SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_6_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 Nextera: 0, count Illumina: 0, count smallRNA: 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_6_1.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 195.559 s (3.678 µs/read; 16.31 M reads/minute).

=== Summary ===

Total reads processed:              53,174,813
Reads with adapters:                11,740,470 (22.1%)
Reads written (passing filters):    53,174,813 (100.0%)

Total basepairs processed: 5,604,235,324 bp
Quality-trimmed:               1,144,174 bp (0.0%)
Total written (filtered):  5,590,261,182 bp (99.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11740470 times

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

Bases preceding removed adapters:
  A: 47.8%
  C: 11.3%
  G: 6.1%
  T: 34.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11270287	13293703.2	0	11270287
2	12875	3323425.8	0	12875
3	296695	830856.5	0	296695
4	159783	207714.1	0	159783
5	715	51928.5	0	715
6	9	12982.1	0	9
7	4	3245.5	0	4
9	5	202.8	0	0 5
10	57	50.7	1	0 57
11	38	12.7	1	0 38
12	2	3.2	1	0 2

RUN STATISTICS FOR INPUT FILE: zr3644_6_1.fastq.gz
=============================================
53174813 sequences processed in total