SUMMARISING RUN PARAMETERS
==========================
Input filename: Undetermined_L001_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.15
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
Output file will be GZIP compressed


This is cutadapt 1.15 with Python 2.7.14+
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA Undetermined_L001_R2_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 266.19 s (24 us/read; 2.54 M reads/minute).

=== Summary ===

Total reads processed:              11,279,426
Reads with adapters:                 2,818,345 (25.0%)
Reads written (passing filters):    11,279,426 (100.0%)

Total basepairs processed:   857,236,376 bp
Quality-trimmed:             156,222,080 bp (18.2%)
Total written (filtered):    697,058,933 bp (81.3%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 2818345 times.

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

Bases preceding removed adapters:
  A: 25.0%
  C: 29.5%
  G: 20.8%
  T: 22.7%
  none/other: 2.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	2188261	2819856.5	0	2188261
2	405113	704964.1	0	405113
3	167498	176241.0	0	167498
4	38582	44060.3	0	38582
5	8621	11015.1	0	8621
6	2713	2753.8	0	2713
7	1280	688.4	0	1280
8	266	172.1	0	266
9	364	43.0	0	114 250
10	412	10.8	1	33 379
11	166	2.7	1	13 153
12	93	0.7	1	17 76
13	31	0.7	1	8 23
14	67	0.7	1	6 61
15	65	0.7	1	6 59
16	95	0.7	1	7 88
17	96	0.7	1	5 91
18	55	0.7	1	4 51
19	100	0.7	1	4 96
20	98	0.7	1	11 87
21	82	0.7	1	11 71
22	78	0.7	1	4 74
23	101	0.7	1	9 92
24	66	0.7	1	8 58
25	115	0.7	1	8 107
26	73	0.7	1	3 70
27	76	0.7	1	5 71
28	65	0.7	1	10 55
29	111	0.7	1	9 102
30	85	0.7	1	7 78
31	75	0.7	1	1 74
32	58	0.7	1	2 56
33	83	0.7	1	2 81
34	98	0.7	1	3 95
35	105	0.7	1	7 98
36	78	0.7	1	9 69
37	66	0.7	1	6 60
38	73	0.7	1	1 72
39	85	0.7	1	2 83
40	69	0.7	1	1 68
41	72	0.7	1	0 72
42	60	0.7	1	2 58
43	110	0.7	1	2 108
44	59	0.7	1	0 59
45	66	0.7	1	0 66
46	73	0.7	1	1 72
47	78	0.7	1	0 78
48	117	0.7	1	1 116
49	64	0.7	1	0 64
50	55	0.7	1	0 55
51	50	0.7	1	0 50
52	60	0.7	1	0 60
53	91	0.7	1	2 89
54	71	0.7	1	0 71
55	55	0.7	1	1 54
56	80	0.7	1	1 79
57	51	0.7	1	0 51
58	89	0.7	1	2 87
59	51	0.7	1	1 50
60	63	0.7	1	1 62
61	64	0.7	1	0 64
62	135	0.7	1	0 135
63	119	0.7	1	1 118
64	85	0.7	1	0 85
65	72	0.7	1	0 72
66	168	0.7	1	1 167
67	67	0.7	1	6 61
68	157	0.7	1	0 157
69	29	0.7	1	0 29
70	118	0.7	1	1 117
71	32	0.7	1	0 32
72	116	0.7	1	3 113
73	47	0.7	1	1 46
74	43	0.7	1	0 43
75	44	0.7	1	0 44
76	16	0.7	1	0 16


RUN STATISTICS FOR INPUT FILE: Undetermined_L001_R2_001.fastq.gz
=============================================
11279426 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 11279426

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1956196 (17.34%)