SUMMARISING RUN PARAMETERS
==========================
Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P11-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/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-P11-GAGTGG-READ1-Sequences.txt.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 868.13 s (20 us/read; 3.01 M reads/minute).

=== Summary ===

Total reads processed:              43,493,444
Reads with adapters:                16,896,044 (38.8%)
Reads written (passing filters):    43,493,444 (100.0%)

Total basepairs processed: 4,349,344,400 bp
Quality-trimmed:              17,521,483 bp (0.4%)
Total written (filtered):  4,252,103,759 bp (97.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16896044 times.

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

Bases preceding removed adapters:
  A: 36.3%
  C: 25.5%
  G: 17.6%
  T: 17.5%
  none/other: 3.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11830295	10873361.0	0	11830295
2	2725990	2718340.2	0	2725990
3	876296	679585.1	0	876296
4	243559	169896.3	0	243559
5	82882	42474.1	0	82882
6	44480	10618.5	0	44480
7	36912	2654.6	0	36912
8	33011	663.7	0	33011
9	31482	165.9	0	30418 1064
10	34474	41.5	1	28061 6413
11	27071	10.4	1	25104 1967
12	25327	2.6	1	23917 1410
13	23491	0.6	1	22278 1213
14	21624	0.6	1	20466 1158
15	21071	0.6	1	19891 1180
16	19142	0.6	1	18057 1085
17	18461	0.6	1	17460 1001
18	17398	0.6	1	16390 1008
19	15821	0.6	1	14886 935
20	14590	0.6	1	13802 788
21	13565	0.6	1	12806 759
22	12033	0.6	1	11335 698
23	11048	0.6	1	10439 609
24	10067	0.6	1	9432 635
25	9388	0.6	1	8907 481
26	8791	0.6	1	8349 442
27	8313	0.6	1	7835 478
28	7798	0.6	1	7354 444
29	7260	0.6	1	6842 418
30	7002	0.6	1	6625 377
31	6574	0.6	1	6221 353
32	6207	0.6	1	5857 350
33	5464	0.6	1	5165 299
34	5408	0.6	1	5063 345
35	5302	0.6	1	5001 301
36	4847	0.6	1	4465 382
37	5124	0.6	1	4484 640
38	4208	0.6	1	3949 259
39	3686	0.6	1	3427 259
40	3484	0.6	1	3226 258
41	3348	0.6	1	3102 246
42	2652	0.6	1	2447 205
43	3564	0.6	1	3338 226
44	1373	0.6	1	1262 111
45	2117	0.6	1	1974 143
46	2187	0.6	1	2031 156
47	2271	0.6	1	2096 175
48	2347	0.6	1	2170 177
49	2229	0.6	1	2083 146
50	2125	0.6	1	1956 169
51	2176	0.6	1	2019 157
52	1953	0.6	1	1799 154
53	1842	0.6	1	1679 163
54	1683	0.6	1	1510 173
55	1700	0.6	1	1527 173
56	1234	0.6	1	1099 135
57	1180	0.6	1	1076 104
58	1085	0.6	1	967 118
59	1060	0.6	1	950 110
60	971	0.6	1	897 74
61	874	0.6	1	792 82
62	918	0.6	1	803 115
63	769	0.6	1	664 105
64	785	0.6	1	656 129
65	922	0.6	1	674 248
66	753	0.6	1	612 141
67	702	0.6	1	578 124
68	813	0.6	1	662 151
69	827	0.6	1	673 154
70	870	0.6	1	661 209
71	944	0.6	1	641 303
72	1120	0.6	1	608 512
73	1799	0.6	1	713 1086
74	3883	0.6	1	748 3135
75	48006	0.6	1	916 47090
76	80426	0.6	1	2421 78005
77	74744	0.6	1	3327 71417
78	56889	0.6	1	2622 54267
79	37949	0.6	1	1941 36008
80	25623	0.6	1	1342 24281
81	16392	0.6	1	985 15407
82	11313	0.6	1	688 10625
83	6786	0.6	1	560 6226
84	4646	0.6	1	405 4241
85	3842	0.6	1	432 3410
86	3050	0.6	1	371 2679
87	2372	0.6	1	345 2027
88	1952	0.6	1	299 1653
89	1596	0.6	1	282 1314
90	1383	0.6	1	205 1178
91	1349	0.6	1	261 1088
92	1259	0.6	1	160 1099
93	1302	0.6	1	148 1154
94	1383	0.6	1	126 1257
95	1813	0.6	1	148 1665
96	2385	0.6	1	144 2241
97	3541	0.6	1	287 3254
98	4648	0.6	1	131 4517
99	16578	0.6	1	194 16384
100	140795	0.6	1	251 140544


RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P11-GAGTGG-READ1-Sequences.txt.gz
=============================================
43493444 sequences processed in total