SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/2_CGATGT_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/2_CGATGT_L001_R1_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 217.76 s (18 us/read; 3.29 M reads/minute).

=== Summary ===

Total reads processed:              11,954,873
Reads with adapters:                 4,759,817 (39.8%)
Reads written (passing filters):    11,954,873 (100.0%)

Total basepairs processed:   609,698,523 bp
Quality-trimmed:               1,934,183 bp (0.3%)
Total written (filtered):    595,521,684 bp (97.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4759817 times.

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

Bases preceding removed adapters:
  A: 30.6%
  C: 2.2%
  G: 21.7%
  T: 45.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	3158682	2988718.2	0	3158682
2	762522	747179.6	0	762522
3	283079	186794.9	0	283079
4	123149	46698.7	0	123149
5	33918	11674.7	0	33918
6	29520	2918.7	0	29520
7	26966	729.7	0	26966
8	26048	182.4	0	26048
9	26083	45.6	0	25757 326
10	23691	11.4	1	22611 1080
11	22687	2.9	1	21775 912
12	21992	0.7	1	21251 741
13	18838	0.2	1	18122 716
14	19991	0.2	1	19139 852
15	18228	0.2	1	17261 967
16	17515	0.2	1	16720 795
17	15543	0.2	1	14889 654
18	14803	0.2	1	14230 573
19	13744	0.2	1	13084 660
20	13268	0.2	1	12580 688
21	12071	0.2	1	11465 606
22	11254	0.2	1	10660 594
23	10146	0.2	1	9659 487
24	9365	0.2	1	8841 524
25	8059	0.2	1	7635 424
26	6645	0.2	1	6261 384
27	5757	0.2	1	5367 390
28	5293	0.2	1	4964 329
29	4478	0.2	1	4163 315
30	3459	0.2	1	3247 212
31	2708	0.2	1	2539 169
32	2250	0.2	1	2116 134
33	1610	0.2	1	1520 90
34	928	0.2	1	877 51
35	581	0.2	1	549 32
36	282	0.2	1	264 18
37	181	0.2	1	171 10
38	146	0.2	1	128 18
39	111	0.2	1	103 8
40	90	0.2	1	79 11
41	136	0.2	1	133 3
42	230	0.2	1	218 12
43	275	0.2	1	260 15
44	517	0.2	1	497 20
45	700	0.2	1	669 31
46	841	0.2	1	800 41
47	561	0.2	1	499 62
48	119	0.2	1	109 10
49	54	0.2	1	47 7
50	67	0.2	1	59 8
51	636	0.2	1	513 123


RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/2_CGATGT_L001_R1_001.fastq.gz
=============================================
11954873 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	75475 (0.6%)