Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_example_results2gz.txt @ 16:cd7e644cae1d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
equal deleted inserted replaced
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 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 Output file will be GZIP compressed 17 Output file will be GZIP compressed
16 18
17 19
18 This is cutadapt 2.4 with Python 3.7.3 20 This is cutadapt 3.4 with Python 3.9.6
19 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz 21 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
20 Processing reads on 1 core in single-end mode ... 22 Processing reads on 4 cores in single-end mode ...
21 Finished in 0.03 s (287 us/read; 0.21 M reads/minute). 23 Finished in 0.01 s (114 µs/read; 0.53 M reads/minute).
22 24
23 === Summary === 25 === Summary ===
24 26
25 Total reads processed: 99 27 Total reads processed: 99
26 Reads with adapters: 52 (52.5%) 28 Reads with adapters: 52 (52.5%)
30 Quality-trimmed: 205 bp (0.8%) 32 Quality-trimmed: 205 bp (0.8%)
31 Total written (filtered): 23,339 bp (93.9%) 33 Total written (filtered): 23,339 bp (93.9%)
32 34
33 === Adapter 1 === 35 === Adapter 1 ===
34 36
35 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times. 37 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times
36 38
37 No. of allowed errors: 39 No. of allowed errors:
38 0-9 bp: 0; 10-12 bp: 1 40 1-9 bp: 0; 10-12 bp: 1
39 41
40 Bases preceding removed adapters: 42 Bases preceding removed adapters:
41 A: 9.6% 43 A: 9.6%
42 C: 38.5% 44 C: 38.5%
43 G: 23.1% 45 G: 23.1%
82 84
83 SUMMARISING RUN PARAMETERS 85 SUMMARISING RUN PARAMETERS
84 ========================== 86 ==========================
85 Input filename: input_2.fastq.gz 87 Input filename: input_2.fastq.gz
86 Trimming mode: paired-end 88 Trimming mode: paired-end
87 Trim Galore version: 0.6.3 89 Trim Galore version: 0.6.7
88 Cutadapt version: 2.4 90 Cutadapt version: 3.4
89 Number of cores used for trimming: 1 91 Python version: could not detect
92 Number of cores used for trimming: 4
90 Quality Phred score cutoff: 20 93 Quality Phred score cutoff: 20
91 Quality encoding type selected: ASCII+33 94 Quality encoding type selected: ASCII+33
95 Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)
92 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 96 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
93 Maximum trimming error rate: 0.1 (default) 97 Maximum trimming error rate: 0.1 (default)
94 Minimum required adapter overlap (stringency): 1 bp 98 Minimum required adapter overlap (stringency): 1 bp
95 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 99 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
96 Output file will be GZIP compressed 100 Output file will be GZIP compressed
97 101
98 102
99 This is cutadapt 2.4 with Python 3.7.3 103 This is cutadapt 3.4 with Python 3.9.6
100 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz 104 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
101 Processing reads on 1 core in single-end mode ... 105 Processing reads on 4 cores in single-end mode ...
102 Finished in 0.02 s (170 us/read; 0.35 M reads/minute). 106 Finished in 0.02 s (232 µs/read; 0.26 M reads/minute).
103 107
104 === Summary === 108 === Summary ===
105 109
106 Total reads processed: 99 110 Total reads processed: 99
107 Reads with adapters: 58 (58.6%) 111 Reads with adapters: 58 (58.6%)
111 Quality-trimmed: 745 bp (3.0%) 115 Quality-trimmed: 745 bp (3.0%)
112 Total written (filtered): 23,035 bp (92.7%) 116 Total written (filtered): 23,035 bp (92.7%)
113 117
114 === Adapter 1 === 118 === Adapter 1 ===
115 119
116 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times. 120 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times
117 121
118 No. of allowed errors: 122 No. of allowed errors:
119 0-9 bp: 0; 10-12 bp: 1 123 1-9 bp: 0; 10-12 bp: 1
120 124
121 Bases preceding removed adapters: 125 Bases preceding removed adapters:
122 A: 12.1% 126 A: 12.1%
123 C: 37.9% 127 C: 37.9%
124 G: 8.6% 128 G: 8.6%