SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_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_5_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 3406.19 s (23 µs/read; 2.62 M reads/minute).

=== Summary ===

Total reads processed:             148,703,891
Reads with adapters:                64,090,433 (43.1%)
Reads written (passing filters):   148,703,891 (100.0%)

Total basepairs processed: 14,312,976,515 bp
Quality-trimmed:              12,726,746 bp (0.1%)
Total written (filtered):  14,227,316,196 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64090433 times

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

Bases preceding removed adapters:
  A: 44.9%
  C: 10.8%
  G: 7.4%
  T: 36.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	58036774	37175972.8	0	58036774
2	3974093	9293993.2	0	3974093
3	1393864	2323498.3	0	1393864
4	676909	580874.6	0	676909
5	3986	145218.6	0	3986
6	1509	36304.7	0	1509
7	647	9076.2	0	647
8	117	2269.0	0	117
9	801	567.3	0	51 750
10	1395	141.8	1	12 1383
11	286	35.5	1	3 283
12	45	8.9	1	0 45
13	7	2.2	1	0 7

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_R1_val_1.fq.gz
=============================================
148703891 sequences processed in total