
SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR3192400_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 SRR3192400_2.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 2198.06 s (23 us/read; 2.61 M reads/minute).

=== Summary ===

Total reads processed:              95,791,942
Reads with adapters:                36,966,867 (38.6%)
Reads written (passing filters):    95,791,942 (100.0%)

Total basepairs processed: 9,579,194,200 bp
Quality-trimmed:             459,057,679 bp (4.8%)
Total written (filtered):  8,893,887,057 bp (92.8%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 36966867 times.

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

Bases preceding removed adapters:
  A: 19.0%
  C: 32.4%
  G: 24.0%
  T: 24.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	19223579	23947985.5	0	19223579
2	5928936	5986996.4	0	5928936
3	2345857	1496749.1	0	2345857
4	771017	374187.3	0	771017
5	492222	93546.8	0	492222
6	425050	23386.7	0	425050
7	381856	5846.7	0	381856
8	406812	1461.7	0	406812
9	446449	365.4	0	443507 2942
10	386155	91.4	1	381466 4689
11	395176	22.8	1	391286 3890
12	387150	5.7	1	384113 3037
13	346829	5.7	1	344319 2510
14	338762	5.7	1	336107 2655
15	261955	5.7	1	259778 2177
16	240099	5.7	1	237878 2221
17	204167	5.7	1	202277 1890
18	166340	5.7	1	164723 1617
19	180625	5.7	1	178600 2025
20	165988	5.7	1	164217 1771
21	159350	5.7	1	157754 1596
22	162796	5.7	1	160834 1962
23	133784	5.7	1	132320 1464
24	141625	5.7	1	140203 1422
25	129943	5.7	1	128101 1842
26	115900	5.7	1	114194 1706
27	115919	5.7	1	114337 1582
28	143758	5.7	1	141697 2061
29	147927	5.7	1	145993 1934
30	90487	5.7	1	88917 1570
31	106596	5.7	1	105175 1421
32	113111	5.7	1	110962 2149
33	97734	5.7	1	96224 1510
34	94392	5.7	1	93117 1275
35	142349	5.7	1	140657 1692
36	88319	5.7	1	86671 1648
37	92268	5.7	1	90496 1772
38	77211	5.7	1	76084 1127
39	97240	5.7	1	95708 1532
40	59252	5.7	1	58194 1058
41	79530	5.7	1	78068 1462
42	227324	5.7	1	224144 3180
43	14087	5.7	1	13556 531
44	52570	5.7	1	51364 1206
45	28034	5.7	1	27359 675
46	34384	5.7	1	33409 975
47	42698	5.7	1	41884 814
48	41544	5.7	1	40849 695
49	45470	5.7	1	44608 862
50	41237	5.7	1	40424 813
51	46203	5.7	1	45329 874
52	45479	5.7	1	44297 1182
53	50707	5.7	1	49408 1299
54	85236	5.7	1	83320 1916
55	23527	5.7	1	22683 844
56	39957	5.7	1	38762 1195
57	51866	5.7	1	50252 1614
58	18044	5.7	1	17475 569
59	19367	5.7	1	18598 769
60	18528	5.7	1	17825 703
61	20929	5.7	1	20304 625
62	25842	5.7	1	24811 1031
63	28351	5.7	1	27556 795
64	12310	5.7	1	11804 506
65	6907	5.7	1	6440 467
66	6151	5.7	1	5707 444
67	5948	5.7	1	5064 884
68	3820	5.7	1	3399 421
69	3615	5.7	1	3088 527
70	3972	5.7	1	3664 308
71	4429	5.7	1	4084 345
72	5681	5.7	1	4956 725
73	5463	5.7	1	5029 434
74	6081	5.7	1	2341 3740
75	1266	5.7	1	539 727
76	775	5.7	1	405 370
77	1556	5.7	1	457 1099
78	489	5.7	1	185 304
79	938	5.7	1	110 828
80	350	5.7	1	33 317
81	410	5.7	1	5 405
82	811	5.7	1	9 802
83	324	5.7	1	1 323
84	2192	5.7	1	6 2186
85	408	5.7	1	3 405
86	331	5.7	1	0 331
87	854	5.7	1	0 854
88	290	5.7	1	1 289
89	319	5.7	1	0 319
90	450	5.7	1	4 446
91	489	5.7	1	0 489
92	1646	5.7	1	5 1641
93	182	5.7	1	1 181
94	313	5.7	1	0 313
95	109	5.7	1	1 108
96	232	5.7	1	1 231
97	1053	5.7	1	2 1051
98	327	5.7	1	0 327
99	368	5.7	1	0 368
100	109	5.7	1	0 109


RUN STATISTICS FOR INPUT FILE: SRR3192400_2.fastq.gz
=============================================
95791942 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 95791942

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 866463 (0.90%)
