SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_16_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_16_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 190.365 s (3.778 µs/read; 15.88 M reads/minute).

=== Summary ===

Total reads processed:              50,386,602
Reads with adapters:                11,103,068 (22.0%)
Reads written (passing filters):    50,386,602 (100.0%)

Total basepairs processed: 5,216,369,199 bp
Quality-trimmed:               1,319,878 bp (0.0%)
Total written (filtered):  5,202,938,705 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11103068 times

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

Bases preceding removed adapters:
  A: 48.0%
  C: 11.5%
  G: 6.0%
  T: 34.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10668570	12596650.5	0	10668570
2	12349	3149162.6	0	12349
3	272590	787290.7	0	272590
4	148755	196822.7	0	148755
5	698	49205.7	0	698
6	8	12301.4	0	8
7	4	3075.4	0	4
10	49	48.1	1	1 48
11	38	12.0	1	0 38
12	7	3.0	1	0 7

RUN STATISTICS FOR INPUT FILE: zr3644_16_2.fastq.gz
=============================================
50386602 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 50386602

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 20069 (0.04%)