SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_10_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 smallRNA: 0, count Illumina: 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_10_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 204.494 s (3.940 µs/read; 15.23 M reads/minute).

=== Summary ===

Total reads processed:              51,902,712
Reads with adapters:                11,461,920 (22.1%)
Reads written (passing filters):    51,902,712 (100.0%)

Total basepairs processed: 5,448,414,856 bp
Quality-trimmed:               1,559,787 bp (0.0%)
Total written (filtered):  5,434,349,231 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11461920 times

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

Bases preceding removed adapters:
  A: 48.2%
  C: 11.4%
  G: 5.9%
  T: 34.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11010720	12975678.0	0	11010720
2	13379	3243919.5	0	13379
3	284461	810979.9	0	284461
4	152433	202745.0	0	152433
5	801	50686.2	0	801
6	11	12671.6	0	11
7	6	3167.9	0	6
9	7	198.0	0	0 7
10	55	49.5	1	0 55
11	45	12.4	1	0 45
12	2	3.1	1	0 2

RUN STATISTICS FOR INPUT FILE: zr3644_10_2.fastq.gz
=============================================
51902712 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 51902712

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21389 (0.04%)