SUMMARISING RUN PARAMETERS
==========================
Input filename: EPI-162_S9_L002_R2_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-162_S9_L002_R2_001.fastq.gz_qual_trimmed.fastq
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 438.01 s (19 us/read; 3.20 M reads/minute).

=== Summary ===

Total reads processed:              23,358,871
Reads with adapters:                16,623,316 (71.2%)
Reads written (passing filters):    23,358,871 (100.0%)

Total basepairs processed: 2,330,642,472 bp
Total written (filtered):  1,961,117,691 bp (84.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16623316 times.

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

Bases preceding removed adapters:
  A: 36.2%
  C: 23.0%
  G: 10.1%
  T: 30.3%
  none/other: 0.4%

Overview of removed sequences
length	count	expect	max.err	error counts
1	6002978	5839717.8	0	6002978
2	219993	1459929.4	0	219993
3	181974	364982.4	0	181974
4	158959	91245.6	0	158959
5	161535	22811.4	0	161535
6	164750	5702.8	0	164750
7	157609	1425.7	0	157609
8	166337	356.4	0	166337
9	160998	89.1	0	160303 695
10	163419	22.3	1	158839 4580
11	157494	5.6	1	151687 5807
12	162268	1.4	1	156624 5644
13	157642	0.3	1	152268 5374
14	171678	0.3	1	165703 5975
15	161960	0.3	1	156095 5865
16	163712	0.3	1	158056 5656
17	174302	0.3	1	168319 5983
18	157485	0.3	1	152106 5379
19	168815	0.3	1	162973 5842
20	167093	0.3	1	161264 5829
21	172080	0.3	1	165528 6552
22	175195	0.3	1	168612 6583
23	172607	0.3	1	166340 6267
24	183495	0.3	1	176628 6867
25	167319	0.3	1	161095 6224
26	171316	0.3	1	164032 7284
27	176530	0.3	1	168373 8157
28	182259	0.3	1	175593 6666
29	179715	0.3	1	172270 7445
30	195093	0.3	1	188352 6741
31	171592	0.3	1	164955 6637
32	180459	0.3	1	174627 5832
33	191657	0.3	1	184460 7197
34	198190	0.3	1	189955 8235
35	186581	0.3	1	180971 5610
36	180387	0.3	1	173816 6571
37	180094	0.3	1	173928 6166
38	162245	0.3	1	156726 5519
39	170999	0.3	1	164973 6026
40	168786	0.3	1	162986 5800
41	168588	0.3	1	163416 5172
42	167022	0.3	1	162294 4728
43	149684	0.3	1	144798 4886
44	154331	0.3	1	149540 4791
45	192478	0.3	1	187461 5017
46	148978	0.3	1	144577 4401
47	107202	0.3	1	103473 3729
48	150200	0.3	1	146349 3851
49	107936	0.3	1	104772 3164
50	113844	0.3	1	110201 3643
51	156487	0.3	1	152944 3543
52	96437	0.3	1	93318 3119
53	100043	0.3	1	96922 3121
54	89058	0.3	1	86124 2934
55	103550	0.3	1	100610 2940
56	99466	0.3	1	96364 3102
57	91001	0.3	1	88220 2781
58	88611	0.3	1	85847 2764
59	84417	0.3	1	81630 2787
60	80787	0.3	1	78214 2573
61	80428	0.3	1	77733 2695
62	80538	0.3	1	77883 2655
63	78488	0.3	1	75763 2725
64	76213	0.3	1	73595 2618
65	78832	0.3	1	76188 2644
66	83670	0.3	1	80684 2986
67	110162	0.3	1	104037 6125
68	347873	0.3	1	340674 7199
69	126664	0.3	1	123109 3555
70	60331	0.3	1	58288 2043
71	33312	0.3	1	31955 1357
72	24107	0.3	1	23038 1069
73	18359	0.3	1	17433 926
74	15230	0.3	1	14419 811
75	12912	0.3	1	12260 652
76	11396	0.3	1	10801 595
77	10184	0.3	1	9639 545
78	9241	0.3	1	8748 493
79	7740	0.3	1	7315 425
80	6748	0.3	1	6375 373
81	5905	0.3	1	5560 345
82	4889	0.3	1	4608 281
83	3970	0.3	1	3730 240
84	3371	0.3	1	3180 191
85	2583	0.3	1	2425 158
86	1937	0.3	1	1803 134
87	1820	0.3	1	1675 145
88	1385	0.3	1	1260 125
89	1439	0.3	1	1300 139
90	1791	0.3	1	1626 165
91	2322	0.3	1	2117 205
92	3405	0.3	1	3085 320
93	6857	0.3	1	6284 573
94	19646	0.3	1	18296 1350
95	34434	0.3	1	32162 2272
96	16438	0.3	1	15369 1069
97	12178	0.3	1	11305 873
98	5101	0.3	1	4753 348
99	5175	0.3	1	4802 373
100	5922	0.3	1	5506 416
101	12600	0.3	1	11553 1047


RUN STATISTICS FOR INPUT FILE: EPI-162_S9_L002_R2_001.fastq.gz
=============================================
23358871 sequences processed in total
Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20):	3102080 (13.3%)
RRBS reads trimmed by additional 2 bp when adapter contamination was detected:	0 (0.0%)

Total number of sequences analysed for the sequence pair length validation: 23358871

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 589325 (2.52%)