
SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR3192397_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 SRR3192397_2.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 2040.01 s (22 us/read; 2.72 M reads/minute).

=== Summary ===

Total reads processed:              92,494,632
Reads with adapters:                29,937,340 (32.4%)
Reads written (passing filters):    92,494,632 (100.0%)

Total basepairs processed: 9,341,957,832 bp
Quality-trimmed:             283,316,439 bp (3.0%)
Total written (filtered):  9,015,621,178 bp (96.5%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 29937340 times.

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

Bases preceding removed adapters:
  A: 32.4%
  C: 29.8%
  G: 20.3%
  T: 17.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	20943420	23123658.0	0	20943420
2	6804121	5780914.5	0	6804121
3	1663664	1445228.6	0	1663664
4	339911	361307.2	0	339911
5	77230	90326.8	0	77230
6	15697	22581.7	0	15697
7	8480	5645.4	0	8480
8	6428	1411.4	0	6428
9	6832	352.8	0	5304 1528
10	7699	88.2	1	5674 2025
11	6629	22.1	1	4456 2173
12	6657	5.5	1	6125 532
13	5561	1.4	1	5359 202
14	8517	1.4	1	8363 154
15	2875	1.4	1	2757 118
16	3934	1.4	1	3817 117
17	5541	1.4	1	5398 143
18	1194	1.4	1	1110 84
19	2071	1.4	1	1992 79
20	1014	1.4	1	967 47
21	421	1.4	1	368 53
22	657	1.4	1	631 26
23	699	1.4	1	648 51
24	1087	1.4	1	1007 80
25	474	1.4	1	433 41
26	596	1.4	1	519 77
27	488	1.4	1	408 80
28	805	1.4	1	747 58
29	648	1.4	1	499 149
30	2186	1.4	1	2112 74
31	122	1.4	1	67 55
32	508	1.4	1	469 39
33	302	1.4	1	232 70
34	385	1.4	1	333 52
35	1077	1.4	1	1003 74
36	593	1.4	1	552 41
37	1026	1.4	1	959 67
38	466	1.4	1	420 46
39	477	1.4	1	417 60
40	338	1.4	1	253 85
41	403	1.4	1	349 54
42	767	1.4	1	676 91
43	233	1.4	1	125 108
44	369	1.4	1	305 64
45	626	1.4	1	558 68
46	171	1.4	1	111 60
47	189	1.4	1	105 84
48	210	1.4	1	125 85
49	202	1.4	1	119 83
50	209	1.4	1	142 67
51	220	1.4	1	182 38
52	139	1.4	1	69 70
53	107	1.4	1	54 53
54	92	1.4	1	48 44
55	97	1.4	1	53 44
56	105	1.4	1	51 54
57	110	1.4	1	71 39
58	124	1.4	1	71 53
59	218	1.4	1	162 56
60	114	1.4	1	75 39
61	111	1.4	1	44 67
62	65	1.4	1	50 15
63	132	1.4	1	74 58
64	127	1.4	1	61 66
65	141	1.4	1	60 81
66	71	1.4	1	16 55
67	60	1.4	1	6 54
68	59	1.4	1	4 55
69	40	1.4	1	1 39
70	49	1.4	1	0 49
71	23	1.4	1	0 23
72	33	1.4	1	1 32
73	50	1.4	1	0 50
74	31	1.4	1	1 30
75	31	1.4	1	0 31
76	36	1.4	1	0 36
77	43	1.4	1	0 43
78	78	1.4	1	0 78
79	28	1.4	1	0 28
80	33	1.4	1	0 33
81	31	1.4	1	0 31
82	19	1.4	1	0 19
83	25	1.4	1	1 24
84	25	1.4	1	1 24
85	37	1.4	1	0 37
86	21	1.4	1	0 21
87	23	1.4	1	0 23
88	26	1.4	1	0 26
89	22	1.4	1	1 21
90	17	1.4	1	0 17
91	29	1.4	1	0 29
92	46	1.4	1	0 46
93	31	1.4	1	0 31
94	16	1.4	1	0 16
95	34	1.4	1	0 34
96	22	1.4	1	1 21
97	35	1.4	1	0 35
98	37	1.4	1	0 37
99	27	1.4	1	0 27
100	13	1.4	1	2 11
101	28	1.4	1	0 28


RUN STATISTICS FOR INPUT FILE: SRR3192397_2.fastq.gz
=============================================
92494632 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 92494632

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 524737 (0.57%)
