SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-3_S9_L003_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-3_S9_L003_R2_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.76 s (33 us/read; 1.82 M reads/minute).

=== Summary ===

Total reads processed:                  53,313
Reads with adapters:                    11,291 (21.2%)
Reads written (passing filters):        53,313 (100.0%)

Total basepairs processed:     6,567,162 bp
Quality-trimmed:               1,650,357 bp (25.1%)
Total written (filtered):      4,897,123 bp (74.6%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11291 times.

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

Bases preceding removed adapters:
  A: 31.2%
  C: 26.3%
  G: 13.1%
  T: 29.0%
  none/other: 0.5%

Overview of removed sequences
length	count	expect	max.err	error counts
1	8487	13328.2	0	8487
2	2076	3332.1	0	2076
3	445	833.0	0	445
4	147	208.3	0	147
5	29	52.1	0	29
6	3	13.0	0	3
7	4	3.3	0	4
8	1	0.8	0	1
10	4	0.1	1	1 3
11	1	0.0	1	0 1
12	2	0.0	1	0 2
14	4	0.0	1	3 1
16	2	0.0	1	2
17	3	0.0	1	2 1
20	1	0.0	1	0 1
21	1	0.0	1	0 1
23	1	0.0	1	1
24	2	0.0	1	2
25	1	0.0	1	0 1
26	2	0.0	1	2
27	1	0.0	1	1
28	1	0.0	1	0 1
30	2	0.0	1	2
32	1	0.0	1	1
33	2	0.0	1	2
34	1	0.0	1	0 1
35	1	0.0	1	1
36	2	0.0	1	1 1
40	2	0.0	1	2
41	2	0.0	1	2
42	3	0.0	1	2 1
45	2	0.0	1	1 1
47	1	0.0	1	1
48	4	0.0	1	3 1
51	3	0.0	1	1 2
52	2	0.0	1	2
53	1	0.0	1	0 1
54	1	0.0	1	1
56	2	0.0	1	2
57	2	0.0	1	1 1
59	1	0.0	1	1
60	1	0.0	1	1
63	2	0.0	1	1 1
64	2	0.0	1	2
65	3	0.0	1	1 2
66	1	0.0	1	0 1
67	2	0.0	1	1 1
68	8	0.0	1	7 1
69	5	0.0	1	5
71	2	0.0	1	2
72	2	0.0	1	1 1
78	1	0.0	1	1
85	1	0.0	1	1
87	1	0.0	1	1
95	1	0.0	1	0 1
98	1	0.0	1	0 1
103	1	0.0	1	1
104	1	0.0	1	1
116	2	0.0	1	0 2
132	1	0.0	1	1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-3_S9_L003_R2_001.fastq.gz
=============================================
53313 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 53313

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 12116 (22.73%)