SUMMARISING RUN PARAMETERS
==========================
Input filename: zr1394_14_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_14_s456.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1678.65 s (19 us/read; 3.17 M reads/minute).

=== Summary ===

Total reads processed:              88,771,906
Reads with adapters:                35,258,873 (39.7%)
Reads written (passing filters):    88,771,906 (100.0%)

Total basepairs processed: 4,466,488,793 bp
Quality-trimmed:               4,892,927 bp (0.1%)
Total written (filtered):  4,424,568,817 bp (99.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 35258873 times.

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

Bases preceding removed adapters:
  A: 47.0%
  C: 10.0%
  G: 3.1%
  T: 39.1%
  none/other: 0.7%

Overview of removed sequences
length	count	expect	max.err	error counts
1	34062365	22192976.5	0	34062365
2	773540	5548244.1	0	773540
3	330019	1387061.0	0	330019
4	74729	346765.3	0	74729
5	9827	86691.3	0	9827
6	972	21672.8	0	972
7	2801	5418.2	0	2801
8	877	1354.6	0	877
9	531	338.6	0	40 491
10	1365	84.7	1	5 1360
11	365	21.2	1	35 330
12	159	5.3	1	0 159
13	67	1.3	1	0 67
14	58	1.3	1	0 58
15	70	1.3	1	0 70
16	216	1.3	1	0 216
17	461	1.3	1	0 461
18	365	1.3	1	0 365
19	26	1.3	1	0 26
20	10	1.3	1	0 10
21	3	1.3	1	0 3
22	1	1.3	1	0 1
23	1	1.3	1	0 1
24	2	1.3	1	0 2
25	5	1.3	1	0 5
26	5	1.3	1	0 5
27	13	1.3	1	0 13
28	3	1.3	1	0 3
29	2	1.3	1	0 2
30	2	1.3	1	0 2
32	2	1.3	1	0 2
33	6	1.3	1	0 6
34	3	1.3	1	0 3
35	1	1.3	1	0 1
36	1	1.3	1	0 1


RUN STATISTICS FOR INPUT FILE: zr1394_14_s456.fastq.gz
=============================================
88771906 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	937269 (1.1%)