SUMMARISING RUN PARAMETERS
==========================
Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P03-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/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-P03-ACTGAT-READ1-Sequences.txt.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 460.43 s (20 us/read; 3.03 M reads/minute).

=== Summary ===

Total reads processed:              23,215,719
Reads with adapters:                 8,194,852 (35.3%)
Reads written (passing filters):    23,215,719 (100.0%)

Total basepairs processed: 2,321,571,900 bp
Quality-trimmed:               5,207,744 bp (0.2%)
Total written (filtered):  2,292,790,871 bp (98.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8194852 times.

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

Bases preceding removed adapters:
  A: 34.6%
  C: 28.5%
  G: 16.5%
  T: 19.2%
  none/other: 1.3%

Overview of removed sequences
length	count	expect	max.err	error counts
1	6038992	5803929.8	0	6038992
2	1352531	1450982.4	0	1352531
3	379888	362745.6	0	379888
4	97837	90686.4	0	97837
5	31884	22671.6	0	31884
6	14491	5667.9	0	14491
7	11346	1417.0	0	11346
8	10207	354.2	0	10207
9	9872	88.6	0	9494 378
10	10524	22.1	1	8528 1996
11	8358	5.5	1	7760 598
12	7763	1.4	1	7297 466
13	7288	0.3	1	6847 441
14	6636	0.3	1	6272 364
15	6517	0.3	1	6143 374
16	6035	0.3	1	5741 294
17	5754	0.3	1	5469 285
18	5542	0.3	1	5220 322
19	4796	0.3	1	4557 239
20	4421	0.3	1	4156 265
21	4150	0.3	1	3875 275
22	3675	0.3	1	3448 227
23	3405	0.3	1	3197 208
24	3108	0.3	1	2926 182
25	2867	0.3	1	2705 162
26	2654	0.3	1	2502 152
27	2554	0.3	1	2380 174
28	2503	0.3	1	2347 156
29	2337	0.3	1	2189 148
30	2215	0.3	1	2064 151
31	1968	0.3	1	1857 111
32	1898	0.3	1	1766 132
33	1703	0.3	1	1606 97
34	1818	0.3	1	1699 119
35	1567	0.3	1	1441 126
36	1595	0.3	1	1457 138
37	1399	0.3	1	1272 127
38	1386	0.3	1	1285 101
39	1241	0.3	1	1148 93
40	1096	0.3	1	1019 77
41	1067	0.3	1	976 91
42	863	0.3	1	803 60
43	1117	0.3	1	1044 73
44	476	0.3	1	427 49
45	650	0.3	1	594 56
46	673	0.3	1	625 48
47	750	0.3	1	687 63
48	730	0.3	1	668 62
49	690	0.3	1	635 55
50	698	0.3	1	643 55
51	651	0.3	1	590 61
52	496	0.3	1	445 51
53	532	0.3	1	472 60
54	490	0.3	1	431 59
55	447	0.3	1	399 48
56	316	0.3	1	277 39
57	336	0.3	1	300 36
58	293	0.3	1	247 46
59	309	0.3	1	268 41
60	286	0.3	1	249 37
61	268	0.3	1	238 30
62	228	0.3	1	197 31
63	258	0.3	1	223 35
64	233	0.3	1	197 36
65	240	0.3	1	202 38
66	260	0.3	1	223 37
67	227	0.3	1	200 27
68	238	0.3	1	185 53
69	261	0.3	1	218 43
70	290	0.3	1	241 49
71	294	0.3	1	228 66
72	338	0.3	1	216 122
73	448	0.3	1	243 205
74	732	0.3	1	286 446
75	8248	0.3	1	346 7902
76	13400	0.3	1	917 12483
77	14730	0.3	1	1375 13355
78	12864	0.3	1	1066 11798
79	8187	0.3	1	984 7203
80	5871	0.3	1	637 5234
81	3977	0.3	1	469 3508
82	2808	0.3	1	327 2481
83	1759	0.3	1	301 1458
84	1233	0.3	1	213 1020
85	992	0.3	1	176 816
86	862	0.3	1	201 661
87	608	0.3	1	167 441
88	499	0.3	1	117 382
89	433	0.3	1	122 311
90	408	0.3	1	114 294
91	371	0.3	1	133 238
92	341	0.3	1	94 247
93	328	0.3	1	83 245
94	392	0.3	1	65 327
95	418	0.3	1	75 343
96	560	0.3	1	78 482
97	851	0.3	1	146 705
98	1042	0.3	1	78 964
99	3418	0.3	1	43 3375
100	28246	0.3	1	60 28186


RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P03-ACTGAT-READ1-Sequences.txt.gz
=============================================
23215719 sequences processed in total