Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_example_results2.txt @ 6:11962ce40855 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
author bgruening
date Wed, 07 Oct 2015 08:39:59 -0400
parents 2c1f0fe810f7
children b4e39d993fc8
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5:f11ff7be8c78 6:11962ce40855
1 1
2 SUMMARISING RUN PARAMETERS 2 SUMMARISING RUN PARAMETERS
3 ========================== 3 ==========================
4 Input filename: ./input_mate1 4 Input filename: ./input_mate1
5 Trimming mode: paired-end 5 Trimming mode: paired-end
6 Trim Galore version: 0.3.7 6 Trim Galore version: 0.4.0
7 Cutadapt version: 1.8
7 Quality Phred score cutoff: 20 8 Quality Phred score cutoff: 20
8 Quality encoding type selected: ASCII+33 9 Quality encoding type selected: ASCII+33
9 Adapter sequence: 'AGATCGGAAGAGC' 10 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
10 Maximum trimming error rate: 0.1 (default) 11 Maximum trimming error rate: 0.1 (default)
11 Minimum required adapter overlap (stringency): 1 bp 12 Minimum required adapter overlap (stringency): 1 bp
12 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 13 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
13 14
14 15
15 cutadapt version 1.1 16 This is cutadapt 1.8 with Python 2.7.9
16 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate1 17 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate1
17 Maximum error rate: 10.00% 18 Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ...
18 Processed reads: 100 19 Finished in 0.10 s (1010 us/read; 0.06 M reads/minute).
19 Trimmed reads: 20 ( 20.0%) 20
20 Total basepairs: 24894 (0.0 Mbp) 21 === Summary ===
21 Trimmed basepairs: 26 (0.0 Mbp) (0.10% of total) 22
22 Too short reads: 0 ( 0.0% of processed reads) 23 Total reads processed: 99
23 Too long reads: 0 ( 0.0% of processed reads) 24 Reads with adapters: 52 (52.5%)
24 Total time: 0.00 s 25 Reads written (passing filters): 99 (100.0%)
25 Time per read: 0.02 ms 26
27 Total basepairs processed: 24,849 bp
28 Quality-trimmed: 205 bp (0.8%)
29 Total written (filtered): 23,339 bp (93.9%)
26 30
27 === Adapter 1 === 31 === Adapter 1 ===
28 32
29 Adapter 'AGATCGGAAGAGC', length 13, was trimmed 20 times. 33 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.
30 34
31 Lengths of removed sequences 35 No. of allowed errors:
32 length count expected 36 0-9 bp: 0; 10-12 bp: 1
33 1 16 25.0 37
34 2 2 6.2 38 Bases preceding removed adapters:
35 3 2 1.6 39 A: 9.6%
40 C: 38.5%
41 G: 23.1%
42 T: 28.8%
43 none/other: 0.0%
44
45 Overview of removed sequences
46 length count expect max.err error counts
47 1 11 24.8 0 11
48 2 5 6.2 0 5
49 3 3 1.5 0 3
50 4 3 0.4 0 3
51 12 1 0.0 1 1
52 13 2 0.0 1 2
53 14 1 0.0 1 1
54 16 1 0.0 1 1
55 17 1 0.0 1 0 1
56 20 2 0.0 1 2
57 21 1 0.0 1 1
58 24 1 0.0 1 1
59 26 2 0.0 1 2
60 31 1 0.0 1 1
61 33 1 0.0 1 1
62 41 2 0.0 1 2
63 49 1 0.0 1 1
64 50 1 0.0 1 1
65 54 1 0.0 1 1
66 56 1 0.0 1 1
67 58 2 0.0 1 2
68 60 1 0.0 1 1
69 67 2 0.0 1 2
70 68 1 0.0 1 1
71 69 1 0.0 1 1
72 73 1 0.0 1 1
73 80 1 0.0 1 1
74 86 1 0.0 1 1
36 75
37 76
38 RUN STATISTICS FOR INPUT FILE: ./input_mate1 77 RUN STATISTICS FOR INPUT FILE: ./input_mate1
39 ============================================= 78 =============================================
40 100 sequences processed in total 79 99 sequences processed in total
41 80
42 81
43 SUMMARISING RUN PARAMETERS 82 SUMMARISING RUN PARAMETERS
44 ========================== 83 ==========================
45 Input filename: ./input_mate2 84 Input filename: ./input_mate2
46 Trimming mode: paired-end 85 Trimming mode: paired-end
47 Trim Galore version: 0.3.7 86 Trim Galore version: 0.4.0
87 Cutadapt version: 1.8
48 Quality Phred score cutoff: 20 88 Quality Phred score cutoff: 20
49 Quality encoding type selected: ASCII+33 89 Quality encoding type selected: ASCII+33
50 Adapter sequence: 'AGATCGGAAGAGC' 90 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
51 Maximum trimming error rate: 0.1 (default) 91 Maximum trimming error rate: 0.1 (default)
52 Minimum required adapter overlap (stringency): 1 bp 92 Minimum required adapter overlap (stringency): 1 bp
53 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 93 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
54 94
55 95
56 cutadapt version 1.1 96 This is cutadapt 1.8 with Python 2.7.9
57 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate2 97 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate2
58 Maximum error rate: 10.00% 98 Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ...
59 Processed reads: 100 99 Finished in 0.10 s (1000 us/read; 0.06 M reads/minute).
60 Trimmed reads: 24 ( 24.0%) 100
61 Total basepairs: 24354 (0.0 Mbp) 101 === Summary ===
62 Trimmed basepairs: 36 (0.0 Mbp) (0.15% of total) 102
63 Too short reads: 0 ( 0.0% of processed reads) 103 Total reads processed: 100
64 Too long reads: 0 ( 0.0% of processed reads) 104 Reads with adapters: 59 (59.0%)
65 Total time: 0.01 s 105 Reads written (passing filters): 100 (100.0%)
66 Time per read: 0.12 ms 106
107 Total basepairs processed: 25,100 bp
108 Quality-trimmed: 746 bp (3.0%)
109 Total written (filtered): 23,276 bp (92.7%)
67 110
68 === Adapter 1 === 111 === Adapter 1 ===
69 112
70 Adapter 'AGATCGGAAGAGC', length 13, was trimmed 24 times. 113 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times.
71 114
72 Lengths of removed sequences 115 No. of allowed errors:
73 length count expected 116 0-9 bp: 0; 10-12 bp: 1
74 1 15 25.0 117
75 2 7 6.2 118 Bases preceding removed adapters:
76 3 1 1.6 119 A: 11.9%
77 4 1 0.4 120 C: 39.0%
121 G: 8.5%
122 T: 40.7%
123 none/other: 0.0%
124
125 Overview of removed sequences
126 length count expect max.err error counts
127 1 16 25.0 0 16
128 2 7 6.2 0 7
129 3 1 1.6 0 1
130 4 2 0.4 0 2
131 6 2 0.0 0 2
132 9 2 0.0 0 2
133 10 1 0.0 1 1
134 13 1 0.0 1 1
135 14 2 0.0 1 2
136 15 1 0.0 1 1
137 16 1 0.0 1 1
138 17 1 0.0 1 1
139 19 2 0.0 1 2
140 21 1 0.0 1 1
141 25 1 0.0 1 1
142 30 1 0.0 1 1
143 32 2 0.0 1 2
144 34 1 0.0 1 1
145 36 2 0.0 1 2
146 38 1 0.0 1 1
147 40 1 0.0 1 1
148 41 1 0.0 1 1
149 42 1 0.0 1 1
150 43 1 0.0 1 1
151 49 1 0.0 1 1
152 51 1 0.0 1 1
153 56 1 0.0 1 1
154 57 1 0.0 1 1
155 60 1 0.0 1 1
156 67 1 0.0 1 1
157 80 1 0.0 1 1
78 158
79 159
80 RUN STATISTICS FOR INPUT FILE: ./input_mate2 160 RUN STATISTICS FOR INPUT FILE: ./input_mate2
81 ============================================= 161 =============================================
82 100 sequences processed in total 162 100 sequences processed in total
83 163
84 Total number of sequences analysed for the sequence pair length validation: 100 164 Total number of sequences analysed for the sequence pair length validation: 99
85 165
86 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.00%) 166 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)