SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_19_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 Illumina: 0, count smallRNA: 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_19_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 181.025 s (3.722 µs/read; 16.12 M reads/minute).

=== Summary ===

Total reads processed:              48,641,567
Reads with adapters:                10,698,385 (22.0%)
Reads written (passing filters):    48,641,567 (100.0%)

Total basepairs processed: 5,104,109,532 bp
Quality-trimmed:               1,449,787 bp (0.0%)
Total written (filtered):  5,090,975,285 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10698385 times

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

Bases preceding removed adapters:
  A: 48.1%
  C: 11.3%
  G: 6.0%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10272320	12160391.8	0	10272320
2	13188	3040097.9	0	13188
3	267040	760024.5	0	267040
4	145073	190006.1	0	145073
5	650	47501.5	0	650
6	16	11875.4	0	16
7	3	2968.8	0	3
8	2	742.2	0	2
9	4	185.6	0	1 3
10	48	46.4	1	0 48
11	39	11.6	1	0 39
12	2	2.9	1	0 2

RUN STATISTICS FOR INPUT FILE: zr3644_19_2.fastq.gz
=============================================
48641567 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 48641567

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 19087 (0.04%)