SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_11_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_11_1.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 211.346 s (3.770 µs/read; 15.92 M reads/minute).

=== Summary ===

Total reads processed:              56,063,348
Reads with adapters:                12,389,539 (22.1%)
Reads written (passing filters):    56,063,348 (100.0%)

Total basepairs processed: 5,885,791,637 bp
Quality-trimmed:               1,060,995 bp (0.0%)
Total written (filtered):  5,871,175,460 bp (99.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12389539 times

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

Bases preceding removed adapters:
  A: 47.7%
  C: 11.4%
  G: 6.1%
  T: 34.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11887969	14015837.0	0	11887969
2	11869	3503959.2	0	11869
3	316693	875989.8	0	316693
4	172280	218997.5	0	172280
5	601	54749.4	0	601
6	9	13687.3	0	9
7	1	3421.8	0	1
8	1	855.5	0	1
9	9	213.9	0	0 9
10	58	53.5	1	0 58
11	47	13.4	1	1 46
12	2	3.3	1	0 2

RUN STATISTICS FOR INPUT FILE: zr3644_11_1.fastq.gz
=============================================
56063348 sequences processed in total