SUMMARISING RUN PARAMETERS
==========================
Input filename: zr1394_13_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_13_s456.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1223.51 s (19 us/read; 3.19 M reads/minute).

=== Summary ===

Total reads processed:              65,081,682
Reads with adapters:                25,664,309 (39.4%)
Reads written (passing filters):    65,081,682 (100.0%)

Total basepairs processed: 3,272,837,182 bp
Quality-trimmed:               3,459,477 bp (0.1%)
Total written (filtered):  3,242,234,024 bp (99.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25664309 times.

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

Bases preceding removed adapters:
  A: 46.6%
  C: 10.8%
  G: 3.7%
  T: 38.2%
  none/other: 0.7%

Overview of removed sequences
length	count	expect	max.err	error counts
1	24665742	16270420.5	0	24665742
2	643781	4067605.1	0	643781
3	280330	1016901.3	0	280330
4	58268	254225.3	0	58268
5	8366	63556.3	0	8366
6	798	15889.1	0	798
7	2561	3972.3	0	2561
8	1035	993.1	0	1035
9	508	248.3	0	36 472
10	1126	62.1	1	2 1124
11	347	15.5	1	36 311
12	174	3.9	1	1 173
13	64	1.0	1	0 64
14	56	1.0	1	0 56
15	81	1.0	1	0 81
16	200	1.0	1	0 200
17	428	1.0	1	0 428
18	365	1.0	1	0 365
19	29	1.0	1	0 29
20	6	1.0	1	0 6
21	1	1.0	1	0 1
22	1	1.0	1	0 1
23	6	1.0	1	0 6
24	6	1.0	1	0 6
25	3	1.0	1	0 3
26	5	1.0	1	0 5
27	6	1.0	1	0 6
28	1	1.0	1	0 1
29	2	1.0	1	0 2
30	2	1.0	1	0 2
31	1	1.0	1	0 1
32	4	1.0	1	0 4
33	1	1.0	1	0 1
34	2	1.0	1	0 2
35	1	1.0	1	0 1
36	2	1.0	1	0 2


RUN STATISTICS FOR INPUT FILE: zr1394_13_s456.fastq.gz
=============================================
65081682 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	729132 (1.1%)