
SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR3192401_2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.1
Cutadapt version: 1.9.1
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
Running FastQC on the data once trimming has completed
Output file will be GZIP compressed


This is cutadapt 1.9.1 with Python 2.7.6
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA SRR3192401_2.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 2151.00 s (22 us/read; 2.67 M reads/minute).

=== Summary ===

Total reads processed:              95,735,344
Reads with adapters:                38,037,448 (39.7%)
Reads written (passing filters):    95,735,344 (100.0%)

Total basepairs processed: 9,573,534,400 bp
Quality-trimmed:             328,931,711 bp (3.4%)
Total written (filtered):  8,974,093,171 bp (93.7%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 38037448 times.

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

Bases preceding removed adapters:
  A: 18.7%
  C: 32.6%
  G: 24.0%
  T: 24.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	18994292	23933836.0	0	18994292
2	5857733	5983459.0	0	5857733
3	2296990	1495864.8	0	2296990
4	758450	373966.2	0	758450
5	495196	93491.5	0	495196
6	423881	23372.9	0	423881
7	385943	5843.2	0	385943
8	412898	1460.8	0	412898
9	445517	365.2	0	442559 2958
10	395118	91.3	1	390548 4570
11	399678	22.8	1	395958 3720
12	395485	5.7	1	392574 2911
13	341547	5.7	1	339210 2337
14	323004	5.7	1	320444 2560
15	282795	5.7	1	280436 2359
16	266409	5.7	1	264066 2343
17	243983	5.7	1	241975 2008
18	239757	5.7	1	237715 2042
19	261017	5.7	1	258589 2428
20	227818	5.7	1	225600 2218
21	232894	5.7	1	231013 1881
22	230583	5.7	1	228083 2500
23	187494	5.7	1	185692 1802
24	198719	5.7	1	196943 1776
25	175321	5.7	1	173048 2273
26	165554	5.7	1	163498 2056
27	164063	5.7	1	162153 1910
28	197382	5.7	1	194871 2511
29	202125	5.7	1	199801 2324
30	122210	5.7	1	120172 2038
31	142664	5.7	1	141005 1659
32	136400	5.7	1	133915 2485
33	117967	5.7	1	116185 1782
34	151714	5.7	1	149898 1816
35	128081	5.7	1	126545 1536
36	123745	5.7	1	121822 1923
37	90063	5.7	1	88228 1835
38	86248	5.7	1	85108 1140
39	91962	5.7	1	90577 1385
40	112038	5.7	1	110416 1622
41	101085	5.7	1	99421 1664
42	135220	5.7	1	133295 1925
43	90993	5.7	1	89770 1223
44	101064	5.7	1	99304 1760
45	75598	5.7	1	74423 1175
46	74472	5.7	1	72938 1534
47	69362	5.7	1	68274 1088
48	71036	5.7	1	70024 1012
49	80279	5.7	1	79084 1195
50	62878	5.7	1	61861 1017
51	63598	5.7	1	62486 1112
52	61750	5.7	1	60294 1456
53	60872	5.7	1	59363 1509
54	88690	5.7	1	86625 2065
55	35845	5.7	1	34833 1012
56	48906	5.7	1	47684 1222
57	55573	5.7	1	53831 1742
58	25399	5.7	1	24673 726
59	27121	5.7	1	26242 879
60	24099	5.7	1	23306 793
61	25352	5.7	1	24593 759
62	30033	5.7	1	28891 1142
63	28567	5.7	1	27649 918
64	13684	5.7	1	13149 535
65	7743	5.7	1	7288 455
66	6835	5.7	1	6407 428
67	6827	5.7	1	5825 1002
68	4746	5.7	1	4324 422
69	4905	5.7	1	4284 621
70	5418	5.7	1	5087 331
71	5876	5.7	1	5498 378
72	7118	5.7	1	6293 825
73	6673	5.7	1	6215 458
74	7018	5.7	1	2679 4339
75	1435	5.7	1	584 851
76	836	5.7	1	456 380
77	1819	5.7	1	578 1241
78	565	5.7	1	258 307
79	1085	5.7	1	118 967
80	358	5.7	1	43 315
81	417	5.7	1	4 413
82	927	5.7	1	8 919
83	350	5.7	1	2 348
84	2557	5.7	1	5 2552
85	449	5.7	1	4 445
86	337	5.7	1	1 336
87	965	5.7	1	0 965
88	286	5.7	1	2 284
89	370	5.7	1	0 370
90	421	5.7	1	5 416
91	448	5.7	1	3 445
92	1701	5.7	1	5 1696
93	204	5.7	1	0 204
94	322	5.7	1	0 322
95	118	5.7	1	0 118
96	183	5.7	1	0 183
97	1077	5.7	1	1 1076
98	340	5.7	1	0 340
99	408	5.7	1	0 408
100	97	5.7	1	0 97


RUN STATISTICS FOR INPUT FILE: SRR3192401_2.fastq.gz
=============================================
95735344 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 95735344

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 498707 (0.52%)
