Mercurial > repos > bgruening > trim_galore

comparison test-data/paired_example_results2.txt @ 4:2c1f0fe810f7 draft

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author bgruening
date Wed, 15 Apr 2015 11:32:11 -0400
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3:eb546ac2aab2 4:2c1f0fe810f7
1
2 SUMMARISING RUN PARAMETERS
3 ==========================
4 Input filename: ./input_mate1
5 Trimming mode: paired-end
6 Trim Galore version: 0.3.7
7 Quality Phred score cutoff: 20
8 Quality encoding type selected: ASCII+33
9 Adapter sequence: 'AGATCGGAAGAGC'
10 Maximum trimming error rate: 0.1 (default)
11 Minimum required adapter overlap (stringency): 1 bp
12 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
13
14
15 cutadapt version 1.1
16 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate1
17 Maximum error rate: 10.00%
18 Processed reads: 100
19 Trimmed reads: 20 ( 20.0%)
20 Total basepairs: 24894 (0.0 Mbp)
21 Trimmed basepairs: 26 (0.0 Mbp) (0.10% of total)
22 Too short reads: 0 ( 0.0% of processed reads)
23 Too long reads: 0 ( 0.0% of processed reads)
24 Total time: 0.00 s
25 Time per read: 0.02 ms
26
27 === Adapter 1 ===
28
29 Adapter 'AGATCGGAAGAGC', length 13, was trimmed 20 times.
30
31 Lengths of removed sequences
32 length count expected
33 1 16 25.0
34 2 2 6.2
35 3 2 1.6
36
37
38 RUN STATISTICS FOR INPUT FILE: ./input_mate1
39 =============================================
40 100 sequences processed in total
41
42
43 SUMMARISING RUN PARAMETERS
44 ==========================
45 Input filename: ./input_mate2
46 Trimming mode: paired-end
47 Trim Galore version: 0.3.7
48 Quality Phred score cutoff: 20
49 Quality encoding type selected: ASCII+33
50 Adapter sequence: 'AGATCGGAAGAGC'
51 Maximum trimming error rate: 0.1 (default)
52 Minimum required adapter overlap (stringency): 1 bp
53 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
54
55
56 cutadapt version 1.1
57 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_mate2
58 Maximum error rate: 10.00%
59 Processed reads: 100
60 Trimmed reads: 24 ( 24.0%)
61 Total basepairs: 24354 (0.0 Mbp)
62 Trimmed basepairs: 36 (0.0 Mbp) (0.15% of total)
63 Too short reads: 0 ( 0.0% of processed reads)
64 Too long reads: 0 ( 0.0% of processed reads)
65 Total time: 0.01 s
66 Time per read: 0.12 ms
67
68 === Adapter 1 ===
69
70 Adapter 'AGATCGGAAGAGC', length 13, was trimmed 24 times.
71
72 Lengths of removed sequences
73 length count expected
74 1 15 25.0
75 2 7 6.2
76 3 1 1.6
77 4 1 0.4
78
79
80 RUN STATISTICS FOR INPUT FILE: ./input_mate2
81 =============================================
82 100 sequences processed in total
83
84 Total number of sequences analysed for the sequence pair length validation: 100
85
86 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.00%)