SUMMARISING RUN PARAMETERS
==========================
Input filename: SIM_2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
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
All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases
All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications)
All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases
All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases
Running FastQC on the data once trimming has completed
Output file will be GZIP compressed


This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SIM_2.fastq.gz
Processing reads on 8 cores in single-end mode ...
Finished in 3.25 s (3 µs/read; 18.46 M reads/minute).

=== Summary ===

Total reads processed:               1,000,000
Reads with adapters:                   500,263 (50.0%)
Reads written (passing filters):     1,000,000 (100.0%)

Total basepairs processed:   150,000,000 bp
Quality-trimmed:                       0 bp (0.0%)
Total written (filtered):    149,499,737 bp (99.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 500263 times

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

Bases preceding removed adapters:
  A: 53.7%
  C: 19.7%
  G: 0.0%
  T: 26.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	500263	250000.0	0	500263

RUN STATISTICS FOR INPUT FILE: SIM_2.fastq.gz
=============================================
1000000 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 1000000

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 0 (0.00%)