
SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR3192398_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 SRR3192398_2.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1552.56 s (23 us/read; 2.66 M reads/minute).

=== Summary ===

Total reads processed:              68,765,938
Reads with adapters:                25,752,326 (37.4%)
Reads written (passing filters):    68,765,938 (100.0%)

Total basepairs processed: 6,876,593,800 bp
Quality-trimmed:             282,522,512 bp (4.1%)
Total written (filtered):  6,533,246,681 bp (95.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25752326 times.

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

Bases preceding removed adapters:
  A: 32.5%
  C: 29.4%
  G: 21.1%
  T: 16.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	16564140	17191484.5	0	16564140
2	4962759	4297871.1	0	4962759
3	1622779	1074467.8	0	1622779
4	502960	268616.9	0	502960
5	261263	67154.2	0	261263
6	189650	16788.6	0	189650
7	172380	4197.1	0	172380
8	151946	1049.3	0	151946
9	143312	262.3	0	141928 1384
10	126353	65.6	1	121951 4402
11	116318	16.4	1	112914 3404
12	115082	4.1	1	111975 3107
13	107501	1.0	1	104629 2872
14	92108	1.0	1	89429 2679
15	76639	1.0	1	74504 2135
16	75434	1.0	1	73259 2175
17	58571	1.0	1	56829 1742
18	38866	1.0	1	37651 1215
19	34770	1.0	1	33709 1061
20	25685	1.0	1	24865 820
21	22593	1.0	1	21898 695
22	24593	1.0	1	23818 775
23	28123	1.0	1	27213 910
24	28200	1.0	1	27282 918
25	19612	1.0	1	18980 632
26	18924	1.0	1	18057 867
27	18378	1.0	1	17789 589
28	22029	1.0	1	21304 725
29	14864	1.0	1	14337 527
30	17938	1.0	1	17378 560
31	6556	1.0	1	6309 247
32	7698	1.0	1	7439 259
33	6090	1.0	1	5885 205
34	12855	1.0	1	12460 395
35	6528	1.0	1	6305 223
36	5619	1.0	1	5401 218
37	5002	1.0	1	4788 214
38	5565	1.0	1	5376 189
39	4812	1.0	1	4645 167
40	4447	1.0	1	4257 190
41	3554	1.0	1	3361 193
42	3080	1.0	1	2940 140
43	1823	1.0	1	1719 104
44	2075	1.0	1	1945 130
45	2015	1.0	1	1909 106
46	1509	1.0	1	1413 96
47	1508	1.0	1	1398 110
48	1165	1.0	1	1081 84
49	1033	1.0	1	958 75
50	854	1.0	1	772 82
51	801	1.0	1	721 80
52	382	1.0	1	305 77
53	340	1.0	1	273 67
54	380	1.0	1	310 70
55	329	1.0	1	286 43
56	301	1.0	1	250 51
57	302	1.0	1	255 47
58	392	1.0	1	306 86
59	355	1.0	1	317 38
60	332	1.0	1	253 79
61	288	1.0	1	226 62
62	455	1.0	1	337 118
63	1175	1.0	1	917 258
64	1889	1.0	1	1380 509
65	3415	1.0	1	2455 960
66	1487	1.0	1	1133 354
67	213	1.0	1	159 54
68	112	1.0	1	45 67
69	70	1.0	1	15 55
70	57	1.0	1	8 49
71	54	1.0	1	5 49
72	36	1.0	1	2 34
73	45	1.0	1	2 43
74	56	1.0	1	5 51
75	46	1.0	1	3 43
76	58	1.0	1	3 55
77	40	1.0	1	3 37
78	69	1.0	1	6 63
79	48	1.0	1	9 39
80	52	1.0	1	6 46
81	50	1.0	1	7 43
82	96	1.0	1	7 89
83	70	1.0	1	10 60
84	57	1.0	1	9 48
85	70	1.0	1	7 63
86	54	1.0	1	11 43
87	36	1.0	1	8 28
88	52	1.0	1	14 38
89	42	1.0	1	10 32
90	42	1.0	1	5 37
91	76	1.0	1	11 65
92	54	1.0	1	6 48
93	62	1.0	1	4 58
94	33	1.0	1	3 30
95	78	1.0	1	7 71
96	41	1.0	1	2 39
97	112	1.0	1	9 103
98	49	1.0	1	3 46
99	44	1.0	1	3 41
100	71	1.0	1	3 68


RUN STATISTICS FOR INPUT FILE: SRR3192398_2.fastq.gz
=============================================
68765938 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 68765938

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2200242 (3.20%)
