SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_21_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 smallRNA: 0, count Nextera: 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_21_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 190.228 s (3.770 µs/read; 15.91 M reads/minute).

=== Summary ===

Total reads processed:              50,457,301
Reads with adapters:                11,151,844 (22.1%)
Reads written (passing filters):    50,457,301 (100.0%)

Total basepairs processed: 5,328,038,707 bp
Quality-trimmed:               1,319,584 bp (0.0%)
Total written (filtered):  5,314,571,238 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11151844 times

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

Bases preceding removed adapters:
  A: 48.3%
  C: 11.3%
  G: 5.8%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10721926	12614325.2	0	10721926
2	11964	3153581.3	0	11964
3	270902	788395.3	0	270902
4	146345	197098.8	0	146345
5	621	49274.7	0	621
6	10	12318.7	0	10
7	3	3079.7	0	3
9	3	192.5	0	1 2
10	39	48.1	1	1 38
11	30	12.0	1	0 30
12	1	3.0	1	0 1

RUN STATISTICS FOR INPUT FILE: zr3644_21_2.fastq.gz
=============================================
50457301 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 50457301

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 17592 (0.03%)