SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR546473_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: 10729). 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 SRR546473_2.fastq.gz
Processing single-end reads on 1 core ...
Finished in 2593.154 s (32.897 µs/read; 1.82 M reads/minute).

=== Summary ===

Total reads processed:              78,826,347
Reads with adapters:                40,061,251 (50.8%)
Reads written (passing filters):    78,826,347 (100.0%)

Total basepairs processed: 7,094,371,230 bp
Quality-trimmed:             112,335,482 bp (1.6%)
Total written (filtered):  6,915,331,195 bp (97.5%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 40061251 times

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

Bases preceding removed adapters:
  A: 52.6%
  C: 17.9%
  G: 0.3%
  T: 29.2%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	38558109	19706586.8	0	38558109
2	68858	4926646.7	0	68858
3	65435	1231661.7	0	65435
4	58305	307915.4	0	58305
5	61014	76978.9	0	61014
6	47346	19244.7	0	47346
7	44364	4811.2	0	44364
8	50102	1202.8	0	50102
9	53237	300.7	0	53078 159
10	45222	75.2	1	44670 552
11	48242	18.8	1	47441 801
12	41762	4.7	1	41142 620
13	44469	1.2	1	43673 796
14	39648	1.2	1	38954 694
15	41157	1.2	1	40314 843
16	43308	1.2	1	42506 802
17	38973	1.2	1	38328 645
18	39458	1.2	1	38702 756
19	36003	1.2	1	35382 621
20	36383	1.2	1	35663 720
21	39745	1.2	1	38973 772
22	34917	1.2	1	34300 617
23	31353	1.2	1	30792 561
24	30408	1.2	1	29931 477
25	30141	1.2	1	29527 614
26	32551	1.2	1	31872 679
27	32329	1.2	1	31670 659
28	28484	1.2	1	27924 560
29	29929	1.2	1	29348 581
30	24980	1.2	1	24598 382
31	21847	1.2	1	21494 353
32	20511	1.2	1	20211 300
33	19350	1.2	1	19039 311
34	20268	1.2	1	19929 339
35	17809	1.2	1	17517 292
36	17900	1.2	1	17615 285
37	17003	1.2	1	16681 322
38	16468	1.2	1	16172 296
39	16291	1.2	1	15991 300
40	17034	1.2	1	16724 310
41	13018	1.2	1	12811 207
42	11537	1.2	1	11334 203
43	12245	1.2	1	11996 249
44	10441	1.2	1	10005 436
45	9410	1.2	1	9026 384
46	6345	1.2	1	6228 117
47	6507	1.2	1	6386 121
48	4921	1.2	1	4741 180
49	4265	1.2	1	4182 83
50	5352	1.2	1	5174 178
51	3009	1.2	1	2962 47
52	2183	1.2	1	2104 79
53	2240	1.2	1	2156 84
54	1934	1.2	1	1861 73
55	1251	1.2	1	1205 46
56	1162	1.2	1	1151 11
57	922	1.2	1	907 15
58	865	1.2	1	854 11
59	462	1.2	1	453 9
60	454	1.2	1	441 13
61	520	1.2	1	501 19
62	395	1.2	1	385 10
63	518	1.2	1	498 20
64	523	1.2	1	517 6
65	35	1.2	1	33 2
66	12	1.2	1	12
67	1	1.2	1	1
69	1	1.2	1	1
70	4	1.2	1	4
71	4	1.2	1	4
72	1	1.2	1	1
75	1	1.2	1	1

RUN STATISTICS FOR INPUT FILE: SRR546473_2.fastq.gz
=============================================
78826347 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 78826347

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 540668 (0.69%)