SUMMARISING RUN PARAMETERS
==========================
Input filename: zr1394_11_s456.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 zr1394_11_s456.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1032.71 s (19 us/read; 3.20 M reads/minute).

=== Summary ===

Total reads processed:              55,109,528
Reads with adapters:                21,238,441 (38.5%)
Reads written (passing filters):    55,109,528 (100.0%)

Total basepairs processed: 2,769,826,173 bp
Quality-trimmed:               3,100,652 bp (0.1%)
Total written (filtered):  2,744,305,038 bp (99.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21238441 times.

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

Bases preceding removed adapters:
  A: 46.1%
  C: 10.8%
  G: 3.8%
  T: 38.6%
  none/other: 0.7%

Overview of removed sequences
length	count	expect	max.err	error counts
1	20439811	13777382.0	0	20439811
2	513654	3444345.5	0	513654
3	226149	861086.4	0	226149
4	45757	215271.6	0	45757
5	7219	53817.9	0	7219
6	683	13454.5	0	683
7	1872	3363.6	0	1872
8	730	840.9	0	730
9	346	210.2	0	39 307
10	807	52.6	1	7 800
11	265	13.1	1	28 237
12	147	3.3	1	0 147
13	59	0.8	1	0 59
14	45	0.8	1	0 45
15	67	0.8	1	0 67
16	182	0.8	1	0 182
17	371	0.8	1	0 371
18	222	0.8	1	0 222
19	24	0.8	1	0 24
20	3	0.8	1	0 3
21	3	0.8	1	0 3
22	2	0.8	1	0 2
23	3	0.8	1	0 3
24	1	0.8	1	0 1
25	3	0.8	1	0 3
26	2	0.8	1	0 2
27	3	0.8	1	0 3
28	3	0.8	1	0 3
29	2	0.8	1	0 2
30	1	0.8	1	0 1
31	1	0.8	1	0 1
34	1	0.8	1	0 1
36	1	0.8	1	0 1
37	1	0.8	1	0 1
38	1	0.8	1	0 1


RUN STATISTICS FOR INPUT FILE: zr1394_11_s456.fastq.gz
=============================================
55109528 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	650956 (1.2%)