SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_3_R1_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.6
Cutadapt version: 3.1
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined)
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/yaaminiv/Hawes/analyses/trimgalore-2 --threads 28
Output file will be GZIP compressed


This is cutadapt 3.1 with Python 3.8.5
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_3_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1069.32 s (27 µs/read; 2.21 M reads/minute).

=== Summary ===

Total reads processed:              39,446,621
Reads with adapters:                17,287,588 (43.8%)
Reads written (passing filters):    39,446,621 (100.0%)

Total basepairs processed: 4,198,659,045 bp
Quality-trimmed:               5,258,040 bp (0.1%)
Total written (filtered):  4,173,950,912 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17287588 times

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

Bases preceding removed adapters:
  A: 45.6%
  C: 10.4%
  G: 6.5%
  T: 37.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	15807468	9861655.2	0	15807468
2	966064	2465413.8	0	966064
3	351561	616353.5	0	351561
4	160330	154088.4	0	160330
5	1021	38522.1	0	1021
6	389	9630.5	0	389
7	123	2407.6	0	123
8	25	601.9	0	25
9	187	150.5	0	7 180
10	342	37.6	1	6 336
11	60	9.4	1	2 58
12	13	2.4	1	0 13
13	2	0.6	1	0 2
14	1	0.6	1	0 1
17	1	0.6	1	0 1
18	1	0.6	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_3_R1_val_1.fq.gz
=============================================
39446621 sequences processed in total