SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-2to4kb-2_S6_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-2to4kb-2_S6_L002_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 (47 us/read; 1.27 M reads/minute).

=== Summary ===

Total reads processed:                  46,064
Reads with adapters:                    12,711 (27.6%)
Reads written (passing filters):        46,064 (100.0%)

Total basepairs processed:     6,334,661 bp
Quality-trimmed:                 208,056 bp (3.3%)
Total written (filtered):      6,110,027 bp (96.5%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12711 times.

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

Bases preceding removed adapters:
  A: 35.7%
  C: 24.3%
  G: 13.0%
  T: 26.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10159	11516.0	0	10159
2	1792	2879.0	0	1792
3	557	719.8	0	557
4	163	179.9	0	163
5	22	45.0	0	22
6	6	11.2	0	6
7	3	2.8	0	3
10	1	0.0	1	1
12	1	0.0	1	1
30	1	0.0	1	0 1
31	1	0.0	1	1
34	1	0.0	1	0 1
44	1	0.0	1	1
51	1	0.0	1	1
60	1	0.0	1	1
73	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R1_001.fastq.gz
=============================================
46064 sequences processed in total