Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_collection_example_results3.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
14 Length cut-off for read 1: 35 bp (default)
15 Length cut-off for read 2: 35 bp (default)
13 16
14 17
15 cutadapt version 1.1 18 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 19 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate1
17 Maximum error rate: 10.00% 20 Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ...
18 Processed reads: 100 21 Finished in 0.10 s (1010 us/read; 0.06 M reads/minute).
19 Trimmed reads: 20 ( 20.0%) 22
20 Total basepairs: 24894 (0.0 Mbp) 23 === Summary ===
21 Trimmed basepairs: 26 (0.0 Mbp) (0.10% of total) 24
22 Too short reads: 0 ( 0.0% of processed reads) 25 Total reads processed: 99
23 Too long reads: 0 ( 0.0% of processed reads) 26 Reads with adapters: 52 (52.5%)
24 Total time: 0.00 s 27 Reads written (passing filters): 99 (100.0%)
25 Time per read: 0.03 ms 28
29 Total basepairs processed: 24,849 bp
30 Quality-trimmed: 205 bp (0.8%)
31 Total written (filtered): 23,339 bp (93.9%)
26 32
27 === Adapter 1 === 33 === Adapter 1 ===
28 34
29 Adapter 'AGATCGGAAGAGC', length 13, was trimmed 20 times. 35 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.
30 36
31 Lengths of removed sequences 37 No. of allowed errors:
32 length count expected 38 0-9 bp: 0; 10-12 bp: 1
33 1 16 25.0 39
34 2 2 6.2 40 Bases preceding removed adapters:
35 3 2 1.6 41 A: 9.6%
42 C: 38.5%
43 G: 23.1%
44 T: 28.8%
45 none/other: 0.0%
46
47 Overview of removed sequences
48 length count expect max.err error counts
49 1 11 24.8 0 11
50 2 5 6.2 0 5
51 3 3 1.5 0 3
52 4 3 0.4 0 3
53 12 1 0.0 1 1
54 13 2 0.0 1 2
55 14 1 0.0 1 1
56 16 1 0.0 1 1
57 17 1 0.0 1 0 1
58 20 2 0.0 1 2
59 21 1 0.0 1 1
60 24 1 0.0 1 1
61 26 2 0.0 1 2
62 31 1 0.0 1 1
63 33 1 0.0 1 1
64 41 2 0.0 1 2
65 49 1 0.0 1 1
66 50 1 0.0 1 1
67 54 1 0.0 1 1
68 56 1 0.0 1 1
69 58 2 0.0 1 2
70 60 1 0.0 1 1
71 67 2 0.0 1 2
72 68 1 0.0 1 1
73 69 1 0.0 1 1
74 73 1 0.0 1 1
75 80 1 0.0 1 1
76 86 1 0.0 1 1
36 77
37 78
38 RUN STATISTICS FOR INPUT FILE: ./input_mate1 79 RUN STATISTICS FOR INPUT FILE: ./input_mate1
39 ============================================= 80 =============================================
40 100 sequences processed in total 81 99 sequences processed in total
41 82
42 83
43 SUMMARISING RUN PARAMETERS 84 SUMMARISING RUN PARAMETERS
44 ========================== 85 ==========================
45 Input filename: ./input_mate2 86 Input filename: ./input_mate2
46 Trimming mode: paired-end 87 Trimming mode: paired-end
47 Trim Galore version: 0.3.7 88 Trim Galore version: 0.4.0
89 Cutadapt version: 1.8
48 Quality Phred score cutoff: 20 90 Quality Phred score cutoff: 20
49 Quality encoding type selected: ASCII+33 91 Quality encoding type selected: ASCII+33
50 Adapter sequence: 'AGATCGGAAGAGC' 92 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
51 Maximum trimming error rate: 0.1 (default) 93 Maximum trimming error rate: 0.1 (default)
52 Minimum required adapter overlap (stringency): 1 bp 94 Minimum required adapter overlap (stringency): 1 bp
53 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 95 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
96 Length cut-off for read 1: 35 bp (default)
97 Length cut-off for read 2: 35 bp (default)
54 98
55 99
56 cutadapt version 1.1 100 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 101 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate2
58 Maximum error rate: 10.00% 102 Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ...
59 Processed reads: 100 103 Finished in 0.10 s (1000 us/read; 0.06 M reads/minute).
60 Trimmed reads: 24 ( 24.0%) 104
61 Total basepairs: 24354 (0.0 Mbp) 105 === Summary ===
62 Trimmed basepairs: 36 (0.0 Mbp) (0.15% of total) 106
63 Too short reads: 0 ( 0.0% of processed reads) 107 Total reads processed: 100
64 Too long reads: 0 ( 0.0% of processed reads) 108 Reads with adapters: 59 (59.0%)
65 Total time: 0.01 s 109 Reads written (passing filters): 100 (100.0%)
66 Time per read: 0.10 ms 110
111 Total basepairs processed: 25,100 bp
112 Quality-trimmed: 746 bp (3.0%)
113 Total written (filtered): 23,276 bp (92.7%)
67 114
68 === Adapter 1 === 115 === Adapter 1 ===
69 116
70 Adapter 'AGATCGGAAGAGC', length 13, was trimmed 24 times. 117 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times.
71 118
72 Lengths of removed sequences 119 No. of allowed errors:
73 length count expected 120 0-9 bp: 0; 10-12 bp: 1
74 1 15 25.0 121
75 2 7 6.2 122 Bases preceding removed adapters:
76 3 1 1.6 123 A: 11.9%
77 4 1 0.4 124 C: 39.0%
125 G: 8.5%
126 T: 40.7%
127 none/other: 0.0%
128
129 Overview of removed sequences
130 length count expect max.err error counts
131 1 16 25.0 0 16
132 2 7 6.2 0 7
133 3 1 1.6 0 1
134 4 2 0.4 0 2
135 6 2 0.0 0 2
136 9 2 0.0 0 2
137 10 1 0.0 1 1
138 13 1 0.0 1 1
139 14 2 0.0 1 2
140 15 1 0.0 1 1
141 16 1 0.0 1 1
142 17 1 0.0 1 1
143 19 2 0.0 1 2
144 21 1 0.0 1 1
145 25 1 0.0 1 1
146 30 1 0.0 1 1
147 32 2 0.0 1 2
148 34 1 0.0 1 1
149 36 2 0.0 1 2
150 38 1 0.0 1 1
151 40 1 0.0 1 1
152 41 1 0.0 1 1
153 42 1 0.0 1 1
154 43 1 0.0 1 1
155 49 1 0.0 1 1
156 51 1 0.0 1 1
157 56 1 0.0 1 1
158 57 1 0.0 1 1
159 60 1 0.0 1 1
160 67 1 0.0 1 1
161 80 1 0.0 1 1
78 162
79 163
80 RUN STATISTICS FOR INPUT FILE: ./input_mate2 164 RUN STATISTICS FOR INPUT FILE: ./input_mate2
81 ============================================= 165 =============================================
82 100 sequences processed in total 166 100 sequences processed in total
83 167
84 Total number of sequences analysed for the sequence pair length validation: 100 168 Total number of sequences analysed for the sequence pair length validation: 99
85 169
86 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.00%) 170 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)