Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_collection_example_results3.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 Length cut-off for read 1: 35 bp (default) 15 Length cut-off for read 1: 35 bp (default)
15 Length cut-off for read 2: 35 bp (default) 16 Length cut-off for read 2: 35 bp (default)
16 17
17 18
18 This is cutadapt 1.13 with Python 3.5.3 19 This is cutadapt 2.4 with Python 3.7.3
19 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq 20 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
20 Trimming 1 adapter with at most 10.0% errors in single-end mode ... 21 Processing reads on 1 core in single-end mode ...
21 Finished in 0.01 s (101 us/read; 0.59 M reads/minute). 22 Finished in 0.01 s (72 us/read; 0.83 M reads/minute).
22 23
23 === Summary === 24 === Summary ===
24 25
25 Total reads processed: 99 26 Total reads processed: 99
26 Reads with adapters: 52 (52.5%) 27 Reads with adapters: 52 (52.5%)
73 69 1 0.0 1 1 74 69 1 0.0 1 1
74 73 1 0.0 1 1 75 73 1 0.0 1 1
75 80 1 0.0 1 1 76 80 1 0.0 1 1
76 86 1 0.0 1 1 77 86 1 0.0 1 1
77 78
78
79 RUN STATISTICS FOR INPUT FILE: input_1.fastq 79 RUN STATISTICS FOR INPUT FILE: input_1.fastq
80 ============================================= 80 =============================================
81 99 sequences processed in total 81 99 sequences processed in total
82 82
83 83
84 SUMMARISING RUN PARAMETERS 84 SUMMARISING RUN PARAMETERS
85 ========================== 85 ==========================
86 Input filename: input_2.fastq 86 Input filename: input_2.fastq
87 Trimming mode: paired-end 87 Trimming mode: paired-end
88 Trim Galore version: 0.4.3 88 Trim Galore version: 0.6.3
89 Cutadapt version: 1.13 89 Cutadapt version: 2.4
90 Number of cores used for trimming: 1
90 Quality Phred score cutoff: 20 91 Quality Phred score cutoff: 20
91 Quality encoding type selected: ASCII+33 92 Quality encoding type selected: ASCII+33
92 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 93 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
93 Maximum trimming error rate: 0.1 (default) 94 Maximum trimming error rate: 0.1 (default)
94 Minimum required adapter overlap (stringency): 1 bp 95 Minimum required adapter overlap (stringency): 1 bp
95 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 96 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 1: 35 bp (default)
97 Length cut-off for read 2: 35 bp (default) 98 Length cut-off for read 2: 35 bp (default)
98 99
99 100
100 This is cutadapt 1.13 with Python 3.5.3 101 This is cutadapt 2.4 with Python 3.7.3
101 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq 102 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
102 Trimming 1 adapter with at most 10.0% errors in single-end mode ... 103 Processing reads on 1 core in single-end mode ...
103 Finished in 0.01 s (100 us/read; 0.60 M reads/minute). 104 Finished in 0.01 s (55 us/read; 1.08 M reads/minute).
104 105
105 === Summary === 106 === Summary ===
106 107
107 Total reads processed: 100 108 Total reads processed: 99
108 Reads with adapters: 59 (59.0%) 109 Reads with adapters: 58 (58.6%)
109 Reads written (passing filters): 100 (100.0%) 110 Reads written (passing filters): 99 (100.0%)
110 111
111 Total basepairs processed: 25,100 bp 112 Total basepairs processed: 24,849 bp
112 Quality-trimmed: 746 bp (3.0%) 113 Quality-trimmed: 745 bp (3.0%)
113 Total written (filtered): 23,276 bp (92.7%) 114 Total written (filtered): 23,035 bp (92.7%)
114 115
115 === Adapter 1 === 116 === Adapter 1 ===
116 117
117 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times. 118 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.
118 119
119 No. of allowed errors: 120 No. of allowed errors:
120 0-9 bp: 0; 10-12 bp: 1 121 0-9 bp: 0; 10-12 bp: 1
121 122
122 Bases preceding removed adapters: 123 Bases preceding removed adapters:
123 A: 11.9% 124 A: 12.1%
124 C: 39.0% 125 C: 37.9%
125 G: 8.5% 126 G: 8.6%
126 T: 40.7% 127 T: 41.4%
127 none/other: 0.0% 128 none/other: 0.0%
128 129
129 Overview of removed sequences 130 Overview of removed sequences
130 length count expect max.err error counts 131 length count expect max.err error counts
131 1 16 25.0 0 16 132 1 16 24.8 0 16
132 2 7 6.2 0 7 133 2 7 6.2 0 7
133 3 1 1.6 0 1 134 3 1 1.5 0 1
134 4 2 0.4 0 2 135 4 2 0.4 0 2
135 6 2 0.0 0 2 136 6 2 0.0 0 2
136 9 2 0.0 0 2 137 9 1 0.0 0 1
137 10 1 0.0 1 1 138 10 1 0.0 1 1
138 13 1 0.0 1 1 139 13 1 0.0 1 1
139 14 2 0.0 1 2 140 14 2 0.0 1 2
140 15 1 0.0 1 1 141 15 1 0.0 1 1
141 16 1 0.0 1 1 142 16 1 0.0 1 1
158 57 1 0.0 1 1 159 57 1 0.0 1 1
159 60 1 0.0 1 1 160 60 1 0.0 1 1
160 67 1 0.0 1 1 161 67 1 0.0 1 1
161 80 1 0.0 1 1 162 80 1 0.0 1 1
162 163
163
164 RUN STATISTICS FOR INPUT FILE: input_2.fastq 164 RUN STATISTICS FOR INPUT FILE: input_2.fastq
165 ============================================= 165 =============================================
166 100 sequences processed in total 166 99 sequences processed in total
167 167
168 Total number of sequences analysed for the sequence pair length validation: 99 168 Total number of sequences analysed for the sequence pair length validation: 99
169 169
170 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%) 170 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)