SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-8to10kb-2_S8_L002_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-8to10kb-2_S8_L002_R2_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.71 s (33 us/read; 1.83 M reads/minute).

=== Summary ===

Total reads processed:                  21,702
Reads with adapters:                     4,540 (20.9%)
Reads written (passing filters):        21,702 (100.0%)

Total basepairs processed:     2,476,067 bp
Quality-trimmed:                 944,413 bp (38.1%)
Total written (filtered):      1,522,669 bp (61.5%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4540 times.

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

Bases preceding removed adapters:
  A: 29.3%
  C: 27.8%
  G: 14.0%
  T: 28.1%
  none/other: 0.9%

Overview of removed sequences
length	count	expect	max.err	error counts
1	3291	5425.5	0	3291
2	926	1356.4	0	926
3	183	339.1	0	183
4	75	84.8	0	75
5	12	21.2	0	12
6	1	5.3	0	1
7	1	1.3	0	1
8	1	0.3	0	1
12	2	0.0	1	1 1
14	2	0.0	1	2
17	1	0.0	1	1
19	1	0.0	1	0 1
26	1	0.0	1	1
28	1	0.0	1	0 1
30	1	0.0	1	1
35	1	0.0	1	1
36	1	0.0	1	0 1
41	2	0.0	1	1 1
44	1	0.0	1	0 1
51	3	0.0	1	3
54	1	0.0	1	1
58	1	0.0	1	0 1
59	1	0.0	1	1
60	2	0.0	1	2
61	1	0.0	1	1
62	2	0.0	1	0 2
63	1	0.0	1	1
64	1	0.0	1	0 1
65	1	0.0	1	1
66	2	0.0	1	2
67	4	0.0	1	1 3
68	4	0.0	1	3 1
69	1	0.0	1	1
71	1	0.0	1	0 1
72	2	0.0	1	2
74	2	0.0	1	1 1
78	1	0.0	1	0 1
95	1	0.0	1	1
103	1	0.0	1	0 1
110	1	0.0	1	1
115	1	0.0	1	1
117	1	0.0	1	1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R2_001.fastq.gz
=============================================
21702 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 21702

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 7398 (34.09%)