
SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR3192657_2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.1
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
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
Running FastQC on the data once trimming has completed
Output file will be GZIP compressed


This is cutadapt 1.9.1 with Python 2.7.6
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192657_2.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1986.06 s (21 us/read; 2.83 M reads/minute).

=== Summary ===

Total reads processed:              93,555,584
Reads with adapters:                30,516,092 (32.6%)
Reads written (passing filters):    93,555,584 (100.0%)

Total basepairs processed: 9,449,113,984 bp
Quality-trimmed:             247,487,419 bp (2.6%)
Total written (filtered):  9,157,670,096 bp (96.9%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 30516092 times.

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

Bases preceding removed adapters:
  A: 32.5%
  C: 30.4%
  G: 22.3%
  T: 14.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	20709985	23388896.0	0	20709985
2	7337450	5847224.0	0	7337450
3	1932874	1461806.0	0	1932874
4	393575	365451.5	0	393575
5	93056	91362.9	0	93056
6	15073	22840.7	0	15073
7	4869	5710.2	0	4869
8	1687	1427.5	0	1687
9	3798	356.9	0	1549 2249
10	3911	89.2	1	1262 2649
11	4890	22.3	1	1038 3852
12	1908	5.6	1	1265 643
13	1075	1.4	1	960 115
14	1220	1.4	1	1161 59
15	758	1.4	1	631 127
16	757	1.4	1	684 73
17	861	1.4	1	757 104
18	281	1.4	1	242 39
19	271	1.4	1	237 34
20	212	1.4	1	152 60
21	142	1.4	1	92 50
22	169	1.4	1	120 49
23	219	1.4	1	129 90
24	294	1.4	1	224 70
25	183	1.4	1	106 77
26	222	1.4	1	114 108
27	189	1.4	1	121 68
28	228	1.4	1	165 63
29	260	1.4	1	130 130
30	406	1.4	1	326 80
31	51	1.4	1	15 36
32	113	1.4	1	73 40
33	119	1.4	1	88 31
34	183	1.4	1	95 88
35	256	1.4	1	175 81
36	140	1.4	1	92 48
37	234	1.4	1	176 58
38	104	1.4	1	69 35
39	103	1.4	1	72 31
40	131	1.4	1	80 51
41	148	1.4	1	100 48
42	165	1.4	1	103 62
43	67	1.4	1	16 51
44	126	1.4	1	43 83
45	152	1.4	1	72 80
46	73	1.4	1	12 61
47	111	1.4	1	14 97
48	78	1.4	1	15 63
49	53	1.4	1	14 39
50	64	1.4	1	20 44
51	65	1.4	1	24 41
52	55	1.4	1	11 44
53	57	1.4	1	2 55
54	80	1.4	1	15 65
55	51	1.4	1	7 44
56	48	1.4	1	3 45
57	89	1.4	1	9 80
58	62	1.4	1	7 55
59	46	1.4	1	18 28
60	74	1.4	1	14 60
61	79	1.4	1	3 76
62	92	1.4	1	12 80
63	77	1.4	1	36 41
64	65	1.4	1	31 34
65	96	1.4	1	37 59
66	70	1.4	1	11 59
67	42	1.4	1	2 40
68	63	1.4	1	0 63
69	94	1.4	1	1 93
70	83	1.4	1	0 83
71	45	1.4	1	0 45
72	73	1.4	1	1 72
73	73	1.4	1	11 62
74	67	1.4	1	0 67
75	14	1.4	1	0 14
76	67	1.4	1	0 67
77	61	1.4	1	0 61
78	56	1.4	1	1 55
79	30	1.4	1	0 30
80	55	1.4	1	0 55
81	38	1.4	1	0 38
82	39	1.4	1	0 39
83	34	1.4	1	0 34
84	69	1.4	1	0 69
85	22	1.4	1	0 22
86	28	1.4	1	0 28
87	44	1.4	1	0 44
88	72	1.4	1	0 72
89	50	1.4	1	0 50
90	40	1.4	1	0 40
91	26	1.4	1	0 26
92	151	1.4	1	0 151
93	40	1.4	1	0 40
94	36	1.4	1	0 36
95	31	1.4	1	0 31
97	1	1.4	1	0 1
98	56	1.4	1	0 56
99	18	1.4	1	0 18
100	42	1.4	1	0 42
101	32	1.4	1	0 32


RUN STATISTICS FOR INPUT FILE: SRR3192657_2.fastq.gz
=============================================
93555584 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 93555584

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 410939 (0.44%)
