SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_23_1.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_1.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 147.534 s (3.697 µs/read; 16.23 M reads/minute).

=== Summary ===

Total reads processed:              39,902,509
Reads with adapters:                 8,788,336 (22.0%)
Reads written (passing filters):    39,902,509 (100.0%)

Total basepairs processed: 4,176,673,289 bp
Quality-trimmed:                 757,303 bp (0.0%)
Total written (filtered):  4,166,299,640 bp (99.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8788336 times

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

Bases preceding removed adapters:
  A: 47.7%
  C: 11.5%
  G: 6.2%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	8432381	9975627.2	0	8432381
2	7877	2493906.8	0	7877
3	224983	623476.7	0	224983
4	122576	155869.2	0	122576
5	447	38967.3	0	447
6	6	9741.8	0	6
7	1	2435.5	0	1
8	1	608.9	0	1
9	2	152.2	0	0 2
10	29	38.1	1	0 29
11	32	9.5	1	0 32
12	1	2.4	1	0 1

RUN STATISTICS FOR INPUT FILE: zr3644_23_1.fastq.gz
=============================================
39902509 sequences processed in total