SUMMARISING RUN PARAMETERS
==========================
Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P05-GAGTGG-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/porites/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/porites/4R041-L7-P05-GAGTGG-READ1-Sequences.txt.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 536.88 s (20 us/read; 2.99 M reads/minute).

=== Summary ===

Total reads processed:              26,724,234
Reads with adapters:                10,486,555 (39.2%)
Reads written (passing filters):    26,724,234 (100.0%)

Total basepairs processed: 2,672,423,400 bp
Quality-trimmed:              16,508,006 bp (0.6%)
Total written (filtered):  2,587,883,920 bp (96.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10486555 times.

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

Bases preceding removed adapters:
  A: 35.5%
  C: 25.2%
  G: 16.0%
  T: 18.2%
  none/other: 5.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	7211785	6681058.5	0	7211785
2	1603420	1670264.6	0	1603420
3	502061	417566.2	0	502061
4	137281	104391.5	0	137281
5	51475	26097.9	0	51475
6	30001	6524.5	0	30001
7	26169	1631.1	0	26169
8	23638	407.8	0	23638
9	22327	101.9	0	21914 413
10	23967	25.5	1	20695 3272
11	19521	6.4	1	18461 1060
12	17758	1.6	1	16909 849
13	17054	0.4	1	16229 825
14	15600	0.4	1	14887 713
15	15199	0.4	1	14522 677
16	14210	0.4	1	13608 602
17	13475	0.4	1	12803 672
18	13394	0.4	1	12772 622
19	11958	0.4	1	11423 535
20	11038	0.4	1	10528 510
21	9903	0.4	1	9388 515
22	9158	0.4	1	8681 477
23	8508	0.4	1	8074 434
24	7687	0.4	1	7236 451
25	6887	0.4	1	6540 347
26	6856	0.4	1	6486 370
27	6493	0.4	1	6182 311
28	6337	0.4	1	6029 308
29	5722	0.4	1	5446 276
30	5394	0.4	1	5103 291
31	5275	0.4	1	5019 256
32	4901	0.4	1	4608 293
33	4533	0.4	1	4298 235
34	4291	0.4	1	4077 214
35	4136	0.4	1	3877 259
36	3741	0.4	1	3486 255
37	4071	0.4	1	3631 440
38	3129	0.4	1	2937 192
39	3089	0.4	1	2849 240
40	2942	0.4	1	2744 198
41	2573	0.4	1	2390 183
42	2110	0.4	1	1983 127
43	2890	0.4	1	2745 145
44	1162	0.4	1	1077 85
45	1723	0.4	1	1612 111
46	1679	0.4	1	1582 97
47	1905	0.4	1	1761 144
48	1874	0.4	1	1764 110
49	1901	0.4	1	1795 106
50	1771	0.4	1	1659 112
51	1864	0.4	1	1750 114
52	1731	0.4	1	1582 149
53	1535	0.4	1	1416 119
54	1339	0.4	1	1204 135
55	1347	0.4	1	1231 116
56	888	0.4	1	808 80
57	996	0.4	1	908 88
58	888	0.4	1	821 67
59	786	0.4	1	727 59
60	727	0.4	1	659 68
61	815	0.4	1	752 63
62	681	0.4	1	616 65
63	581	0.4	1	515 66
64	676	0.4	1	590 86
65	716	0.4	1	514 202
66	605	0.4	1	515 90
67	613	0.4	1	529 84
68	587	0.4	1	488 99
69	628	0.4	1	496 132
70	750	0.4	1	536 214
71	734	0.4	1	459 275
72	907	0.4	1	476 431
73	1510	0.4	1	504 1006
74	3436	0.4	1	529 2907
75	53016	0.4	1	777 52239
76	76935	0.4	1	1889 75046
77	73954	0.4	1	2706 71248
78	59704	0.4	1	2061 57643
79	35471	0.4	1	1514 33957
80	24120	0.4	1	1026 23094
81	15842	0.4	1	719 15123
82	10769	0.4	1	485 10284
83	6440	0.4	1	432 6008
84	4174	0.4	1	315 3859
85	3430	0.4	1	265 3165
86	2791	0.4	1	264 2527
87	2100	0.4	1	250 1850
88	1776	0.4	1	205 1571
89	1577	0.4	1	168 1409
90	1389	0.4	1	167 1222
91	1233	0.4	1	218 1015
92	1119	0.4	1	123 996
93	1196	0.4	1	99 1097
94	1438	0.4	1	94 1344
95	1639	0.4	1	114 1525
96	2274	0.4	1	108 2166
97	3385	0.4	1	228 3157
98	4572	0.4	1	130 4442
99	16559	0.4	1	162 16397
100	140340	0.4	1	501 139839


RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P05-GAGTGG-READ1-Sequences.txt.gz
=============================================
26724234 sequences processed in total