SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-5to7kb-2_S7_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-5to7kb-2_S7_L002_R1_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 3.03 s (44 us/read; 1.36 M reads/minute).

=== Summary ===

Total reads processed:                  68,454
Reads with adapters:                    16,462 (24.0%)
Reads written (passing filters):        68,454 (100.0%)

Total basepairs processed:     9,072,717 bp
Quality-trimmed:                 256,864 bp (2.8%)
Total written (filtered):      8,793,704 bp (96.9%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16462 times.

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

Bases preceding removed adapters:
  A: 34.6%
  C: 24.3%
  G: 13.5%
  T: 27.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	13052	17113.5	0	13052
2	2407	4278.4	0	2407
3	685	1069.6	0	685
4	238	267.4	0	238
5	46	66.8	0	46
6	11	16.7	0	11
7	2	4.2	0	2
8	1	1.0	0	1
11	2	0.0	1	1 1
15	1	0.0	1	0 1
24	1	0.0	1	1
25	1	0.0	1	0 1
34	2	0.0	1	2
36	1	0.0	1	0 1
38	1	0.0	1	1
53	2	0.0	1	1 1
57	1	0.0	1	1
59	1	0.0	1	0 1
60	1	0.0	1	0 1
62	1	0.0	1	1
66	1	0.0	1	1
68	1	0.0	1	0 1
74	1	0.0	1	0 1
81	1	0.0	1	0 1
97	1	0.0	1	1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R1_001.fastq.gz
=============================================
68454 sequences processed in total