SUMMARISING RUN PARAMETERS
==========================
Input filename: Geoduck-NMP-gDNA-6_S21_L006_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-6_S21_L006_R2_001.fastq.gz
Running on 1 core
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.97 s (33 us/read; 1.81 M reads/minute).

=== Summary ===

Total reads processed:                  29,238
Reads with adapters:                     6,008 (20.5%)
Reads written (passing filters):        29,238 (100.0%)

Total basepairs processed:     3,157,431 bp
Quality-trimmed:                 833,914 bp (26.4%)
Total written (filtered):      2,312,523 bp (73.2%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6008 times.

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

Bases preceding removed adapters:
  A: 27.5%
  C: 26.9%
  G: 15.8%
  T: 29.2%
  none/other: 0.6%

Overview of removed sequences
length	count	expect	max.err	error counts
1	4275	7309.5	0	4275
2	1295	1827.4	0	1295
3	260	456.8	0	260
4	101	114.2	0	101
5	25	28.6	0	25
6	3	7.1	0	3
8	1	0.4	0	1
10	1	0.0	1	0 1
11	1	0.0	1	0 1
13	1	0.0	1	0 1
24	2	0.0	1	1 1
26	1	0.0	1	0 1
28	2	0.0	1	0 2
30	3	0.0	1	1 2
33	1	0.0	1	0 1
39	1	0.0	1	0 1
43	1	0.0	1	0 1
45	1	0.0	1	0 1
46	1	0.0	1	1
48	1	0.0	1	1
50	2	0.0	1	0 2
51	1	0.0	1	1
54	2	0.0	1	1 1
55	1	0.0	1	1
58	1	0.0	1	0 1
60	1	0.0	1	1
63	1	0.0	1	1
67	4	0.0	1	3 1
68	7	0.0	1	7
69	3	0.0	1	2 1
71	1	0.0	1	0 1
72	1	0.0	1	1
81	1	0.0	1	0 1
92	1	0.0	1	0 1
112	1	0.0	1	0 1
113	1	0.0	1	0 1
149	1	0.0	1	0 1
150	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: Geoduck-NMP-gDNA-6_S21_L006_R2_001.fastq.gz
=============================================
29238 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 29238

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 8435 (28.85%)