SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-8_S29_L008_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-8_S29_L008_R2_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.39 s (37 us/read; 1.62 M reads/minute).

=== Summary ===

Total reads processed:                  10,428
Reads with adapters:                     2,215 (21.2%)
Reads written (passing filters):        10,428 (100.0%)

Total basepairs processed:     1,167,532 bp
Quality-trimmed:                 376,873 bp (32.3%)
Total written (filtered):        786,368 bp (67.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2215 times.

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

Bases preceding removed adapters:
  A: 29.0%
  C: 28.0%
  G: 14.3%
  T: 26.5%
  none/other: 2.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	1607	2607.0	0	1607
2	464	651.8	0	464
3	92	162.9	0	92
4	24	40.7	0	24
5	4	10.2	0	4
6	1	2.5	0	1
7	2	0.6	0	2
16	1	0.0	1	1
24	1	0.0	1	1
30	1	0.0	1	0 1
42	1	0.0	1	1
51	2	0.0	1	2
58	1	0.0	1	1
62	1	0.0	1	1
63	1	0.0	1	1
64	1	0.0	1	1
67	3	0.0	1	1 2
68	2	0.0	1	2
69	2	0.0	1	1 1
70	1	0.0	1	0 1
72	1	0.0	1	0 1
117	1	0.0	1	0 1
149	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-8_S29_L008_R2_001.fastq.gz
=============================================
10428 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 10428

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3616 (34.68%)