
SUMMARISING RUN PARAMETERS
==========================
Input filename: /data/local/buyar/pigx/pigx_rnaseq/tests/sample_data/reads/UHR_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/UHR_Rep3.read2.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.04 s (37 us/read; 1.60 M reads/minute).

=== Summary ===

Total reads processed:                     951
Reads with adapters:                       319 (33.5%)
Reads written (passing filters):           951 (100.0%)

Total basepairs processed:        95,100 bp
Quality-trimmed:                   1,824 bp (1.9%)
Total written (filtered):         92,832 bp (97.6%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 319 times.

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

Bases preceding removed adapters:
  A: 27.9%
  C: 35.1%
  G: 21.6%
  T: 15.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	220	237.8	0	220
2	74	59.4	0	74
3	24	14.9	0	24
4	1	3.7	0	1


RUN STATISTICS FOR INPUT FILE: /data/local/buyar/pigx/pigx_rnaseq/tests/sample_data/reads/UHR_Rep3.read2.fastq.gz
=============================================
951 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 951

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