SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_11_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 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_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 213.200 s (3.803 µs/read; 15.78 M reads/minute).

=== Summary ===

Total reads processed:              56,063,348
Reads with adapters:                12,366,580 (22.1%)
Reads written (passing filters):    56,063,348 (100.0%)

Total basepairs processed: 5,882,642,906 bp
Quality-trimmed:               1,526,273 bp (0.0%)
Total written (filtered):  5,867,625,450 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12366580 times

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

Bases preceding removed adapters:
  A: 48.2%
  C: 11.3%
  G: 5.9%
  T: 34.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11881670	14015837.0	0	11881670
2	13677	3503959.2	0	13677
3	304285	875989.8	0	304285
4	166045	218997.5	0	166045
5	782	54749.4	0	782
6	10	13687.3	0	10
7	1	3421.8	0	1
8	3	855.5	0	3
9	3	213.9	0	0 3
10	48	53.5	1	0 48
11	56	13.4	1	0 56

RUN STATISTICS FOR INPUT FILE: zr3644_11_2.fastq.gz
=============================================
56063348 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 56063348

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 20359 (0.04%)