SUMMARISING RUN PARAMETERS
==========================
Input filename: A-15171-1.end2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.16
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; 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 sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1
Output file will be GZIP compressed


This is cutadapt 1.16 with Python 2.7.13
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA A-15171-1.end2.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 935.38 s (36 us/read; 1.65 M reads/minute).

=== Summary ===

Total reads processed:              25,789,699
Reads with adapters:                10,229,897 (39.7%)
Reads written (passing filters):    25,789,699 (100.0%)

Total basepairs processed: 1,627,130,474 bp
Quality-trimmed:                  71,881 bp (0.0%)
Total written (filtered):  1,609,439,424 bp (98.9%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 10229897 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 28.3%
  C: 27.5%
  G: 22.9%
  T: 21.3%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	8111889	6447424.8	0	8111889
2	1458286	1611856.2	0	1458286
3	364976	402964.0	0	364976
4	79410	100741.0	0	79410
5	20433	25185.3	0	20433
6	10723	6296.3	0	10723
7	4613	1574.1	0	4613
8	4027	393.5	0	4027
9	4103	98.4	0	3377 726
10	4088	24.6	1	2926 1162
11	4928	6.1	1	3060 1868
12	4182	1.5	1	3155 1027
13	3950	1.5	1	3247 703
14	4945	1.5	1	3125 1820
15	4485	1.5	1	2775 1710
16	3657	1.5	1	2734 923
17	3571	1.5	1	2806 765
18	3278	1.5	1	3014 264
19	4224	1.5	1	3657 567
20	4307	1.5	1	3699 608
21	4616	1.5	1	4272 344
22	5929	1.5	1	4538 1391
23	5986	1.5	1	5615 371
24	6582	1.5	1	6103 479
25	5098	1.5	1	4809 289
26	4217	1.5	1	3903 314
27	4099	1.5	1	3671 428
28	4574	1.5	1	4131 443
29	5187	1.5	1	4765 422
30	5720	1.5	1	5416 304
31	5808	1.5	1	5475 333
32	6019	1.5	1	5649 370
33	10662	1.5	1	10100 562
34	4761	1.5	1	4414 347
35	8454	1.5	1	8069 385
36	4372	1.5	1	4086 286
37	4224	1.5	1	3982 242
38	6707	1.5	1	6288 419
39	2013	1.5	1	1806 207
40	2803	1.5	1	2535 268
41	1261	1.5	1	1059 202
42	784	1.5	1	637 147
43	976	1.5	1	415 561
44	521	1.5	1	312 209
45	735	1.5	1	309 426
46	615	1.5	1	335 280
47	443	1.5	1	258 185
48	901	1.5	1	529 372
49	1006	1.5	1	752 254
50	2275	1.5	1	80 2195
51	412	1.5	1	13 399
52	344	1.5	1	9 335
53	564	1.5	1	4 560
54	102	1.5	1	0 102
55	495	1.5	1	2 493
56	234	1.5	1	4 230
57	177	1.5	1	1 176
58	450	1.5	1	5 445
59	350	1.5	1	2 348
60	1235	1.5	1	3 1232
61	169	1.5	1	4 165
62	251	1.5	1	17 234
63	459	1.5	1	4 455
64	103	1.5	1	0 103
65	146	1.5	1	3 143
66	134	1.5	1	3 131
67	258	1.5	1	5 253
68	373	1.5	1	3 370
69	76	1.5	1	2 74
70	73	1.5	1	7 66
71	49	1.5	1	3 46
72	83	1.5	1	4 79
73	413	1.5	1	6 407
74	125	1.5	1	35 90
75	1325	1.5	1	1112 213
76	74	1.5	1	8 66


RUN STATISTICS FOR INPUT FILE: A-15171-1.end2.fastq.gz
=============================================
25789699 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 25789699

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 20776 (0.08%)