SUMMARISING RUN PARAMETERS
==========================
Input filename: WT_rep1_1_Ch6.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.4_dev
Cutadapt version: 2.1
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Using Illumina adapter for trimming (count: 10). Second best hit was smallRNA (count: 0)
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Removing Ns from the start and end of reads
Running FastQC on the data once trimming has completed
Output file will be GZIP compressed


This is cutadapt 2.1 with Python 3.4.3
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 --trim-n -a AGATCGGAAGAGC WT_rep1_1_Ch6.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 72.25 s (54 us/read; 1.11 M reads/minute).

=== Summary ===

Total reads processed:               1,340,546
Reads with adapters:                   473,901 (35.4%)
Reads written (passing filters):     1,340,546 (100.0%)

Total basepairs processed:   135,395,146 bp
Quality-trimmed:               3,974,452 bp (2.9%)
Total written (filtered):    130,761,940 bp (96.6%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 473901 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 37.0%
  C: 27.3%
  G: 17.6%
  T: 18.2%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	351033	335136.5	0	351033
2	89096	83784.1	0	89096
3	24988	20946.0	0	24988
4	6609	5236.5	0	6609
5	1446	1309.1	0	1446
6	141	327.3	0	141
7	31	81.8	0	31
8	13	20.5	0	13
9	76	5.1	0	18 58
10	83	1.3	1	1 82
11	18	0.3	1	2 16
12	7	0.1	1	0 7
13	6	0.0	1	0 6
14	4	0.0	1	0 4
15	37	0.0	1	1 36
16	4	0.0	1	0 4
17	1	0.0	1	0 1
19	2	0.0	1	0 2
20	1	0.0	1	0 1
21	2	0.0	1	0 2
22	4	0.0	1	0 4
23	2	0.0	1	0 2
24	1	0.0	1	0 1
25	3	0.0	1	0 3
26	2	0.0	1	0 2
27	5	0.0	1	0 5
28	9	0.0	1	0 9
29	14	0.0	1	0 14
30	8	0.0	1	1 7
31	4	0.0	1	0 4
33	6	0.0	1	1 5
34	8	0.0	1	0 8
35	19	0.0	1	0 19
36	15	0.0	1	0 15
37	1	0.0	1	0 1
38	4	0.0	1	0 4
39	3	0.0	1	2 1
40	12	0.0	1	0 12
41	6	0.0	1	0 6
42	12	0.0	1	0 12
44	2	0.0	1	0 2
45	2	0.0	1	0 2
46	5	0.0	1	0 5
47	5	0.0	1	0 5
48	5	0.0	1	0 5
49	4	0.0	1	0 4
50	3	0.0	1	1 2
52	3	0.0	1	1 2
53	1	0.0	1	0 1
54	1	0.0	1	0 1
55	12	0.0	1	0 12
56	3	0.0	1	0 3
57	5	0.0	1	2 3
58	3	0.0	1	0 3
59	3	0.0	1	0 3
60	6	0.0	1	0 6
61	1	0.0	1	0 1
62	5	0.0	1	0 5
63	5	0.0	1	0 5
64	6	0.0	1	0 6
66	1	0.0	1	0 1
67	5	0.0	1	1 4
68	8	0.0	1	1 7
69	2	0.0	1	0 2
70	2	0.0	1	0 2
72	7	0.0	1	0 7
73	7	0.0	1	0 7
74	6	0.0	1	0 6
76	1	0.0	1	0 1
77	2	0.0	1	0 2
79	3	0.0	1	0 3
80	4	0.0	1	0 4
81	2	0.0	1	0 2
83	1	0.0	1	0 1
84	2	0.0	1	0 2
87	3	0.0	1	0 3
88	1	0.0	1	0 1
89	1	0.0	1	0 1
90	1	0.0	1	0 1
91	5	0.0	1	0 5
93	1	0.0	1	0 1
94	1	0.0	1	0 1
95	2	0.0	1	0 2
97	4	0.0	1	0 4
98	12	0.0	1	0 12
99	1	0.0	1	0 1

RUN STATISTICS FOR INPUT FILE: WT_rep1_1_Ch6.fastq.gz
=============================================
1340546 sequences processed in total