SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_18_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/Hawes/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/Hawes/analyses/trimgalore/zr3644_18_R1_val_1.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1378.13 s (27 µs/read; 2.25 M reads/minute).

=== Summary ===

Total reads processed:              51,713,176
Reads with adapters:                22,562,188 (43.6%)
Reads written (passing filters):    51,713,176 (100.0%)

Total basepairs processed: 5,465,399,814 bp
Quality-trimmed:               6,523,423 bp (0.1%)
Total written (filtered):  5,433,434,497 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22562188 times

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

Bases preceding removed adapters:
  A: 45.6%
  C: 10.4%
  G: 6.6%
  T: 37.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	20591166	12928294.0	0	20591166
2	1288102	3232073.5	0	1288102
3	464974	808018.4	0	464974
4	215050	202004.6	0	215050
5	1399	50501.1	0	1399
6	504	12625.3	0	504
7	141	3156.3	0	141
8	34	789.1	0	34
9	237	197.3	0	19 218
10	446	49.3	1	6 440
11	110	12.3	1	0 110
12	16	3.1	1	0 16
13	7	0.8	1	0 7
18	1	0.8	1	0 1
20	1	0.8	1	0 1

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_18_R1_val_1.fq.gz
=============================================
51713176 sequences processed in total