SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_20_2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.10
Cutadapt version: 4.9
Python version: could not detect
Number of cores used for trimming: 8
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Unable to auto-detect most prominent adapter from the first specified file (count Nextera: 0, count smallRNA: 0, count Illumina: 0)
Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
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 4.9 with Python 3.12.8
Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr3644_20_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 198.127 s (3.711 µs/read; 16.17 M reads/minute).

=== Summary ===

Total reads processed:              53,390,071
Reads with adapters:                11,641,581 (21.8%)
Reads written (passing filters):    53,390,071 (100.0%)

Total basepairs processed: 5,654,746,380 bp
Quality-trimmed:               1,085,705 bp (0.0%)
Total written (filtered):  5,640,947,601 bp (99.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11641581 times

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

Bases preceding removed adapters:
  A: 48.0%
  C: 10.9%
  G: 6.0%
  T: 35.1%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11182496	13347517.8	0	11182496
2	10563	3336879.4	0	10563
3	285899	834219.9	0	285899
4	161927	208555.0	0	161927
5	585	52138.7	0	585
6	4	13034.7	0	4
7	2	3258.7	0	2
8	3	814.7	0	3
9	2	203.7	0	0 2
10	59	50.9	1	0 59
11	40	12.7	1	0 40
12	1	3.2	1	0 1

RUN STATISTICS FOR INPUT FILE: zr3644_20_2.fastq.gz
=============================================
53390071 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 53390071

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 14088 (0.03%)