SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_12_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_12_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 172.172 s (3.675 µs/read; 16.33 M reads/minute).

=== Summary ===

Total reads processed:              46,849,571
Reads with adapters:                10,405,504 (22.2%)
Reads written (passing filters):    46,849,571 (100.0%)

Total basepairs processed: 4,923,606,473 bp
Quality-trimmed:               1,191,353 bp (0.0%)
Total written (filtered):  4,911,158,319 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10405504 times

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

Bases preceding removed adapters:
  A: 48.6%
  C: 11.2%
  G: 5.4%
  T: 34.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10040028	11712392.8	0	10040028
2	9932	2928098.2	0	9932
3	226310	732024.5	0	226310
4	128539	183006.1	0	128539
5	621	45751.5	0	621
6	8	11437.9	0	8
7	3	2859.5	0	3
8	1	714.9	0	1
9	3	178.7	0	1 2
10	35	44.7	1	0 35
11	24	11.2	1	0 24

RUN STATISTICS FOR INPUT FILE: zr3644_12_2.fastq.gz
=============================================
46849571 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 46849571

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 15335 (0.03%)