SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_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_3_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 4163.00 s (22 µs/read; 2.72 M reads/minute).

=== Summary ===

Total reads processed:             188,570,462
Reads with adapters:                80,733,395 (42.8%)
Reads written (passing filters):   188,570,462 (100.0%)

Total basepairs processed: 17,936,139,623 bp
Quality-trimmed:              13,556,549 bp (0.1%)
Total written (filtered):  17,830,717,001 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 80733395 times

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

Bases preceding removed adapters:
  A: 44.9%
  C: 10.8%
  G: 7.3%
  T: 37.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	73137967	47142615.5	0	73137967
2	4966325	11785653.9	0	4966325
3	1752381	2946413.5	0	1752381
4	865292	736603.4	0	865292
5	5112	184150.8	0	5112
6	2087	46037.7	0	2087
7	791	11509.4	0	791
8	123	2877.4	0	123
9	1079	719.3	0	66 1013
10	1861	179.8	1	25 1836
11	308	45.0	1	1 307
12	64	11.2	1	0 64
13	5	2.8	1	0 5

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_R1_val_1.fq.gz
=============================================
188570462 sequences processed in total