SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_24_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_24_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 194.881 s (3.730 µs/read; 16.08 M reads/minute).

=== Summary ===

Total reads processed:              52,244,045
Reads with adapters:                11,513,322 (22.0%)
Reads written (passing filters):    52,244,045 (100.0%)

Total basepairs processed: 5,504,855,813 bp
Quality-trimmed:               1,399,478 bp (0.0%)
Total written (filtered):  5,490,898,393 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11513322 times

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

Bases preceding removed adapters:
  A: 48.2%
  C: 11.3%
  G: 5.9%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11062873	13061011.2	0	11062873
2	12570	3265252.8	0	12570
3	282814	816313.2	0	282814
4	154309	204078.3	0	154309
5	663	51019.6	0	663
6	8	12754.9	0	8
7	2	3188.7	0	2
9	3	199.3	0	0 3
10	37	49.8	1	1 36
11	39	12.5	1	0 39
12	4	3.1	1	0 4

RUN STATISTICS FOR INPUT FILE: zr3644_24_2.fastq.gz
=============================================
52244045 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 52244045

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 19892 (0.04%)