SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_1_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 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_1.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 186.283 s (3.653 µs/read; 16.42 M reads/minute).

=== Summary ===

Total reads processed:              50,993,451
Reads with adapters:                11,202,687 (22.0%)
Reads written (passing filters):    50,993,451 (100.0%)

Total basepairs processed: 5,326,077,021 bp
Quality-trimmed:                 977,056 bp (0.0%)
Total written (filtered):  5,312,841,062 bp (99.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11202687 times

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

Bases preceding removed adapters:
  A: 47.6%
  C: 11.5%
  G: 6.2%
  T: 34.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10748806	12748362.8	0	10748806
2	9899	3187090.7	0	9899
3	286907	796772.7	0	286907
4	156439	199193.2	0	156439
5	509	49798.3	0	509
6	8	12449.6	0	8
7	2	3112.4	0	2
9	8	194.5	0	0 8
10	60	48.6	1	0 60
11	45	12.2	1	0 45
12	4	3.0	1	0 4

RUN STATISTICS FOR INPUT FILE: zr3644_1_1.fastq.gz
=============================================
50993451 sequences processed in total