SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_22_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/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_22_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1304.96 s (27 µs/read; 2.19 M reads/minute).

=== Summary ===

Total reads processed:              47,725,182
Reads with adapters:                20,746,534 (43.5%)
Reads written (passing filters):    47,725,182 (100.0%)

Total basepairs processed: 5,064,153,931 bp
Quality-trimmed:               8,600,269 bp (0.2%)
Total written (filtered):  5,032,244,815 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20746534 times

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

Bases preceding removed adapters:
  A: 45.7%
  C: 10.3%
  G: 6.4%
  T: 37.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	19018813	11931295.5	0	19018813
2	1102799	2982823.9	0	1102799
3	422330	745706.0	0	422330
4	199471	186426.5	0	199471
5	1874	46606.6	0	1874
6	427	11651.7	0	427
7	136	2912.9	0	136
8	34	728.2	0	34
9	193	182.1	0	12 181
10	376	45.5	1	2 374
11	65	11.4	1	0 65
12	14	2.8	1	0 14
13	2	0.7	1	0 2

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_22_R2_val_2.fq.gz
=============================================
47725182 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 47725182

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 26554 (0.06%)