SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4_dev
Cutadapt version: 1.16
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
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
Running FastQC on the data once trimming has completed
Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/20180328_fastqc_trimmed_hiseq_geoduck --threads 28
Output file will be GZIP compressed


This is cutadapt 1.16 with Python 2.7.14
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R1_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.20 s (56 us/read; 1.07 M reads/minute).

=== Summary ===

Total reads processed:                  21,429
Reads with adapters:                     5,461 (25.5%)
Reads written (passing filters):        21,429 (100.0%)

Total basepairs processed:     2,970,617 bp
Quality-trimmed:                 104,883 bp (3.5%)
Total written (filtered):      2,858,543 bp (96.2%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5461 times.

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

Bases preceding removed adapters:
  A: 34.5%
  C: 24.4%
  G: 13.8%
  T: 27.2%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	4378	5357.2	0	4378
2	786	1339.3	0	786
3	223	334.8	0	223
4	55	83.7	0	55
5	9	20.9	0	9
6	2	5.2	0	2
10	1	0.0	1	0 1
18	1	0.0	1	0 1
19	1	0.0	1	0 1
28	1	0.0	1	1
38	1	0.0	1	1
52	1	0.0	1	1
60	1	0.0	1	1
70	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R1_001.fastq.gz
=============================================
21429 sequences processed in total