SUMMARISING RUN PARAMETERS
==========================
Input filename: zr1394_10_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_10_s456.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1484.68 s (19 us/read; 3.20 M reads/minute).

=== Summary ===

Total reads processed:              79,264,583
Reads with adapters:                30,297,063 (38.2%)
Reads written (passing filters):    79,264,583 (100.0%)

Total basepairs processed: 3,978,999,570 bp
Quality-trimmed:               5,235,908 bp (0.1%)
Total written (filtered):  3,941,256,193 bp (99.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 30297063 times.

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

Bases preceding removed adapters:
  A: 44.6%
  C: 10.4%
  G: 4.9%
  T: 39.4%
  none/other: 0.7%

Overview of removed sequences
length	count	expect	max.err	error counts
1	28762957	19816145.8	0	28762957
2	1012763	4954036.4	0	1012763
3	417959	1238509.1	0	417959
4	81634	309627.3	0	81634
5	12134	77406.8	0	12134
6	1255	19351.7	0	1255
7	4142	4837.9	0	4142
8	1302	1209.5	0	1302
9	671	302.4	0	46 625
10	1592	75.6	1	5 1587
11	253	18.9	1	16 237
12	147	4.7	1	0 147
13	36	1.2	1	0 36
14	23	1.2	1	0 23
15	10	1.2	1	0 10
16	27	1.2	1	0 27
17	77	1.2	1	0 77
18	36	1.2	1	0 36
19	11	1.2	1	0 11
20	3	1.2	1	0 3
22	1	1.2	1	0 1
23	3	1.2	1	0 3
25	1	1.2	1	0 1
26	2	1.2	1	0 2
27	5	1.2	1	0 5
28	4	1.2	1	0 4
29	11	1.2	1	0 11
30	1	1.2	1	0 1
31	2	1.2	1	0 2
33	1	1.2	1	0 1


RUN STATISTICS FOR INPUT FILE: zr1394_10_s456.fastq.gz
=============================================
79264583 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	1043126 (1.3%)