SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_8_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_8_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1157.87 s (27 µs/read; 2.23 M reads/minute).

=== Summary ===

Total reads processed:              42,944,059
Reads with adapters:                18,771,452 (43.7%)
Reads written (passing filters):    42,944,059 (100.0%)

Total basepairs processed: 4,553,628,990 bp
Quality-trimmed:               5,628,517 bp (0.1%)
Total written (filtered):  4,526,859,091 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18771452 times

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

Bases preceding removed adapters:
  A: 45.6%
  C: 10.4%
  G: 6.6%
  T: 37.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	17148689	10736014.8	0	17148689
2	1061835	2684003.7	0	1061835
3	381925	671000.9	0	381925
4	175925	167750.2	0	175925
5	1790	41937.6	0	1790
6	435	10484.4	0	435
7	125	2621.1	0	125
8	31	655.3	0	31
9	202	163.8	0	14 188
10	411	41.0	1	4 407
11	72	10.2	1	1 71
12	11	2.6	1	0 11
13	1	0.6	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_8_R1_val_1.fq.gz
=============================================
42944059 sequences processed in total