SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-8to10kb-6_S24_L006_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-6_S24_L006_R2_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 3.23 s (33 us/read; 1.84 M reads/minute).

=== Summary ===

Total reads processed:                  99,111
Reads with adapters:                    21,130 (21.3%)
Reads written (passing filters):        99,111 (100.0%)

Total basepairs processed:    11,417,041 bp
Quality-trimmed:               2,151,435 bp (18.8%)
Total written (filtered):      9,219,206 bp (80.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21130 times.

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

Bases preceding removed adapters:
  A: 29.8%
  C: 25.8%
  G: 13.8%
  T: 29.8%
  none/other: 0.9%

Overview of removed sequences
length	count	expect	max.err	error counts
1	15526	24777.8	0	15526
2	4041	6194.4	0	4041
3	787	1548.6	0	787
4	377	387.2	0	377
5	93	96.8	0	93
6	12	24.2	0	12
7	8	6.0	0	8
8	3	1.5	0	3
9	1	0.4	0	1
10	3	0.1	1	0 3
11	1	0.0	1	1
12	4	0.0	1	4
13	2	0.0	1	0 2
14	5	0.0	1	4 1
16	4	0.0	1	1 3
17	3	0.0	1	2 1
22	2	0.0	1	1 1
23	1	0.0	1	1
24	3	0.0	1	3
25	2	0.0	1	2
26	4	0.0	1	4
28	5	0.0	1	3 2
32	2	0.0	1	2
33	5	0.0	1	2 3
36	1	0.0	1	1
37	2	0.0	1	1 1
38	2	0.0	1	1 1
39	1	0.0	1	1
42	5	0.0	1	5
44	4	0.0	1	3 1
45	2	0.0	1	1 1
46	2	0.0	1	0 2
48	1	0.0	1	1
50	1	0.0	1	1
51	8	0.0	1	6 2
52	1	0.0	1	1
55	2	0.0	1	1 1
56	3	0.0	1	2 1
57	1	0.0	1	0 1
58	1	0.0	1	1
59	5	0.0	1	5
61	1	0.0	1	0 1
62	3	0.0	1	3
63	2	0.0	1	2
64	3	0.0	1	2 1
65	2	0.0	1	2
66	2	0.0	1	2
67	39	0.0	1	4 35
68	55	0.0	1	23 32
69	29	0.0	1	14 15
70	12	0.0	1	2 10
71	6	0.0	1	2 4
72	1	0.0	1	0 1
73	1	0.0	1	0 1
74	2	0.0	1	1 1
77	1	0.0	1	0 1
81	1	0.0	1	1
85	1	0.0	1	1
90	1	0.0	1	0 1
92	1	0.0	1	0 1
98	1	0.0	1	0 1
102	1	0.0	1	1
106	2	0.0	1	0 2
110	1	0.0	1	1
111	1	0.0	1	1
114	1	0.0	1	0 1
117	1	0.0	1	0 1
118	1	0.0	1	0 1
121	1	0.0	1	1
123	1	0.0	1	0 1
127	1	0.0	1	1
131	1	0.0	1	0 1
133	2	0.0	1	1 1
137	1	0.0	1	0 1
147	1	0.0	1	1
149	4	0.0	1	1 3
150	9	0.0	1	2 7
151	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R2_001.fastq.gz
=============================================
99111 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 99111

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 23739 (23.95%)