
SUMMARISING RUN PARAMETERS
==========================
Input filename: /data/local/buyar/pigx/pigx_rnaseq/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.3
Cutadapt version: 1.15
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
Output file will be GZIP compressed


This is cutadapt 1.15 with Python 3.5.4
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /data/local/buyar/pigx/pigx_rnaseq/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.03 s (35 us/read; 1.72 M reads/minute).

=== Summary ===

Total reads processed:                     817
Reads with adapters:                       237 (29.0%)
Reads written (passing filters):           817 (100.0%)

Total basepairs processed:        81,700 bp
Quality-trimmed:                     725 bp (0.9%)
Total written (filtered):         80,651 bp (98.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 237 times.

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

Bases preceding removed adapters:
  A: 28.7%
  C: 35.9%
  G: 19.4%
  T: 16.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	168	204.2	0	168
2	54	51.1	0	54
3	12	12.8	0	12
4	3	3.2	0	3


RUN STATISTICS FOR INPUT FILE: /data/local/buyar/pigx/pigx_rnaseq/tests/sample_data/reads/HBR_Rep2.read2.fastq.gz
=============================================
817 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 817

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