SUMMARISING RUN PARAMETERS
==========================
Input filename: zr1394_9_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_9_s456.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1517.94 s (19 us/read; 3.09 M reads/minute).

=== Summary ===

Total reads processed:              78,146,508
Reads with adapters:                32,115,155 (41.1%)
Reads written (passing filters):    78,146,508 (100.0%)

Total basepairs processed: 3,934,245,065 bp
Quality-trimmed:               3,699,261 bp (0.1%)
Total written (filtered):  3,896,717,530 bp (99.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 32115155 times.

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

Bases preceding removed adapters:
  A: 47.1%
  C: 10.3%
  G: 3.1%
  T: 38.8%
  none/other: 0.7%

Overview of removed sequences
length	count	expect	max.err	error counts
1	30946269	19536627.0	0	30946269
2	755555	4884156.8	0	755555
3	325643	1221039.2	0	325643
4	73128	305259.8	0	73128
5	8030	76314.9	0	8030
6	742	19078.7	0	742
7	2218	4769.7	0	2218
8	800	1192.4	0	800
9	473	298.1	0	40 433
10	852	74.5	1	8 844
11	285	18.6	1	24 261
12	140	4.7	1	0 140
13	50	1.2	1	0 50
14	51	1.2	1	0 51
15	69	1.2	1	0 69
16	154	1.2	1	0 154
17	392	1.2	1	0 392
18	245	1.2	1	0 245
19	20	1.2	1	0 20
20	4	1.2	1	0 4
21	2	1.2	1	0 2
22	2	1.2	1	0 2
23	1	1.2	1	0 1
24	5	1.2	1	0 5
25	3	1.2	1	0 3
26	3	1.2	1	0 3
27	6	1.2	1	0 6
28	5	1.2	1	0 5
29	2	1.2	1	0 2
31	1	1.2	1	0 1
32	2	1.2	1	0 2
33	2	1.2	1	0 2
34	1	1.2	1	0 1


RUN STATISTICS FOR INPUT FILE: zr1394_9_s456.fastq.gz
=============================================
78146508 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	795586 (1.0%)