SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_23_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_23_R2_val_2.fq.gz
Processing reads on 1 core in single-end mode ...
Finished in 1116.39 s (28 µs/read; 2.18 M reads/minute).

=== Summary ===

Total reads processed:              40,539,021
Reads with adapters:                17,635,972 (43.5%)
Reads written (passing filters):    40,539,021 (100.0%)

Total basepairs processed: 4,279,858,954 bp
Quality-trimmed:               7,142,575 bp (0.2%)
Total written (filtered):  4,252,914,909 bp (99.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17635972 times

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

Bases preceding removed adapters:
  A: 45.8%
  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	16178776	10134755.2	0	16178776
2	927146	2533688.8	0	927146
3	358259	633422.2	0	358259
4	169076	158355.6	0	169076
5	1577	39588.9	0	1577
6	361	9897.2	0	361
7	118	2474.3	0	118
8	22	618.6	0	22
9	196	154.6	0	12 184
10	356	38.7	1	2 354
11	76	9.7	1	0 76
12	9	2.4	1	0 9

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_23_R2_val_2.fq.gz
=============================================
40539021 sequences processed in total

Total number of sequences analysed for the sequence pair length validation: 40539021

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 23114 (0.06%)