SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_9_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 Illumina: 0, count smallRNA: 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_9_1.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 189.277 s (3.979 µs/read; 15.08 M reads/minute).

=== Summary ===

Total reads processed:              47,573,665
Reads with adapters:                10,467,499 (22.0%)
Reads written (passing filters):    47,573,665 (100.0%)

Total basepairs processed: 4,891,509,161 bp
Quality-trimmed:               1,127,583 bp (0.0%)
Total written (filtered):  4,878,912,465 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10467499 times

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

Bases preceding removed adapters:
  A: 47.5%
  C: 11.6%
  G: 6.4%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10036253	11893416.2	0	10036253
2	9587	2973354.1	0	9587
3	274122	743338.5	0	274122
4	146882	185834.6	0	146882
5	554	46458.7	0	554
6	4	11614.7	0	4
7	4	2903.7	0	4
8	3	725.9	0	3
10	46	45.4	1	0 46
11	42	11.3	1	0 42
12	2	2.8	1	0 2

RUN STATISTICS FOR INPUT FILE: zr3644_9_1.fastq.gz
=============================================
47573665 sequences processed in total