SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-8to10kb-2_S8_L002_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-2_S8_L002_R1_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.18 s (54 us/read; 1.11 M reads/minute).

=== Summary ===

Total reads processed:                  21,702
Reads with adapters:                     5,593 (25.8%)
Reads written (passing filters):        21,702 (100.0%)

Total basepairs processed:     2,994,474 bp
Quality-trimmed:                 110,023 bp (3.7%)
Total written (filtered):      2,876,687 bp (96.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5593 times.

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

Bases preceding removed adapters:
  A: 35.3%
  C: 23.9%
  G: 13.5%
  T: 27.2%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	4384	5425.5	0	4384
2	900	1356.4	0	900
3	217	339.1	0	217
4	67	84.8	0	67
5	10	21.2	0	10
6	1	5.3	0	1
8	1	0.3	0	1
10	2	0.0	1	1 1
12	1	0.0	1	0 1
18	1	0.0	1	1
32	1	0.0	1	0 1
33	1	0.0	1	1
40	1	0.0	1	0 1
60	1	0.0	1	1
64	1	0.0	1	1
66	1	0.0	1	0 1
70	1	0.0	1	0 1
73	1	0.0	1	0 1
109	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R1_001.fastq.gz
=============================================
21702 sequences processed in total