
SUMMARISING RUN PARAMETERS
==========================
Input filename: /data/local/buyar/pigx/pigx_rnaseq/tests/sample_data/reads/UHR_Rep3.read1.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/UHR_Rep3.read1.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.03 s (36 us/read; 1.67 M reads/minute).

=== Summary ===

Total reads processed:                     951
Reads with adapters:                       302 (31.8%)
Reads written (passing filters):           951 (100.0%)

Total basepairs processed:        95,100 bp
Quality-trimmed:                     623 bp (0.7%)
Total written (filtered):         94,027 bp (98.9%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 302 times.

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

Bases preceding removed adapters:
  A: 25.8%
  C: 37.4%
  G: 25.2%
  T: 11.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	190	237.8	0	190
2	86	59.4	0	86
3	19	14.9	0	19
4	4	3.7	0	4
5	3	0.9	0	3


RUN STATISTICS FOR INPUT FILE: /data/local/buyar/pigx/pigx_rnaseq/tests/sample_data/reads/UHR_Rep3.read1.fastq.gz
=============================================
951 sequences processed in total

