SUMMARISING RUN PARAMETERS
==========================
Input filename: zr2096_2_s1_R2_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4_dev
Cutadapt version: 1.16
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
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 Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases
Running FastQC on the data once trimming has completed
Running FastQC with the following extra arguments: --outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18
Output file will be GZIP compressed


This is cutadapt 1.16 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_2_s1_R2_val_2.fq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 496.66 s (16 us/read; 3.69 M reads/minute).

=== Summary ===

Total reads processed:              30,577,202
Reads with adapters:                10,310,937 (33.7%)
Reads written (passing filters):    30,577,202 (100.0%)

Total basepairs processed: 2,210,198,514 bp
Quality-trimmed:               1,435,870 bp (0.1%)
Total written (filtered):  2,196,492,805 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10310937 times.

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

Bases preceding removed adapters:
  A: 45.0%
  C: 16.0%
  G: 4.3%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	9512775	7644300.5	0	9512775
2	538390	1911075.1	0	538390
3	156475	477768.8	0	156475
4	26348	119442.2	0	26348
5	2581	29860.5	0	2581
6	3032	7465.1	0	3032
7	734	1866.3	0	734
8	400	466.6	0	400
9	2281	116.6	0	1872 409
10	1990	29.2	1	280 1710
11	2737	7.3	1	1038 1699
12	2694	1.8	1	424 2270
13	5326	0.5	1	0 5326
14	9353	0.5	1	0 9353
15	14674	0.5	1	0 14674
16	17913	0.5	1	0 17913
17	10146	0.5	1	0 10146
18	1035	0.5	1	0 1035
19	201	0.5	1	0 201
20	113	0.5	1	0 113
21	73	0.5	1	0 73
22	101	0.5	1	0 101
23	102	0.5	1	0 102
24	98	0.5	1	0 98
25	114	0.5	1	0 114
26	95	0.5	1	0 95
27	76	0.5	1	0 76
28	70	0.5	1	0 70
29	80	0.5	1	0 80
30	79	0.5	1	0 79
31	71	0.5	1	0 71
32	56	0.5	1	0 56
33	49	0.5	1	0 49
34	52	0.5	1	0 52
35	48	0.5	1	0 48
36	29	0.5	1	0 29
37	32	0.5	1	0 32
38	28	0.5	1	0 28
39	34	0.5	1	0 34
40	24	0.5	1	0 24
41	25	0.5	1	0 25
42	30	0.5	1	0 30
43	28	0.5	1	0 28
44	25	0.5	1	0 25
45	25	0.5	1	0 25
46	19	0.5	1	0 19
47	17	0.5	1	0 17
48	19	0.5	1	0 19
49	27	0.5	1	0 27
50	22	0.5	1	0 22
51	15	0.5	1	0 15
52	18	0.5	1	0 18
53	8	0.5	1	0 8
54	15	0.5	1	0 15
55	15	0.5	1	0 15
56	11	0.5	1	0 11
57	5	0.5	1	0 5
58	13	0.5	1	0 13
59	12	0.5	1	0 12
60	10	0.5	1	0 10
61	10	0.5	1	0 10
62	8	0.5	1	0 8
63	8	0.5	1	0 8
64	6	0.5	1	0 6
65	6	0.5	1	0 6
66	4	0.5	1	0 4
67	4	0.5	1	0 4
68	4	0.5	1	0 4
69	8	0.5	1	0 8
70	5	0.5	1	0 5
71	2	0.5	1	0 2
72	3	0.5	1	0 3
75	1	0.5	1	0 1


RUN STATISTICS FOR INPUT FILE: zr2096_2_s1_R2_val_2.fq.gz
=============================================
30577202 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 30577202

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 173241 (0.57%)