SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-6_S21_L006_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-6_S21_L006_R1_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.40 s (48 us/read; 1.25 M reads/minute).

=== Summary ===

Total reads processed:                  29,238
Reads with adapters:                     6,900 (23.6%)
Reads written (passing filters):        29,238 (100.0%)

Total basepairs processed:     3,979,508 bp
Quality-trimmed:                 101,141 bp (2.5%)
Total written (filtered):      3,868,128 bp (97.2%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6900 times.

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

Bases preceding removed adapters:
  A: 32.3%
  C: 24.0%
  G: 14.8%
  T: 28.7%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	5416	7309.5	0	5416
2	1049	1827.4	0	1049
3	295	456.8	0	295
4	96	114.2	0	96
5	22	28.6	0	22
6	2	7.1	0	2
7	1	1.8	0	1
10	1	0.0	1	0 1
28	1	0.0	1	1
30	1	0.0	1	1
41	1	0.0	1	1
53	1	0.0	1	0 1
62	1	0.0	1	0 1
66	1	0.0	1	1
69	1	0.0	1	1
70	1	0.0	1	1
74	1	0.0	1	0 1
76	3	0.0	1	3
77	1	0.0	1	1
79	1	0.0	1	0 1
81	1	0.0	1	1
82	1	0.0	1	0 1
134	1	0.0	1	0 1
143	1	0.0	1	1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-6_S21_L006_R1_001.fastq.gz
=============================================
29238 sequences processed in total