SUMMARISING RUN PARAMETERS
==========================
Input filename: zr1394_5_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_5_s456.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 907.10 s (19 us/read; 3.18 M reads/minute).

=== Summary ===

Total reads processed:              48,050,056
Reads with adapters:                19,818,564 (41.2%)
Reads written (passing filters):    48,050,056 (100.0%)

Total basepairs processed: 2,414,803,052 bp
Quality-trimmed:               2,459,373 bp (0.1%)
Total written (filtered):  2,391,223,773 bp (99.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19818564 times.

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

Bases preceding removed adapters:
  A: 46.2%
  C: 11.2%
  G: 4.0%
  T: 37.9%
  none/other: 0.7%

Overview of removed sequences
length	count	expect	max.err	error counts
1	18984030	12012514.0	0	18984030
2	513786	3003128.5	0	513786
3	253524	750782.1	0	253524
4	51698	187695.5	0	51698
5	6400	46923.9	0	6400
6	650	11731.0	0	650
7	1757	2932.7	0	1757
8	1013	733.2	0	1013
9	476	183.3	0	60 416
10	803	45.8	1	16 787
11	402	11.5	1	50 352
12	289	2.9	1	1 288
13	129	0.7	1	0 129
14	140	0.7	1	0 140
15	231	0.7	1	0 231
16	572	0.7	1	0 572
17	1330	0.7	1	0 1330
18	1058	0.7	1	0 1058
19	104	0.7	1	0 104
20	22	0.7	1	0 22
21	10	0.7	1	0 10
22	10	0.7	1	0 10
23	11	0.7	1	0 11
24	10	0.7	1	0 10
25	9	0.7	1	0 9
26	17	0.7	1	0 17
27	18	0.7	1	0 18
28	11	0.7	1	0 11
29	8	0.7	1	0 8
30	11	0.7	1	0 11
31	7	0.7	1	0 7
32	4	0.7	1	0 4
33	7	0.7	1	0 7
34	10	0.7	1	0 10
35	5	0.7	1	0 5
36	2	0.7	1	0 2


RUN STATISTICS FOR INPUT FILE: zr1394_5_s456.fastq.gz
=============================================
48050056 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	648320 (1.3%)