SUMMARISING RUN PARAMETERS
==========================
Input filename: /Volumes/Serine/wd/18-04-10/sub-zr2096_5_s1_R2.fastq
Trimming mode: paired-end
Trim Galore version: 0.4.4_dev
Cutadapt version: 1.16
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
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


This is cutadapt 1.16 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Volumes/Serine/wd/18-04-10/sub-zr2096_5_s1_R2.fastq
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.15 s (15 us/read; 3.92 M reads/minute).

=== Summary ===

Total reads processed:                  10,000
Reads with adapters:                     3,714 (37.1%)
Reads written (passing filters):        10,000 (100.0%)

Total basepairs processed:       905,579 bp
Quality-trimmed:                   3,382 bp (0.4%)
Total written (filtered):        897,751 bp (99.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 3714 times.

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

Bases preceding removed adapters:
  A: 43.2%
  C: 13.2%
  G: 9.8%
  T: 33.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	3232	2500.0	0	3232
2	342	625.0	0	342
3	99	156.2	0	99
4	37	39.1	0	37
15	1	0.0	1	0 1
16	2	0.0	1	0 2
38	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: /Volumes/Serine/wd/18-04-10/sub-zr2096_5_s1_R2.fastq
=============================================
10000 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 10000

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 104 (1.04%)