
SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR3192396_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 SRR3192396_2.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 2246.39 s (21 us/read; 2.81 M reads/minute).

=== Summary ===

Total reads processed:             105,089,150
Reads with adapters:                32,883,672 (31.3%)
Reads written (passing filters):   105,089,150 (100.0%)

Total basepairs processed: 10,614,004,150 bp
Quality-trimmed:             373,151,687 bp (3.5%)
Total written (filtered):  10,194,057,791 bp (96.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 32883672 times.

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

Bases preceding removed adapters:
  A: 31.6%
  C: 30.7%
  G: 21.2%
  T: 16.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	22961688	26272287.5	0	22961688
2	7631789	6568071.9	0	7631789
3	1774925	1642018.0	0	1774925
4	352001	410504.5	0	352001
5	85236	102626.1	0	85236
6	14948	25656.5	0	14948
7	5781	6414.1	0	5781
8	2947	1603.5	0	2947
9	4332	400.9	0	2702 1630
10	4609	100.2	1	2721 1888
11	4651	25.1	1	2206 2445
12	3142	6.3	1	2694 448
13	2715	1.6	1	2575 140
14	3889	1.6	1	3787 102
15	1551	1.6	1	1462 89
16	1876	1.6	1	1792 84
17	2296	1.6	1	2204 92
18	601	1.6	1	550 51
19	1322	1.6	1	1268 54
20	814	1.6	1	765 49
21	433	1.6	1	359 74
22	766	1.6	1	684 82
23	971	1.6	1	903 68
24	1405	1.6	1	1323 82
25	724	1.6	1	646 78
26	873	1.6	1	777 96
27	666	1.6	1	582 84
28	1132	1.6	1	1082 50
29	813	1.6	1	701 112
30	2529	1.6	1	2431 98
31	221	1.6	1	135 86
32	751	1.6	1	699 52
33	325	1.6	1	276 49
34	449	1.6	1	361 88
35	770	1.6	1	667 103
36	704	1.6	1	618 86
37	862	1.6	1	800 62
38	468	1.6	1	419 49
39	551	1.6	1	501 50
40	361	1.6	1	277 84
41	438	1.6	1	366 72
42	838	1.6	1	728 110
43	196	1.6	1	84 112
44	356	1.6	1	275 81
45	580	1.6	1	458 122
46	175	1.6	1	84 91
47	203	1.6	1	111 92
48	183	1.6	1	124 59
49	204	1.6	1	120 84
50	256	1.6	1	172 84
51	197	1.6	1	157 40
52	104	1.6	1	52 52
53	62	1.6	1	33 29
54	86	1.6	1	34 52
55	150	1.6	1	52 98
56	78	1.6	1	37 41
57	113	1.6	1	40 73
58	100	1.6	1	45 55
59	81	1.6	1	36 45
60	100	1.6	1	51 49
61	126	1.6	1	46 80
62	98	1.6	1	59 39
63	259	1.6	1	152 107
64	161	1.6	1	133 28
65	187	1.6	1	139 48
66	100	1.6	1	39 61
67	68	1.6	1	31 37
68	69	1.6	1	5 64
69	35	1.6	1	1 34
70	48	1.6	1	1 47
71	41	1.6	1	2 39
72	36	1.6	1	1 35
73	39	1.6	1	0 39
74	45	1.6	1	1 44
75	49	1.6	1	0 49
76	69	1.6	1	0 69
77	17	1.6	1	0 17
78	59	1.6	1	1 58
79	33	1.6	1	0 33
80	51	1.6	1	1 50
81	14	1.6	1	0 14
82	41	1.6	1	0 41
83	52	1.6	1	0 52
84	67	1.6	1	1 66
85	21	1.6	1	0 21
86	47	1.6	1	1 46
87	31	1.6	1	0 31
88	31	1.6	1	1 30
89	24	1.6	1	0 24
90	12	1.6	1	0 12
91	40	1.6	1	0 40
92	41	1.6	1	0 41
93	29	1.6	1	0 29
94	48	1.6	1	0 48
95	21	1.6	1	0 21
96	7	1.6	1	0 7
97	28	1.6	1	0 28
98	52	1.6	1	0 52
99	32	1.6	1	0 32
100	24	1.6	1	0 24
101	33	1.6	1	0 33


RUN STATISTICS FOR INPUT FILE: SRR3192396_2.fastq.gz
=============================================
105089150 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 105089150

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 675966 (0.64%)
