1 0.0 1 1
153 40 1 0.0 1 1
154 41 1 0.0 1 1
155 42 1 0.0 1 1
156 43 1 0.0 1 1
157 49 1 0.0 1 1
158 51 1 0.0 1 1
159 56 1 0.0 1 1
160 57 1 0.0 1 1
161 60 1 0.0 1 1
162 67 1 0.0 1 1
163 80 1 0.0 1 1
164
165
166 RUN STATISTICS FOR INPUT FILE: input_2.fastq.gz
167 =============================================
168 100 sequences processed in total
169
170 Total number of sequences analysed for the sequence pair length validation: 99
171
172 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)