SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-4_S13_L004_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-4_S13_L004_R1_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 2.44 s (45 us/read; 1.34 M reads/minute).

=== Summary ===

Total reads processed:                  54,441
Reads with adapters:                    13,028 (23.9%)
Reads written (passing filters):        54,441 (100.0%)

Total basepairs processed:     7,139,942 bp
Quality-trimmed:                 243,519 bp (3.4%)
Total written (filtered):      6,878,887 bp (96.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13028 times.

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

Bases preceding removed adapters:
  A: 34.4%
  C: 23.5%
  G: 14.0%
  T: 28.1%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10104	13610.2	0	10104
2	2184	3402.6	0	2184
3	511	850.6	0	511
4	178	212.7	0	178
5	32	53.2	0	32
6	3	13.3	0	3
7	2	3.3	0	2
8	2	0.8	0	2
9	1	0.2	0	1
14	1	0.0	1	0 1
17	1	0.0	1	0 1
36	1	0.0	1	1
42	1	0.0	1	1
43	1	0.0	1	0 1
48	1	0.0	1	0 1
55	1	0.0	1	0 1
56	1	0.0	1	0 1
78	1	0.0	1	1
96	1	0.0	1	0 1
117	1	0.0	1	1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-4_S13_L004_R1_001.fastq.gz
=============================================
54441 sequences processed in total