Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_collection_example_results3.txt @ 16:cd7e644cae1d draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 276a0ec327f5369c16563696047f0d31577c353f"
author bgruening
date Fri, 08 Oct 2021 09:57:52 +0000
parents 084bbd8ba7b8
children
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15:084bbd8ba7b8 16:cd7e644cae1d
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: 0.6.3 6 Trim Galore version: 0.6.7
7 Cutadapt version: 2.4 7 Cutadapt version: 3.4
8 Number of cores used for trimming: 1 8 Python version: could not detect
9 Number of cores used for trimming: 4
9 Quality Phred score cutoff: 20 10 Quality Phred score cutoff: 20
10 Quality encoding type selected: ASCII+33 11 Quality encoding type selected: ASCII+33
12 Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)
11 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 13 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
12 Maximum trimming error rate: 0.1 (default) 14 Maximum trimming error rate: 0.1 (default)
13 Minimum required adapter overlap (stringency): 1 bp 15 Minimum required adapter overlap (stringency): 1 bp
14 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 16 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
15 Length cut-off for read 1: 35 bp (default) 17 Length cut-off for read 1: 35 bp (default)
16 Length cut-off for read 2: 35 bp (default) 18 Length cut-off for read 2: 35 bp (default)
17 19
18 20
19 This is cutadapt 2.4 with Python 3.7.3 21 This is cutadapt 3.4 with Python 3.9.6
20 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq 22 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
21 Processing reads on 1 core in single-end mode ... 23 Processing reads on 4 cores in single-end mode ...
22 Finished in 0.01 s (72 us/read; 0.83 M reads/minute). 24 Finished in 0.01 s (115 µs/read; 0.52 M reads/minute).
23 25
24 === Summary === 26 === Summary ===
25 27
26 Total reads processed: 99 28 Total reads processed: 99
27 Reads with adapters: 52 (52.5%) 29 Reads with adapters: 52 (52.5%)
31 Quality-trimmed: 205 bp (0.8%) 33 Quality-trimmed: 205 bp (0.8%)
32 Total written (filtered): 23,339 bp (93.9%) 34 Total written (filtered): 23,339 bp (93.9%)
33 35
34 === Adapter 1 === 36 === Adapter 1 ===
35 37
36 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times. 38 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times
37 39
38 No. of allowed errors: 40 No. of allowed errors:
39 0-9 bp: 0; 10-12 bp: 1 41 1-9 bp: 0; 10-12 bp: 1
40 42
41 Bases preceding removed adapters: 43 Bases preceding removed adapters:
42 A: 9.6% 44 A: 9.6%
43 C: 38.5% 45 C: 38.5%
44 G: 23.1% 46 G: 23.1%
83 85
84 SUMMARISING RUN PARAMETERS 86 SUMMARISING RUN PARAMETERS
85 ========================== 87 ==========================
86 Input filename: input_2.fastq 88 Input filename: input_2.fastq
87 Trimming mode: paired-end 89 Trimming mode: paired-end
88 Trim Galore version: 0.6.3 90 Trim Galore version: 0.6.7
89 Cutadapt version: 2.4 91 Cutadapt version: 3.4
90 Number of cores used for trimming: 1 92 Python version: could not detect
93 Number of cores used for trimming: 4
91 Quality Phred score cutoff: 20 94 Quality Phred score cutoff: 20
92 Quality encoding type selected: ASCII+33 95 Quality encoding type selected: ASCII+33
96 Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)
93 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 97 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
94 Maximum trimming error rate: 0.1 (default) 98 Maximum trimming error rate: 0.1 (default)
95 Minimum required adapter overlap (stringency): 1 bp 99 Minimum required adapter overlap (stringency): 1 bp
96 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 100 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
97 Length cut-off for read 1: 35 bp (default) 101 Length cut-off for read 1: 35 bp (default)
98 Length cut-off for read 2: 35 bp (default) 102 Length cut-off for read 2: 35 bp (default)
99 103
100 104
101 This is cutadapt 2.4 with Python 3.7.3 105 This is cutadapt 3.4 with Python 3.9.6
102 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq 106 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
103 Processing reads on 1 core in single-end mode ... 107 Processing reads on 4 cores in single-end mode ...
104 Finished in 0.01 s (55 us/read; 1.08 M reads/minute). 108 Finished in 0.02 s (159 µs/read; 0.38 M reads/minute).
105 109
106 === Summary === 110 === Summary ===
107 111
108 Total reads processed: 99 112 Total reads processed: 99
109 Reads with adapters: 58 (58.6%) 113 Reads with adapters: 58 (58.6%)
113 Quality-trimmed: 745 bp (3.0%) 117 Quality-trimmed: 745 bp (3.0%)
114 Total written (filtered): 23,035 bp (92.7%) 118 Total written (filtered): 23,035 bp (92.7%)
115 119
116 === Adapter 1 === 120 === Adapter 1 ===
117 121
118 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times. 122 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times
119 123
120 No. of allowed errors: 124 No. of allowed errors:
121 0-9 bp: 0; 10-12 bp: 1 125 1-9 bp: 0; 10-12 bp: 1
122 126
123 Bases preceding removed adapters: 127 Bases preceding removed adapters:
124 A: 12.1% 128 A: 12.1%
125 C: 37.9% 129 C: 37.9%
126 G: 8.6% 130 G: 8.6%