SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_13_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 smallRNA: 0, count Nextera: 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_13_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 204.571 s (3.838 µs/read; 15.63 M reads/minute).

=== Summary ===

Total reads processed:              53,303,436
Reads with adapters:                11,790,806 (22.1%)
Reads written (passing filters):    53,303,436 (100.0%)

Total basepairs processed: 5,645,188,934 bp
Quality-trimmed:               1,514,110 bp (0.0%)
Total written (filtered):  5,630,822,049 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11790806 times

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

Bases preceding removed adapters:
  A: 48.4%
  C: 11.2%
  G: 5.8%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11332259	13325859.0	0	11332259
2	13372	3331464.8	0	13372
3	288409	832866.2	0	288409
4	155917	208216.5	0	155917
5	719	52054.1	0	719
6	13	13013.5	0	13
7	3	3253.4	0	3
9	7	203.3	0	0 7
10	61	50.8	1	0 61
11	42	12.7	1	0 42
12	4	3.2	1	0 4

RUN STATISTICS FOR INPUT FILE: zr3644_13_2.fastq.gz
=============================================
53303436 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 53303436

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 20356 (0.04%)