SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_23_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 Illumina: 0, count Nextera: 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_23_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 151.686 s (3.801 µs/read; 15.78 M reads/minute).

=== Summary ===

Total reads processed:              39,902,509
Reads with adapters:                 8,756,139 (21.9%)
Reads written (passing filters):    39,902,509 (100.0%)

Total basepairs processed: 4,174,401,309 bp
Quality-trimmed:               1,068,818 bp (0.0%)
Total written (filtered):  4,163,776,556 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8756139 times

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

Bases preceding removed adapters:
  A: 48.1%
  C: 11.4%
  G: 5.9%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	8411031	9975627.2	0	8411031
2	10054	2493906.8	0	10054
3	216481	623476.7	0	216481
4	117892	155869.2	0	117892
5	603	38967.3	0	603
6	6	9741.8	0	6
7	4	2435.5	0	4
8	2	608.9	0	2
9	1	152.2	0	0 1
10	35	38.1	1	0 35
11	29	9.5	1	0 29
12	1	2.4	1	0 1

RUN STATISTICS FOR INPUT FILE: zr3644_23_2.fastq.gz
=============================================
39902509 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 39902509

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 15835 (0.04%)