SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/6_GCCAAT_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/6_GCCAAT_L001_R1_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 226.82 s (18 us/read; 3.30 M reads/minute).

=== Summary ===

Total reads processed:              12,489,766
Reads with adapters:                 4,926,737 (39.4%)
Reads written (passing filters):    12,489,766 (100.0%)

Total basepairs processed:   636,978,066 bp
Quality-trimmed:               2,185,070 bp (0.3%)
Total written (filtered):    622,210,082 bp (97.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4926737 times.

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

Bases preceding removed adapters:
  A: 30.5%
  C: 2.0%
  G: 21.7%
  T: 45.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	3276852	3122441.5	0	3276852
2	794601	780610.4	0	794601
3	285283	195152.6	0	285283
4	128704	48788.1	0	128704
5	34517	12197.0	0	34517
6	30844	3049.3	0	30844
7	27794	762.3	0	27794
8	26986	190.6	0	26986
9	26705	47.6	0	26364 341
10	24540	11.9	1	23408 1132
11	22952	3.0	1	21953 999
12	22249	0.7	1	21427 822
13	19064	0.2	1	18363 701
14	20118	0.2	1	19165 953
15	18116	0.2	1	17196 920
16	17610	0.2	1	16786 824
17	15552	0.2	1	14920 632
18	14792	0.2	1	14184 608
19	13580	0.2	1	12901 679
20	13017	0.2	1	12408 609
21	12046	0.2	1	11420 626
22	11133	0.2	1	10543 590
23	10274	0.2	1	9720 554
24	9512	0.2	1	8930 582
25	8110	0.2	1	7681 429
26	7068	0.2	1	6648 420
27	6240	0.2	1	5852 388
28	5751	0.2	1	5401 350
29	5135	0.2	1	4807 328
30	3946	0.2	1	3711 235
31	2969	0.2	1	2764 205
32	2533	0.2	1	2391 142
33	1882	0.2	1	1783 99
34	1129	0.2	1	1075 54
35	677	0.2	1	633 44
36	417	0.2	1	393 24
37	181	0.2	1	171 10
38	147	0.2	1	140 7
39	94	0.2	1	87 7
40	78	0.2	1	73 5
41	108	0.2	1	97 11
42	189	0.2	1	173 16
43	214	0.2	1	201 13
44	419	0.2	1	390 29
45	541	0.2	1	524 17
46	683	0.2	1	649 34
47	542	0.2	1	494 48
48	110	0.2	1	96 14
49	49	0.2	1	37 12
50	61	0.2	1	59 2
51	623	0.2	1	514 109


RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/6_GCCAAT_L001_R1_001.fastq.gz
=============================================
12489766 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	80117 (0.6%)