SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-2to4kb-1_S2_L001_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-2to4kb-1_S2_L001_R2_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.28 s (28 us/read; 2.13 M reads/minute).

=== Summary ===

Total reads processed:                  45,471
Reads with adapters:                     8,828 (19.4%)
Reads written (passing filters):        45,471 (100.0%)

Total basepairs processed:     5,183,367 bp
Quality-trimmed:               2,042,773 bp (39.4%)
Total written (filtered):      3,126,445 bp (60.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8828 times.

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

Bases preceding removed adapters:
  A: 29.5%
  C: 26.9%
  G: 13.8%
  T: 28.6%
  none/other: 1.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	6546	11367.8	0	6546
2	1699	2841.9	0	1699
3	382	710.5	0	382
4	121	177.6	0	121
5	27	44.4	0	27
6	4	11.1	0	4
7	4	2.8	0	4
12	2	0.0	1	1 1
13	1	0.0	1	1
17	1	0.0	1	0 1
20	2	0.0	1	1 1
23	1	0.0	1	1
28	1	0.0	1	0 1
30	2	0.0	1	1 1
34	1	0.0	1	1
35	1	0.0	1	1
36	1	0.0	1	1
38	1	0.0	1	1
44	1	0.0	1	0 1
45	1	0.0	1	0 1
46	1	0.0	1	1
48	2	0.0	1	2
51	2	0.0	1	2
54	1	0.0	1	1
55	3	0.0	1	3
59	1	0.0	1	0 1
62	2	0.0	1	2
67	3	0.0	1	2 1
68	8	0.0	1	7 1
69	1	0.0	1	1
86	1	0.0	1	1
87	1	0.0	1	1
91	1	0.0	1	1
112	1	0.0	1	0 1
115	1	0.0	1	1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R2_001.fastq.gz
=============================================
45471 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 45471

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 15918 (35.01%)