SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_2_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_2_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 4025.76 s (24 µs/read; 2.49 M reads/minute).

=== Summary ===

Total reads processed:             166,968,754
Reads with adapters:                72,030,649 (43.1%)
Reads written (passing filters):   166,968,754 (100.0%)

Total basepairs processed: 16,652,184,280 bp
Quality-trimmed:              18,025,036 bp (0.1%)
Total written (filtered):  16,552,510,285 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 72030649 times

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

Bases preceding removed adapters:
  A: 45.3%
  C: 10.7%
  G: 7.1%
  T: 36.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	65474090	41742188.5	0	65474090
2	4278730	10435547.1	0	4278730
3	1522141	2608886.8	0	1522141
4	744071	652221.7	0	744071
5	6464	163055.4	0	6464
6	1663	40763.9	0	1663
7	592	10191.0	0	592
8	148	2547.7	0	148
9	908	636.9	0	87 821
10	1470	159.2	1	13 1457
11	311	39.8	1	6 305
12	52	10.0	1	0 52
13	7	2.5	1	0 7
33	1	2.5	1	0 1
35	1	2.5	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_2_R2_val_2.fq.gz
=============================================
166968754 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 166968754

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 136735 (0.08%)