SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-5_S17_L005_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-5_S17_L005_R2_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.91 s (35 us/read; 1.71 M reads/minute).

=== Summary ===

Total reads processed:                  25,880
Reads with adapters:                     5,305 (20.5%)
Reads written (passing filters):        25,880 (100.0%)

Total basepairs processed:     2,796,540 bp
Quality-trimmed:                 750,455 bp (26.8%)
Total written (filtered):      2,035,872 bp (72.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 5305 times.

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

Bases preceding removed adapters:
  A: 27.9%
  C: 26.9%
  G: 15.1%
  T: 29.4%
  none/other: 0.7%

Overview of removed sequences
length	count	expect	max.err	error counts
1	3767	6470.0	0	3767
2	1155	1617.5	0	1155
3	224	404.4	0	224
4	87	101.1	0	87
5	15	25.3	0	15
6	3	6.3	0	3
7	2	1.6	0	2
11	1	0.0	1	0 1
13	1	0.0	1	0 1
14	1	0.0	1	0 1
15	1	0.0	1	1
22	1	0.0	1	1
23	1	0.0	1	0 1
24	1	0.0	1	1
30	1	0.0	1	1
44	1	0.0	1	1
46	3	0.0	1	3
48	3	0.0	1	2 1
50	1	0.0	1	1
51	4	0.0	1	3 1
53	1	0.0	1	0 1
57	1	0.0	1	1
58	1	0.0	1	1
59	1	0.0	1	1
60	1	0.0	1	1
63	1	0.0	1	0 1
65	2	0.0	1	2
66	3	0.0	1	1 2
67	5	0.0	1	0 5
68	6	0.0	1	5 1
69	5	0.0	1	3 2
70	2	0.0	1	0 2
104	1	0.0	1	1
118	1	0.0	1	0 1
149	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-5_S17_L005_R2_001.fastq.gz
=============================================
25880 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 25880

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 7597 (29.35%)