SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-5_S17_L005_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-5_S17_L005_R1_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.35 s (52 us/read; 1.15 M reads/minute).

=== Summary ===

Total reads processed:                  25,880
Reads with adapters:                     5,985 (23.1%)
Reads written (passing filters):        25,880 (100.0%)

Total basepairs processed:     3,517,457 bp
Quality-trimmed:                  92,838 bp (2.6%)
Total written (filtered):      3,415,401 bp (97.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5985 times.

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

Bases preceding removed adapters:
  A: 33.5%
  C: 25.0%
  G: 13.7%
  T: 27.7%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	4640	6470.0	0	4640
2	988	1617.5	0	988
3	241	404.4	0	241
4	82	101.1	0	82
5	10	25.3	0	10
6	1	6.3	0	1
7	1	1.6	0	1
10	2	0.0	1	0 2
11	1	0.0	1	1
34	1	0.0	1	1
43	1	0.0	1	0 1
53	1	0.0	1	1
62	1	0.0	1	1
67	1	0.0	1	1
70	1	0.0	1	0 1
73	3	0.0	1	0 3
75	1	0.0	1	0 1
76	4	0.0	1	4
77	1	0.0	1	1
80	1	0.0	1	0 1
94	1	0.0	1	0 1
128	1	0.0	1	0 1
151	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-5_S17_L005_R1_001.fastq.gz
=============================================
25880 sequences processed in total