SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_5_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_5_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 164.210 s (3.725 µs/read; 16.11 M reads/minute).

=== Summary ===

Total reads processed:              44,083,656
Reads with adapters:                 9,695,976 (22.0%)
Reads written (passing filters):    44,083,656 (100.0%)

Total basepairs processed: 4,660,205,454 bp
Quality-trimmed:               1,059,127 bp (0.0%)
Total written (filtered):  4,648,569,766 bp (99.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9695976 times

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

Bases preceding removed adapters:
  A: 48.2%
  C: 11.1%
  G: 5.9%
  T: 34.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	9316949	11020914.0	0	9316949
2	9817	2755228.5	0	9817
3	237908	688807.1	0	237908
4	130639	172201.8	0	130639
5	585	43050.4	0	585
6	7	10762.6	0	7
7	3	2690.7	0	3
8	1	672.7	0	1
9	2	168.2	0	0 2
10	32	42.0	1	0 32
11	32	10.5	1	0 32
12	1	2.6	1	0 1

RUN STATISTICS FOR INPUT FILE: zr3644_5_2.fastq.gz
=============================================
44083656 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 44083656

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 13188 (0.03%)