SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_20_1.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_1.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 229.147 s (4.292 µs/read; 13.98 M reads/minute).

=== Summary ===

Total reads processed:              53,390,071
Reads with adapters:                11,871,545 (22.2%)
Reads written (passing filters):    53,390,071 (100.0%)

Total basepairs processed: 5,643,601,239 bp
Quality-trimmed:               1,699,620 bp (0.0%)
Total written (filtered):  5,628,931,774 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11871545 times

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

Bases preceding removed adapters:
  A: 47.4%
  C: 11.9%
  G: 6.1%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11380348	13347517.8	0	11380348
2	38677	3336879.4	0	38677
3	299891	834219.9	0	299891
4	151300	208555.0	0	151300
5	1192	52138.7	0	1192
6	20	13034.7	0	20
7	5	3258.7	0	5
8	2	814.7	0	2
9	9	203.7	0	1 8
10	55	50.9	1	0 55
11	44	12.7	1	1 43
12	2	3.2	1	0 2

RUN STATISTICS FOR INPUT FILE: zr3644_20_1.fastq.gz
=============================================
53390071 sequences processed in total