SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_1_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_1_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 197.878 s (3.880 µs/read; 15.46 M reads/minute).

=== Summary ===

Total reads processed:              50,993,451
Reads with adapters:                11,315,972 (22.2%)
Reads written (passing filters):    50,993,451 (100.0%)

Total basepairs processed: 5,320,352,930 bp
Quality-trimmed:               1,686,240 bp (0.0%)
Total written (filtered):  5,306,337,413 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11315972 times

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

Bases preceding removed adapters:
  A: 48.2%
  C: 11.5%
  G: 5.9%
  T: 34.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10876605	12748362.8	0	10876605
2	16325	3187090.7	0	16325
3	273549	796772.7	0	273549
4	148568	199193.2	0	148568
5	821	49798.3	0	821
6	17	12449.6	0	17
7	3	3112.4	0	3
8	4	778.1	0	4
9	3	194.5	0	0 3
10	34	48.6	1	1 33
11	40	12.2	1	0 40
12	3	3.0	1	0 3

RUN STATISTICS FOR INPUT FILE: zr3644_1_2.fastq.gz
=============================================
50993451 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 50993451

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21577 (0.04%)