SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_7_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 Nextera: 0, count smallRNA: 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_7_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 308.089 s (3.777 µs/read; 15.89 M reads/minute).

=== Summary ===

Total reads processed:              81,572,749
Reads with adapters:                18,087,574 (22.2%)
Reads written (passing filters):    81,572,749 (100.0%)

Total basepairs processed: 8,620,461,579 bp
Quality-trimmed:               2,728,639 bp (0.0%)
Total written (filtered):  8,598,021,745 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18087574 times

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

Bases preceding removed adapters:
  A: 48.5%
  C: 11.1%
  G: 5.8%
  T: 34.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	17384393	20393187.2	0	17384393
2	22907	5098296.8	0	22907
3	442429	1274574.2	0	442429
4	236449	318643.6	0	236449
5	1209	79660.9	0	1209
6	12	19915.2	0	12
7	8	4978.8	0	8
8	1	1244.7	0	1
9	7	311.2	0	1 6
10	92	77.8	1	0 92
11	63	19.4	1	0 63
12	4	4.9	1	0 4

RUN STATISTICS FOR INPUT FILE: zr3644_7_2.fastq.gz
=============================================
81572749 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 81572749

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 36243 (0.04%)