SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_2_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 Illumina: 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_2_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 209.226 s (3.802 µs/read; 15.78 M reads/minute).

=== Summary ===

Total reads processed:              55,025,914
Reads with adapters:                12,192,720 (22.2%)
Reads written (passing filters):    55,025,914 (100.0%)

Total basepairs processed: 5,853,339,301 bp
Quality-trimmed:               1,525,987 bp (0.0%)
Total written (filtered):  5,838,528,615 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12192720 times

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

Bases preceding removed adapters:
  A: 48.6%
  C: 11.1%
  G: 5.7%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11721044	13756478.5	0	11721044
2	14050	3439119.6	0	14050
3	296327	859779.9	0	296327
4	160427	214945.0	0	160427
5	772	53736.2	0	772
6	4	13434.1	0	4
7	3	3358.5	0	3
8	2	839.6	0	2
9	1	209.9	0	1
10	55	52.5	1	0 55
11	34	13.1	1	0 34
12	1	3.3	1	0 1

RUN STATISTICS FOR INPUT FILE: zr3644_2_2.fastq.gz
=============================================
55025914 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 55025914

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 17888 (0.03%)