SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-2to4kb-2_S6_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-2to4kb-2_S6_L002_R2_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.41 s (31 us/read; 1.97 M reads/minute).

=== Summary ===

Total reads processed:                  46,064
Reads with adapters:                     9,262 (20.1%)
Reads written (passing filters):        46,064 (100.0%)

Total basepairs processed:     5,308,036 bp
Quality-trimmed:               2,045,052 bp (38.5%)
Total written (filtered):      3,247,224 bp (61.2%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9262 times.

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

Bases preceding removed adapters:
  A: 29.4%
  C: 27.3%
  G: 13.9%
  T: 28.5%
  none/other: 0.9%

Overview of removed sequences
length	count	expect	max.err	error counts
1	6857	11516.0	0	6857
2	1778	2879.0	0	1778
3	396	719.8	0	396
4	127	179.9	0	127
5	33	45.0	0	33
6	4	11.2	0	4
7	3	2.8	0	3
8	1	0.7	0	1
10	3	0.0	1	2 1
11	2	0.0	1	0 2
12	1	0.0	1	0 1
13	2	0.0	1	1 1
16	1	0.0	1	0 1
19	1	0.0	1	0 1
21	1	0.0	1	0 1
24	1	0.0	1	1
30	1	0.0	1	1
31	1	0.0	1	1
32	1	0.0	1	0 1
33	3	0.0	1	3
36	1	0.0	1	1
38	1	0.0	1	0 1
44	1	0.0	1	1
45	2	0.0	1	1 1
48	1	0.0	1	1
49	3	0.0	1	3
51	3	0.0	1	3
53	1	0.0	1	0 1
56	1	0.0	1	1
57	1	0.0	1	1
60	1	0.0	1	1
61	1	0.0	1	1
64	1	0.0	1	0 1
65	1	0.0	1	0 1
66	1	0.0	1	1
67	5	0.0	1	2 3
68	7	0.0	1	6 1
70	1	0.0	1	0 1
71	1	0.0	1	0 1
77	1	0.0	1	0 1
80	2	0.0	1	1 1
91	1	0.0	1	0 1
96	1	0.0	1	1
97	2	0.0	1	0 2
100	1	0.0	1	1
114	1	0.0	1	0 1
122	1	0.0	1	0 1
127	1	0.0	1	1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R2_001.fastq.gz
=============================================
46064 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 46064

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 15644 (33.96%)