SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-5to7kb-1_S3_L001_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-5to7kb-1_S3_L001_R1_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 2.93 s (46 us/read; 1.30 M reads/minute).

=== Summary ===

Total reads processed:                  63,365
Reads with adapters:                    15,099 (23.8%)
Reads written (passing filters):        63,365 (100.0%)

Total basepairs processed:     8,424,415 bp
Quality-trimmed:                 237,122 bp (2.8%)
Total written (filtered):      8,166,503 bp (96.9%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15099 times.

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

Bases preceding removed adapters:
  A: 34.9%
  C: 24.3%
  G: 13.6%
  T: 27.2%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11998	15841.2	0	11998
2	2190	3960.3	0	2190
3	621	990.1	0	621
4	205	247.5	0	205
5	45	61.9	0	45
6	9	15.5	0	9
7	3	3.9	0	3
8	1	1.0	0	1
10	1	0.1	1	0 1
12	2	0.0	1	1 1
15	3	0.0	1	1 2
17	1	0.0	1	0 1
22	1	0.0	1	0 1
23	1	0.0	1	1
26	1	0.0	1	0 1
34	1	0.0	1	0 1
36	1	0.0	1	1
41	1	0.0	1	0 1
47	1	0.0	1	1
54	2	0.0	1	1 1
55	1	0.0	1	1
63	1	0.0	1	1
69	1	0.0	1	1
70	1	0.0	1	1
71	1	0.0	1	1
89	1	0.0	1	0 1
98	1	0.0	1	0 1
102	2	0.0	1	1 1
122	1	0.0	1	0 1
147	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R1_001.fastq.gz
=============================================
63365 sequences processed in total