SUMMARISING RUN PARAMETERS
==========================
Input filename: zr3644_3_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_3_2.fastq.gz
Processing single-end reads on 8 cores ...
Finished in 147.665 s (3.795 µs/read; 15.81 M reads/minute).

=== Summary ===

Total reads processed:              38,913,609
Reads with adapters:                 8,570,201 (22.0%)
Reads written (passing filters):    38,913,609 (100.0%)

Total basepairs processed: 4,104,947,111 bp
Quality-trimmed:               1,144,651 bp (0.0%)
Total written (filtered):  4,094,443,064 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8570201 times

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

Bases preceding removed adapters:
  A: 48.1%
  C: 11.2%
  G: 5.9%
  T: 34.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	8229341	9728402.2	0	8229341
2	10493	2432100.6	0	10493
3	213504	608025.1	0	213504
4	116217	152006.3	0	116217
5	553	38001.6	0	553
6	10	9500.4	0	10
8	2	593.8	0	2
9	1	148.4	0	0 1
10	42	37.1	1	0 42
11	37	9.3	1	0 37
12	1	2.3	1	0 1

RUN STATISTICS FOR INPUT FILE: zr3644_3_2.fastq.gz
=============================================
38913609 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 38913609

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 14660 (0.04%)