Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_example_results2.txt @ 15:084bbd8ba7b8 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7
author bgruening
date Tue, 30 Jul 2019 06:26:49 -0400
parents 80cd83b11214
children cd7e644cae1d
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14:949f01671246 15:084bbd8ba7b8
1 1
2 SUMMARISING RUN PARAMETERS 2 SUMMARISING RUN PARAMETERS
3 ========================== 3 ==========================
4 Input filename: input_1.fastq 4 Input filename: input_1.fastq
5 Trimming mode: paired-end 5 Trimming mode: paired-end
6 Trim Galore version: 0.4.3 6 Trim Galore version: 0.6.3
7 Cutadapt version: 1.13 7 Cutadapt version: 2.4
8 Number of cores used for trimming: 1
8 Quality Phred score cutoff: 20 9 Quality Phred score cutoff: 20
9 Quality encoding type selected: ASCII+33 10 Quality encoding type selected: ASCII+33
10 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 11 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
11 Maximum trimming error rate: 0.1 (default) 12 Maximum trimming error rate: 0.1 (default)
12 Minimum required adapter overlap (stringency): 1 bp 13 Minimum required adapter overlap (stringency): 1 bp
13 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 14 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
14 15
15 16
16 This is cutadapt 1.13 with Python 3.5.3 17 This is cutadapt 2.4 with Python 3.7.3
17 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq 18 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
18 Trimming 1 adapter with at most 10.0% errors in single-end mode ... 19 Processing reads on 1 core in single-end mode ...
19 Finished in 0.01 s (101 us/read; 0.59 M reads/minute). 20 Finished in 0.01 s (75 us/read; 0.80 M reads/minute).
20 21
21 === Summary === 22 === Summary ===
22 23
23 Total reads processed: 99 24 Total reads processed: 99
24 Reads with adapters: 52 (52.5%) 25 Reads with adapters: 52 (52.5%)
71 69 1 0.0 1 1 72 69 1 0.0 1 1
72 73 1 0.0 1 1 73 73 1 0.0 1 1
73 80 1 0.0 1 1 74 80 1 0.0 1 1
74 86 1 0.0 1 1 75 86 1 0.0 1 1
75 76
76
77 RUN STATISTICS FOR INPUT FILE: input_1.fastq 77 RUN STATISTICS FOR INPUT FILE: input_1.fastq
78 ============================================= 78 =============================================
79 99 sequences processed in total 79 99 sequences processed in total
80 80
81 81
82 SUMMARISING RUN PARAMETERS 82 SUMMARISING RUN PARAMETERS
83 ========================== 83 ==========================
84 Input filename: input_2.fastq 84 Input filename: input_2.fastq
85 Trimming mode: paired-end 85 Trimming mode: paired-end
86 Trim Galore version: 0.4.3 86 Trim Galore version: 0.6.3
87 Cutadapt version: 1.13 87 Cutadapt version: 2.4
88 Number of cores used for trimming: 1
88 Quality Phred score cutoff: 20 89 Quality Phred score cutoff: 20
89 Quality encoding type selected: ASCII+33 90 Quality encoding type selected: ASCII+33
90 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 91 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
91 Maximum trimming error rate: 0.1 (default) 92 Maximum trimming error rate: 0.1 (default)
92 Minimum required adapter overlap (stringency): 1 bp 93 Minimum required adapter overlap (stringency): 1 bp
93 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 94 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
94 95
95 96
96 This is cutadapt 1.13 with Python 3.5.3 97 This is cutadapt 2.4 with Python 3.7.3
97 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq 98 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
98 Trimming 1 adapter with at most 10.0% errors in single-end mode ... 99 Processing reads on 1 core in single-end mode ...
99 Finished in 0.01 s (100 us/read; 0.60 M reads/minute). 100 Finished in 0.00 s (50 us/read; 1.19 M reads/minute).
100 101
101 === Summary === 102 === Summary ===
102 103
103 Total reads processed: 100 104 Total reads processed: 99
104 Reads with adapters: 59 (59.0%) 105 Reads with adapters: 58 (58.6%)
105 Reads written (passing filters): 100 (100.0%) 106 Reads written (passing filters): 99 (100.0%)
106 107
107 Total basepairs processed: 25,100 bp 108 Total basepairs processed: 24,849 bp
108 Quality-trimmed: 746 bp (3.0%) 109 Quality-trimmed: 745 bp (3.0%)
109 Total written (filtered): 23,276 bp (92.7%) 110 Total written (filtered): 23,035 bp (92.7%)
110 111
111 === Adapter 1 === 112 === Adapter 1 ===
112 113
113 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times. 114 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.
114 115
115 No. of allowed errors: 116 No. of allowed errors:
116 0-9 bp: 0; 10-12 bp: 1 117 0-9 bp: 0; 10-12 bp: 1
117 118
118 Bases preceding removed adapters: 119 Bases preceding removed adapters:
119 A: 11.9% 120 A: 12.1%
120 C: 39.0% 121 C: 37.9%
121 G: 8.5% 122 G: 8.6%
122 T: 40.7% 123 T: 41.4%
123 none/other: 0.0% 124 none/other: 0.0%
124 125
125 Overview of removed sequences 126 Overview of removed sequences
126 length count expect max.err error counts 127 length count expect max.err error counts
127 1 16 25.0 0 16 128 1 16 24.8 0 16
128 2 7 6.2 0 7 129 2 7 6.2 0 7
129 3 1 1.6 0 1 130 3 1 1.5 0 1
130 4 2 0.4 0 2 131 4 2 0.4 0 2
131 6 2 0.0 0 2 132 6 2 0.0 0 2
132 9 2 0.0 0 2 133 9 1 0.0 0 1
133 10 1 0.0 1 1 134 10 1 0.0 1 1
134 13 1 0.0 1 1 135 13 1 0.0 1 1
135 14 2 0.0 1 2 136 14 2 0.0 1 2
136 15 1 0.0 1 1 137 15 1 0.0 1 1
137 16 1 0.0 1 1 138 16 1 0.0 1 1
154 57 1 0.0 1 1 155 57 1 0.0 1 1
155 60 1 0.0 1 1 156 60 1 0.0 1 1
156 67 1 0.0 1 1 157 67 1 0.0 1 1
157 80 1 0.0 1 1 158 80 1 0.0 1 1
158 159
159
160 RUN STATISTICS FOR INPUT FILE: input_2.fastq 160 RUN STATISTICS FOR INPUT FILE: input_2.fastq
161 ============================================= 161 =============================================
162 100 sequences processed in total 162 99 sequences processed in total
163 163
164 Total number of sequences analysed for the sequence pair length validation: 99 164 Total number of sequences analysed for the sequence pair length validation: 99
165 165
166 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%) 166 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)