SUMMARISING RUN PARAMETERS
==========================
Input filename: zr1394_3_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_3_s456.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 928.08 s (19 us/read; 3.16 M reads/minute).

=== Summary ===

Total reads processed:              48,926,620
Reads with adapters:                19,871,742 (40.6%)
Reads written (passing filters):    48,926,620 (100.0%)

Total basepairs processed: 2,461,374,827 bp
Quality-trimmed:               2,449,172 bp (0.1%)
Total written (filtered):  2,437,911,467 bp (99.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19871742 times.

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

Bases preceding removed adapters:
  A: 46.6%
  C: 10.4%
  G: 3.5%
  T: 38.8%
  none/other: 0.7%

Overview of removed sequences
length	count	expect	max.err	error counts
1	19123736	12231655.0	0	19123736
2	469996	3057913.8	0	469996
3	219964	764478.4	0	219964
4	45745	191119.6	0	45745
5	5398	47779.9	0	5398
6	518	11945.0	0	518
7	1564	2986.2	0	1564
8	655	746.6	0	655
9	292	186.6	0	30 262
10	785	46.7	1	17 768
11	299	11.7	1	20 279
12	194	2.9	1	2 192
13	108	0.7	1	0 108
14	60	0.7	1	0 60
15	155	0.7	1	0 155
16	357	0.7	1	0 357
17	945	0.7	1	0 945
18	761	0.7	1	0 761
19	71	0.7	1	0 71
20	18	0.7	1	0 18
21	7	0.7	1	0 7
22	3	0.7	1	0 3
23	6	0.7	1	0 6
24	5	0.7	1	0 5
25	9	0.7	1	0 9
26	12	0.7	1	0 12
27	10	0.7	1	0 10
28	13	0.7	1	0 13
29	6	0.7	1	0 6
30	8	0.7	1	0 8
31	10	0.7	1	0 10
32	8	0.7	1	0 8
33	5	0.7	1	0 5
34	10	0.7	1	0 10
35	3	0.7	1	0 3
36	2	0.7	1	0 2
37	2	0.7	1	0 2
38	2	0.7	1	0 2


RUN STATISTICS FOR INPUT FILE: zr1394_3_s456.fastq.gz
=============================================
48926620 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	549891 (1.1%)