SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_R2_val_2.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_3_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 4261.97 s (23 µs/read; 2.65 M reads/minute).

=== Summary ===

Total reads processed:             188,570,462
Reads with adapters:                80,665,127 (42.8%)
Reads written (passing filters):   188,570,462 (100.0%)

Total basepairs processed: 17,936,143,783 bp
Quality-trimmed:              19,692,763 bp (0.1%)
Total written (filtered):  17,824,830,257 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 80665127 times

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

Bases preceding removed adapters:
  A: 45.0%
  C: 10.8%
  G: 7.3%
  T: 37.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	73217738	47142615.5	0	73217738
2	4849872	11785653.9	0	4849872
3	1721795	2946413.5	0	1721795
4	861358	736603.4	0	861358
5	7989	184150.8	0	7989
6	2062	46037.7	0	2062
7	713	11509.4	0	713
8	175	2877.4	0	175
9	1044	719.3	0	85 959
10	1897	179.8	1	14 1883
11	424	45.0	1	1 423
12	54	11.2	1	0 54
13	6	2.8	1	0 6

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_R2_val_2.fq.gz
=============================================
188570462 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 188570462

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 194796 (0.10%)