SUMMARISING RUN PARAMETERS
==========================
Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P08-ACTGAT-READ1-Sequences.txt.gz
Trimming mode: paired-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 for both reads before a sequence pair gets removed: 20 bp
All Read 1 sequences will be trimmed by 15 bp from their 5' end to avoid poor qualities or biases
All Read 2 sequences will be trimmed by 15 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications)
All Read 1 sequences will be trimmed by 4 bp from their 3' end to avoid poor qualities or biases
All Read 2 sequences will be trimmed by 4 bp from their 3' end to avoid poor qualities or biases
Running FastQC on the data once trimming has completed
Running FastQC with the following extra arguments: --outdir /mnt/data/coral_RNAseq_2017/montipora/20180415_trimmed/fastqc --threads 24
Output file will be GZIP compressed


This is cutadapt 1.16 with Python 3.6.4
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P08-ACTGAT-READ1-Sequences.txt.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 804.99 s (19 us/read; 3.08 M reads/minute).

=== Summary ===

Total reads processed:              41,291,102
Reads with adapters:                14,466,467 (35.0%)
Reads written (passing filters):    41,291,102 (100.0%)

Total basepairs processed: 4,129,110,200 bp
Quality-trimmed:               8,835,488 bp (0.2%)
Total written (filtered):  4,082,776,233 bp (98.9%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14466467 times.

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

Bases preceding removed adapters:
  A: 34.9%
  C: 29.0%
  G: 16.8%
  T: 18.2%
  none/other: 1.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10798854	10322775.5	0	10798854
2	2340224	2580693.9	0	2340224
3	662545	645173.5	0	662545
4	179322	161293.4	0	179322
5	56519	40323.3	0	56519
6	24042	10080.8	0	24042
7	17791	2520.2	0	17791
8	15095	630.1	0	15095
9	14800	157.5	0	14092 708
10	18454	39.4	1	12727 5727
11	12641	9.8	1	11705 936
12	11495	2.5	1	10846 649
13	10513	0.6	1	9978 535
14	9674	0.6	1	9183 491
15	9494	0.6	1	8998 496
16	8869	0.6	1	8377 492
17	8198	0.6	1	7733 465
18	7595	0.6	1	7185 410
19	7070	0.6	1	6691 379
20	6406	0.6	1	6067 339
21	5767	0.6	1	5438 329
22	5221	0.6	1	4922 299
23	4670	0.6	1	4399 271
24	4459	0.6	1	4205 254
25	4041	0.6	1	3814 227
26	3799	0.6	1	3620 179
27	3379	0.6	1	3182 197
28	3302	0.6	1	3139 163
29	3150	0.6	1	2992 158
30	2832	0.6	1	2677 155
31	2750	0.6	1	2587 163
32	2657	0.6	1	2499 158
33	2392	0.6	1	2261 131
34	2292	0.6	1	2135 157
35	1859	0.6	1	1735 124
36	2052	0.6	1	1879 173
37	1767	0.6	1	1651 116
38	1703	0.6	1	1599 104
39	1515	0.6	1	1428 87
40	1329	0.6	1	1235 94
41	1236	0.6	1	1112 124
42	1076	0.6	1	991 85
43	1307	0.6	1	1247 60
44	639	0.6	1	566 73
45	853	0.6	1	777 76
46	799	0.6	1	741 58
47	810	0.6	1	741 69
48	861	0.6	1	789 72
49	741	0.6	1	676 65
50	751	0.6	1	687 64
51	715	0.6	1	644 71
52	647	0.6	1	574 73
53	572	0.6	1	500 72
54	523	0.6	1	436 87
55	477	0.6	1	405 72
56	325	0.6	1	266 59
57	378	0.6	1	330 48
58	292	0.6	1	254 38
59	362	0.6	1	302 60
60	331	0.6	1	281 50
61	251	0.6	1	213 38
62	320	0.6	1	268 52
63	242	0.6	1	204 38
64	266	0.6	1	212 54
65	323	0.6	1	242 81
66	366	0.6	1	324 42
67	265	0.6	1	208 57
68	293	0.6	1	239 54
69	311	0.6	1	241 70
70	283	0.6	1	192 91
71	340	0.6	1	250 90
72	430	0.6	1	289 141
73	535	0.6	1	294 241
74	1071	0.6	1	394 677
75	11032	0.6	1	448 10584
76	20217	0.6	1	1415 18802
77	21589	0.6	1	2189 19400
78	17912	0.6	1	1769 16143
79	12905	0.6	1	1404 11501
80	9087	0.6	1	1001 8086
81	6011	0.6	1	739 5272
82	4239	0.6	1	553 3686
83	2735	0.6	1	449 2286
84	1935	0.6	1	365 1570
85	1581	0.6	1	358 1223
86	1353	0.6	1	325 1028
87	926	0.6	1	282 644
88	860	0.6	1	266 594
89	720	0.6	1	212 508
90	530	0.6	1	148 382
91	636	0.6	1	252 384
92	493	0.6	1	116 377
93	500	0.6	1	126 374
94	508	0.6	1	117 391
95	698	0.6	1	154 544
96	943	0.6	1	149 794
97	1335	0.6	1	297 1038
98	1615	0.6	1	142 1473
99	5106	0.6	1	81 5025
100	41473	0.6	1	237 41236


RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P08-ACTGAT-READ1-Sequences.txt.gz
=============================================
41291102 sequences processed in total