SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-7_S25_L007_R2_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-7_S25_L007_R2_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.45 s (36 us/read; 1.66 M reads/minute).

=== Summary ===

Total reads processed:                  12,504
Reads with adapters:                     2,708 (21.7%)
Reads written (passing filters):        12,504 (100.0%)

Total basepairs processed:     1,395,904 bp
Quality-trimmed:                 425,569 bp (30.5%)
Total written (filtered):        964,713 bp (69.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2708 times.

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

Bases preceding removed adapters:
  A: 29.5%
  C: 27.4%
  G: 13.7%
  T: 27.4%
  none/other: 2.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	1964	3126.0	0	1964
2	532	781.5	0	532
3	128	195.4	0	128
4	47	48.8	0	47
5	7	12.2	0	7
6	1	3.1	0	1
7	1	0.8	0	1
12	1	0.0	1	0 1
18	1	0.0	1	0 1
42	1	0.0	1	0 1
45	1	0.0	1	1
51	2	0.0	1	0 2
52	1	0.0	1	0 1
54	1	0.0	1	0 1
55	1	0.0	1	1
64	1	0.0	1	1
65	2	0.0	1	2
67	1	0.0	1	0 1
68	6	0.0	1	5 1
69	2	0.0	1	2
70	1	0.0	1	1
96	1	0.0	1	0 1
100	1	0.0	1	1
105	1	0.0	1	0 1
116	1	0.0	1	0 1
150	2	0.0	1	1 1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-7_S25_L007_R2_001.fastq.gz
=============================================
12504 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 12504

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 4218 (33.73%)