Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_example_results2gz.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
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 Output file will be GZIP compressed 15 Output file will be GZIP compressed
15 16
16 17
17 This is cutadapt 1.13 with Python 3.5.3 18 This is cutadapt 2.4 with Python 3.7.3
18 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz 19 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
19 Trimming 1 adapter with at most 10.0% errors in single-end mode ... 20 Processing reads on 1 core in single-end mode ...
20 Finished in 0.01 s (101 us/read; 0.59 M reads/minute). 21 Finished in 0.03 s (287 us/read; 0.21 M reads/minute).
21 22
22 === Summary === 23 === Summary ===
23 24
24 Total reads processed: 99 25 Total reads processed: 99
25 Reads with adapters: 52 (52.5%) 26 Reads with adapters: 52 (52.5%)
72 69 1 0.0 1 1 73 69 1 0.0 1 1
73 73 1 0.0 1 1 74 73 1 0.0 1 1
74 80 1 0.0 1 1 75 80 1 0.0 1 1
75 86 1 0.0 1 1 76 86 1 0.0 1 1
76 77
77
78 RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz 78 RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz
79 ============================================= 79 =============================================
80 99 sequences processed in total 80 99 sequences processed in total
81 81
82 82
83 SUMMARISING RUN PARAMETERS 83 SUMMARISING RUN PARAMETERS
84 ========================== 84 ==========================
85 Input filename: input_2.fastq.gz 85 Input filename: input_2.fastq.gz
86 Trimming mode: paired-end 86 Trimming mode: paired-end
87 Trim Galore version: 0.4.3 87 Trim Galore version: 0.6.3
88 Cutadapt version: 1.13 88 Cutadapt version: 2.4
89 Number of cores used for trimming: 1
89 Quality Phred score cutoff: 20 90 Quality Phred score cutoff: 20
90 Quality encoding type selected: ASCII+33 91 Quality encoding type selected: ASCII+33
91 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 92 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
92 Maximum trimming error rate: 0.1 (default) 93 Maximum trimming error rate: 0.1 (default)
93 Minimum required adapter overlap (stringency): 1 bp 94 Minimum required adapter overlap (stringency): 1 bp
94 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
95 Output file will be GZIP compressed 96 Output file will be GZIP compressed
96 97
97 98
98 This is cutadapt 1.13 with Python 3.5.3 99 This is cutadapt 2.4 with Python 3.7.3
99 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz 100 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
100 Trimming 1 adapter with at most 10.0% errors in single-end mode ... 101 Processing reads on 1 core in single-end mode ...
101 Finished in 0.01 s (100 us/read; 0.60 M reads/minute). 102 Finished in 0.02 s (170 us/read; 0.35 M reads/minute).
102 103
103 === Summary === 104 === Summary ===
104 105
105 Total reads processed: 100 106 Total reads processed: 99
106 Reads with adapters: 59 (59.0%) 107 Reads with adapters: 58 (58.6%)
107 Reads written (passing filters): 100 (100.0%) 108 Reads written (passing filters): 99 (100.0%)
108 109
109 Total basepairs processed: 25,100 bp 110 Total basepairs processed: 24,849 bp
110 Quality-trimmed: 746 bp (3.0%) 111 Quality-trimmed: 745 bp (3.0%)
111 Total written (filtered): 23,276 bp (92.7%) 112 Total written (filtered): 23,035 bp (92.7%)
112 113
113 === Adapter 1 === 114 === Adapter 1 ===
114 115
115 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times. 116 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.
116 117
117 No. of allowed errors: 118 No. of allowed errors:
118 0-9 bp: 0; 10-12 bp: 1 119 0-9 bp: 0; 10-12 bp: 1
119 120
120 Bases preceding removed adapters: 121 Bases preceding removed adapters:
121 A: 11.9% 122 A: 12.1%
122 C: 39.0% 123 C: 37.9%
123 G: 8.5% 124 G: 8.6%
124 T: 40.7% 125 T: 41.4%
125 none/other: 0.0% 126 none/other: 0.0%
126 127
127 Overview of removed sequences 128 Overview of removed sequences
128 length count expect max.err error counts 129 length count expect max.err error counts
129 1 16 25.0 0 16 130 1 16 24.8 0 16
130 2 7 6.2 0 7 131 2 7 6.2 0 7
131 3 1 1.6 0 1 132 3 1 1.5 0 1
132 4 2 0.4 0 2 133 4 2 0.4 0 2
133 6 2 0.0 0 2 134 6 2 0.0 0 2
134 9 2 0.0 0 2 135 9 1 0.0 0 1
135 10 1 0.0 1 1 136 10 1 0.0 1 1
136 13 1 0.0 1 1 137 13 1 0.0 1 1
137 14 2 0.0 1 2 138 14 2 0.0 1 2
138 15 1 0.0 1 1 139 15 1 0.0 1 1
139 16 1 0.0 1 1 140 16 1 0.0 1 1
156 57 1 0.0 1 1 157 57 1 0.0 1 1
157 60 1 0.0 1 1 158 60 1 0.0 1 1
158 67 1 0.0 1 1 159 67 1 0.0 1 1
159 80 1 0.0 1 1 160 80 1 0.0 1 1
160 161
161
162 RUN STATISTICS FOR INPUT FILE: input_2.fastq.gz 162 RUN STATISTICS FOR INPUT FILE: input_2.fastq.gz
163 ============================================= 163 =============================================
164 100 sequences processed in total 164 99 sequences processed in total
165 165
166 Total number of sequences analysed for the sequence pair length validation: 99 166 Total number of sequences analysed for the sequence pair length validation: 99
167 167
168 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%) 168 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)