SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_15_2.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_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 219.451 s (3.755 µs/read; 15.98 M reads/minute).

=== Summary ===

Total reads processed:              58,435,477
Reads with adapters:                12,899,394 (22.1%)
Reads written (passing filters):    58,435,477 (100.0%)

Total basepairs processed: 6,162,906,442 bp
Quality-trimmed:               1,645,680 bp (0.0%)
Total written (filtered):  6,147,193,745 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12899394 times

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

Bases preceding removed adapters:
  A: 48.3%
  C: 11.2%
  G: 5.9%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	12395155	14608869.2	0	12395155
2	14341	3652217.3	0	14341
3	317980	913054.3	0	317980
4	170941	228263.6	0	170941
5	854	57065.9	0	854
6	14	14266.5	0	14
7	3	3566.6	0	3
8	1	891.7	0	1
9	5	222.9	0	1 4
10	55	55.7	1	0 55
11	42	13.9	1	0 42
12	3	3.5	1	0 3

RUN STATISTICS FOR INPUT FILE: zr3644_15_2.fastq.gz
=============================================
58435477 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 58435477

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21296 (0.04%)