SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR546474_2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.10
Cutadapt version: 4.2
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Using Illumina adapter for trimming (count: 3595). Second best hit was Nextera (count: 0)
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
Output file will be GZIP compressed


This is cutadapt 4.2 with Python 3.10.8
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR546474_2.fastq.gz
Processing single-end reads on 1 core ...
Finished in 2480.783 s (32.129 µs/read; 1.87 M reads/minute).

=== Summary ===

Total reads processed:              77,213,856
Reads with adapters:                38,809,726 (50.3%)
Reads written (passing filters):    77,213,856 (100.0%)

Total basepairs processed: 6,949,247,040 bp
Quality-trimmed:             164,918,292 bp (2.4%)
Total written (filtered):  6,737,075,150 bp (96.9%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 38809726 times

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

Bases preceding removed adapters:
  A: 53.0%
  C: 17.3%
  G: 0.3%
  T: 29.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	38305781	19303464.0	0	38305781
2	32652	4825866.0	0	32652
3	29306	1206466.5	0	29306
4	24931	301616.6	0	24931
5	26569	75404.2	0	26569
6	14118	18851.0	0	14118
7	12966	4712.8	0	12966
8	16041	1178.2	0	16041
9	17960	294.5	0	17923 37
10	13643	73.6	1	13438 205
11	14987	18.4	1	14545 442
12	12225	4.6	1	11989 236
13	13278	1.2	1	12952 326
14	11761	1.2	1	11511 250
15	12652	1.2	1	12284 368
16	14254	1.2	1	13755 499
17	11726	1.2	1	11424 302
18	12854	1.2	1	12430 424
19	11098	1.2	1	10825 273
20	12619	1.2	1	12166 453
21	13954	1.2	1	13473 481
22	11074	1.2	1	10789 285
23	9493	1.2	1	9266 227
24	9055	1.2	1	8856 199
25	9174	1.2	1	8940 234
26	10204	1.2	1	9907 297
27	10372	1.2	1	10086 286
28	8639	1.2	1	8435 204
29	9282	1.2	1	9034 248
30	7488	1.2	1	7334 154
31	6676	1.2	1	6524 152
32	6283	1.2	1	6171 112
33	6345	1.2	1	6227 118
34	6314	1.2	1	6175 139
35	5270	1.2	1	5154 116
36	5562	1.2	1	5457 105
37	5327	1.2	1	5223 104
38	5183	1.2	1	5041 142
39	5413	1.2	1	5250 163
40	5890	1.2	1	5727 163
41	3872	1.2	1	3777 95
42	3290	1.2	1	3221 69
43	3869	1.2	1	3789 80
44	3034	1.2	1	2959 75
45	2498	1.2	1	2463 35
46	2080	1.2	1	2046 34
47	1937	1.2	1	1887 50
48	1569	1.2	1	1546 23
49	1412	1.2	1	1380 32
50	1566	1.2	1	1540 26
51	1032	1.2	1	1016 16
52	891	1.2	1	877 14
53	808	1.2	1	793 15
54	666	1.2	1	649 17
55	533	1.2	1	526 7
56	457	1.2	1	449 8
57	349	1.2	1	342 7
58	312	1.2	1	308 4
59	188	1.2	1	183 5
60	177	1.2	1	172 5
61	187	1.2	1	179 8
62	132	1.2	1	126 6
63	131	1.2	1	125 6
64	269	1.2	1	260 9
65	34	1.2	1	34
66	10	1.2	1	10
67	2	1.2	1	2
70	1	1.2	1	1
71	1	1.2	1	1

RUN STATISTICS FOR INPUT FILE: SRR546474_2.fastq.gz
=============================================
77213856 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 77213856

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1008780 (1.31%)