Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_example_results2gz.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
comparison
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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.gz 4 Input filename: input_1.fastq.gz
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 Illumina (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 Output file will be GZIP compressed 17 Output file will be GZIP compressed
18 18
19 19
20 This is cutadapt 3.4 with Python 3.9.6 20 This is cutadapt 5.0 with Python 3.12.10
21 Command line parameters: -j 4 -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
22 Processing reads on 4 cores in single-end mode ... 22 Processing single-end reads on 4 cores ...
23 Finished in 0.01 s (114 µs/read; 0.53 M reads/minute).
24 23
25 === Summary === 24 === Summary ===
26 25
27 Total reads processed: 99 26 Total reads processed: 99
28 Reads with adapters: 52 (52.5%) 27 Reads with adapters: 52 (52.5%)
34 33
35 === Adapter 1 === 34 === Adapter 1 ===
36 35
37 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times 36 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times
38 37
38 Minimum overlap: 1
39 No. of allowed errors: 39 No. of allowed errors:
40 1-9 bp: 0; 10-12 bp: 1 40 1-9 bp: 0; 10-12 bp: 1
41 41
42 Bases preceding removed adapters: 42 Bases preceding removed adapters:
43 A: 9.6% 43 A: 9.6%
84 84
85 SUMMARISING RUN PARAMETERS 85 SUMMARISING RUN PARAMETERS
86 ========================== 86 ==========================
87 Input filename: input_2.fastq.gz 87 Input filename: input_2.fastq.gz
88 Trimming mode: paired-end 88 Trimming mode: paired-end
89 Trim Galore version: 0.6.7 89 Trim Galore version: 0.6.10
90 Cutadapt version: 3.4 90 Cutadapt version: 5.0
91 Python version: could not detect 91 Python version: 3.12.10
92 Number of cores used for trimming: 4 92 Number of cores used for trimming: 4
93 Quality Phred score cutoff: 20 93 Quality Phred score cutoff: 20
94 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) 95 Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)
96 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 96 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
97 Maximum trimming error rate: 0.1 (default) 97 Maximum trimming error rate: 0.1 (default)
98 Minimum required adapter overlap (stringency): 1 bp 98 Minimum required adapter overlap (stringency): 1 bp
99 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
100 Output file will be GZIP compressed 100 Output file will be GZIP compressed
101 101
102 102
103 This is cutadapt 3.4 with Python 3.9.6 103 This is cutadapt 5.0 with Python 3.12.10
104 Command line parameters: -j 4 -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
105 Processing reads on 4 cores in single-end mode ... 105 Processing single-end reads on 4 cores ...
106 Finished in 0.02 s (232 µs/read; 0.26 M reads/minute).
107 106
108 === Summary === 107 === Summary ===
109 108
110 Total reads processed: 99 109 Total reads processed: 99
111 Reads with adapters: 58 (58.6%) 110 Reads with adapters: 58 (58.6%)
117 116
118 === Adapter 1 === 117 === Adapter 1 ===
119 118
120 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times 119 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times
121 120
121 Minimum overlap: 1
122 No. of allowed errors: 122 No. of allowed errors:
123 1-9 bp: 0; 10-12 bp: 1 123 1-9 bp: 0; 10-12 bp: 1
124 124
125 Bases preceding removed adapters: 125 Bases preceding removed adapters:
126 A: 12.1% 126 A: 12.1%