SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/5_ACAGTG_L001_R1_001.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 8 bp from their 5' end to avoid poor qualities or biases
Running FastQC on the data once trimming has completed
Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimmed_fastqc --threads 28
Output file will be GZIP compressed


This is cutadapt 1.16 with Python 2.7.14
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/5_ACAGTG_L001_R1_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 230.03 s (18 us/read; 3.28 M reads/minute).

=== Summary ===

Total reads processed:              12,589,609
Reads with adapters:                 5,003,685 (39.7%)
Reads written (passing filters):    12,589,609 (100.0%)

Total basepairs processed:   642,070,059 bp
Quality-trimmed:               2,594,232 bp (0.4%)
Total written (filtered):    626,202,947 bp (97.5%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5003685 times.

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

Bases preceding removed adapters:
  A: 30.4%
  C: 2.0%
  G: 21.9%
  T: 45.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	3295604	3147402.2	0	3295604
2	802076	786850.6	0	802076
3	289174	196712.6	0	289174
4	132748	49178.2	0	132748
5	37772	12294.5	0	37772
6	33518	3073.6	0	33518
7	30685	768.4	0	30685
8	29675	192.1	0	29675
9	29294	48.0	0	28914 380
10	26932	12.0	1	25771 1161
11	25424	3.0	1	24438 986
12	24576	0.8	1	23687 889
13	21216	0.2	1	20361 855
14	22921	0.2	1	21965 956
15	18687	0.2	1	17712 975
16	19766	0.2	1	18777 989
17	16813	0.2	1	16133 680
18	16135	0.2	1	15502 633
19	15003	0.2	1	14260 743
20	13995	0.2	1	13335 660
21	12979	0.2	1	12295 684
22	12172	0.2	1	11539 633
23	11217	0.2	1	10663 554
24	10242	0.2	1	9608 634
25	8811	0.2	1	8346 465
26	7468	0.2	1	7010 458
27	6717	0.2	1	6246 471
28	6216	0.2	1	5834 382
29	5562	0.2	1	5215 347
30	4179	0.2	1	3933 246
31	3458	0.2	1	3263 195
32	2742	0.2	1	2590 152
33	2233	0.2	1	2128 105
34	1264	0.2	1	1197 67
35	813	0.2	1	766 47
36	417	0.2	1	393 24
37	250	0.2	1	236 14
38	182	0.2	1	174 8
39	98	0.2	1	94 4
40	96	0.2	1	94 2
41	112	0.2	1	107 5
42	235	0.2	1	225 10
43	281	0.2	1	265 16
44	521	0.2	1	505 16
45	769	0.2	1	747 22
46	900	0.2	1	865 35
47	653	0.2	1	593 60
48	123	0.2	1	117 6
49	71	0.2	1	63 8
50	66	0.2	1	62 4
51	824	0.2	1	707 117


RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/5_ACAGTG_L001_R1_001.fastq.gz
=============================================
12589609 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	87428 (0.7%)