SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_14_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_14_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 132.823 s (3.655 µs/read; 16.42 M reads/minute).

=== Summary ===

Total reads processed:              36,340,861
Reads with adapters:                 7,985,325 (22.0%)
Reads written (passing filters):    36,340,861 (100.0%)

Total basepairs processed: 3,824,508,213 bp
Quality-trimmed:                 817,245 bp (0.0%)
Total written (filtered):  3,814,988,882 bp (99.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7985325 times

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

Bases preceding removed adapters:
  A: 48.2%
  C: 11.2%
  G: 5.9%
  T: 34.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	7677254	9085215.2	0	7677254
2	7685	2271303.8	0	7685
3	193008	567826.0	0	193008
4	106855	141956.5	0	106855
5	445	35489.1	0	445
6	5	8872.3	0	5
9	4	138.6	0	0 4
10	33	34.7	1	0 33
11	35	8.7	1	0 35
12	1	2.2	1	0 1

RUN STATISTICS FOR INPUT FILE: zr3644_14_2.fastq.gz
=============================================
36340861 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 36340861

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 10706 (0.03%)