SUMMARISING RUN PARAMETERS
==========================
Input filename: EPI-119_S31_L005_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4_dev
Cutadapt version: 1.9.1
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. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction
All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications)
Running FastQC on the data once trimming has completed
Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc --threads 16
Output file will be GZIP compressed


This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/EPI-119_S31_L005_R1_001.fastq.gz_qual_trimmed.fastq
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 552.58 s (19 us/read; 3.15 M reads/minute).

=== Summary ===

Total reads processed:              29,018,872
Reads with adapters:                14,945,774 (51.5%)
Reads written (passing filters):    29,018,872 (100.0%)

Total basepairs processed: 2,919,648,747 bp
Total written (filtered):  2,701,752,596 bp (92.5%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14945774 times.

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

Bases preceding removed adapters:
  A: 26.6%
  C: 6.5%
  G: 23.9%
  T: 43.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	6190802	7254718.0	0	6190802
2	1416952	1813679.5	0	1416952
3	528181	453419.9	0	528181
4	341864	113355.0	0	341864
5	144965	28338.7	0	144965
6	152127	7084.7	0	152127
7	146993	1771.2	0	146993
8	170386	442.8	0	170386
9	152866	110.7	0	151486 1380
10	149965	27.7	1	143748 6217
11	142341	6.9	1	135647 6694
12	137753	1.7	1	131563 6190
13	128964	0.4	1	123370 5594
14	146517	0.4	1	138762 7755
15	134849	0.4	1	128728 6121
16	141865	0.4	1	134264 7601
17	132955	0.4	1	126797 6158
18	120614	0.4	1	115272 5342
19	132847	0.4	1	125556 7291
20	121479	0.4	1	116123 5356
21	137034	0.4	1	129542 7492
22	127895	0.4	1	122021 5874
23	114673	0.4	1	109056 5617
24	120904	0.4	1	114560 6344
25	109352	0.4	1	104420 4932
26	121103	0.4	1	114671 6432
27	109335	0.4	1	104391 4944
28	105003	0.4	1	100237 4766
29	112686	0.4	1	107259 5427
30	107490	0.4	1	102848 4642
31	110686	0.4	1	105216 5470
32	102107	0.4	1	97682 4425
33	108458	0.4	1	103361 5097
34	97708	0.4	1	93448 4260
35	97974	0.4	1	93317 4657
36	96228	0.4	1	91975 4253
37	102500	0.4	1	97670 4830
38	94200	0.4	1	89985 4215
39	92800	0.4	1	88304 4496
40	96886	0.4	1	92107 4779
41	141622	0.4	1	136489 5133
42	75579	0.4	1	72696 2883
43	35589	0.4	1	33546 2043
44	79104	0.4	1	75615 3489
45	73701	0.4	1	70467 3234
46	74415	0.4	1	71304 3111
47	81279	0.4	1	77578 3701
48	76890	0.4	1	73424 3466
49	76572	0.4	1	72916 3656
50	70076	0.4	1	67100 2976
51	66114	0.4	1	63314 2800
52	62234	0.4	1	59644 2590
53	62422	0.4	1	59971 2451
54	62231	0.4	1	59621 2610
55	63774	0.4	1	61322 2452
56	62691	0.4	1	60157 2534
57	60227	0.4	1	57872 2355
58	56514	0.4	1	54560 1954
59	55589	0.4	1	53567 2022
60	50300	0.4	1	48558 1742
61	50412	0.4	1	48691 1721
62	54716	0.4	1	52811 1905
63	54717	0.4	1	52767 1950
64	56115	0.4	1	54254 1861
65	50693	0.4	1	49025 1668
66	46957	0.4	1	45356 1601
67	40646	0.4	1	39235 1411
68	33548	0.4	1	32437 1111
69	34486	0.4	1	33331 1155
70	31256	0.4	1	30204 1052
71	30849	0.4	1	29811 1038
72	29471	0.4	1	28343 1128
73	32424	0.4	1	30970 1454
74	52965	0.4	1	51557 1408
75	22944	0.4	1	22288 656
76	10556	0.4	1	10180 376
77	6398	0.4	1	6165 233
78	4367	0.4	1	4215 152
79	2823	0.4	1	2736 87
80	2034	0.4	1	1954 80
81	1354	0.4	1	1292 62
82	986	0.4	1	945 41
83	706	0.4	1	682 24
84	448	0.4	1	420 28
85	272	0.4	1	257 15
86	168	0.4	1	154 14
87	141	0.4	1	125 16
88	108	0.4	1	100 8
89	109	0.4	1	98 11
90	116	0.4	1	106 10
91	190	0.4	1	175 15
92	268	0.4	1	250 18
93	432	0.4	1	401 31
94	901	0.4	1	857 44
95	1201	0.4	1	1138 63
96	1067	0.4	1	1011 56
97	562	0.4	1	519 43
98	169	0.4	1	151 18
99	105	0.4	1	85 20
100	213	0.4	1	163 50
101	651	0.4	1	465 186


RUN STATISTICS FOR INPUT FILE: EPI-119_S31_L005_R1_001.fastq.gz
=============================================
29018872 sequences processed in total
Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20):	2899376 (10.0%)
RRBS reads trimmed by additional 2 bp when adapter contamination was detected:	14942640 (51.5%)