SUMMARISING RUN PARAMETERS
==========================
Input filename: 1_ATCACG_L001_R1_001.fastq.gz
Trimming mode: single-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; 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
All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases
All Read 1 sequences will be trimmed by 10 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 /home/sam/analyses/20180503_trimgalore/20180503_trim_fastqc --threads 16
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 1_ATCACG_L001_R1_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 178.25 s (19 us/read; 3.16 M reads/minute).

=== Summary ===

Total reads processed:               9,402,890
Reads with adapters:                 3,614,450 (38.4%)
Reads written (passing filters):     9,402,890 (100.0%)

Total basepairs processed:   479,547,390 bp
Quality-trimmed:               1,696,655 bp (0.4%)
Total written (filtered):    470,451,893 bp (98.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3614450 times.

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

Bases preceding removed adapters:
  A: 31.4%
  C: 1.4%
  G: 20.7%
  T: 46.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	2534817	2350722.5	0	2534817
2	588836	587680.6	0	588836
3	204258	146920.2	0	204258
4	88103	36730.0	0	88103
5	17429	9182.5	0	17429
6	15373	2295.6	0	15373
7	13444	573.9	0	13444
8	12820	143.5	0	12820
9	12758	35.9	0	12524 234
10	11538	9.0	1	10942 596
11	10792	2.2	1	10254 538
12	10254	0.6	1	9851 403
13	8731	0.1	1	8342 389
14	9191	0.1	1	8738 453
15	8084	0.1	1	7583 501
16	7876	0.1	1	7481 395
17	6938	0.1	1	6639 299
18	6454	0.1	1	6171 283
19	5903	0.1	1	5610 293
20	5383	0.1	1	5103 280
21	5083	0.1	1	4790 293
22	4643	0.1	1	4397 246
23	4171	0.1	1	3933 238
24	3683	0.1	1	3464 219
25	3166	0.1	1	2987 179
26	2610	0.1	1	2451 159
27	2135	0.1	1	1984 151
28	1995	0.1	1	1857 138
29	1717	0.1	1	1614 103
30	1262	0.1	1	1188 74
31	987	0.1	1	907 80
32	773	0.1	1	723 50
33	587	0.1	1	556 31
34	338	0.1	1	315 23
35	167	0.1	1	159 8
36	102	0.1	1	95 7
37	53	0.1	1	50 3
38	53	0.1	1	51 2
39	33	0.1	1	31 2
40	32	0.1	1	28 4
41	41	0.1	1	37 4
42	100	0.1	1	90 10
43	111	0.1	1	107 4
44	262	0.1	1	252 10
45	411	0.1	1	399 12
46	385	0.1	1	361 24
47	255	0.1	1	228 27
48	45	0.1	1	42 3
49	27	0.1	1	20 7
50	17	0.1	1	16 1
51	224	0.1	1	183 41


RUN STATISTICS FOR INPUT FILE: 1_ATCACG_L001_R1_001.fastq.gz
=============================================
9402890 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	156572 (1.7%)