SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_22_1.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_1.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 170.969 s (3.636 µs/read; 16.50 M reads/minute).

=== Summary ===

Total reads processed:              47,019,646
Reads with adapters:                10,343,637 (22.0%)
Reads written (passing filters):    47,019,646 (100.0%)

Total basepairs processed: 4,947,908,715 bp
Quality-trimmed:                 896,580 bp (0.0%)
Total written (filtered):  4,935,698,587 bp (99.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10343637 times

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

Bases preceding removed adapters:
  A: 47.8%
  C: 11.5%
  G: 6.1%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	9926473	11754911.5	0	9926473
2	9640	2938727.9	0	9640
3	263340	734682.0	0	263340
4	143572	183670.5	0	143572
5	529	45917.6	0	529
6	3	11479.4	0	3
7	3	2869.9	0	3
8	1	717.5	0	1
9	5	179.4	0	0 5
10	32	44.8	1	0 32
11	38	11.2	1	0 38
12	1	2.8	1	0 1

RUN STATISTICS FOR INPUT FILE: zr3644_22_1.fastq.gz
=============================================
47019646 sequences processed in total