SUMMARISING RUN PARAMETERS
==========================
Input filename: zr1394_12_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_12_s456.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1139.67 s (19 us/read; 3.17 M reads/minute).

=== Summary ===

Total reads processed:              60,153,246
Reads with adapters:                24,436,298 (40.6%)
Reads written (passing filters):    60,153,246 (100.0%)

Total basepairs processed: 3,025,392,455 bp
Quality-trimmed:               3,405,348 bp (0.1%)
Total written (filtered):  2,996,148,248 bp (99.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24436298 times.

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

Bases preceding removed adapters:
  A: 46.7%
  C: 10.8%
  G: 3.4%
  T: 38.4%
  none/other: 0.7%

Overview of removed sequences
length	count	expect	max.err	error counts
1	23481319	15038311.5	0	23481319
2	618279	3759577.9	0	618279
3	262540	939894.5	0	262540
4	61274	234973.6	0	61274
5	6867	58743.4	0	6867
6	674	14685.9	0	674
7	2226	3671.5	0	2226
8	854	917.9	0	854
9	404	229.5	0	34 370
10	865	57.4	1	10 855
11	211	14.3	1	23 188
12	105	3.6	1	3 102
13	36	0.9	1	0 36
14	27	0.9	1	0 27
15	33	0.9	1	0 33
16	112	0.9	1	0 112
17	273	0.9	1	0 273
18	148	0.9	1	0 148
19	21	0.9	1	0 21
20	5	0.9	1	0 5
21	1	0.9	1	0 1
22	3	0.9	1	0 3
23	2	0.9	1	0 2
24	1	0.9	1	0 1
25	5	0.9	1	0 5
26	2	0.9	1	0 2
27	3	0.9	1	0 3
28	1	0.9	1	0 1
29	1	0.9	1	0 1
30	1	0.9	1	0 1
31	1	0.9	1	0 1
32	1	0.9	1	0 1
34	2	0.9	1	0 2
36	1	0.9	1	0 1


RUN STATISTICS FOR INPUT FILE: zr1394_12_s456.fastq.gz
=============================================
60153246 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	693815 (1.2%)