SUMMARISING RUN PARAMETERS
==========================
Input filename: EPI-145_S38_L005_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.2
Cutadapt version: 1.12
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 for both reads before a sequence pair gets removed: 20 bp
File was specified to be an MspI-digested RRBS sample. Sequences with adapter contamination will be trimmed a further 2 bp to remove potential methylation-biased bases from the end-repair reaction
Running FastQC on the data once trimming has completed
Output file will be GZIP compressed


This is cutadapt 1.12 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /home/sean/Documents/Geoduck/trimmed-data/EPI-145_S38_L005_R2_001.fastq.gz_qual_trimmed.fastq
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 518.76 s (20 us/read; 2.95 M reads/minute).

=== Summary ===

Total reads processed:              25,512,585
Reads with adapters:                15,613,126 (61.2%)
Reads written (passing filters):    25,512,585 (100.0%)

Total basepairs processed: 2,553,685,509 bp
Total written (filtered):  2,356,058,789 bp (92.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15613126 times.

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

Bases preceding removed adapters:
  A: 39.3%
  C: 25.0%
  G: 7.1%
  T: 28.6%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	9077013	6378146.2	0	9077013
2	191849	1594536.6	0	191849
3	188524	398634.1	0	188524
4	143336	99658.5	0	143336
5	142647	24914.6	0	142647
6	146034	6228.7	0	146034
7	139792	1557.2	0	139792
8	178001	389.3	0	178001
9	135673	97.3	0	135104 569
10	136613	24.3	1	131617 4996
11	128613	6.1	1	122097 6516
12	128881	1.5	1	122858 6023
13	122163	0.4	1	116317 5846
14	136318	0.4	1	129872 6446
15	124861	0.4	1	118909 5952
16	124856	0.4	1	118914 5942
17	131964	0.4	1	125918 6046
18	110142	0.4	1	104971 5171
19	119375	0.4	1	114042 5333
20	115744	0.4	1	109986 5758
21	121855	0.4	1	115367 6488
22	123970	0.4	1	117835 6135
23	114419	0.4	1	108954 5465
24	122162	0.4	1	116393 5769
25	103220	0.4	1	98078 5142
26	109614	0.4	1	103443 6171
27	114021	0.4	1	106971 7050
28	114371	0.4	1	109126 5245
29	111847	0.4	1	105127 6720
30	121246	0.4	1	116039 5207
31	98509	0.4	1	93194 5315
32	103407	0.4	1	99169 4238
33	107769	0.4	1	102375 5394
34	113829	0.4	1	107389 6440
35	101643	0.4	1	97779 3864
36	96504	0.4	1	91368 5136
37	91281	0.4	1	86804 4477
38	83854	0.4	1	79689 4165
39	85543	0.4	1	81147 4396
40	85429	0.4	1	80999 4430
41	83091	0.4	1	79482 3609
42	87925	0.4	1	84702 3223
43	69788	0.4	1	66229 3559
44	77087	0.4	1	73629 3458
45	115625	0.4	1	111938 3687
46	68373	0.4	1	65332 3041
47	46242	0.4	1	43635 2607
48	77224	0.4	1	74590 2634
49	43134	0.4	1	41113 2021
50	49609	0.4	1	47114 2495
51	77797	0.4	1	75369 2428
52	37403	0.4	1	35614 1789
53	42599	0.4	1	40472 2127
54	36131	0.4	1	34264 1867
55	48945	0.4	1	46830 2115
56	47254	0.4	1	44959 2295
57	42774	0.4	1	40818 1956
58	41425	0.4	1	39658 1767
59	38922	0.4	1	36999 1923
60	39145	0.4	1	37236 1909
61	40063	0.4	1	38092 1971
62	43002	0.4	1	40884 2118
63	46639	0.4	1	44376 2263
64	47439	0.4	1	45216 2223
65	48155	0.4	1	45925 2230
66	49461	0.4	1	47212 2249
67	56049	0.4	1	53086 2963
68	119070	0.4	1	115969 3101
69	39067	0.4	1	37462 1605
70	19519	0.4	1	18466 1053
71	11722	0.4	1	11006 716
72	9271	0.4	1	8616 655
73	7363	0.4	1	6876 487
74	6135	0.4	1	5668 467
75	5168	0.4	1	4792 376
76	4305	0.4	1	4012 293
77	3649	0.4	1	3390 259
78	2978	0.4	1	2768 210
79	2470	0.4	1	2295 175
80	1809	0.4	1	1691 118
81	1380	0.4	1	1281 99
82	1043	0.4	1	968 75
83	721	0.4	1	663 58
84	549	0.4	1	491 58
85	401	0.4	1	362 39
86	315	0.4	1	281 34
87	296	0.4	1	253 43
88	304	0.4	1	264 40
89	339	0.4	1	291 48
90	379	0.4	1	320 59
91	540	0.4	1	499 41
92	974	0.4	1	889 85
93	2147	0.4	1	1910 237
94	5784	0.4	1	5196 588
95	9468	0.4	1	8607 861
96	3934	0.4	1	3588 346
97	1691	0.4	1	1544 147
98	549	0.4	1	503 46
99	438	0.4	1	403 35
100	398	0.4	1	355 43
101	757	0.4	1	670 87


RUN STATISTICS FOR INPUT FILE: EPI-145_S38_L005_R2_001.fastq.gz
=============================================
25512585 sequences processed in total
Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20):	3020088 (11.8%)
RRBS reads trimmed by additional 2 bp when adapter contamination was detected:	15602506 (61.2%)

Total number of sequences analysed for the sequence pair length validation: 25512585

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 197332 (0.77%)