SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_22_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 Nextera: 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_22_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 173.142 s (3.682 µs/read; 16.29 M reads/minute).

=== Summary ===

Total reads processed:              47,019,646
Reads with adapters:                10,294,626 (21.9%)
Reads written (passing filters):    47,019,646 (100.0%)

Total basepairs processed: 4,944,442,652 bp
Quality-trimmed:               1,310,489 bp (0.0%)
Total written (filtered):  4,931,891,613 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10294626 times

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

Bases preceding removed adapters:
  A: 48.1%
  C: 11.3%
  G: 6.0%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	9886833	11754911.5	0	9886833
2	11235	2938727.9	0	11235
3	256133	734682.0	0	256133
4	139703	183670.5	0	139703
5	638	45917.6	0	638
6	3	11479.4	0	3
7	4	2869.9	0	4
8	1	717.5	0	1
9	3	179.4	0	0 3
10	41	44.8	1	0 41
11	29	11.2	1	0 29
12	3	2.8	1	0 3

RUN STATISTICS FOR INPUT FILE: zr3644_22_2.fastq.gz
=============================================
47019646 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 47019646

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 17479 (0.04%)