SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_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/Manchester/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/Manchester/analyses/trimgalore/zr3616_6_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 4492.65 s (23 µs/read; 2.60 M reads/minute).

=== Summary ===

Total reads processed:             195,031,602
Reads with adapters:                83,929,651 (43.0%)
Reads written (passing filters):   195,031,602 (100.0%)

Total basepairs processed: 18,448,842,626 bp
Quality-trimmed:              17,583,668 bp (0.1%)
Total written (filtered):  18,335,636,313 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 83929651 times

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

Bases preceding removed adapters:
  A: 44.7%
  C: 10.9%
  G: 7.5%
  T: 36.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	75945182	48757900.5	0	75945182
2	5221016	12189475.1	0	5221016
3	1854537	3047368.8	0	1854537
4	893411	761842.2	0	893411
5	9023	190460.5	0	9023
6	2110	47615.1	0	2110
7	805	11903.8	0	805
8	137	2975.9	0	137
9	1139	744.0	0	81 1058
10	1883	186.0	1	16 1867
11	336	46.5	1	4 332
12	64	11.6	1	0 64
13	5	2.9	1	0 5
20	3	2.9	1	0 3

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_R1_val_1.fq.gz
=============================================
195031602 sequences processed in total