SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR546471_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: 21296). 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 SRR546471_2.fastq.gz
Processing single-end reads on 1 core ...
Finished in 2212.098 s (31.244 µs/read; 1.92 M reads/minute).

=== Summary ===

Total reads processed:              70,799,691
Reads with adapters:                36,121,202 (51.0%)
Reads written (passing filters):    70,799,691 (100.0%)

Total basepairs processed: 6,371,972,190 bp
Quality-trimmed:              97,584,075 bp (1.5%)
Total written (filtered):  6,193,677,286 bp (97.2%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36121202 times

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

Bases preceding removed adapters:
  A: 52.1%
  C: 18.9%
  G: 0.4%
  T: 28.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	33748938	17699922.8	0	33748938
2	92983	4424980.7	0	92983
3	89416	1106245.2	0	89416
4	83273	276561.3	0	83273
5	90596	69140.3	0	90596
6	67629	17285.1	0	67629
7	64447	4321.3	0	64447
8	75032	1080.3	0	75032
9	80858	270.1	0	80655 203
10	67754	67.5	1	66993 761
11	72848	16.9	1	71700 1148
12	63356	4.2	1	62370 986
13	67918	1.1	1	66750 1168
14	60037	1.1	1	59030 1007
15	62709	1.1	1	61520 1189
16	67739	1.1	1	66488 1251
17	60083	1.1	1	58997 1086
18	61149	1.1	1	60051 1098
19	56530	1.1	1	55573 957
20	58003	1.1	1	56812 1191
21	65091	1.1	1	63812 1279
22	55962	1.1	1	54974 988
23	50119	1.1	1	49219 900
24	48996	1.1	1	48248 748
25	50086	1.1	1	49159 927
26	54823	1.1	1	53612 1211
27	55756	1.1	1	54645 1111
28	46869	1.1	1	46015 854
29	51842	1.1	1	50958 884
30	42206	1.1	1	41530 676
31	36756	1.1	1	36180 576
32	35154	1.1	1	34629 525
33	33827	1.1	1	33270 557
34	35365	1.1	1	34829 536
35	30312	1.1	1	29831 481
36	31670	1.1	1	31152 518
37	29916	1.1	1	29376 540
38	29414	1.1	1	27873 1541
39	29298	1.1	1	28695 603
40	31552	1.1	1	31029 523
41	23858	1.1	1	23445 413
42	20337	1.1	1	19259 1078
43	22599	1.1	1	21566 1033
44	18925	1.1	1	18574 351
45	16525	1.1	1	16248 277
46	11402	1.1	1	10880 522
47	11338	1.1	1	11190 148
48	9024	1.1	1	8588 436
49	8101	1.1	1	7955 146
50	9733	1.1	1	9620 113
51	5512	1.1	1	5441 71
52	4083	1.1	1	4026 57
53	4101	1.1	1	4049 52
54	3584	1.1	1	3538 46
55	2481	1.1	1	2441 40
56	2114	1.1	1	2088 26
57	1853	1.1	1	1814 39
58	1823	1.1	1	1804 19
59	1079	1.1	1	1070 9
60	1067	1.1	1	1048 19
61	1287	1.1	1	1256 31
62	917	1.1	1	897 20
63	1344	1.1	1	1303 41
64	1654	1.1	1	1630 24
65	113	1.1	1	112 1
66	20	1.1	1	18 2
67	2	1.1	1	2
68	1	1.1	1	1
70	5	1.1	1	3 2
71	7	1.1	1	6 1
75	1	1.1	1	1

RUN STATISTICS FOR INPUT FILE: SRR546471_2.fastq.gz
=============================================
70799691 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 70799691

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 476907 (0.67%)