Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_example_results2.txt @ 18:b94789823aad draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f8ccc97b827b98db1bcf42073d3c5eb4e3f134c4
author bgruening
date Sat, 10 May 2025 08:09:10 +0000
parents cd7e644cae1d
children
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17:eefb644655a5 18:b94789823aad
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: 0.6.7 6 Trim Galore version: 0.6.10
7 Cutadapt version: 3.4 7 Cutadapt version: 5.0
8 Python version: could not detect 8 Python version: 3.12.10
9 Number of cores used for trimming: 4 9 Number of cores used for trimming: 4
10 Quality Phred score cutoff: 20 10 Quality Phred score cutoff: 20
11 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) 12 Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
13 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 13 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
14 Maximum trimming error rate: 0.1 (default) 14 Maximum trimming error rate: 0.1 (default)
15 Minimum required adapter overlap (stringency): 1 bp 15 Minimum required adapter overlap (stringency): 1 bp
16 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
17 17
18 18
19 This is cutadapt 3.4 with Python 3.9.6 19 This is cutadapt 5.0 with Python 3.12.10
20 Command line parameters: -j 4 -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
21 Processing reads on 4 cores in single-end mode ... 21 Processing single-end reads on 4 cores ...
22 Finished in 0.01 s (117 µs/read; 0.51 M reads/minute).
23 22
24 === Summary === 23 === Summary ===
25 24
26 Total reads processed: 99 25 Total reads processed: 99
27 Reads with adapters: 52 (52.5%) 26 Reads with adapters: 52 (52.5%)
33 32
34 === Adapter 1 === 33 === Adapter 1 ===
35 34
36 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times 35 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times
37 36
37 Minimum overlap: 1
38 No. of allowed errors: 38 No. of allowed errors:
39 1-9 bp: 0; 10-12 bp: 1 39 1-9 bp: 0; 10-12 bp: 1
40 40
41 Bases preceding removed adapters: 41 Bases preceding removed adapters:
42 A: 9.6% 42 A: 9.6%
83 83
84 SUMMARISING RUN PARAMETERS 84 SUMMARISING RUN PARAMETERS
85 ========================== 85 ==========================
86 Input filename: input_2.fastq 86 Input filename: input_2.fastq
87 Trimming mode: paired-end 87 Trimming mode: paired-end
88 Trim Galore version: 0.6.7 88 Trim Galore version: 0.6.10
89 Cutadapt version: 3.4 89 Cutadapt version: 5.0
90 Python version: could not detect 90 Python version: 3.12.10
91 Number of cores used for trimming: 4 91 Number of cores used for trimming: 4
92 Quality Phred score cutoff: 20 92 Quality Phred score cutoff: 20
93 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) 94 Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
95 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 95 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
96 Maximum trimming error rate: 0.1 (default) 96 Maximum trimming error rate: 0.1 (default)
97 Minimum required adapter overlap (stringency): 1 bp 97 Minimum required adapter overlap (stringency): 1 bp
98 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
99 99
100 100
101 This is cutadapt 3.4 with Python 3.9.6 101 This is cutadapt 5.0 with Python 3.12.10
102 Command line parameters: -j 4 -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
103 Processing reads on 4 cores in single-end mode ... 103 Processing single-end reads on 4 cores ...
104 Finished in 0.03 s (256 µs/read; 0.23 M reads/minute).
105 104
106 === Summary === 105 === Summary ===
107 106
108 Total reads processed: 99 107 Total reads processed: 99
109 Reads with adapters: 58 (58.6%) 108 Reads with adapters: 58 (58.6%)
115 114
116 === Adapter 1 === 115 === Adapter 1 ===
117 116
118 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times 117 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times
119 118
119 Minimum overlap: 1
120 No. of allowed errors: 120 No. of allowed errors:
121 1-9 bp: 0; 10-12 bp: 1 121 1-9 bp: 0; 10-12 bp: 1
122 122
123 Bases preceding removed adapters: 123 Bases preceding removed adapters:
124 A: 12.1% 124 A: 12.1%