SUMMARISING RUN PARAMETERS
==========================
Input filename: zr1394_8_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_8_s456.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 737.40 s (19 us/read; 3.18 M reads/minute).

=== Summary ===

Total reads processed:              39,136,514
Reads with adapters:                15,691,880 (40.1%)
Reads written (passing filters):    39,136,514 (100.0%)

Total basepairs processed: 1,968,545,164 bp
Quality-trimmed:               2,012,847 bp (0.1%)
Total written (filtered):  1,949,900,521 bp (99.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15691880 times.

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

Bases preceding removed adapters:
  A: 46.8%
  C: 10.5%
  G: 3.7%
  T: 38.3%
  none/other: 0.7%

Overview of removed sequences
length	count	expect	max.err	error counts
1	15065221	9784128.5	0	15065221
2	395817	2446032.1	0	395817
3	184704	611508.0	0	184704
4	36406	152877.0	0	36406
5	4814	38219.3	0	4814
6	470	9554.8	0	470
7	1447	2388.7	0	1447
8	486	597.2	0	486
9	271	149.3	0	21 250
10	614	37.3	1	13 601
11	250	9.3	1	26 224
12	135	2.3	1	0 135
13	62	0.6	1	0 62
14	50	0.6	1	0 50
15	78	0.6	1	0 78
16	178	0.6	1	0 178
17	460	0.6	1	0 460
18	320	0.6	1	0 320
19	42	0.6	1	0 42
20	4	0.6	1	0 4
21	5	0.6	1	0 5
22	4	0.6	1	0 4
23	3	0.6	1	0 3
24	3	0.6	1	0 3
25	7	0.6	1	0 7
26	3	0.6	1	0 3
27	6	0.6	1	0 6
28	7	0.6	1	0 7
29	2	0.6	1	0 2
30	1	0.6	1	0 1
31	1	0.6	1	0 1
32	2	0.6	1	0 2
33	3	0.6	1	0 3
34	2	0.6	1	0 2
35	1	0.6	1	0 1
37	1	0.6	1	0 1


RUN STATISTICS FOR INPUT FILE: zr1394_8_s456.fastq.gz
=============================================
39136514 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	439325 (1.1%)