SUMMARISING RUN PARAMETERS
==========================
Input filename: zr1394_1_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_1_s456.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 894.57 s (19 us/read; 3.18 M reads/minute).

=== Summary ===

Total reads processed:              47,399,413
Reads with adapters:                19,203,284 (40.5%)
Reads written (passing filters):    47,399,413 (100.0%)

Total basepairs processed: 2,382,626,805 bp
Quality-trimmed:               2,279,442 bp (0.1%)
Total written (filtered):  2,359,943,952 bp (99.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19203284 times.

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

Bases preceding removed adapters:
  A: 46.5%
  C: 10.8%
  G: 3.8%
  T: 38.3%
  none/other: 0.7%

Overview of removed sequences
length	count	expect	max.err	error counts
1	18444214	11849853.2	0	18444214
2	469739	2962463.3	0	469739
3	227505	740615.8	0	227505
4	45947	185154.0	0	45947
5	6341	46288.5	0	6341
6	636	11572.1	0	636
7	1722	2893.0	0	1722
8	731	723.3	0	731
9	358	180.8	0	43 315
10	835	45.2	1	19 816
11	429	11.3	1	46 383
12	264	2.8	1	4 260
13	130	0.7	1	0 130
14	131	0.7	1	0 131
15	205	0.7	1	0 205
16	539	0.7	1	0 539
17	1620	0.7	1	0 1620
18	1478	0.7	1	0 1478
19	166	0.7	1	0 166
20	33	0.7	1	0 33
21	15	0.7	1	0 15
22	7	0.7	1	0 7
23	14	0.7	1	0 14
24	13	0.7	1	0 13
25	14	0.7	1	0 14
26	38	0.7	1	0 38
27	34	0.7	1	0 34
28	17	0.7	1	0 17
29	12	0.7	1	0 12
30	11	0.7	1	0 11
31	21	0.7	1	0 21
32	15	0.7	1	0 15
33	15	0.7	1	0 15
34	19	0.7	1	0 19
35	11	0.7	1	0 11
36	3	0.7	1	0 3
37	1	0.7	1	0 1
38	1	0.7	1	0 1


RUN STATISTICS FOR INPUT FILE: zr1394_1_s456.fastq.gz
=============================================
47399413 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	607127 (1.3%)