
SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR3192658_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 SRR3192658_2.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1971.98 s (20 us/read; 2.97 M reads/minute).

=== Summary ===

Total reads processed:              97,548,052
Reads with adapters:                30,622,375 (31.4%)
Reads written (passing filters):    97,548,052 (100.0%)

Total basepairs processed: 9,852,353,252 bp
Quality-trimmed:             287,989,645 bp (2.9%)
Total written (filtered):  9,520,194,936 bp (96.6%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 30622375 times.

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

Bases preceding removed adapters:
  A: 31.5%
  C: 31.2%
  G: 23.1%
  T: 14.3%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	20624337	24387013.0	0	20624337
2	7568536	6096753.2	0	7568536
3	1899525	1524188.3	0	1899525
4	388085	381047.1	0	388085
5	96465	95261.8	0	96465
6	15464	23815.4	0	15464
7	4786	5953.9	0	4786
8	1171	1488.5	0	1171
9	2846	372.1	0	896 1950
10	3353	93.0	1	762 2591
11	4399	23.3	1	717 3682
12	1353	5.8	1	710 643
13	703	1.5	1	631 72
14	803	1.5	1	728 75
15	560	1.5	1	423 137
16	528	1.5	1	434 94
17	510	1.5	1	450 60
18	222	1.5	1	146 76
19	266	1.5	1	207 59
20	298	1.5	1	200 98
21	215	1.5	1	127 88
22	196	1.5	1	152 44
23	322	1.5	1	234 88
24	396	1.5	1	342 54
25	240	1.5	1	175 65
26	319	1.5	1	184 135
27	235	1.5	1	161 74
28	270	1.5	1	212 58
29	376	1.5	1	200 176
30	528	1.5	1	438 90
31	104	1.5	1	38 66
32	190	1.5	1	133 57
33	151	1.5	1	74 77
34	169	1.5	1	72 97
35	243	1.5	1	146 97
36	175	1.5	1	116 59
37	209	1.5	1	142 67
38	142	1.5	1	72 70
39	170	1.5	1	97 73
40	109	1.5	1	71 38
41	117	1.5	1	62 55
42	139	1.5	1	69 70
43	105	1.5	1	16 89
44	124	1.5	1	39 85
45	120	1.5	1	41 79
46	60	1.5	1	13 47
47	112	1.5	1	12 100
48	82	1.5	1	5 77
49	181	1.5	1	6 175
50	82	1.5	1	13 69
51	32	1.5	1	12 20
52	41	1.5	1	5 36
53	89	1.5	1	8 81
54	64	1.5	1	3 61
55	69	1.5	1	3 66
56	57	1.5	1	2 55
57	93	1.5	1	0 93
58	37	1.5	1	6 31
59	30	1.5	1	6 24
60	43	1.5	1	11 32
61	69	1.5	1	12 57
62	51	1.5	1	10 41
63	96	1.5	1	30 66
64	90	1.5	1	43 47
65	91	1.5	1	23 68
66	36	1.5	1	15 21
67	56	1.5	1	2 54
68	44	1.5	1	2 42
69	64	1.5	1	0 64
70	57	1.5	1	0 57
71	56	1.5	1	0 56
72	61	1.5	1	0 61
73	50	1.5	1	0 50
74	58	1.5	1	0 58
75	17	1.5	1	0 17
76	44	1.5	1	0 44
77	63	1.5	1	0 63
78	34	1.5	1	0 34
79	23	1.5	1	0 23
80	55	1.5	1	0 55
81	53	1.5	1	0 53
82	26	1.5	1	0 26
83	47	1.5	1	0 47
84	38	1.5	1	0 38
85	41	1.5	1	0 41
86	19	1.5	1	1 18
87	36	1.5	1	0 36
88	20	1.5	1	0 20
89	32	1.5	1	0 32
90	16	1.5	1	0 16
91	16	1.5	1	0 16
92	54	1.5	1	0 54
93	32	1.5	1	0 32
94	17	1.5	1	0 17
95	17	1.5	1	0 17
96	33	1.5	1	0 33
97	38	1.5	1	0 38
98	30	1.5	1	0 30
99	10	1.5	1	0 10
100	25	1.5	1	0 25
101	14	1.5	1	0 14


RUN STATISTICS FOR INPUT FILE: SRR3192658_2.fastq.gz
=============================================
97548052 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 97548052

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 476884 (0.49%)
