Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_example_results2.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
comparison
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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 smallRNA (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 17
16 18
17 This is cutadapt 2.4 with Python 3.7.3 19 This is cutadapt 3.4 with Python 3.9.6
18 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq 20 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
19 Processing reads on 1 core in single-end mode ... 21 Processing reads on 4 cores in single-end mode ...
20 Finished in 0.01 s (75 us/read; 0.80 M reads/minute). 22 Finished in 0.01 s (117 µs/read; 0.51 M reads/minute).
21 23
22 === Summary === 24 === Summary ===
23 25
24 Total reads processed: 99 26 Total reads processed: 99
25 Reads with adapters: 52 (52.5%) 27 Reads with adapters: 52 (52.5%)
29 Quality-trimmed: 205 bp (0.8%) 31 Quality-trimmed: 205 bp (0.8%)
30 Total written (filtered): 23,339 bp (93.9%) 32 Total written (filtered): 23,339 bp (93.9%)
31 33
32 === Adapter 1 === 34 === Adapter 1 ===
33 35
34 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times. 36 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times
35 37
36 No. of allowed errors: 38 No. of allowed errors:
37 0-9 bp: 0; 10-12 bp: 1 39 1-9 bp: 0; 10-12 bp: 1
38 40
39 Bases preceding removed adapters: 41 Bases preceding removed adapters:
40 A: 9.6% 42 A: 9.6%
41 C: 38.5% 43 C: 38.5%
42 G: 23.1% 44 G: 23.1%
81 83
82 SUMMARISING RUN PARAMETERS 84 SUMMARISING RUN PARAMETERS
83 ========================== 85 ==========================
84 Input filename: input_2.fastq 86 Input filename: input_2.fastq
85 Trimming mode: paired-end 87 Trimming mode: paired-end
86 Trim Galore version: 0.6.3 88 Trim Galore version: 0.6.7
87 Cutadapt version: 2.4 89 Cutadapt version: 3.4
88 Number of cores used for trimming: 1 90 Python version: could not detect
91 Number of cores used for trimming: 4
89 Quality Phred score cutoff: 20 92 Quality Phred score cutoff: 20
90 Quality encoding type selected: ASCII+33 93 Quality encoding type selected: ASCII+33
94 Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
91 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 95 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
92 Maximum trimming error rate: 0.1 (default) 96 Maximum trimming error rate: 0.1 (default)
93 Minimum required adapter overlap (stringency): 1 bp 97 Minimum required adapter overlap (stringency): 1 bp
94 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 98 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
95 99
96 100
97 This is cutadapt 2.4 with Python 3.7.3 101 This is cutadapt 3.4 with Python 3.9.6
98 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq 102 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
99 Processing reads on 1 core in single-end mode ... 103 Processing reads on 4 cores in single-end mode ...
100 Finished in 0.00 s (50 us/read; 1.19 M reads/minute). 104 Finished in 0.03 s (256 µs/read; 0.23 M reads/minute).
101 105
102 === Summary === 106 === Summary ===
103 107
104 Total reads processed: 99 108 Total reads processed: 99
105 Reads with adapters: 58 (58.6%) 109 Reads with adapters: 58 (58.6%)
109 Quality-trimmed: 745 bp (3.0%) 113 Quality-trimmed: 745 bp (3.0%)
110 Total written (filtered): 23,035 bp (92.7%) 114 Total written (filtered): 23,035 bp (92.7%)
111 115
112 === Adapter 1 === 116 === Adapter 1 ===
113 117
114 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times. 118 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times
115 119
116 No. of allowed errors: 120 No. of allowed errors:
117 0-9 bp: 0; 10-12 bp: 1 121 1-9 bp: 0; 10-12 bp: 1
118 122
119 Bases preceding removed adapters: 123 Bases preceding removed adapters:
120 A: 12.1% 124 A: 12.1%
121 C: 37.9% 125 C: 37.9%
122 G: 8.6% 126 G: 8.6%