SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_9_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 Illumina: 0, count smallRNA: 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_9_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 176.076 s (3.701 µs/read; 16.21 M reads/minute).

=== Summary ===

Total reads processed:              47,573,665
Reads with adapters:                10,518,319 (22.1%)
Reads written (passing filters):    47,573,665 (100.0%)

Total basepairs processed: 4,888,982,120 bp
Quality-trimmed:               1,484,662 bp (0.0%)
Total written (filtered):  4,876,006,620 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10518319 times

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

Bases preceding removed adapters:
  A: 48.0%
  C: 11.6%
  G: 6.1%
  T: 34.3%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10098209	11893416.2	0	10098209
2	12101	2973354.1	0	12101
3	264984	743338.5	0	264984
4	142230	185834.6	0	142230
5	683	46458.7	0	683
6	4	11614.7	0	4
7	5	2903.7	0	5
8	2	725.9	0	2
9	5	181.5	0	0 5
10	43	45.4	1	0 43
11	46	11.3	1	0 46
12	7	2.8	1	0 7

RUN STATISTICS FOR INPUT FILE: zr3644_9_2.fastq.gz
=============================================
47573665 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 47573665

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 24492 (0.05%)