SUMMARISING RUN PARAMETERS
==========================
Input filename: illumina_10K.fastq.gz
Trimming mode: single-end
Trim Galore version: 0.6.4
Cutadapt version: 1.18
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Using Illumina adapter for trimming (count: 2862). Second best hit was smallRNA (count: 0)
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 before a sequence gets removed: 20 bp
Output file will be GZIP compressed


This is cutadapt 1.18 with Python 3.5.1
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC illumina_10K.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 0.45 s (45 us/read; 1.33 M reads/minute).

=== Summary ===

Total reads processed:                  10,000
Reads with adapters:                     6,382 (63.8%)
Reads written (passing filters):        10,000 (100.0%)

Total basepairs processed:     1,500,000 bp
Quality-trimmed:                  13,264 bp (0.9%)
Total written (filtered):      1,302,140 bp (86.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6382 times.

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

Bases preceding removed adapters:
  A: 40.9%
  C: 16.0%
  G: 12.0%
  T: 31.1%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	2549	2500.0	0	2549
2	216	625.0	0	216
3	85	156.2	0	85
4	59	39.1	0	59
5	43	9.8	0	43
6	42	2.4	0	42
7	44	0.6	0	44
8	41	0.2	0	41
9	57	0.0	0	54 3
10	53	0.0	1	47 6
11	41	0.0	1	37 4
12	46	0.0	1	44 2
13	26	0.0	1	23 3
14	54	0.0	1	51 3
15	44	0.0	1	40 4
16	41	0.0	1	35 6
17	46	0.0	1	39 7
18	50	0.0	1	48 2
19	54	0.0	1	52 2
20	38	0.0	1	36 2
21	45	0.0	1	37 8
22	36	0.0	1	30 6
23	44	0.0	1	41 3
24	32	0.0	1	27 5
25	29	0.0	1	26 3
26	43	0.0	1	38 5
27	40	0.0	1	36 4
28	41	0.0	1	35 6
29	29	0.0	1	29
30	51	0.0	1	46 5
31	39	0.0	1	37 2
32	31	0.0	1	28 3
33	32	0.0	1	30 2
34	42	0.0	1	36 6
35	41	0.0	1	34 7
36	41	0.0	1	40 1
37	43	0.0	1	41 2
38	39	0.0	1	34 5
39	38	0.0	1	36 2
40	34	0.0	1	32 2
41	29	0.0	1	27 2
42	38	0.0	1	32 6
43	41	0.0	1	40 1
44	31	0.0	1	25 6
45	43	0.0	1	41 2
46	33	0.0	1	32 1
47	18	0.0	1	15 3
48	38	0.0	1	36 2
49	30	0.0	1	29 1
50	24	0.0	1	21 3
51	40	0.0	1	39 1
52	33	0.0	1	32 1
53	33	0.0	1	29 4
54	24	0.0	1	23 1
55	36	0.0	1	32 4
56	33	0.0	1	26 7
57	31	0.0	1	30 1
58	34	0.0	1	30 4
59	31	0.0	1	29 2
60	24	0.0	1	22 2
61	28	0.0	1	27 1
62	31	0.0	1	29 2
63	28	0.0	1	26 2
64	13	0.0	1	12 1
65	19	0.0	1	18 1
66	25	0.0	1	25
67	28	0.0	1	25 3
68	27	0.0	1	23 4
69	31	0.0	1	31
70	16	0.0	1	15 1
71	29	0.0	1	28 1
72	30	0.0	1	28 2
73	31	0.0	1	29 2
74	24	0.0	1	23 1
75	24	0.0	1	22 2
76	29	0.0	1	27 2
77	19	0.0	1	16 3
78	33	0.0	1	31 2
79	29	0.0	1	24 5
80	30	0.0	1	30
81	33	0.0	1	32 1
82	41	0.0	1	36 5
83	69	0.0	1	64 5
84	63	0.0	1	58 5
85	67	0.0	1	60 7
86	53	0.0	1	53
87	24	0.0	1	23 1
88	34	0.0	1	32 2
89	16	0.0	1	16
90	14	0.0	1	14
91	13	0.0	1	13
92	10	0.0	1	8 2
93	19	0.0	1	17 2
94	9	0.0	1	9
95	9	0.0	1	8 1
96	13	0.0	1	13
97	12	0.0	1	11 1
98	10	0.0	1	9 1
99	13	0.0	1	13
100	12	0.0	1	11 1
101	12	0.0	1	11 1
102	9	0.0	1	8 1
103	12	0.0	1	11 1
104	13	0.0	1	12 1
105	8	0.0	1	6 2
106	11	0.0	1	9 2
107	12	0.0	1	11 1
108	11	0.0	1	11
109	7	0.0	1	5 2
110	5	0.0	1	5
111	10	0.0	1	9 1
112	17	0.0	1	16 1
113	4	0.0	1	3 1
114	7	0.0	1	5 2
115	9	0.0	1	8 1
116	6	0.0	1	6
117	6	0.0	1	3 3
118	10	0.0	1	9 1
119	9	0.0	1	8 1
120	4	0.0	1	4
121	5	0.0	1	5
122	6	0.0	1	5 1
123	5	0.0	1	5
124	10	0.0	1	8 2
125	9	0.0	1	8 1
126	6	0.0	1	5 1
127	4	0.0	1	4
128	10	0.0	1	9 1
129	6	0.0	1	6
130	4	0.0	1	4
131	7	0.0	1	6 1
132	5	0.0	1	5
133	2	0.0	1	2
134	5	0.0	1	5
135	2	0.0	1	2
136	2	0.0	1	2
137	1	0.0	1	1
138	2	0.0	1	1 1
139	2	0.0	1	1 1
140	2	0.0	1	2
141	1	0.0	1	1
142	2	0.0	1	2
149	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: illumina_10K.fastq.gz
=============================================
10000 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	73 (0.7%)