SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_15_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_15_1.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 218.407 s (3.738 µs/read; 16.05 M reads/minute).

=== Summary ===

Total reads processed:              58,435,477
Reads with adapters:                12,883,656 (22.0%)
Reads written (passing filters):    58,435,477 (100.0%)

Total basepairs processed: 6,163,827,525 bp
Quality-trimmed:               1,141,239 bp (0.0%)
Total written (filtered):  6,148,605,765 bp (99.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12883656 times

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

Bases preceding removed adapters:
  A: 47.9%
  C: 11.3%
  G: 6.1%
  T: 34.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	12368284	14608869.2	0	12368284
2	12304	3652217.3	0	12304
3	326139	913054.3	0	326139
4	176052	228263.6	0	176052
5	756	57065.9	0	756
6	9	14266.5	0	9
7	2	3566.6	0	2
9	1	222.9	0	0 1
10	57	55.7	1	3 54
11	47	13.9	1	0 47
12	5	3.5	1	0 5

RUN STATISTICS FOR INPUT FILE: zr3644_15_1.fastq.gz
=============================================
58435477 sequences processed in total