SUMMARISING RUN PARAMETERS
==========================
Input filename: zr2096_9_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_9_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 533.88 s (17 us/read; 3.61 M reads/minute).

=== Summary ===

Total reads processed:              32,090,732
Reads with adapters:                12,065,165 (37.6%)
Reads written (passing filters):    32,090,732 (100.0%)

Total basepairs processed: 2,435,867,609 bp
Quality-trimmed:               1,897,278 bp (0.1%)
Total written (filtered):  2,420,389,815 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12065165 times.

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

Bases preceding removed adapters:
  A: 47.3%
  C: 14.5%
  G: 3.3%
  T: 34.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11369976	8022683.0	0	11369976
2	480206	2005670.8	0	480206
3	135922	501417.7	0	135922
4	26588	125354.4	0	26588
5	3510	31338.6	0	3510
6	1945	7834.7	0	1945
7	456	1958.7	0	456
8	286	489.7	0	286
9	1414	122.4	0	1191 223
10	1205	30.6	1	159 1046
11	2243	7.7	1	628 1615
12	1796	1.9	1	276 1520
13	3224	0.5	1	0 3224
14	6064	0.5	1	0 6064
15	9139	0.5	1	0 9139
16	12213	0.5	1	0 12213
17	7453	0.5	1	0 7453
18	550	0.5	1	0 550
19	63	0.5	1	0 63
20	39	0.5	1	0 39
21	37	0.5	1	0 37
22	20	0.5	1	0 20
23	32	0.5	1	0 32
24	34	0.5	1	0 34
25	44	0.5	1	0 44
26	30	0.5	1	0 30
27	25	0.5	1	0 25
28	46	0.5	1	0 46
29	32	0.5	1	0 32
30	43	0.5	1	0 43
31	37	0.5	1	0 37
32	42	0.5	1	0 42
33	24	0.5	1	0 24
34	23	0.5	1	0 23
35	19	0.5	1	0 19
36	16	0.5	1	0 16
37	9	0.5	1	0 9
38	17	0.5	1	0 17
39	17	0.5	1	0 17
40	14	0.5	1	0 14
41	22	0.5	1	0 22
42	17	0.5	1	0 17
43	15	0.5	1	0 15
44	20	0.5	1	0 20
45	13	0.5	1	0 13
46	19	0.5	1	0 19
47	16	0.5	1	0 16
48	17	0.5	1	0 17
49	12	0.5	1	0 12
50	12	0.5	1	0 12
51	10	0.5	1	0 10
52	15	0.5	1	0 15
53	8	0.5	1	0 8
54	12	0.5	1	0 12
55	10	0.5	1	0 10
56	11	0.5	1	0 11
57	8	0.5	1	0 8
58	13	0.5	1	0 13
59	4	0.5	1	0 4
60	3	0.5	1	0 3
61	6	0.5	1	0 6
62	9	0.5	1	0 9
63	7	0.5	1	0 7
64	5	0.5	1	0 5
65	7	0.5	1	0 7
66	6	0.5	1	0 6
67	1	0.5	1	0 1
68	5	0.5	1	0 5
70	5	0.5	1	0 5
71	1	0.5	1	0 1
72	1	0.5	1	0 1
73	2	0.5	1	0 2


RUN STATISTICS FOR INPUT FILE: zr2096_9_s1_R2_val_2.fq.gz
=============================================
32090732 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 32090732

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 199437 (0.62%)