Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_collection_example_results3gz.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
comparison
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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.gz 4 Input filename: input_1.fastq.gz
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
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 Output file will be GZIP compressed 17 Output file will be GZIP compressed
17 18
18 19
19 This is cutadapt 1.13 with Python 3.5.3 20 This is cutadapt 2.4 with Python 3.7.3
20 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz 21 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
21 Trimming 1 adapter with at most 10.0% errors in single-end mode ... 22 Processing reads on 1 core in single-end mode ...
22 Finished in 0.01 s (101 us/read; 0.59 M reads/minute). 23 Finished in 0.02 s (176 us/read; 0.34 M reads/minute).
23 24
24 === Summary === 25 === Summary ===
25 26
26 Total reads processed: 99 27 Total reads processed: 99
27 Reads with adapters: 52 (52.5%) 28 Reads with adapters: 52 (52.5%)
74 69 1 0.0 1 1 75 69 1 0.0 1 1
75 73 1 0.0 1 1 76 73 1 0.0 1 1
76 80 1 0.0 1 1 77 80 1 0.0 1 1
77 86 1 0.0 1 1 78 86 1 0.0 1 1
78 79
79
80 RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz 80 RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz
81 ============================================= 81 =============================================
82 99 sequences processed in total 82 99 sequences processed in total
83 83
84 84
85 SUMMARISING RUN PARAMETERS 85 SUMMARISING RUN PARAMETERS
86 ========================== 86 ==========================
87 Input filename: input_2.fastq.gz 87 Input filename: input_2.fastq.gz
88 Trimming mode: paired-end 88 Trimming mode: paired-end
89 Trim Galore version: 0.4.3 89 Trim Galore version: 0.6.3
90 Cutadapt version: 1.13 90 Cutadapt version: 2.4
91 Number of cores used for trimming: 1
91 Quality Phred score cutoff: 20 92 Quality Phred score cutoff: 20
92 Quality encoding type selected: ASCII+33 93 Quality encoding type selected: ASCII+33
93 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 94 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
94 Maximum trimming error rate: 0.1 (default) 95 Maximum trimming error rate: 0.1 (default)
95 Minimum required adapter overlap (stringency): 1 bp 96 Minimum required adapter overlap (stringency): 1 bp
97 Length cut-off for read 1: 35 bp (default) 98 Length cut-off for read 1: 35 bp (default)
98 Length cut-off for read 2: 35 bp (default) 99 Length cut-off for read 2: 35 bp (default)
99 Output file will be GZIP compressed 100 Output file will be GZIP compressed
100 101
101 102
102 This is cutadapt 1.13 with Python 3.5.3 103 This is cutadapt 2.4 with Python 3.7.3
103 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz 104 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
104 Trimming 1 adapter with at most 10.0% errors in single-end mode ... 105 Processing reads on 1 core in single-end mode ...
105 Finished in 0.01 s (100 us/read; 0.60 M reads/minute). 106 Finished in 0.02 s (169 us/read; 0.36 M reads/minute).
106 107
107 === Summary === 108 === Summary ===
108 109
109 Total reads processed: 100 110 Total reads processed: 99
110 Reads with adapters: 59 (59.0%) 111 Reads with adapters: 58 (58.6%)
111 Reads written (passing filters): 100 (100.0%) 112 Reads written (passing filters): 99 (100.0%)
112 113
113 Total basepairs processed: 25,100 bp 114 Total basepairs processed: 24,849 bp
114 Quality-trimmed: 746 bp (3.0%) 115 Quality-trimmed: 745 bp (3.0%)
115 Total written (filtered): 23,276 bp (92.7%) 116 Total written (filtered): 23,035 bp (92.7%)
116 117
117 === Adapter 1 === 118 === Adapter 1 ===
118 119
119 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times. 120 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.
120 121
121 No. of allowed errors: 122 No. of allowed errors:
122 0-9 bp: 0; 10-12 bp: 1 123 0-9 bp: 0; 10-12 bp: 1
123 124
124 Bases preceding removed adapters: 125 Bases preceding removed adapters:
125 A: 11.9% 126 A: 12.1%
126 C: 39.0% 127 C: 37.9%
127 G: 8.5% 128 G: 8.6%
128 T: 40.7% 129 T: 41.4%
129 none/other: 0.0% 130 none/other: 0.0%
130 131
131 Overview of removed sequences 132 Overview of removed sequences
132 length count expect max.err error counts 133 length count expect max.err error counts
133 1 16 25.0 0 16 134 1 16 24.8 0 16
134 2 7 6.2 0 7 135 2 7 6.2 0 7
135 3 1 1.6 0 1 136 3 1 1.5 0 1
136 4 2 0.4 0 2 137 4 2 0.4 0 2
137 6 2 0.0 0 2 138 6 2 0.0 0 2
138 9 2 0.0 0 2 139 9 1 0.0 0 1
139 10 1 0.0 1 1 140 10 1 0.0 1 1
140 13 1 0.0 1 1 141 13 1 0.0 1 1
141 14 2 0.0 1 2 142 14 2 0.0 1 2
142 15 1 0.0 1 1 143 15 1 0.0 1 1
143 16 1 0.0 1 1 144 16 1 0.0 1 1
160 57 1 0.0 1 1 161 57 1 0.0 1 1
161 60 1 0.0 1 1 162 60 1 0.0 1 1
162 67 1 0.0 1 1 163 67 1 0.0 1 1
163 80 1 0.0 1 1 164 80 1 0.0 1 1
164 165
165
166 RUN STATISTICS FOR INPUT FILE: input_2.fastq.gz 166 RUN STATISTICS FOR INPUT FILE: input_2.fastq.gz
167 ============================================= 167 =============================================
168 100 sequences processed in total 168 99 sequences processed in total
169 169
170 Total number of sequences analysed for the sequence pair length validation: 99 170 Total number of sequences analysed for the sequence pair length validation: 99
171 171
172 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%) 172 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)