SUMMARISING RUN PARAMETERS
==========================
Input filename: raw_reads.fq.gz
Trimming mode: single-end
Trim Galore version: 0.4.1
Cutadapt version: 1.10
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 before a sequence gets removed: 20 bp
Output file will be GZIP compressed


This is cutadapt 1.10 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC raw_reads.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.03 s (31 us/read; 1.92 M reads/minute).

=== Summary ===

Total reads processed:                   1,000
Reads with adapters:                       353 (35.3%)
Reads written (passing filters):         1,000 (100.0%)

Total basepairs processed:        51,000 bp
Quality-trimmed:                      58 bp (0.1%)
Total written (filtered):         50,363 bp (98.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 353 times.

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

Bases preceding removed adapters:
  A: 34.0%
  C: 31.7%
  G: 17.0%
  T: 16.7%
  none/other: 0.6%

Overview of removed sequences
length	count	expect	max.err	error counts
1	247	250.0	0	247
2	83	62.5	0	83
3	20	15.6	0	20
4	1	3.9	0	1
51	2	0.0	1	0 2


RUN STATISTICS FOR INPUT FILE: raw_reads.fq.gz
=============================================
1000 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	2 (0.2%)