
SUMMARISING RUN PARAMETERS
==========================
Input filename: /data/local/buyar/pigx/pigx_rnaseq/tests/sample_data/reads/HBR_Rep3.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_Rep3.read2.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.02 s (36 us/read; 1.67 M reads/minute).

=== Summary ===

Total reads processed:                     679
Reads with adapters:                       203 (29.9%)
Reads written (passing filters):           679 (100.0%)

Total basepairs processed:        67,900 bp
Quality-trimmed:                     944 bp (1.4%)
Total written (filtered):         66,683 bp (98.2%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 203 times.

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

Bases preceding removed adapters:
  A: 25.1%
  C: 34.5%
  G: 24.6%
  T: 15.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	144	169.8	0	144
2	50	42.4	0	50
3	8	10.6	0	8
5	1	0.7	0	1


RUN STATISTICS FOR INPUT FILE: /data/local/buyar/pigx/pigx_rnaseq/tests/sample_data/reads/HBR_Rep3.read2.fastq.gz
=============================================
679 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 679

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