SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_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_1_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 3834.05 s (24 µs/read; 2.52 M reads/minute).

=== Summary ===

Total reads processed:             161,236,355
Reads with adapters:                69,191,738 (42.9%)
Reads written (passing filters):   161,236,355 (100.0%)

Total basepairs processed: 16,097,674,230 bp
Quality-trimmed:              12,874,747 bp (0.1%)
Total written (filtered):  16,006,234,206 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 69191738 times

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

Bases preceding removed adapters:
  A: 45.1%
  C: 10.9%
  G: 7.2%
  T: 36.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	62763288	40309088.8	0	62763288
2	4229388	10077272.2	0	4229388
3	1479655	2519318.0	0	1479655
4	709665	629829.5	0	709665
5	4423	157457.4	0	4423
6	1782	39364.3	0	1782
7	615	9841.1	0	615
8	147	2460.3	0	147
9	864	615.1	0	65 799
10	1561	153.8	1	10 1551
11	290	38.4	1	6 284
12	56	9.6	1	0 56
13	4	2.4	1	0 4

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_R1_val_1.fq.gz
=============================================
161236355 sequences processed in total