SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R1_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-5_S20_L005_R1_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 3.66 s (42 us/read; 1.43 M reads/minute).

=== Summary ===

Total reads processed:                  87,562
Reads with adapters:                    20,789 (23.7%)
Reads written (passing filters):        87,562 (100.0%)

Total basepairs processed:    11,436,175 bp
Quality-trimmed:                 304,214 bp (2.7%)
Total written (filtered):     11,089,885 bp (97.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20789 times.

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

Bases preceding removed adapters:
  A: 34.3%
  C: 22.8%
  G: 13.7%
  T: 28.6%
  none/other: 0.6%

Overview of removed sequences
length	count	expect	max.err	error counts
1	16267	21890.5	0	16267
2	3095	5472.6	0	3095
3	873	1368.2	0	873
4	298	342.0	0	298
5	56	85.5	0	56
6	7	21.4	0	7
7	6	5.3	0	6
8	2	1.3	0	2
9	1	0.3	0	0 1
10	1	0.1	1	0 1
16	3	0.0	1	3
17	1	0.0	1	0 1
18	1	0.0	1	0 1
21	1	0.0	1	1
25	1	0.0	1	1
30	2	0.0	1	1 1
31	2	0.0	1	2
34	1	0.0	1	0 1
36	1	0.0	1	0 1
38	1	0.0	1	1
39	2	0.0	1	2
40	2	0.0	1	1 1
41	1	0.0	1	1
42	1	0.0	1	0 1
43	1	0.0	1	0 1
48	2	0.0	1	2
49	1	0.0	1	1
59	1	0.0	1	1
66	2	0.0	1	1 1
68	2	0.0	1	2
69	1	0.0	1	1
70	1	0.0	1	0 1
71	1	0.0	1	0 1
72	1	0.0	1	1
73	2	0.0	1	1 1
74	4	0.0	1	0 4
75	21	0.0	1	3 18
76	27	0.0	1	9 18
77	17	0.0	1	5 12
78	19	0.0	1	9 10
79	5	0.0	1	3 2
80	6	0.0	1	5 1
81	1	0.0	1	1
82	2	0.0	1	0 2
83	2	0.0	1	0 2
85	2	0.0	1	2
86	1	0.0	1	1
87	2	0.0	1	1 1
88	1	0.0	1	0 1
90	1	0.0	1	0 1
96	1	0.0	1	0 1
102	1	0.0	1	0 1
108	1	0.0	1	1
109	1	0.0	1	1
118	1	0.0	1	0 1
122	1	0.0	1	0 1
126	1	0.0	1	0 1
131	1	0.0	1	1
146	1	0.0	1	0 1
148	1	0.0	1	1
149	3	0.0	1	1 2
150	19	0.0	1	3 16
151	5	0.0	1	0 5


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R1_001.fastq.gz
=============================================
87562 sequences processed in total