SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-2to4kb-1_S2_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-2to4kb-1_S2_L001_R1_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 2.17 s (48 us/read; 1.26 M reads/minute).

=== Summary ===

Total reads processed:                  45,471
Reads with adapters:                    12,498 (27.5%)
Reads written (passing filters):        45,471 (100.0%)

Total basepairs processed:     6,281,433 bp
Quality-trimmed:                 196,524 bp (3.1%)
Total written (filtered):      6,068,398 bp (96.6%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12498 times.

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

Bases preceding removed adapters:
  A: 36.2%
  C: 24.6%
  G: 12.5%
  T: 26.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10043	11367.8	0	10043
2	1721	2841.9	0	1721
3	526	710.5	0	526
4	157	177.6	0	157
5	27	44.4	0	27
6	6	11.1	0	6
7	3	2.8	0	3
8	1	0.7	0	1
11	1	0.0	1	0 1
12	1	0.0	1	1
13	1	0.0	1	0 1
19	1	0.0	1	0 1
30	1	0.0	1	1
33	1	0.0	1	0 1
36	1	0.0	1	0 1
37	1	0.0	1	1
39	1	0.0	1	1
40	1	0.0	1	1
53	1	0.0	1	1
65	1	0.0	1	1
82	1	0.0	1	0 1
150	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R1_001.fastq.gz
=============================================
45471 sequences processed in total