SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_4_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_4_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 191.401 s (3.882 µs/read; 15.46 M reads/minute).

=== Summary ===

Total reads processed:              49,306,248
Reads with adapters:                10,876,701 (22.1%)
Reads written (passing filters):    49,306,248 (100.0%)

Total basepairs processed: 5,196,883,196 bp
Quality-trimmed:               1,144,034 bp (0.0%)
Total written (filtered):  5,183,912,909 bp (99.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10876701 times

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

Bases preceding removed adapters:
  A: 48.3%
  C: 11.2%
  G: 5.7%
  T: 34.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10468383	12326562.0	0	10468383
2	10557	3081640.5	0	10557
3	255543	770410.1	0	255543
4	141508	192602.5	0	141508
5	602	48150.6	0	602
6	5	12037.7	0	5
7	4	3009.4	0	4
8	1	752.4	0	1
9	9	188.1	0	0 9
10	44	47.0	1	0 44
11	42	11.8	1	0 42
12	3	2.9	1	0 3

RUN STATISTICS FOR INPUT FILE: zr3644_4_2.fastq.gz
=============================================
49306248 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 49306248

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 14817 (0.03%)