SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_8_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 smallRNA: 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_8_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 156.595 s (3.699 µs/read; 16.22 M reads/minute).

=== Summary ===

Total reads processed:              42,336,845
Reads with adapters:                 9,369,504 (22.1%)
Reads written (passing filters):    42,336,845 (100.0%)

Total basepairs processed: 4,447,437,363 bp
Quality-trimmed:               1,380,266 bp (0.0%)
Total written (filtered):  4,435,834,604 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9369504 times

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

Bases preceding removed adapters:
  A: 48.2%
  C: 11.3%
  G: 5.9%
  T: 34.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	9000162	10584211.2	0	9000162
2	12631	2646052.8	0	12631
3	230974	661513.2	0	230974
4	124965	165378.3	0	124965
5	677	41344.6	0	677
6	15	10336.1	0	15
7	3	2584.0	0	3
8	2	646.0	0	2
9	4	161.5	0	0 4
10	44	40.4	1	0 44
11	25	10.1	1	0 25
12	2	2.5	1	0 2

RUN STATISTICS FOR INPUT FILE: zr3644_8_2.fastq.gz
=============================================
42336845 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 42336845

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 17083 (0.04%)