SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_18_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 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_18_1.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 209.114 s (4.105 µs/read; 14.62 M reads/minute).

=== Summary ===

Total reads processed:              50,943,423
Reads with adapters:                11,217,786 (22.0%)
Reads written (passing filters):    50,943,423 (100.0%)

Total basepairs processed: 5,337,357,833 bp
Quality-trimmed:                 912,711 bp (0.0%)
Total written (filtered):  5,324,164,501 bp (99.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11217786 times

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

Bases preceding removed adapters:
  A: 47.6%
  C: 11.5%
  G: 6.2%
  T: 34.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10760538	12735855.8	0	10760538
2	10533	3183963.9	0	10533
3	289286	795991.0	0	289286
4	156664	198997.7	0	156664
5	637	49749.4	0	637
6	4	12437.4	0	4
8	1	777.3	0	1
9	1	194.3	0	0 1
10	68	48.6	1	0 68
11	51	12.1	1	0 51
12	3	3.0	1	0 3

RUN STATISTICS FOR INPUT FILE: zr3644_18_1.fastq.gz
=============================================
50943423 sequences processed in total