SUMMARISING RUN PARAMETERS
==========================
Input filename: KO-13004-2.end2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.16
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; 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
All sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1
Output file will be GZIP compressed


This is cutadapt 1.16 with Python 2.7.13
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA KO-13004-2.end2.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 656.67 s (36 us/read; 1.67 M reads/minute).

=== Summary ===

Total reads processed:              18,231,944
Reads with adapters:                 7,186,760 (39.4%)
Reads written (passing filters):    18,231,944 (100.0%)

Total basepairs processed: 1,171,551,201 bp
Quality-trimmed:                  79,931 bp (0.0%)
Total written (filtered):  1,158,766,093 bp (98.9%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 7186760 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 27.1%
  C: 27.5%
  G: 23.3%
  T: 22.0%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	5607754	4557986.0	0	5607754
2	1062029	1139496.5	0	1062029
3	293772	284874.1	0	293772
4	64692	71218.5	0	64692
5	17584	17804.6	0	17584
6	10009	4451.2	0	10009
7	3728	1112.8	0	3728
8	2884	278.2	0	2884
9	2986	69.5	0	2364 622
10	2896	17.4	1	1986 910
11	3264	4.3	1	2145 1119
12	2886	1.1	1	2205 681
13	2764	1.1	1	2278 486
14	2869	1.1	1	2003 866
15	2724	1.1	1	1892 832
16	2174	1.1	1	1709 465
17	2287	1.1	1	1853 434
18	2177	1.1	1	1969 208
19	2800	1.1	1	2432 368
20	2814	1.1	1	2490 324
21	3088	1.1	1	2843 245
22	4004	1.1	1	3274 730
23	4427	1.1	1	4135 292
24	4537	1.1	1	4191 346
25	3327	1.1	1	3121 206
26	2764	1.1	1	2504 260
27	2650	1.1	1	2318 332
28	3095	1.1	1	2815 280
29	3368	1.1	1	3095 273
30	3844	1.1	1	3582 262
31	3995	1.1	1	3707 288
32	4439	1.1	1	4150 289
33	7942	1.1	1	7479 463
34	3359	1.1	1	3130 229
35	6190	1.1	1	5850 340
36	3343	1.1	1	3089 254
37	3101	1.1	1	2873 228
38	5014	1.1	1	4665 349
39	1641	1.1	1	1431 210
40	2378	1.1	1	2160 218
41	1154	1.1	1	995 159
42	786	1.1	1	646 140
43	834	1.1	1	425 409
44	527	1.1	1	350 177
45	599	1.1	1	352 247
46	546	1.1	1	362 184
47	437	1.1	1	297 140
48	795	1.1	1	545 250
49	910	1.1	1	725 185
50	1225	1.1	1	86 1139
51	263	1.1	1	10 253
52	181	1.1	1	5 176
53	368	1.1	1	6 362
54	85	1.1	1	5 80
55	362	1.1	1	2 360
56	141	1.1	1	6 135
57	129	1.1	1	5 124
58	346	1.1	1	2 344
59	193	1.1	1	5 188
60	804	1.1	1	6 798
61	122	1.1	1	7 115
62	217	1.1	1	49 168
63	290	1.1	1	9 281
64	104	1.1	1	16 88
65	80	1.1	1	8 72
66	126	1.1	1	5 121
67	176	1.1	1	12 164
68	286	1.1	1	7 279
69	59	1.1	1	3 56
70	78	1.1	1	16 62
71	37	1.1	1	4 33
72	103	1.1	1	27 76
73	327	1.1	1	24 303
74	146	1.1	1	61 85
75	2261	1.1	1	2055 206
76	64	1.1	1	9 55


RUN STATISTICS FOR INPUT FILE: KO-13004-2.end2.fastq.gz
=============================================
18231944 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 18231944

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 16874 (0.09%)