Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_collection_example_results3gz.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.gz 4 Input filename: input_1.fastq.gz
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 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 Output file will be GZIP compressed 19 Output file will be GZIP compressed
18 20
19 21
20 This is cutadapt 2.4 with Python 3.7.3 22 This is cutadapt 3.4 with Python 3.9.6
21 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz 23 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
22 Processing reads on 1 core in single-end mode ... 24 Processing reads on 4 cores in single-end mode ...
23 Finished in 0.02 s (176 us/read; 0.34 M reads/minute). 25 Finished in 0.01 s (129 µs/read; 0.47 M reads/minute).
24 26
25 === Summary === 27 === Summary ===
26 28
27 Total reads processed: 99 29 Total reads processed: 99
28 Reads with adapters: 52 (52.5%) 30 Reads with adapters: 52 (52.5%)
32 Quality-trimmed: 205 bp (0.8%) 34 Quality-trimmed: 205 bp (0.8%)
33 Total written (filtered): 23,339 bp (93.9%) 35 Total written (filtered): 23,339 bp (93.9%)
34 36
35 === Adapter 1 === 37 === Adapter 1 ===
36 38
37 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times. 39 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times
38 40
39 No. of allowed errors: 41 No. of allowed errors:
40 0-9 bp: 0; 10-12 bp: 1 42 1-9 bp: 0; 10-12 bp: 1
41 43
42 Bases preceding removed adapters: 44 Bases preceding removed adapters:
43 A: 9.6% 45 A: 9.6%
44 C: 38.5% 46 C: 38.5%
45 G: 23.1% 47 G: 23.1%
84 86
85 SUMMARISING RUN PARAMETERS 87 SUMMARISING RUN PARAMETERS
86 ========================== 88 ==========================
87 Input filename: input_2.fastq.gz 89 Input filename: input_2.fastq.gz
88 Trimming mode: paired-end 90 Trimming mode: paired-end
89 Trim Galore version: 0.6.3 91 Trim Galore version: 0.6.7
90 Cutadapt version: 2.4 92 Cutadapt version: 3.4
91 Number of cores used for trimming: 1 93 Python version: could not detect
94 Number of cores used for trimming: 4
92 Quality Phred score cutoff: 20 95 Quality Phred score cutoff: 20
93 Quality encoding type selected: ASCII+33 96 Quality encoding type selected: ASCII+33
97 Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
94 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 98 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
95 Maximum trimming error rate: 0.1 (default) 99 Maximum trimming error rate: 0.1 (default)
96 Minimum required adapter overlap (stringency): 1 bp 100 Minimum required adapter overlap (stringency): 1 bp
97 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 101 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
98 Length cut-off for read 1: 35 bp (default) 102 Length cut-off for read 1: 35 bp (default)
99 Length cut-off for read 2: 35 bp (default) 103 Length cut-off for read 2: 35 bp (default)
100 Output file will be GZIP compressed 104 Output file will be GZIP compressed
101 105
102 106
103 This is cutadapt 2.4 with Python 3.7.3 107 This is cutadapt 3.4 with Python 3.9.6
104 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz 108 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
105 Processing reads on 1 core in single-end mode ... 109 Processing reads on 4 cores in single-end mode ...
106 Finished in 0.02 s (169 us/read; 0.36 M reads/minute). 110 Finished in 0.04 s (395 µs/read; 0.15 M reads/minute).
107 111
108 === Summary === 112 === Summary ===
109 113
110 Total reads processed: 99 114 Total reads processed: 99
111 Reads with adapters: 58 (58.6%) 115 Reads with adapters: 58 (58.6%)
115 Quality-trimmed: 745 bp (3.0%) 119 Quality-trimmed: 745 bp (3.0%)
116 Total written (filtered): 23,035 bp (92.7%) 120 Total written (filtered): 23,035 bp (92.7%)
117 121
118 === Adapter 1 === 122 === Adapter 1 ===
119 123
120 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times. 124 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times
121 125
122 No. of allowed errors: 126 No. of allowed errors:
123 0-9 bp: 0; 10-12 bp: 1 127 1-9 bp: 0; 10-12 bp: 1
124 128
125 Bases preceding removed adapters: 129 Bases preceding removed adapters:
126 A: 12.1% 130 A: 12.1%
127 C: 37.9% 131 C: 37.9%
128 G: 8.6% 132 G: 8.6%