
SUMMARISING RUN PARAMETERS
==========================
Input filename: illumina_100K.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: 28700). 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_100K.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 4.61 s (46 us/read; 1.30 M reads/minute).

=== Summary ===

Total reads processed:                 100,000
Reads with adapters:                    64,192 (64.2%)
Reads written (passing filters):       100,000 (100.0%)

Total basepairs processed:    15,000,000 bp
Quality-trimmed:                 124,497 bp (0.8%)
Total written (filtered):     13,021,579 bp (86.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64192 times.

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

Bases preceding removed adapters:
  A: 41.0%
  C: 15.5%
  G: 11.6%
  T: 31.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	25485	25000.0	0	25485
2	2462	6250.0	0	2462
3	897	1562.5	0	897
4	634	390.6	0	634
5	453	97.7	0	453
6	478	24.4	0	478
7	495	6.1	0	495
8	383	1.5	0	383
9	453	0.4	0	442 11
10	476	0.1	1	440 36
11	382	0.0	1	351 31
12	440	0.0	1	409 31
13	372	0.0	1	336 36
14	460	0.0	1	430 30
15	484	0.0	1	447 37
16	375	0.0	1	345 30
17	407	0.0	1	374 33
18	464	0.0	1	430 34
19	463	0.0	1	431 32
20	397	0.0	1	359 38
21	455	0.0	1	421 34
22	388	0.0	1	356 32
23	444	0.0	1	403 41
24	376	0.0	1	347 29
25	402	0.0	1	368 34
26	484	0.0	1	445 39
27	389	0.0	1	355 34
28	370	0.0	1	336 34
29	382	0.0	1	344 38
30	429	0.0	1	392 37
31	418	0.0	1	387 31
32	370	0.0	1	339 31
33	313	0.0	1	288 25
34	398	0.0	1	370 28
35	379	0.0	1	348 31
36	377	0.0	1	350 27
37	402	0.0	1	380 22
38	383	0.0	1	347 36
39	349	0.0	1	324 25
40	365	0.0	1	342 23
41	296	0.0	1	276 20
42	351	0.0	1	317 34
43	348	0.0	1	327 21
44	314	0.0	1	286 28
45	363	0.0	1	336 27
46	288	0.0	1	267 21
47	312	0.0	1	287 25
48	397	0.0	1	359 38
49	307	0.0	1	280 27
50	330	0.0	1	301 29
51	378	0.0	1	354 24
52	307	0.0	1	294 13
53	293	0.0	1	269 24
54	250	0.0	1	238 12
55	304	0.0	1	280 24
56	311	0.0	1	282 29
57	287	0.0	1	263 24
58	287	0.0	1	262 25
59	276	0.0	1	246 30
60	262	0.0	1	248 14
61	286	0.0	1	268 18
62	283	0.0	1	262 21
63	350	0.0	1	326 24
64	177	0.0	1	161 16
65	268	0.0	1	255 13
66	261	0.0	1	241 20
67	233	0.0	1	219 14
68	276	0.0	1	249 27
69	276	0.0	1	259 17
70	202	0.0	1	188 14
71	239	0.0	1	223 16
72	230	0.0	1	216 14
73	267	0.0	1	246 21
74	268	0.0	1	242 26
75	204	0.0	1	187 17
76	217	0.0	1	200 17
77	243	0.0	1	229 14
78	258	0.0	1	235 23
79	279	0.0	1	247 32
80	286	0.0	1	255 31
81	331	0.0	1	316 15
82	452	0.0	1	416 36
83	597	0.0	1	540 57
84	806	0.0	1	742 64
85	745	0.0	1	680 65
86	483	0.0	1	459 24
87	331	0.0	1	314 17
88	285	0.0	1	266 19
89	238	0.0	1	226 12
90	172	0.0	1	153 19
91	158	0.0	1	150 8
92	141	0.0	1	125 16
93	132	0.0	1	117 15
94	116	0.0	1	106 10
95	120	0.0	1	110 10
96	138	0.0	1	124 14
97	114	0.0	1	105 9
98	124	0.0	1	118 6
99	112	0.0	1	103 9
100	107	0.0	1	97 10
101	121	0.0	1	112 9
102	102	0.0	1	91 11
103	105	0.0	1	95 10
104	108	0.0	1	101 7
105	105	0.0	1	97 8
106	117	0.0	1	98 19
107	105	0.0	1	96 9
108	90	0.0	1	76 14
109	103	0.0	1	90 13
110	77	0.0	1	68 9
111	87	0.0	1	80 7
112	90	0.0	1	79 11
113	84	0.0	1	75 9
114	83	0.0	1	73 10
115	98	0.0	1	86 12
116	85	0.0	1	76 9
117	91	0.0	1	81 10
118	91	0.0	1	81 10
119	74	0.0	1	64 10
120	58	0.0	1	52 6
121	73	0.0	1	61 12
122	67	0.0	1	59 8
123	66	0.0	1	59 7
124	57	0.0	1	52 5
125	77	0.0	1	73 4
126	61	0.0	1	54 7
127	56	0.0	1	49 7
128	56	0.0	1	50 6
129	37	0.0	1	33 4
130	54	0.0	1	50 4
131	51	0.0	1	43 8
132	27	0.0	1	23 4
133	28	0.0	1	25 3
134	26	0.0	1	21 5
135	24	0.0	1	22 2
136	27	0.0	1	25 2
137	12	0.0	1	11 1
138	20	0.0	1	17 3
139	17	0.0	1	14 3
140	17	0.0	1	17
141	21	0.0	1	15 6
142	20	0.0	1	16 4
143	5	0.0	1	3 2
144	5	0.0	1	2 3
145	6	0.0	1	3 3
146	3	0.0	1	1 2
147	1	0.0	1	0 1
149	4	0.0	1	2 2
150	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: illumina_100K.fastq.gz
=============================================
100000 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	637 (0.6%)

