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comparison test-data/paired_collection_example_results3.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 Illumina (count: 0) 12 Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)
13 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 13 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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 Length cut-off for read 1: 35 bp (default) 17 Length cut-off for read 1: 35 bp (default)
18 Length cut-off for read 2: 35 bp (default) 18 Length cut-off for read 2: 35 bp (default)
19 19
20 20
21 This is cutadapt 3.4 with Python 3.9.6 21 This is cutadapt 5.0 with Python 3.12.10
22 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq 22 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
23 Processing reads on 4 cores in single-end mode ... 23 Processing single-end reads on 4 cores ...
24 Finished in 0.01 s (115 µs/read; 0.52 M reads/minute).
25 24
26 === Summary === 25 === Summary ===
27 26
28 Total reads processed: 99 27 Total reads processed: 99
29 Reads with adapters: 52 (52.5%) 28 Reads with adapters: 52 (52.5%)
35 34
36 === Adapter 1 === 35 === Adapter 1 ===
37 36
38 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times 37 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times
39 38
39 Minimum overlap: 1
40 No. of allowed errors: 40 No. of allowed errors:
41 1-9 bp: 0; 10-12 bp: 1 41 1-9 bp: 0; 10-12 bp: 1
42 42
43 Bases preceding removed adapters: 43 Bases preceding removed adapters:
44 A: 9.6% 44 A: 9.6%
85 85
86 SUMMARISING RUN PARAMETERS 86 SUMMARISING RUN PARAMETERS
87 ========================== 87 ==========================
88 Input filename: input_2.fastq 88 Input filename: input_2.fastq
89 Trimming mode: paired-end 89 Trimming mode: paired-end
90 Trim Galore version: 0.6.7 90 Trim Galore version: 0.6.10
91 Cutadapt version: 3.4 91 Cutadapt version: 5.0
92 Python version: could not detect 92 Python version: 3.12.10
93 Number of cores used for trimming: 4 93 Number of cores used for trimming: 4
94 Quality Phred score cutoff: 20 94 Quality Phred score cutoff: 20
95 Quality encoding type selected: ASCII+33 95 Quality encoding type selected: ASCII+33
96 Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0) 96 Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)
97 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) 97 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
100 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 100 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
101 Length cut-off for read 1: 35 bp (default) 101 Length cut-off for read 1: 35 bp (default)
102 Length cut-off for read 2: 35 bp (default) 102 Length cut-off for read 2: 35 bp (default)
103 103
104 104
105 This is cutadapt 3.4 with Python 3.9.6 105 This is cutadapt 5.0 with Python 3.12.10
106 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq 106 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
107 Processing reads on 4 cores in single-end mode ... 107 Processing single-end reads on 4 cores ...
108 Finished in 0.02 s (159 µs/read; 0.38 M reads/minute).
109 108
110 === Summary === 109 === Summary ===
111 110
112 Total reads processed: 99 111 Total reads processed: 99
113 Reads with adapters: 58 (58.6%) 112 Reads with adapters: 58 (58.6%)
119 118
120 === Adapter 1 === 119 === Adapter 1 ===
121 120
122 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times 121 Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times
123 122
123 Minimum overlap: 1
124 No. of allowed errors: 124 No. of allowed errors:
125 1-9 bp: 0; 10-12 bp: 1 125 1-9 bp: 0; 10-12 bp: 1
126 126
127 Bases preceding removed adapters: 127 Bases preceding removed adapters:
128 A: 12.1% 128 A: 12.1%