SUMMARISING RUN PARAMETERS
==========================
Input filename: zr2096_5_s1_R1_val_1.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_5_s1_R1_val_1.fq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 558.78 s (18 us/read; 3.40 M reads/minute).

=== Summary ===

Total reads processed:              31,629,718
Reads with adapters:                15,896,587 (50.3%)
Reads written (passing filters):    31,629,718 (100.0%)

Total basepairs processed: 2,404,730,852 bp
Quality-trimmed:               2,548,776 bp (0.1%)
Total written (filtered):  2,383,094,134 bp (99.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15896587 times.

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

Bases preceding removed adapters:
  A: 40.4%
  C: 11.8%
  G: 10.9%
  T: 36.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	13584485	7907429.5	0	13584485
2	1763666	1976857.4	0	1763666
3	449266	494214.3	0	449266
4	66342	123553.6	0	66342
5	6358	30888.4	0	6358
6	5668	7722.1	0	5668
7	2600	1930.5	0	2600
8	1104	482.6	0	1104
9	911	120.7	0	268 643
10	1305	30.2	1	278 1027
11	942	7.5	1	120 822
12	675	1.9	1	117 558
13	874	0.5	1	0 874
14	1154	0.5	1	0 1154
15	2172	0.5	1	0 2172
16	4142	0.5	1	0 4142
17	3621	0.5	1	0 3621
18	238	0.5	1	0 238
19	64	0.5	1	0 64
20	38	0.5	1	0 38
21	22	0.5	1	0 22
22	35	0.5	1	0 35
23	32	0.5	1	0 32
24	30	0.5	1	0 30
25	35	0.5	1	0 35
26	40	0.5	1	0 40
27	32	0.5	1	0 32
28	37	0.5	1	0 37
29	30	0.5	1	0 30
30	29	0.5	1	0 29
31	28	0.5	1	0 28
32	33	0.5	1	0 33
33	33	0.5	1	0 33
34	25	0.5	1	0 25
35	24	0.5	1	0 24
36	30	0.5	1	0 30
37	21	0.5	1	0 21
38	28	0.5	1	0 28
39	26	0.5	1	0 26
40	25	0.5	1	0 25
41	23	0.5	1	0 23
42	30	0.5	1	0 30
43	25	0.5	1	0 25
44	27	0.5	1	0 27
45	21	0.5	1	0 21
46	14	0.5	1	0 14
47	23	0.5	1	0 23
48	18	0.5	1	0 18
49	22	0.5	1	0 22
50	17	0.5	1	0 17
51	17	0.5	1	0 17
52	12	0.5	1	0 12
53	15	0.5	1	0 15
54	10	0.5	1	0 10
55	14	0.5	1	0 14
56	10	0.5	1	0 10
57	8	0.5	1	0 8
58	8	0.5	1	0 8
59	13	0.5	1	0 13
60	6	0.5	1	0 6
61	5	0.5	1	0 5
62	3	0.5	1	0 3
63	2	0.5	1	0 2
64	6	0.5	1	0 6
65	2	0.5	1	0 2
66	7	0.5	1	0 7
67	1	0.5	1	0 1
68	2	0.5	1	0 2
69	2	0.5	1	0 2
70	1	0.5	1	0 1
71	2	0.5	1	0 2
73	1	0.5	1	0 1


RUN STATISTICS FOR INPUT FILE: zr2096_5_s1_R1_val_1.fq.gz
=============================================
31629718 sequences processed in total