SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_18_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_18_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 191.662 s (3.762 µs/read; 15.95 M reads/minute).

=== Summary ===

Total reads processed:              50,943,423
Reads with adapters:                11,203,734 (22.0%)
Reads written (passing filters):    50,943,423 (100.0%)

Total basepairs processed: 5,335,048,821 bp
Quality-trimmed:               1,318,749 bp (0.0%)
Total written (filtered):  5,321,501,542 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11203734 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: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10761847	12735855.8	0	10761847
2	12427	3183963.9	0	12427
3	277326	795991.0	0	277326
4	151352	198997.7	0	151352
5	678	49749.4	0	678
6	4	12437.4	0	4
7	4	3109.3	0	4
8	2	777.3	0	2
9	3	194.3	0	0 3
10	49	48.6	1	0 49
11	36	12.1	1	0 36
12	6	3.0	1	0 6

RUN STATISTICS FOR INPUT FILE: zr3644_18_2.fastq.gz
=============================================
50943423 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 50943423

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 18577 (0.04%)