SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_17_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 Illumina: 0, count smallRNA: 0, count Nextera: 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_17_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 211.743 s (3.687 µs/read; 16.27 M reads/minute).

=== Summary ===

Total reads processed:              57,429,743
Reads with adapters:                12,617,361 (22.0%)
Reads written (passing filters):    57,429,743 (100.0%)

Total basepairs processed: 6,011,277,780 bp
Quality-trimmed:               1,504,005 bp (0.0%)
Total written (filtered):  5,995,998,237 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12617361 times

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

Bases preceding removed adapters:
  A: 48.0%
  C: 11.4%
  G: 6.0%
  T: 34.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	12117776	14357435.8	0	12117776
2	14284	3589358.9	0	14284
3	313526	897339.7	0	313526
4	170886	224334.9	0	170886
5	762	56083.7	0	762
6	8	14020.9	0	8
7	7	3505.2	0	7
8	2	876.3	0	2
9	4	219.1	0	2 2
10	56	54.8	1	1 55
11	47	13.7	1	0 47
12	3	3.4	1	0 3

RUN STATISTICS FOR INPUT FILE: zr3644_17_2.fastq.gz
=============================================
57429743 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 57429743

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 23755 (0.04%)